Mercurial > repos > dereeper > sniplay
changeset 1:420b57c3c185 draft
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MDSplot/MDSbasedOnIBSmatrix.pl.org Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,77 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + +my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink"; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --in <input> + -o, --out <output> +~; +$usage .= "\n"; + +my ($in,$out); + + +GetOptions( + "in=s" => \$in, + "out=s" => \$out +); + +die $usage + if ( !$in || !$out); + + +my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1"; +system($plink_command); + +my $awk_cmd = "awk \{\'print \$1\'\} $in.ped"; +my $inds = `$awk_cmd`; +my @individuals = split("\n",$inds); + + +open(my $OUT,">$out.mds_plot.txt"); +my $go = 0; +open(my $O,"$out.mds"); +while(<$O>) +{ + if ($go) + { + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @i = split(/\s+/,$line); + my $ind = $i[1]; + print $OUT "$ind ".$i[4]." ".$i[5]."\n"; + } + if (/C1/){$go = 1;} +} +close($O); +close($OUT); + + +my $j = 0; +open(my $IBS,">$out.ibs_matrix.txt"); +print $IBS "Individuals " . join("\t",@individuals)."\n"; +open(my $O2,"$out.mibs"); +while(<$O2>) +{ + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @i = split(/\s+/,$line); + print $IBS $individuals[$j]. " ". join("\t",@i)."\n"; + $j++; +} +close($O2); +close($IBS); + + + + + +
--- a/MDSplot/mdsplot.xml Mon Mar 23 05:57:27 2015 -0400 +++ b/MDSplot/mdsplot.xml Fri Jul 10 04:39:30 2015 -0400 @@ -6,7 +6,7 @@ <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> <requirements> <requirement type="binary">perl</requirement> - <requirement type="package" version="0.1.13">plink</requirement> + <requirement type="package" version="1.07">plink</requirement> </requirements> <!-- [OPTIONAL] Command to be executed to get the tool's version string --> @@ -63,17 +63,31 @@ <!-- [OPTIONAL] Help displayed in Galaxy --> <help> + .. class:: infomark -**Authors** +**Authors** plink_ + +.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ + + | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +.. class:: infomark + +**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). --------------------------------------------------- -.. class:: infomark -**Please cite** If you use this tool, please cite dereeper et al. 2015 in prep. - ---------------------------------------------------- ======== MDS plot @@ -90,20 +104,14 @@ Workflow position ----------------- -**Upstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= +**Upstream tool** - -**Downstream tools** +=============== ========================== =============== +Name output file(s) format +=============== ========================== =============== +VCFtools Filter PED and MAP file tabular and MAP +=============== ========================== =============== -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= ---------- @@ -137,6 +145,11 @@ Output_name.log Log file +------------ +Dependencies +------------ +plink + version 1.07 --------------------------------------------------- @@ -199,5 +212,21 @@ </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PedToFasta/Ped2Fasta.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,70 @@ + +#!/usr/bin/perl + +use strict; +use Getopt::Long; + +my $usage = qq~Usage:$0 <args> [<opts>] + +where <args> are: + + -i, --in <PED input> + -o, --out <Fasta output> +~; +$usage .= "\n"; + +my ($input,$out); + + + +GetOptions( + "in=s" => \$input, + "out=s" => \$out, +); + + +die $usage + if ( !$input || !$out); + + +my %IUPAC = +( + '00'=> "?", + 'AA'=> "A", + 'CC'=> "C", + 'GG'=> "G", + 'TT'=> "T", + 'AG'=> "R", + 'GA'=> "R", + 'CT'=> "Y", + 'TC'=> "Y", + 'TG'=> "K", + 'GT'=> "K", + 'CG'=> "S", + 'GC'=> "S", + 'AT'=> "W", + 'TA'=> "W", + 'AC'=> "M", + 'CA'=> "M", +); + +open(my $O,">$out"); +open(my $P,$input) or die "File does not exist"; +while(<$P>) +{ + my $line = $_; + $line =~s/\r//g; + $line =~s/\n//g; + my @infos = split("\t",$_); + my $ind = $infos[0]; + print $O ">$ind\n"; + for (my $i = 6; $i <= $#infos; $i= $i+2) + { + my $code = $infos[$i].$infos[$i+1]; + my $letter = $IUPAC{$code}; + print $O $letter; + } + print $O "\n"; +} +close($P); +close($O);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PedToFasta/pedToFasta.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,171 @@ +<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Convert PED file to Fasta File </description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="perl"> + Ped2Fasta.pl --in $filein --out $fileout + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="txt" optional="false" label="PED input" /> + <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <test> + <param name="filein" value="sample.ped" /> + <output name="fileout" file="result.fa" /> + </test> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + +========= +Ped2Fasta +========= + +----------- +Description +----------- + + Convert PED file to Fasta File + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ========================== ======= +Name output file(s) format +=============== ========================== ======= +VCFtools Filter VCF file VCF +=============== ========================== ======= + + +**Downstream tool** + +=========== ========================== ======= +Name input file(s) format +=========== ========================== ======= +Readseq Fasta alignment fasta +=========== ========================== ======= + + +---------- +Input file +---------- + +PED file + PED file usually from VCF tools + +---------- +Parameters +---------- + +Output file name + Prefix for the output fasta file + +------------ +Output files +------------ + +Fasta file + PED file conversion + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +PED file +--------- + +:: + + CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A + +Parameters +========== + +Output name -> pedFile + +Output files +============ + +pedFile.fa +---------- + +:: + + YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY + + + </help> + + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PedToFasta/test-data/result.fa Fri Jul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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PedToFasta/test-data/sample.ped Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,1 @@ +CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A C G C T T C A C T G A G A G T G A C C T A G T G C G A G T G T C A G C T G A T C G T G A G T G A G C T G T G C G C T A G A T C T G C T C G A A G C T G A A G G A A T T C A T A T C T C T A T A G G A C T A G G C A G A T G C C G G A C A T C A G A G T G G C A T A C G C G T A T G A G A C T C T A T C A C T T G T C A T G A C G T C G A T A A G C T C A T A C T C T T C A C G T C T T G C T A T A G C T A G C T A G C T T C T G G T C T T A A G C A A C A T T G C T C T C G C T T C T A A G T C C G T G A G A T G A G C A G A G G A C T T C T A C T T C T C T G T C T C G T T C A G A C T G G T G A C T C T A G T G T C T G T G A T T A T G G A C T T A A G C A T C G A C G A T C T T A T C T C T A G A A G A G A G A G T C G A G C A G G T G A A T T G A T A G G T T G C T T C T C G T A C G T C T T C T C G C T A C G C G C T A G G A T G G A A C C G G T A C T G A G G A G T A G A T G A G A A G G A T C A T A G G T T G C T T A A G T G G A T C T A A T T A G T A C G A G A A G C T A G C T T C T A A T A G T C T C A G T G G T T A T C T C A G G A T A T C T C A G T G C T C G A G G A C T A T A G T C A T G C A T T C C T A T A T G T T C T C G T T C A T T C G A C A A G C T A G T C C T A G A G A T C T C T T C G C G A C T A G G A T G A G G A C T A C C A G C C G G A A G C T C T C T C G A G A C A T G A G A A G A G G C A T G A C T T C C A C T T C A G T C A T C T G A G A G C C G C T C T A C T C A G T G G T A G T G C T T A G T A G G A C T T C G A T C A G C A A C A T T C T A G A T C G C G C T A C T T C T C A G T C A T A T T A A T T A G A T C G A A G T C G A C T A T A T A C A C C T A G T C T C T C A G C G C T C T G A G A G A G A G A C T T C C T A G C T T C A G A G G T G T C A C T C A G A G A G A A G C G T C T G T C G A A G G A T C T A T C A G G A T C T A A G C T G C C T C T G A T C G A G A C T G C A G A C A C G T G A G T T C T C T C C A C A G A A T C T T G T A T C A C A G T C G A C G A T A G T C A G T C A C C T C A A C G A A G T C G C G A C T G A G A A G G C A G A G G C A G A G A C G T G A G T C T C T T C G A A G C T A C C T C T A G C T G A G A G T C T G A G A G A G A G A C T T C G A C T T C A T C T T C G C G A G A A C G T G A C T C T T C C G T C G A A G T C T C A T G A C A T C G C G A C T C T C T C A C A G A G A C T C T G A T A T G A C A T T A A T C T A G G A T A C T T C T C C G T A G A G A T C A G T C G A C T A G A G G A T C G A T C A G C T G A T C C T C T T C G A A G G A A T C A T C T G C A A T A G G A C T C T C T C T G A C A T C C G G C A G G A G A T A C T G A T A A G G A A G A T T C A G A T T C A G T G A T C T C T C A G T G A C T G A C A C T G A C T C A G A G A C T A G T C T C C T C T C T G A A C A G A G A T C T C T G A G C C T T C C G T C A G T C C T T C C T G C A T G T C T A C A G C T T C C T C T C T T C C T G A G A G T A T C T T C C A C T G A C T C A T A C T C T T C C G C T T C A C T A C T A C A T C G T C T A A T T A T C G A C T C T T C C G T C G A C T A C C A G A G A G A T C T G T C A G A T G A T C C T G A A G A G T G C T C T T C T G G A C T C T G A C T C T C A T C G A C A G A C T T C T C G T A T C T T A T A T C C T T G C T G A T C A T T A A G T C G A A C G C G C C T T C C T C T C T T G T C A G T C A G A G C T C T A G C T T C G A C T G A G T G A C T C T G T C T C T C T T A C T A G T C G A G A C T T C C T G A A C C T C T A G G A G A C T A T A G A G G T A G C T C T C T C T A G A G G A C T G A C T C T G T C T T C G A G A G A G A T A C T G T T A G A G A G A C A T C A T G A T C A G G A C G A T C G G C C T C T C T C T G A T C C T C T T C C T C G A G T C T C C A G A A G C T C G G A A T A C T C A G C T C T C T G A G A C T A G C T T A C T T C C T A C A T A T G A G A C T A C G A T C C T C T G A G A A C C T G A G A G C T G G A A G C T C T G C G A T C G T G A G A G A A C A G T A T C T C C A T A C T C T A C G A T A C T C T T A T A T C T C T C G T C G T C T G T C C T C T T C C T C T T C T A C T T C C G A G T A C G C T C T C T T C G A G A T C G C A G A C T C C T T C G A G A T C C G A T C T C T T C C T A T G A C T C T C G A G T C T C T G A G G A C T C T C T A C A T C T C T C T G A T A T A C T T G T C C A C T G A G A A G C A C T T C C G G A T G T C A C A C T C C T G A G A A G A T A G T C G A A G G A A C C T G T C T A G T G G A C T A G T C G A C G C T T C A G C T C G G A C A T C A T A T T A A T T A A T C T T G C T G A C G T C T C T A G T A C G A T A A T C T T A G C A C A C G C C A A G T G T C A G G C A T A T A C G T A T C T T C T C T A G T A G A G G T A G A T G A A T T C T A T A T A T C G C T C A G C G T C T C T C C T T C A G A G T A A C A C G A T A C T A G T C T C A T T C T G A G C A A T A G T C G A T C T C G A A G A T A T G A C T A C T C T C T C G A T C T C C T C A A G C T T C C T A G G A T C A G T A A G T C G A T C A T T A G T A T A C G A T A G A T C C T A G A G A G T C T A G C C T T A G A G C A G T C A T T C C G A G T C T G G A A G C T A G G A T G A G T C G A T C A T G C A T T A C T G A T A A G G A A G T G T C T G C T G A T C C T A T C T G T G T A G C T C T T C G A A G C T T C C T T C T C A G T G G A T C T G T C C A T C T C G A A T T C G T G A T A C A C T G A G A T G C T A G A G G A T C G A T C A G A T T C G C C T G A T C T G T C C A C G C T T C A G A T A G A C T A T G G C G A G C T C C T A G T A G C G A G A A G A G T C C G A C G C G A G A A T T G G A A G A G C T C T T C G A A G C T T A A T T C T C A G G A C T C A T C C A G A A G C T A T T A A G T C C T T C A G A C A G G T T G T C T G A T C A T C C T A G A C T C C T G T C A A T C A T C A G A T G A G T C T G A G C A G C A G T C G C T A G G C C T T C A G A T A C C A C G G C T G G A T C A C C T T G T C A G A T G A G A A G A G A G C T C T C G A G T G C T G A T C C T C T T C G A C T A G A G G T G A T C C T C T T A T C T C T A C T T C T A A G C T A G G T A C G A G T G A A G C T G A T C T A A T C A A C A G G A A G C T C T C T C T A T G C T A G C G A C A T A T A C T G A A T C T G C C T T C T A G A C T C T G A A G C T G A A G C T C T A G G A G A T A T C G C G C G A T C A G C T T C G C G A G A T G T A C T C G C A T C C G C G T G T C T C A G C A G A G A A G C T A T C A G A C T G A G T A G A G G A G A T G C T C T A T C G T C G A T C C T T C T C G A A G A C G A G A C T A T G A A G A G G A T C G C T C A G C T T C G A G A T A C G G A A C G C G A T C G C G A T A T C A G G C A G T C G A T G G T T A T C G A C T T C A T A G A T A G A G C T A C G T G A G T A G T G T G G A G T C T A C C A G T C T A G A C A G G A A G T C A G A G T C T C A G A C T A T A A G G A G A T C T C A T T A T C A G T G G A C T T C C T G A C T T C T C C T C T A G T C C T T A A G G A C T T C A C C T C G G C A T A G A G T G T C A G A G C T C T A G G A G T T C G C A C T A C A A T G A C T G A A C G A A G T C A G A C C T G A G A T A A G T A A G G T A G T C G C T G C T G C G C G A T C G C G A C T T C A C G A A G G A A G T A G T C T A G G C A G G A G T G T C T A G G A A C A C C T G A C A A G A T G A A G G A T G G A A T G A G A C T T C T G A T C T G A G T A G G A G A A C G T A G A G G C C T C T A T C G A G G T A G A G G A A C T C A T A T A T A T T G A G C T G A A G T C T C A C A T C A T C A G A G C T A G G A C A C T C T G C A T T C A C C A T C G A T C G C T G T A T A A G T C T A T C G A T A C T A T A T T C A G G A C T G A G C C G A C C T G T C A C G C T G A C G G A A G C T T C C T T C A C G T T A A T C A T G G C A G C A A G C T G A C G A G C T C A A G A G G A C T A T G A C T C A T G T C G A C T G C A T T A A C C G G T C T C T G C A T T C A G C T G A A G G A A C T C C T T A G C A G A T A T T C C T G A T C C A G C C G C T T C C T A G T C T C T A T C T C A C G A C T C G A C T A G A C T G A C T C T A G T G G A G A G A A G A C A G T C G A G A T A C T G C C T C T T A T C T C C A A T C T G A T C C T G A A T G A C T T C C T C G G A G A T C A G A G A G A C C A C A A G G C C T G T G A T A T A T G A G C T C T G A G A T G C T A G T C T A G A G A A G C T A T G A A G A G C T C A C T T C T C T A C T A T C T C T T A A G G A G A C T G A T C G A C G G A A T A C A G A G A G A T T C T C T C G T A T C T G A G A T C C G G A T G C A G A A G A G G A G C T G T C C A A T G T G A T C C A T G T G A G G C C A T G C T T C A G G A G A A G G T A G T C A G G T C T A G T C A C T C T C T C C T A G G A G A A C T G T G A C G A T A T C T C G T A T T C C A T A T C C G A T T A A G T C G A G T C T G T T A A T A G T G C T A G G A C T A C C T G A A T G A T C T A A T G A T C T A C A A G A G G A G A G A G A A G T G G A G C C T C A G T C T A G G A T G G A G T A T G A T C T C A T G T G C G C T C C T T A C T C A C G C T C G T C A G T A G A G A A G C A A G T A C A A G T A C G T A T C G C A G T C C T C T T A T A G A A G C T G A C G T A A T G C T G C G G A T C T C C T T C C T T C C A T C G A C T C G G A T A C G A T C T T C T C C A T C T A C T G A A G T C A T A G T C C T T C T A G C T C G A T C T C G A G T T A G A T C C T G A T C G A T A G T T C A C C G T C G A G A G A G T G A G A T A T C C T A T G T G C T G C G C T A C C G G A G A C T C T C T T C C T C T C T T C A G C T A G T A G C T A C A T C T A G A T G C T C A G A T A T C G A T G T C G A A G C A A C C T C T G A A C T C C A A T T C T G A T C T T C A G A T A G A G G A T C G A C T C T G A C T C T C T G A C T G C T C C T A T A T C T C T C T A G C T G A G A A G G C G A A G C T A G C A C T A C G T C T T G T C A G T C C G C T G T T C T A G A A T G A A G T C G C C T G A A T G T A G C T C T T A G A C T T C T C C T G T T C C A T A C T C A A T G A C T A C T A G C A G G T A G A T C T A G C A G A T C C T G A C T G T G A G C A G A G G A T A A G C A G A A G G T C T G A T C A G C T A G T C A G G A T C A G G T C T C T G A G A T C G A A G A C C G T G G A G T G A A T G T A G T A A C C T C A T C T G G A T A A G C G G A C T T C C T T G A G T A T C A G G A G A G T G A T C G A G A C T T A T A G T C T C T C T G A A C G A C T A G A G A C A G A T G C C T C G T C A T A T A G C T C A A T C T T G G A G T C G T C A G A C T C T A T G G C G T C G A G T A T C C T T C G A A G A G G C A G T C A G C T T G G A T C A T A T A T G A A C A T C T T C G C C T A G G A T C G T C T T C T C C G A T T C G T G A C A C T A G G T G A G A G A C T C T T A G C T G C T C G G T C T C T A C T C T C T C T C G T G A T G T C C T T C G C G C A G A G A G T C G A C G T A T C A G T C A G G T C A G C C T A G A G T A C A A G G C T C T G G A T C G T G T A T C T C T C T C T A C T G A G C T T A C T T C G A C T A G G A A C G A G C C A C A C T G C A C T G C T C T C T G C G A T G T C G A C T C A C T C G A G G T C T G T C T T C C T G T G A T G T C A T T C T G T C C T T C A G C T A G G A T G C T A T G A A G G A C T C T G C A G C T G A T A T A A G G A A G T A T C A C A G T A G A A G G A A G G A C T C G G A T A G T T C A G A C T A C T C T T C A G T C A G T C G A A G A G A G G A C T A G G A A G C T C T T C C T A T T C C T A G G A C T T C T C G A C A G T T C T C T C T A A T C A A T A G A G A G A G C T A G C T A G A G A G A T A C T G G A A G T C T A G T T G A G T C A G T C C A C T C A T C T C A G C T T C T A A G C T A G G A T A G A A T A G A C T C C T G C G A T A G A C T A G T C C T G A C A G T G A C A A T C G G A A G G T A G G A C T T C G A C T A G G T A T T A A C C G C T G A G A A G A G C G T A G T C T G C A C T G T C T A A G C G C T G C T C C G G C C T G A T G G A A G T G C G C T C T T C A G A T A G T C A T C T C T G A C T G A G A A G C T T C T C A G T C G A T C A G A G C T G A A T A T T C T C G A T C A G G C C T G A A G T C G A A C A G G T T C G C C T T A C T C A A T C T G A C T T C G A T C T C T C C G A T T C C T G A A C G A T G G A T C G C C T A T C T A G A T T C A G C T G A C T G A C T T C C T C T G A G A A C C T G A C T T A C T C T T C T C G A C T G A G C A C G A T C T G G A C T G A T C T G C A C T C T T C C T T C A G C G T A C G A C A G A G C T G A G C A T T C C T T A A T T C C T T A C T G A C T G A A G T C C G G A G A T C T C A G C T T G C T A G C T A G T C T C T C A G G A G A C G C T T G A G C A C T A G C A T C A T T A G C A G T A T C C T C A T C T G T C A G A G C A C T A T A G G T T C G A C T G A G A C T C T G A G T G A T C T C T A C T C T A T C T G A A G G A G A G C A G T C C G C T C T G A C T C T G A A T C T G A A G T A T G G A G A C T G A T A G C C T G A G A T C C T G A T C T C G A C T G A G A G A T C A G T G A C C T T A T C C A G C G A C T G A C T C T T A C G T A T G G A T A C T C T A C G C A C G A A T A G A G T C G T C T C T T C A G T C A G T G A T T C C T G A A G G T T C A G G A A C A T A C T A C T A G G C T G G T G T G T T C A G G C T G T A A T A C T C C T G C C A C T A G A G A C T A A G T G A C T G G A T C T C A G G A T G C A A G G T G T C T C T T A G A T G A T T G C T C T A G G A G A G A A C C T G A T A A G G A A T T G G C A G T G G T T C A C G A T A T C G A C G A G G A G T C T G T C G A T G A G C G A A G G A T C G T C T A T T C A T T C T C A C T C G A T C C T G A G A C T C G G A G A A G C T G A T C T G A T A G A G C T T C G T A C T A T A G T C T C T T A A C G A C A C T A G G A A G C T C G C T C T G A T A C A T C C T A G T C G C C G C T C T C T G A C G G A A T A T G A C G G T A G C T A G A G C A G T C T A T A G A G C G G A A G C T C T G C G A C T A G T C T C A G T C G A C T A C C G C T A G A G C T C A G A T C A G C T T C G A C A A G A T T C A G C T C A T A G T T A G A T C T G C T G A G A G T G A G A G T G C C T C T A C A G G A C T C T C T C T C T T C C A C T G A G A G A G A G T T C T C G T A G G A A T T C T C A T A C A G T C C T G A G A A G C T T C T C G T G A T C C T A G T C T C A G C T A C T G G A A G C T A G C T T A T A C T G A A G A G G A C T G A C T T C C G A T A C C A T A C T T A C A T C A T C G T C T C G A T A T A T A T C G A A G A G G A C T T A C T G T G C T G G A T C G C G C C T C T T C A T G A G A G A A C A C A G C G T C T C T G C T A G G T C T C T C A C T T G A G T C C T T C T G G A C T G C C A T C T C T A T C G A G C A T G A A G T A A G C T G T A G C T A G T C T C T C A G T C A G G T C T T C T C A G C T T G C T C T C T C T G A G C C T G T T A C T A C T A G C A C G A A G C T A G C A T G G A A C A G T C G C G A C T C G A G C T C T T C G A C A T C T G A G G A G A A T A G C T C T G A G A G A A G T C T C A T T C T C A T A G G A T G A T G T T G A G T C A G A T A G A T C T C G C A C T G A G A G C C A G A A T T A A T C G C A A G C A C G G A G T C T T A A G G A C T T C C T A T C T A G T C C G C T A G A C T A A C A G G C A T A G C T T G T G A G A G T A C G G C C T T C T C C T T C G A T C T C T C C A C T C T T C T C A C A G C T G T T C T C A G T A C T T C C T A G C T C T C T C T C T C T G A A C C T C T C T G A G A G A C T T C C T T C A G A G C T T G T A G A C T G A A G G A C T A T A T T C T G A C G A G T C G C T T C T C T C T C G A C T T A G A G A A G A G T G G C T C C G T C C A G A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/Rooting.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,59 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; +use Cwd ; +use FindBin qw ( $Bin $Script ); + +my $CURRENT_DIR = $Bin; + +my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar"; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <newick input> + -o, --output <newick output> +~; +$usage .= "\n"; + +my ($input,$outfile); + + +GetOptions( + "input=s" => \$input, + "output=s" => \$outfile +); + + +die $usage + if ( !$input || !$outfile); + +my $treefile = $input; + + +# replace negative values by 0 +open(T,$treefile); +open(T2,">$treefile.2"); +while(<T>) +{ + my $line = $_; + $line =~s/\-\d+\.*\d*\,/0,/g; + $line =~s/\-\d+\.*\d*\)/0\)/g; + print T2 $line; +} +close(T); +close(T2); + +my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1"; +system($rooting_command); + +unlink("$treefile.all"); +unlink("$treefile.2"); +rename("$treefile.midpoint",$outfile); + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/rooting.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,193 @@ +<tool id="sniplay_rooting" name="Rooting" version="1.0.2"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Midpoint rooting of newick tree </description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package">Rootings_54.jar</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="perl"> + Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> + <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> + <data name="fileout" type="data" format="txt" label="${fileout_label}" /> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + + <test> + <param name="filein" value="newick" /> + <output name="fileout" file="out_tree" /> + <output name="fileout_log" file="out_tree.log" /> + </test> + + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + + +.. class:: infomark + +**Authors** Jean-François Dufayard, CIRAD, South Green platform + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +.. class:: infomark + +**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +--------------------------------------------------- + + + + +======= +Rooting +======= + +----------- +Description +----------- + + Compute a midpoint newick rooted tree. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +fastme Newick tree Newick +=========== ========================== ======= + + + +---------- +Input file +---------- + +Newick file + + +---------- +Parameters +---------- + +Output name + Output base name for the ouput files + + +------------ +Output files +------------ + +Output_name + Resulting tree rooted in newick format + +Output_name.log + Log file + +------------ +Dependencies +------------ +Rooting + CIRAD tool. Contact jean-francois.dufayard@cirad.fr + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Newick file +----------- + +:: + + (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... + + +Parameters +========== + +Output name -> out tree + + +Output files +============ + +out tree +-------- + +:: + + (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/test-data/newick Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,2 @@ +(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/test-data/out_tree Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,1 @@ +(ref:0.575788,(((((((((((((((((((((((PALAWAN:0.032789,KENDINGA5H:0.028863):0.031721,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.004581,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004869,DINORADO:0.065206):0.004898,((LUDAN:0.05423,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):8.8E-5):0.006838,CAAWA/FORT:0.05563):0.011439,CANELADEFE:0.050931):0.002897,PACHOLINHA:0.042509):0.002988,TRESMESES:0.028972):0.001209,((OS4:0.021016,OS6:0.01567):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.006303,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.004673,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.14437):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.04316,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.01418,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.05797):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.00344,(((((KUROKA:0.096901,IRAT144:0.032372):0.04063,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.03418):0.01106,CAIAPO:0.07222):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.001457,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.01125,(((IAC47:0.007321,(IAC165:5.0E-4,VARYLAVA90:0.00165):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.007912,IRAT234:0.037316):0.005647,MANDRIRAVI:0.049833):0.002593,RT1031-69:0.04352):0.005079,((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.00474):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):8.58E-4,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.02711,GRAZI:0.022678):7.63E-4):0.00987,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:0.0,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):9.71E-4):0.009442):0.002985):0.008281,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.02162,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.05943,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.001416,((GANIGI:0.040448,PULULAPA:0.03984):0.020258,GOGO:0.060904):0.005609):0.018877,CUIABANA:0.066182):0.020665,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.03265):0.012575,VIETNAM1:0.049323):0.00311,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.01445):0.01097):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.00624,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.043699,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.015245,(((JUMALI:0.07765,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607):0.14713500000000007);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,124 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <Hapmap input> + -o, --out <output in tabular format> + -s, --step <step (in bp)> +~; +$usage .= "\n"; + +my ($input,$out,$step); + +GetOptions( + "input=s" => \$input, + "out=s" => \$out, + "step=s" => \$step, +); + + +die $usage + if ( !$input || !$step || !$out ); + +my $max_chr_num = 100; + +my %counts; +my %counts_by_ind; +open(my $HAPMAP,$input); +my $headers= <$HAPMAP>; +$headers=~s/\n//g; +$headers=~s/\r//g; +my @ind_names = split(/\t/,$headers); +my @individual_names; +for (my $i = 12; $i <= $#ind_names; $i++) +{ + push(@individual_names,$ind_names[$i]); +} +my %maximums; +while(<$HAPMAP>) +{ + my $line = $_; + $line=~s/\n//g; + $line=~s/\r//g; + my @infos = split(/\t/,$line); + my $chrom = $infos[2]; + my $position = $infos[3]; + if ($position > $maximums{$chrom}){$maximums{$chrom}=$position;} + my $classe_position = int($position/$step); + $counts{$chrom}{$classe_position}++; + + my $ref_allele = $infos[11]; + for (my $i = 12; $i <= $#infos; $i++) + { + if (!$counts_by_ind{$chrom}{$classe_position}{$i}){$counts_by_ind{$chrom}{$classe_position}{$i} = 0;} + if ($infos[$i] ne $ref_allele) + { + $counts_by_ind{$chrom}{$classe_position}{$i}++; + } + } +} +close($HAPMAP); + +####################################################### +# global +####################################################### +open(my $OUT,">$out"); +print $OUT "Chromosome Position SNPs\n"; +my $chr_num = 0; +foreach my $chrom(sort keys(%counts)) +{ + $chr_num++; + my $ref_counts = $counts{$chrom}; + my %final_counts = %$ref_counts; + my $x = 0; + #foreach my $classe_position(sort {$a<=>$b} keys(%final_counts)) + for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) + { + my $nb = 0; + if ($counts{$chrom}{$classe_position}) + { + $nb = $counts{$chrom}{$classe_position}; + } + $x += $step; + print $OUT "$chrom $x $nb\n"; + } + if ($chr_num >= $max_chr_num){last;} +} +close($OUT); + +####################################################### +# For each individual +####################################################### +open(my $OUT2,">$out.by_sample"); +$chr_num = 0; +print $OUT2 "Chromosome ".join("\t",@individual_names) . "\n"; +foreach my $chrom(sort keys(%counts_by_ind)) +{ + $chr_num++; + my $ref_counts = $counts_by_ind{$chrom}; + my %final_counts = %$ref_counts; + for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) + { + print $OUT2 "$chrom"; + my $num_ind = 12; + foreach my $indiv(@individual_names) + { + my $val = 0; + + if ($counts_by_ind{$chrom}{$classe_position}{$num_ind}) + { + $val = $counts_by_ind{$chrom}{$classe_position}{$num_ind}; + } + print $OUT2 " $val"; + $num_ind++; + } + print $OUT2 "\n"; + } + if ($chr_num >= $max_chr_num){last;} +} +close($OUT2);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,207 @@ +<tool id="sniplay_density" name="SNP density" version="1.2.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Calculate SNP densities along chromosome from HapMap</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="bash"> + calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> + <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> + <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> + <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> +<!-- + <test> + <param name="input" value="input_test.txt" /> + <output name="output" file="output_test.txt" /> + </test> +--> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + + + +============= +SNP densities +============= + +----------- +Description +----------- + + Calculate SNP densities along chromosome from HapMap + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Hapmap file hapmap +=============== ====================== =========== + + +---------- +Input file +---------- + +Hapmap file + File with SNPs + + +---------- +Parameters +---------- + +Step + Step in bp for the window to calculate SNP density + +Output name + Output base name for the two ouput files + + +------------ +Output files +------------ + +Output_name + Tabular file with SNP density in each postion + +Output_name.by_sample + Tabular file with SNP density for each sample + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 + chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT + chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA + chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC + chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG + chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG + chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT + +Parameters +========== + +Step -> 200000 + +Output name -> densities + + +Output files +============ + +densities +--------- + +:: + + Chromosome Position SNPs + chr1 200000 355 + chr1 400000 228 + chr1 600000 63 + chr1 800000 191 + + +densities.by_sample +------------------- + +:: + + Chromosome BA58 BA59 BD54 + chr1 220 197 225 + chr1 130 119 133 + chr1 43 43 40 + chr1 139 167 141 + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,13 @@ +#!/bin/bash + +tool_path=$(dirname $0) +hapmap=$1 +fileout=$2 +fileout_bysample=$3 +step=$4 + +perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl -i $hapmap -o $fileout -s $step + +cp $fileout.by_sample $fileout_bysample +rm $fileout.by_sample +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/.svn/entries Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,130 @@ +10 + +dir +39 +svn+ssh://svn.sb-roscoff.fr/svn/logiciel/galaxy/galaxy4sniplay/SNP_density/test-data +svn+ssh://svn.sb-roscoff.fr/svn/logiciel/galaxy + + + +2014-12-05T15:19:39.834618Z +39 +gandres + + + + + + + + + + + + + + +0f93037e-e277-4375-988d-e0ab8f9fda44 + +hapmap +file + + + + +2014-10-10T14:09:09.000000Z +65d1c4316f6d483a62c8bea0f5b9ef2a +2014-12-05T15:19:39.834618Z +39 +gandres + + + + + + + + + + + + + + + + + + + + + +376118 + +result_bysample.txt +file + + + + +2014-12-05T14:21:25.000000Z +4c3d447481c9e55ef17337836c42fc38 +2014-12-05T15:19:39.834618Z +39 +gandres + + + + + + + + + + + + + + + + + + + + + +336 + +result.txt +file + + + + +2014-12-05T14:21:32.000000Z +436c5356d4acc99f8ed023bc681bb787 +2014-12-05T15:19:39.834618Z +39 +gandres + + + + + + + + + + + + + + + + + + + + + +357 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/.svn/text-base/hapmap.svn-base Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,3584 @@ +rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 +chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT +chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA +chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC +chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG +chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG +chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT +chr1:1398 [T/G] chr1 1398 Cc01_g00010:369 exon SYNONYMOUS_CODING gcA/gcC A/A 16.7% 3 TT TT NN TG +chr1:1394 [G/C] chr1 1394 Cc01_g00010:373 exon NON_SYNONYMOUS_CODING Cgt/Ggt R/G 16.7% 3 GG GG NN GC +chr1:1379 [A/T] chr1 1379 Cc01_g00010:388 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 16.7% 3 AA AA NN AT +chr1:1352 [T/C] chr1 1352 Cc01_g00010:415 exon NON_SYNONYMOUS_CODING Act/Gct T/A 33.3% 3 TT CC NN CC +chr1:1252 [T/A] chr1 1252 Cc01_g00010:515 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA +chr1:17176 [T/G] chr1 17176 Cc01_g00030:504 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TT TG TT +chr1:18041 [A/G] chr1 18041 Cc01_g00030:661 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 AA AA GG AG +chr1:18442 [C/A] chr1 18442 Cc01_g00030:929 exon NON_SYNONYMOUS_CODING tCc/tAc S/Y 25.0% 4 CC CC CA CA +chr1:18478 [T/C] chr1 18478 Cc01_g00030:965 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 25.0% 4 TT TT TC TC +chr1:18554 [T/G] chr1 18554 Cc01_g00030:1041 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT TT TG TG +chr1:19062 [T/A] chr1 19062 Cc01_g00030:1151 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN TT AA +chr1:19078 [A/G] chr1 19078 Cc01_g00030:1167 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:19138 [T/C] chr1 19138 Cc01_g00030:1227 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT CT TC +chr1:22125 [C/T] chr1 22125 Cc01_g00030:1773 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC CT CT +chr1:22212 [T/C] chr1 22212 Cc01_g00030:1860 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:22342 [T/A] chr1 22342 Cc01_g00030:1990 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 4 TT TT TA TA +chr1:22404 [C/T] chr1 22404 Cc01_g00030:2052 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC CT CT +chr1:22478 [C/G] chr1 22478 Cc01_g00030:2126 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC GG CC CC +chr1:22613 [C/T] chr1 22613 Cc01_g00030:2261 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 CC TT CC CC +chr1:22657 [C/T] chr1 22657 Cc01_g00030:2305 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC +chr1:22758 [A/G] chr1 22758 Cc01_g00030:2406 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AA AG AG +chr1:22903 [C/A] chr1 22903 Cc01_g00030:2551 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CC CA CA +chr1:22965 [G/T] chr1 22965 Cc01_g00030:2613 exon NON_SYNONYMOUS_CODING atG/atT M/I 12.5% 4 GG GG TG GG +chr1:23037 [A/G] chr1 23037 Cc01_g00030:2685 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA AA AG AG +chr1:24151 [A/G] chr1 24151 Cc01_g00030:3063 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA AG AG +chr1:24436 [T/C] chr1 24436 Cc01_g00030:3240 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT TC TC +chr1:25763 [G/C] chr1 25763 Cc01_g00030:3610 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 25.0% 4 GG GG GC GC +chr1:26910 [T/G] chr1 26910 Cc01_g00030:3889 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 25.0% 4 TT TT TG TG +chr1:26996 [C/T] chr1 26996 Cc01_g00030:3975 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 CC CC CT CT +chr1:27095 [A/T] chr1 27095 Cc01_g00030:4074 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT +chr1:27755 [C/T] chr1 27755 Cc01_g00030:4734 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC CT CT +chr1:30493 [C/T] chr1 30493 Cc01_g00030:4992 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:30505 [C/T] chr1 30505 Cc01_g00030:5004 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CC TT CT +chr1:30560 [A/G] chr1 30560 Cc01_g00030:5059 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AG AA +chr1:30592 [T/C] chr1 30592 Cc01_g00030:5091 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:32950 [A/G] chr1 32950 Cc01_g00030:5337 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AA AG AG +chr1:32968 [A/C] chr1 32968 Cc01_g00030:5355 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 4 AA CC AA AA +chr1:33022 [A/T] chr1 33022 Cc01_g00030:5409 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TT AA AA +chr1:33025 [T/A] chr1 33025 Cc01_g00030:5412 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT AA TT TT +chr1:33167 [T/C] chr1 33167 Cc01_g00030:5554 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 25.0% 4 TT CC TT TT +chr1:33196 [C/T] chr1 33196 Cc01_g00030:5583 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 CC TT CC CC +chr1:33467 [T/C] chr1 33467 Cc01_g00030:5854 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TC TC +chr1:37303 [G/A] chr1 37303 Cc01_g00040:129 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 GG NN NN AA +chr1:37602 [C/G] chr1 37602 Cc01_g00040:428 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC GG GG CG +chr1:37607 [T/G] chr1 37607 Cc01_g00040:433 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 50.0% 3 TT GG NN TG +chr1:38519 [A/C] chr1 38519 Cc01_g00040:507 exon SYNONYMOUS_CODING gcA/gcC A/A 33.3% 3 AA NN CC CC +chr1:38606 [G/A] chr1 38606 Cc01_g00040:594 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 4 GG AA GA GA +chr1:38657 [C/T] chr1 38657 Cc01_g00040:645 exon SYNONYMOUS_CODING caC/caT H/H 37.5% 4 CC TT TT CT +chr1:38927 [G/A] chr1 38927 Cc01_g00040:915 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN NN AA +chr1:38942 [G/C] chr1 38942 Cc01_g00040:930 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG NN CC CC +chr1:38952 [C/T] chr1 38952 Cc01_g00040:940 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 CC NN TT CT +chr1:38956 [T/C] chr1 38956 Cc01_g00040:944 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 3 TT NN CC TC +chr1:39103 [C/T] chr1 39103 Cc01_g00040:1091 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT +chr1:39113 [C/T] chr1 39113 Cc01_g00040:1101 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TT CT +chr1:39164 [T/G] chr1 39164 Cc01_g00040:1152 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TG TT TT +chr1:39389 [T/C] chr1 39389 Cc01_g00040:1377 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 2 TT NN NN TC +chr1:77092 [C/G] chr1 77092 Cc01_g00050:8 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 25.0% 4 CC GG GG GG +chr1:77069 [C/A] chr1 77069 Cc01_g00050:31 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 12.5% 4 CC CA CC CC +chr1:77040 [A/C] chr1 77040 Cc01_g00050:60 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 AA CC CC CC +chr1:77030 [T/C] chr1 77030 Cc01_g00050:70 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC CC CC +chr1:76998 [C/A] chr1 76998 Cc01_g00050:102 exon SYNONYMOUS_CODING ccG/ccT P/P 50.0% 4 CC AA CA CA +chr1:76995 [T/C] chr1 76995 Cc01_g00050:105 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC +chr1:83837 [G/A] chr1 83837 Cc01_g00060:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:84858 [A/C] chr1 84858 Cc01_g00060:392 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 37.5% 4 AA CC AA AC +chr1:84868 [C/T] chr1 84868 Cc01_g00060:402 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 4 CC TT CC TT +chr1:84880 [G/A] chr1 84880 Cc01_g00060:414 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GG AA +chr1:84991 [C/G] chr1 84991 Cc01_g00060:525 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 CC CC CG CC +chr1:105491 [C/A] chr1 105491 Cc01_g00070:36 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA +chr1:100754 [G/C] chr1 100754 Cc01_g00070:660 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 GG GC GG GG +chr1:100458 [A/C] chr1 100458 Cc01_g00070:720 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 37.5% 4 AA CC AA AC +chr1:100367 [C/A] chr1 100367 Cc01_g00070:811 exon STOP_GAINED Gga/Tga G/1 12.5% 4 CC CC CA CC +chr1:99870 [T/C] chr1 99870 Cc01_g00070:1068 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC +chr1:99742 [C/G] chr1 99742 Cc01_g00070:1196 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CC CG +chr1:99729 [G/A] chr1 99729 Cc01_g00070:1209 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GG GA +chr1:99727 [G/C] chr1 99727 Cc01_g00070:1211 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC +chr1:99642 [C/T] chr1 99642 Cc01_g00070:1296 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT +chr1:99567 [T/G] chr1 99567 Cc01_g00070:1371 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 TT TT TT TG +chr1:99549 [T/C] chr1 99549 Cc01_g00070:1389 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT CC TT TT +chr1:99448 [T/G] chr1 99448 Cc01_g00070:1490 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG +chr1:99354 [T/C] chr1 99354 Cc01_g00070:1584 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC +chr1:99162 [T/C] chr1 99162 Cc01_g00070:1776 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:98368 [C/G] chr1 98368 Cc01_g00070:2112 exon NON_SYNONYMOUS_CODING agG/agC R/S 50.0% 2 CC NN NN GG +chr1:97071 [A/C] chr1 97071 Cc01_g00070:2285 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 AA CC CC CC +chr1:96611 [C/T] chr1 96611 Cc01_g00070:2292 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CT CC CC +chr1:95183 [T/C] chr1 95183 Cc01_g00070:2748 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC +chr1:95134 [T/C] chr1 95134 Cc01_g00070:2797 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC TT TC +chr1:95116 [G/A] chr1 95116 Cc01_g00070:2815 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:94898 [G/A] chr1 94898 Cc01_g00070:2895 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA +chr1:94841 [A/T] chr1 94841 Cc01_g00070:2952 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:94700 [C/T] chr1 94700 Cc01_g00070:2994 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:94679 [A/G] chr1 94679 Cc01_g00070:3015 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AA AG +chr1:93879 [T/C] chr1 93879 Cc01_g00070:3411 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 TT CC TT TC +chr1:93873 [C/T] chr1 93873 Cc01_g00070:3417 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CC CT +chr1:92117 [A/T] chr1 92117 Cc01_g00070:3663 exon SYNONYMOUS_CODING ctT/ctA L/L 25.0% 4 AA TT AA AA +chr1:92011 [A/C] chr1 92011 Cc01_g00070:3769 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC +chr1:91347 [G/A] chr1 91347 Cc01_g00070:4194 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG +chr1:90731 [A/C] chr1 90731 Cc01_g00070:4545 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AC AC AC +chr1:90332 [T/A] chr1 90332 Cc01_g00070:4746 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TT TA +chr1:90303 [A/G] chr1 90303 Cc01_g00070:4775 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 25.0% 4 AA GG AA AA +chr1:90289 [C/T] chr1 90289 Cc01_g00070:4789 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 CC TT CC CT +chr1:90161 [A/G] chr1 90161 Cc01_g00070:4917 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:90128 [G/A] chr1 90128 Cc01_g00070:4950 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA +chr1:89792 [G/A] chr1 89792 Cc01_g00070:5127 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA GG GA +chr1:89745 [A/G] chr1 89745 Cc01_g00070:5174 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 37.5% 4 AA GG AA AG +chr1:89720 [T/C] chr1 89720 Cc01_g00070:5199 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC CC CC +chr1:89493 [A/G] chr1 89493 Cc01_g00070:5304 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG +chr1:89423 [A/C] chr1 89423 Cc01_g00070:5374 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC +chr1:89418 [A/T] chr1 89418 Cc01_g00070:5379 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 AA AA AA TA +chr1:88516 [T/G] chr1 88516 Cc01_g00070:5910 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 TT TT TT TG +chr1:87964 [T/C] chr1 87964 Cc01_g00070:6237 exon SYNONYMOUS_CODING agA/agG R/R 37.5% 4 TT CC TT TC +chr1:112990 [T/C] chr1 112990 Cc01_g00080:4 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 50.0% 4 TT TT CC CC +chr1:112983 [A/G] chr1 112983 Cc01_g00080:11 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 4 AA AA GG GG +chr1:112926 [A/T] chr1 112926 Cc01_g00080:68 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 50.0% 4 AA AA TT TT +chr1:112910 [T/C] chr1 112910 Cc01_g00080:84 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:112909 [A/C] chr1 112909 Cc01_g00080:85 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC +chr1:112875 [C/A] chr1 112875 Cc01_g00080:119 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 12.5% 4 CC CC CA CC +chr1:112874 [G/A] chr1 112874 Cc01_g00080:120 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG GG GA GA +chr1:112792 [A/G] chr1 112792 Cc01_g00080:202 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA AA GG GG +chr1:112070 [T/C] chr1 112070 Cc01_g00080:274 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 TT TT TC CC +chr1:111976 [T/C] chr1 111976 Cc01_g00080:368 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TC TT +chr1:111966 [G/C] chr1 111966 Cc01_g00080:378 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG +chr1:111413 [T/C] chr1 111413 Cc01_g00080:741 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 TT CC TT TT +chr1:111011 [T/A] chr1 111011 Cc01_g00080:879 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TT TA TT +chr1:111002 [G/A] chr1 111002 Cc01_g00080:888 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG AA AA AA +chr1:110176 [A/G] chr1 110176 Cc01_g00080:1233 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AA AG AA +chr1:127984 [A/G] chr1 127984 Cc01_g00090:15 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:128022 [T/A] chr1 128022 Cc01_g00090:53 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 TT AA AA AA +chr1:128047 [A/G] chr1 128047 Cc01_g00090:78 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:128072 [A/T] chr1 128072 Cc01_g00090:103 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA TT TT TT +chr1:128252 [T/C] chr1 128252 Cc01_g00090:283 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT CC CC CC +chr1:133985 [C/T] chr1 133985 Cc01_g00100:165 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC TT CC +chr1:133990 [T/G] chr1 133990 Cc01_g00100:170 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 12.5% 4 TT TT TT TG +chr1:134007 [G/T] chr1 134007 Cc01_g00100:187 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT TT GT +chr1:134174 [T/A] chr1 134174 Cc01_g00100:354 exon SYNONYMOUS_CODING gtT/gtA V/V 25.0% 4 TT TT TA TA +chr1:134262 [G/A] chr1 134262 Cc01_g00100:442 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GA GG +chr1:134333 [T/C] chr1 134333 Cc01_g00100:513 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT TC TC +chr1:134393 [C/A] chr1 134393 Cc01_g00100:573 exon SYNONYMOUS_CODING acC/acA T/T 37.5% 4 CC AA CC AC +chr1:134403 [C/T] chr1 134403 Cc01_g00100:583 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC CC TC CC +chr1:134481 [C/A] chr1 134481 Cc01_g00100:661 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC +chr1:134514 [T/C] chr1 134514 Cc01_g00100:694 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT TC TC TC +chr1:134570 [T/C] chr1 134570 Cc01_g00100:750 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TT CC TC +chr1:134580 [C/T] chr1 134580 Cc01_g00100:760 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT +chr1:134592 [C/G] chr1 134592 Cc01_g00100:772 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC GG CC CC +chr1:134603 [G/T] chr1 134603 Cc01_g00100:783 exon SYNONYMOUS_CODING acG/acT T/T 25.0% 4 GG GG TT GG +chr1:134957 [T/G] chr1 134957 Cc01_g00100:1137 exon SYNONYMOUS_CODING ccT/ccG P/P 37.5% 4 TT GG TT TG +chr1:135249 [C/A] chr1 135249 Cc01_g00100:1429 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 12.5% 4 CC CC CC CA +chr1:135260 [G/A] chr1 135260 Cc01_g00100:1440 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GG AA GA +chr1:135922 [T/C] chr1 135922 Cc01_g00110:53 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 37.5% 4 TT CC TT TC +chr1:135925 [A/G] chr1 135925 Cc01_g00110:56 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AA AG +chr1:136539 [G/A] chr1 136539 Cc01_g00120:13 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AA GG +chr1:136654 [A/T] chr1 136654 Cc01_g00120:128 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 AA AA TT AA +chr1:136658 [A/G] chr1 136658 Cc01_g00120:132 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG +chr1:136898 [A/G] chr1 136898 Cc01_g00120:372 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG +chr1:136996 [A/G] chr1 136996 Cc01_g00120:470 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GG AG +chr1:137035 [T/C] chr1 137035 Cc01_g00120:509 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT +chr1:137064 [G/A] chr1 137064 Cc01_g00120:538 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG AA AA GA +chr1:137153 [A/G] chr1 137153 Cc01_g00120:627 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AA AG +chr1:137300 [C/T] chr1 137300 Cc01_g00120:774 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC TT CC +chr1:137483 [G/A] chr1 137483 Cc01_g00120:957 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GG GA +chr1:137525 [A/G] chr1 137525 Cc01_g00120:999 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA GG AA +chr1:137571 [A/G] chr1 137571 Cc01_g00120:1045 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG GG AG +chr1:137669 [C/T] chr1 137669 Cc01_g00120:1143 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT +chr1:137725 [T/C] chr1 137725 Cc01_g00120:1199 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 TT TT TT TC +chr1:137873 [T/C] chr1 137873 Cc01_g00120:1347 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC +chr1:137891 [C/T] chr1 137891 Cc01_g00120:1365 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:138059 [T/C] chr1 138059 Cc01_g00120:1533 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC TT TT +chr1:138108 [C/T] chr1 138108 Cc01_g00120:1582 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT CC CT +chr1:138227 [C/T] chr1 138227 Cc01_g00120:1701 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC TT CC +chr1:138383 [C/T] chr1 138383 Cc01_g00120:1857 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT +chr1:138386 [T/C] chr1 138386 Cc01_g00120:1860 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC +chr1:138497 [G/A] chr1 138497 Cc01_g00120:1971 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG +chr1:144606 [G/C] chr1 144606 Cc01_g00130:45 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG CC GC +chr1:144576 [C/G] chr1 144576 Cc01_g00130:75 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 CC GG GG GG +chr1:144519 [A/G] chr1 144519 Cc01_g00130:132 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA AA GG AA +chr1:144434 [T/A] chr1 144434 Cc01_g00130:217 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 37.5% 4 TT AA TT TA +chr1:144286 [C/G] chr1 144286 Cc01_g00130:365 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 50.0% 4 CC GG GG CC +chr1:147816 [C/T] chr1 147816 Cc01_g00140:18 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC TT NN NN +chr1:147821 [G/T] chr1 147821 Cc01_g00140:23 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 33.3% 3 GG TT NN GG +chr1:147823 [G/A] chr1 147823 Cc01_g00140:25 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG +chr1:147861 [G/A] chr1 147861 Cc01_g00140:63 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 GG GG NN AA +chr1:147863 [G/C] chr1 147863 Cc01_g00140:65 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 33.3% 3 GG GG NN CC +chr1:147872 [C/T] chr1 147872 Cc01_g00140:74 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 33.3% 3 CC TT NN CC +chr1:147974 [G/T] chr1 147974 Cc01_g00140:176 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT TT TT +chr1:148011 [T/G] chr1 148011 Cc01_g00140:213 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT GG TT TT +chr1:148050 [T/C] chr1 148050 Cc01_g00140:252 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT CC TT +chr1:148062 [G/A] chr1 148062 Cc01_g00140:264 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA +chr1:148150 [A/G] chr1 148150 Cc01_g00140:352 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 AA AG AA AA +chr1:148165 [C/G] chr1 148165 Cc01_g00140:367 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 CC CC GG CC +chr1:148179 [C/G] chr1 148179 Cc01_g00140:381 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC +chr1:148184 [A/G] chr1 148184 Cc01_g00140:386 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG +chr1:148230 [C/T] chr1 148230 Cc01_g00140:432 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC TT CC CC +chr1:148933 [G/T] chr1 148933 Cc01_g00140:447 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT +chr1:148935 [G/T] chr1 148935 Cc01_g00140:449 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT +chr1:148943 [G/A] chr1 148943 Cc01_g00140:457 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA AA AA +chr1:148945 [A/G] chr1 148945 Cc01_g00140:459 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA GG GG GG +chr1:149174 [A/G] chr1 149174 Cc01_g00140:492 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 4 AA AG GG AG +chr1:149185 [A/G] chr1 149185 Cc01_g00140:503 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AA GG AA +chr1:149253 [C/T] chr1 149253 Cc01_g00140:571 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT +chr1:149279 [G/A] chr1 149279 Cc01_g00140:597 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG GA AA GA +chr1:150025 [G/C] chr1 150025 Cc01_g00140:698 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 12.5% 4 GG GG GG GC +chr1:150045 [G/A] chr1 150045 Cc01_g00140:718 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG +chr1:150080 [A/T] chr1 150080 Cc01_g00140:753 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA +chr1:150083 [G/A] chr1 150083 Cc01_g00140:756 exon SYNONYMOUS_CODING gtG/gtA V/V 50.0% 4 GG AG AA AG +chr1:151272 [C/T] chr1 151272 Cc01_g00140:847 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:151277 [G/C] chr1 151277 Cc01_g00140:852 exon SYNONYMOUS_CODING ccG/ccC P/P 50.0% 4 GG GC CC CG +chr1:152592 [T/C] chr1 152592 Cc01_g00140:903 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TT TC +chr1:157051 [C/T] chr1 157051 Cc01_g00140:960 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC TT TT TT +chr1:160171 [C/A] chr1 160171 Cc01_g00140:1088 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA AA AA +chr1:160217 [A/G] chr1 160217 Cc01_g00140:1134 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA AG AA AG +chr1:160786 [C/T] chr1 160786 Cc01_g00140:1194 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC TC +chr1:161276 [A/G] chr1 161276 Cc01_g00140:1312 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA +chr1:161769 [A/T] chr1 161769 Cc01_g00140:1461 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 4 AA AT TT AT +chr1:161789 [A/C] chr1 161789 Cc01_g00140:1481 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA CA AA AA +chr1:161808 [A/T] chr1 161808 Cc01_g00140:1500 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA TA AA AA +chr1:161819 [G/A] chr1 161819 Cc01_g00140:1511 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 12.5% 4 GG GA GG GG +chr1:161837 [T/C] chr1 161837 Cc01_g00140:1529 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT +chr1:162050 [C/T] chr1 162050 Cc01_g00140:1545 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC CT CC +chr1:162069 [C/A] chr1 162069 Cc01_g00140:1564 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 12.5% 4 CC CC CC AC +chr1:162112 [A/T] chr1 162112 Cc01_g00140:1607 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 12.5% 4 AA AT AA AA +chr1:162135 [A/C] chr1 162135 Cc01_g00140:1630 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA CA +chr1:162634 [C/G] chr1 162634 Cc01_g00140:1650 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 CC CC CC GC +chr1:163489 [A/T] chr1 163489 Cc01_g00140:1854 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AT AA AA +chr1:168498 [C/T] chr1 168498 Cc01_g00150:90 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC TT CC +chr1:168595 [G/A] chr1 168595 Cc01_g00150:187 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:168747 [A/T] chr1 168747 Cc01_g00150:339 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA AA TT +chr1:174617 [C/G] chr1 174617 Cc01_g00160:6 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC CC GG CC +chr1:174616 [C/T] chr1 174616 Cc01_g00160:7 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC CC TT CC +chr1:174601 [G/C] chr1 174601 Cc01_g00160:22 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 GG GC GG GG +chr1:174600 [A/G] chr1 174600 Cc01_g00160:23 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AA AG AA +chr1:174590 [C/A] chr1 174590 Cc01_g00160:33 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC +chr1:174580 [C/T] chr1 174580 Cc01_g00160:43 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TC TC CT +chr1:174572 [C/T] chr1 174572 Cc01_g00160:51 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TC TC CT +chr1:174565 [T/C] chr1 174565 Cc01_g00160:58 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CT TC TC +chr1:174562 [A/G] chr1 174562 Cc01_g00160:61 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA GA AA AG +chr1:174533 [C/G] chr1 174533 Cc01_g00160:90 exon SYNONYMOUS_CODING ctG/ctC L/L 25.0% 4 CC GG GG GG +chr1:174501 [C/T] chr1 174501 Cc01_g00160:122 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 37.5% 4 CC TC TT CC +chr1:174490 [C/T] chr1 174490 Cc01_g00160:133 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 4 CC TC TT TC +chr1:174472 [C/T] chr1 174472 Cc01_g00160:151 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 CC TC CC CC +chr1:174446 [T/C] chr1 174446 Cc01_g00160:177 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:174440 [G/A] chr1 174440 Cc01_g00160:183 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 GG AG AA GG +chr1:174419 [C/T] chr1 174419 Cc01_g00160:204 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TC CT CC +chr1:174413 [G/C] chr1 174413 Cc01_g00160:210 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG +chr1:174411 [C/T] chr1 174411 Cc01_g00160:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 CC TC CT CC +chr1:174403 [T/C] chr1 174403 Cc01_g00160:220 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT CT TT TT +chr1:174401 [G/A] chr1 174401 Cc01_g00160:222 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GA AG GG +chr1:174374 [G/A] chr1 174374 Cc01_g00160:249 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG GG AA GG +chr1:174353 [G/A] chr1 174353 Cc01_g00160:270 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG +chr1:174324 [G/A] chr1 174324 Cc01_g00160:299 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 37.5% 4 GG GA GA GA +chr1:174310 [C/T] chr1 174310 Cc01_g00160:313 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 CC CT TT CT +chr1:174297 [C/T] chr1 174297 Cc01_g00160:326 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC CT +chr1:174295 [G/A] chr1 174295 Cc01_g00160:328 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GA GG GA +chr1:174280 [G/T] chr1 174280 Cc01_g00160:343 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 GG GT GT GG +chr1:174257 [G/A] chr1 174257 Cc01_g00160:366 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG GA GG +chr1:174251 [C/T] chr1 174251 Cc01_g00160:372 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CC CT CC +chr1:174248 [G/A] chr1 174248 Cc01_g00160:375 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:174242 [A/T] chr1 174242 Cc01_g00160:381 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:174232 [C/T] chr1 174232 Cc01_g00160:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CT CC +chr1:174225 [G/C] chr1 174225 Cc01_g00160:398 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GC GG GG +chr1:174208 [C/G] chr1 174208 Cc01_g00160:415 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 CC CG CC CC +chr1:174205 [G/A] chr1 174205 Cc01_g00160:418 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG GA AG GG +chr1:174192 [G/A] chr1 174192 Cc01_g00160:431 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG GA GA GG +chr1:174190 [G/A] chr1 174190 Cc01_g00160:433 exon STOP_GAINED Cag/Tag Q/5 25.0% 4 GG GA AG GG +chr1:174185 [A/T] chr1 174185 Cc01_g00160:438 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AT TA AA +chr1:174174 [C/T] chr1 174174 Cc01_g00160:449 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT TC CC +chr1:174172 [T/C] chr1 174172 Cc01_g00160:451 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT +chr1:174068 [G/C] chr1 174068 Cc01_g00160:555 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 16.7% 3 GG GC NN GG +chr1:174026 [G/T] chr1 174026 Cc01_g00160:597 exon NON_SYNONYMOUS_CODING agC/agA S/R 33.3% 3 GG TT NN GG +chr1:173945 [C/G] chr1 173945 Cc01_g00160:678 exon SYNONYMOUS_CODING gcG/gcC A/A 12.5% 4 CC CG CC CC +chr1:173942 [C/T] chr1 173942 Cc01_g00160:681 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT TT CT +chr1:173921 [G/A] chr1 173921 Cc01_g00160:702 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG AA AA GA +chr1:173846 [G/A] chr1 173846 Cc01_g00160:777 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 3 GG AA NN GA +chr1:173642 [A/T] chr1 173642 Cc01_g00160:981 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA TT AA AA +chr1:173627 [A/G] chr1 173627 Cc01_g00160:996 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA GG AA AA +chr1:173596 [C/A] chr1 173596 Cc01_g00160:1027 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 CC CA CC CC +chr1:173585 [G/A] chr1 173585 Cc01_g00160:1038 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AG AA AA +chr1:173444 [G/T] chr1 173444 Cc01_g00160:1179 exon SYNONYMOUS_CODING atC/atA I/I 25.0% 2 GG NN NN GT +chr1:173410 [C/T] chr1 173410 Cc01_g00160:1213 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 16.7% 3 CC CC NN CT +chr1:173230 [T/C] chr1 173230 Cc01_g00160:1393 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 16.7% 3 TT TT NN TC +chr1:173180 [C/T] chr1 173180 Cc01_g00160:1443 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 CC TT NN CC +chr1:173126 [A/G] chr1 173126 Cc01_g00160:1497 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA GG AA AA +chr1:172613 [G/C] chr1 172613 Cc01_g00160:2010 exon SYNONYMOUS_CODING ctC/ctG L/L 50.0% 3 GG CC NN GC +chr1:172589 [G/T] chr1 172589 Cc01_g00160:2034 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 16.7% 3 GG GG NN TG +chr1:172499 [A/G] chr1 172499 Cc01_g00160:2124 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA NN GG AG +chr1:172355 [T/C] chr1 172355 Cc01_g00160:2268 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TC NN TT +chr1:172314 [T/C] chr1 172314 Cc01_g00160:2309 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 TT TC NN TT +chr1:172303 [G/A] chr1 172303 Cc01_g00160:2320 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 GG AA NN GG +chr1:172265 [T/C] chr1 172265 Cc01_g00160:2358 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TT NN TC +chr1:172206 [G/A] chr1 172206 Cc01_g00160:2417 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 GG GA NN GG +chr1:172178 [T/C] chr1 172178 Cc01_g00160:2445 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 2 TT NN NN TC +chr1:172150 [T/C] chr1 172150 Cc01_g00160:2473 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 2 TT NN NN TC +chr1:181949 [A/C] chr1 181949 Cc01_g00170:492 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 2 AA NN NN CC +chr1:182195 [C/A] chr1 182195 Cc01_g00170:738 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 2 CC NN NN AA +chr1:182231 [G/A] chr1 182231 Cc01_g00170:774 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA +chr1:182291 [A/G] chr1 182291 Cc01_g00170:834 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 3 AA NN AG GG +chr1:182424 [G/A] chr1 182424 Cc01_g00170:861 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA +chr1:182456 [A/G] chr1 182456 Cc01_g00170:893 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA NN AA AG +chr1:182483 [A/G] chr1 182483 Cc01_g00170:920 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:182874 [A/G] chr1 182874 Cc01_g00170:1113 exon SYNONYMOUS_CODING ccA/ccG P/P 33.3% 3 AA NN AA GG +chr1:183107 [T/C] chr1 183107 Cc01_g00170:1346 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT +chr1:188621 [G/A] chr1 188621 Cc01_g00180:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:188690 [C/A] chr1 188690 Cc01_g00180:81 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC +chr1:189264 [A/G] chr1 189264 Cc01_g00180:254 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AA AG AG +chr1:189346 [C/G] chr1 189346 Cc01_g00180:336 exon SYNONYMOUS_CODING cgC/cgG R/R 25.0% 4 CC GG GG GG +chr1:189357 [G/A] chr1 189357 Cc01_g00180:347 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA +chr1:189499 [G/C] chr1 189499 Cc01_g00180:489 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 4 GG CC CC GG +chr1:189586 [C/T] chr1 189586 Cc01_g00180:576 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT TT CC +chr1:190066 [A/G] chr1 190066 Cc01_g00180:780 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA +chr1:190127 [T/G] chr1 190127 Cc01_g00180:841 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 TT GG GG GG +chr1:190494 [C/T] chr1 190494 Cc01_g00180:1023 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 CC TT TT TT +chr1:190503 [A/G] chr1 190503 Cc01_g00180:1032 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:190584 [T/C] chr1 190584 Cc01_g00180:1113 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT +chr1:190662 [A/G] chr1 190662 Cc01_g00180:1191 exon SYNONYMOUS_STOP taA/taG 3/3 25.0% 4 AA AA GG AA +chr1:193899 [T/C] chr1 193899 Cc01_g00190:67 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 TT CC TT TT +chr1:193871 [T/C] chr1 193871 Cc01_g00190:95 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 TT TT CC TC +chr1:193809 [A/T] chr1 193809 Cc01_g00190:157 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA TA +chr1:193801 [G/C] chr1 193801 Cc01_g00190:165 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 GG GG GG CG +chr1:193793 [C/T] chr1 193793 Cc01_g00190:173 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC TC +chr1:193735 [C/T] chr1 193735 Cc01_g00190:231 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CT CT TC +chr1:193681 [G/C] chr1 193681 Cc01_g00190:240 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG GC GG GC +chr1:193649 [T/G] chr1 193649 Cc01_g00190:272 exon NON_SYNONYMOUS_CODING gAc/gCc D/A 12.5% 4 TT TT TT TG +chr1:193584 [G/A] chr1 193584 Cc01_g00190:337 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 25.0% 4 GG GG AA GG +chr1:193551 [T/A] chr1 193551 Cc01_g00190:370 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 TT AA TT TA +chr1:193129 [T/A] chr1 193129 Cc01_g00190:445 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 25.0% 4 TT TT AA TT +chr1:192625 [A/G] chr1 192625 Cc01_g00190:654 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AA GG AA +chr1:191959 [T/C] chr1 191959 Cc01_g00190:689 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT CC TT +chr1:191385 [T/A] chr1 191385 Cc01_g00190:915 exon SYNONYMOUS_CODING tcA/tcT S/S 25.0% 4 TT AA AA AA +chr1:191370 [A/G] chr1 191370 Cc01_g00190:930 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AA GG AA +chr1:191325 [C/T] chr1 191325 Cc01_g00190:975 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT +chr1:199253 [T/C] chr1 199253 Cc01_g00200:6 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT CC TT +chr1:199193 [G/A] chr1 199193 Cc01_g00200:66 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GG GA +chr1:199148 [T/A] chr1 199148 Cc01_g00200:111 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 12.5% 4 TT TT TT AT +chr1:199134 [G/A] chr1 199134 Cc01_g00200:125 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG AG +chr1:199093 [A/C] chr1 199093 Cc01_g00200:166 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 37.5% 4 AA CC AA CA +chr1:199078 [T/C] chr1 199078 Cc01_g00200:181 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CC TT TT +chr1:198900 [A/T] chr1 198900 Cc01_g00200:262 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 12.5% 4 AA AA AA AT +chr1:198850 [G/A] chr1 198850 Cc01_g00200:312 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA +chr1:198811 [A/G] chr1 198811 Cc01_g00200:351 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 AA GG AA AA +chr1:198805 [A/G] chr1 198805 Cc01_g00200:357 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA AA GG AA +chr1:198802 [C/G] chr1 198802 Cc01_g00200:360 exon SYNONYMOUS_CODING gtG/gtC V/V 25.0% 4 CC CC GG CC +chr1:197996 [A/G] chr1 197996 Cc01_g00200:615 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG +chr1:197551 [A/G] chr1 197551 Cc01_g00200:963 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG AA AA +chr1:197200 [C/T] chr1 197200 Cc01_g00200:1207 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 CC TT CT CT +chr1:197177 [C/T] chr1 197177 Cc01_g00200:1230 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC TT TT TT +chr1:196815 [C/T] chr1 196815 Cc01_g00200:1344 exon SYNONYMOUS_CODING acG/acA T/T 50.0% 4 CC CT TT CT +chr1:196570 [A/T] chr1 196570 Cc01_g00200:1485 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AA AT +chr1:196315 [G/A] chr1 196315 Cc01_g00200:1584 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GG AA GG +chr1:196047 [G/C] chr1 196047 Cc01_g00200:1668 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 GG GG CC GG +chr1:195875 [A/G] chr1 195875 Cc01_g00200:1698 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GG AA AA +chr1:195821 [A/G] chr1 195821 Cc01_g00200:1752 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:208818 [T/C] chr1 208818 Cc01_g00220:430 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TC TT TC +chr1:207744 [G/A] chr1 207744 Cc01_g00220:618 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG GA GG GA +chr1:207027 [T/C] chr1 207027 Cc01_g00220:756 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TC TT TT +chr1:206648 [A/G] chr1 206648 Cc01_g00220:891 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:206440 [T/C] chr1 206440 Cc01_g00220:1099 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC +chr1:206402 [A/G] chr1 206402 Cc01_g00220:1137 exon SYNONYMOUS_CODING ccT/ccC P/P 50.0% 4 AA AA GG GG +chr1:216024 [C/T] chr1 216024 Cc01_g00230:429 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN +chr1:218860 [T/C] chr1 218860 Cc01_g00230:1338 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TT CC +chr1:218862 [G/A] chr1 218862 Cc01_g00230:1340 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 GG GG AA GG +chr1:219273 [C/T] chr1 219273 Cc01_g00230:1566 exon SYNONYMOUS_CODING tcC/tcT S/S 33.3% 3 CC NN TT TT +chr1:219413 [G/A] chr1 219413 Cc01_g00230:1605 exon SYNONYMOUS_CODING ccG/ccA P/P 50.0% 3 GG NN GA AA +chr1:219545 [T/C] chr1 219545 Cc01_g00230:1737 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC +chr1:220134 [A/G] chr1 220134 Cc01_g00230:2126 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA GG GG GG +chr1:220340 [A/G] chr1 220340 Cc01_g00230:2332 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG +chr1:221669 [G/T] chr1 221669 Cc01_g00240:79 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 GG TT TT GG +chr1:221674 [T/C] chr1 221674 Cc01_g00240:84 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT TC +chr1:221714 [G/T] chr1 221714 Cc01_g00240:124 exon NON_SYNONYMOUS_CODING Ggg/Tgg G/W 25.0% 4 GG TT GG GG +chr1:221718 [G/A] chr1 221718 Cc01_g00240:128 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GG AG +chr1:221746 [A/T] chr1 221746 Cc01_g00240:156 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 AA AT AA AA +chr1:221763 [A/T] chr1 221763 Cc01_g00240:173 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA +chr1:221788 [C/T] chr1 221788 Cc01_g00240:198 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 CC CT CC CC +chr1:221833 [T/C] chr1 221833 Cc01_g00240:243 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT CT TT TT +chr1:221852 [C/T] chr1 221852 Cc01_g00240:262 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 CC CC CC CT +chr1:221853 [G/A] chr1 221853 Cc01_g00240:263 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 GG GG GG AA +chr1:221866 [A/T] chr1 221866 Cc01_g00240:276 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT +chr1:222383 [T/C] chr1 222383 Cc01_g00240:354 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT +chr1:222633 [T/C] chr1 222633 Cc01_g00240:417 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:222951 [T/C] chr1 222951 Cc01_g00240:534 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:224386 [T/A] chr1 224386 Cc01_g00240:726 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT +chr1:224660 [A/T] chr1 224660 Cc01_g00240:825 exon SYNONYMOUS_CODING ggA/ggT G/G 37.5% 4 AA TT AA AT +chr1:224706 [G/C] chr1 224706 Cc01_g00240:871 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 GG GG GC GG +chr1:225032 [G/A] chr1 225032 Cc01_g00240:933 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG +chr1:225065 [C/T] chr1 225065 Cc01_g00240:966 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC TC CC CC +chr1:225194 [C/T] chr1 225194 Cc01_g00240:1008 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC TT CC CT +chr1:226501 [T/C] chr1 226501 Cc01_g00240:1072 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC CT +chr1:226539 [C/A] chr1 226539 Cc01_g00240:1110 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA +chr1:226575 [T/C] chr1 226575 Cc01_g00240:1146 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 TT TC TT TT +chr1:226694 [C/G] chr1 226694 Cc01_g00240:1181 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC +chr1:232340 [C/T] chr1 232340 Cc01_g00250:33 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CC TT CC +chr1:232292 [G/A] chr1 232292 Cc01_g00250:81 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA AA AA +chr1:229696 [A/G] chr1 229696 Cc01_g00250:380 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AA AG +chr1:228604 [A/G] chr1 228604 Cc01_g00250:468 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA +chr1:250535 [A/C] chr1 250535 Cc01_g00260:69 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC +chr1:250487 [T/A] chr1 250487 Cc01_g00260:117 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 TT TA TT TT +chr1:250388 [G/A] chr1 250388 Cc01_g00260:216 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA GG GG +chr1:246857 [G/A] chr1 246857 Cc01_g00260:529 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG GA GG +chr1:246722 [T/C] chr1 246722 Cc01_g00260:584 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT CC TT TC +chr1:246700 [A/G] chr1 246700 Cc01_g00260:606 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA GA +chr1:246674 [G/C] chr1 246674 Cc01_g00260:632 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GG GG GC +chr1:244939 [T/C] chr1 244939 Cc01_g00260:648 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TC TC TT +chr1:244750 [T/C] chr1 244750 Cc01_g00260:726 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TT TC +chr1:254013 [C/T] chr1 254013 Cc01_g00270:80 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:254369 [A/G] chr1 254369 Cc01_g00270:114 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AG AA +chr1:254414 [C/T] chr1 254414 Cc01_g00270:159 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:254486 [C/T] chr1 254486 Cc01_g00270:231 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CT CC CC +chr1:256173 [C/T] chr1 256173 Cc01_g00270:426 exon SYNONYMOUS_CODING ggC/ggT G/G 50.0% 4 CC CT TT CT +chr1:256269 [T/A] chr1 256269 Cc01_g00270:522 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 TT TT TT TA +chr1:256296 [C/G] chr1 256296 Cc01_g00270:549 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CC CG CC +chr1:256351 [G/C] chr1 256351 Cc01_g00270:604 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG +chr1:269489 [G/A] chr1 269489 Cc01_g00280:101 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GG GA +chr1:269514 [T/C] chr1 269514 Cc01_g00280:126 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC CC CC +chr1:269516 [T/C] chr1 269516 Cc01_g00280:128 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT TC +chr1:269724 [T/C] chr1 269724 Cc01_g00280:336 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC CC CC +chr1:269781 [G/A] chr1 269781 Cc01_g00280:393 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA +chr1:269793 [T/C] chr1 269793 Cc01_g00280:405 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TT TC +chr1:269833 [G/T] chr1 269833 Cc01_g00280:445 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT +chr1:269843 [T/C] chr1 269843 Cc01_g00280:455 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 TT TT TT CT +chr1:269847 [C/T] chr1 269847 Cc01_g00280:459 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC CT +chr1:269904 [T/C] chr1 269904 Cc01_g00280:516 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:269928 [C/T] chr1 269928 Cc01_g00280:540 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT +chr1:270027 [G/T] chr1 270027 Cc01_g00280:639 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT +chr1:270312 [A/C] chr1 270312 Cc01_g00280:924 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 AA AA CC AA +chr1:270383 [G/C] chr1 270383 Cc01_g00280:995 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GG GC +chr1:270395 [G/T] chr1 270395 Cc01_g00280:1007 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GG GT GG +chr1:270483 [T/C] chr1 270483 Cc01_g00280:1095 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TT TT TC +chr1:276780 [A/C] chr1 276780 Cc01_g00290:10 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 AA CC CC CC +chr1:274650 [T/G] chr1 274650 Cc01_g00290:196 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT +chr1:274413 [T/A] chr1 274413 Cc01_g00290:433 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TA TT +chr1:274345 [A/G] chr1 274345 Cc01_g00290:501 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA +chr1:273652 [G/A] chr1 273652 Cc01_g00290:639 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA GG GA +chr1:273576 [C/T] chr1 273576 Cc01_g00290:715 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC CC TT CC +chr1:273394 [C/T] chr1 273394 Cc01_g00290:897 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CC TT CT +chr1:273220 [G/A] chr1 273220 Cc01_g00290:1071 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GG GA GG +chr1:273180 [C/G] chr1 273180 Cc01_g00290:1111 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 37.5% 4 CC CC GG CG +chr1:273178 [G/A] chr1 273178 Cc01_g00290:1113 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GG AA GA +chr1:288461 [C/T] chr1 288461 Cc01_g00300:50 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:288120 [G/A] chr1 288120 Cc01_g00300:228 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 GG GG GA GG +chr1:287468 [G/A] chr1 287468 Cc01_g00300:469 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GG AA GG +chr1:287403 [A/G] chr1 287403 Cc01_g00300:534 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG GG GG +chr1:287370 [C/T] chr1 287370 Cc01_g00300:567 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT +chr1:286545 [A/G] chr1 286545 Cc01_g00300:774 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA AA GG AA +chr1:286507 [G/A] chr1 286507 Cc01_g00300:812 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG GA +chr1:286482 [G/C] chr1 286482 Cc01_g00300:837 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GG GG CG +chr1:285910 [C/A] chr1 285910 Cc01_g00300:942 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 CC AA CC AA +chr1:285897 [A/G] chr1 285897 Cc01_g00300:955 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG +chr1:285722 [T/G] chr1 285722 Cc01_g00300:1031 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 25.0% 4 TT TT GG TT +chr1:283896 [T/C] chr1 283896 Cc01_g00300:1335 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TT TC +chr1:283878 [G/A] chr1 283878 Cc01_g00300:1353 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG AA AA AA +chr1:283455 [A/T] chr1 283455 Cc01_g00300:1569 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AT AA AA +chr1:283107 [T/C] chr1 283107 Cc01_g00300:1682 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TC TT TT +chr1:280180 [T/C] chr1 280180 Cc01_g00300:1872 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC CC CC +chr1:293608 [T/C] chr1 293608 Cc01_g00310:9 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:293593 [G/A] chr1 293593 Cc01_g00310:24 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA GA GA +chr1:293581 [A/T] chr1 293581 Cc01_g00310:36 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA AT AT AT +chr1:293556 [G/A] chr1 293556 Cc01_g00310:61 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 GG GA GA GA +chr1:293548 [G/A] chr1 293548 Cc01_g00310:69 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 GG GG GA GG +chr1:293524 [A/G] chr1 293524 Cc01_g00310:93 exon SYNONYMOUS_CODING aaT/aaC N/N 37.5% 4 AA GG GG AG +chr1:290571 [T/C] chr1 290571 Cc01_g00310:310 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT +chr1:300689 [C/A] chr1 300689 Cc01_g00320:60 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 CC CC CC CA +chr1:300911 [G/T] chr1 300911 Cc01_g00320:111 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT +chr1:301164 [A/C] chr1 301164 Cc01_g00320:219 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA +chr1:301180 [G/T] chr1 301180 Cc01_g00320:235 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG +chr1:304719 [T/A] chr1 304719 Cc01_g00320:558 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TT TA +chr1:304779 [A/C] chr1 304779 Cc01_g00320:618 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA +chr1:329247 [C/A] chr1 329247 Cc01_g00330:270 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC AA CC CC +chr1:329217 [G/A] chr1 329217 Cc01_g00330:300 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG AA GA GA +chr1:329108 [G/A] chr1 329108 Cc01_g00330:409 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GA GG GG +chr1:329088 [A/G] chr1 329088 Cc01_g00330:429 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA +chr1:328149 [A/G] chr1 328149 Cc01_g00330:456 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA GA AA +chr1:328065 [T/G] chr1 328065 Cc01_g00330:540 exon SYNONYMOUS_CODING tcA/tcC S/S 50.0% 4 TT GG TG TG +chr1:327708 [A/C] chr1 327708 Cc01_g00330:644 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 12.5% 4 AA AC AA AA +chr1:327632 [C/T] chr1 327632 Cc01_g00330:720 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT CC CT +chr1:327519 [A/C] chr1 327519 Cc01_g00330:760 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC +chr1:327109 [T/C] chr1 327109 Cc01_g00330:833 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT TT TT TC +chr1:320096 [C/G] chr1 320096 Cc01_g00330:1285 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 37.5% 4 CC GG GG CG +chr1:319913 [T/C] chr1 319913 Cc01_g00330:1358 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:319903 [G/C] chr1 319903 Cc01_g00330:1368 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 GG GG GC GG +chr1:319887 [G/T] chr1 319887 Cc01_g00330:1384 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 GG TT GG GT +chr1:319879 [C/A] chr1 319879 Cc01_g00330:1392 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA +chr1:319682 [T/A] chr1 319682 Cc01_g00330:1589 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 TT AA AA TA +chr1:319581 [C/T] chr1 319581 Cc01_g00330:1690 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 CC CC CT CC +chr1:319379 [A/G] chr1 319379 Cc01_g00330:1892 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:319299 [A/C] chr1 319299 Cc01_g00330:1972 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 AA AA AC AA +chr1:319123 [G/A] chr1 319123 Cc01_g00330:2148 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:319112 [G/C] chr1 319112 Cc01_g00330:2159 exon NON_SYNONYMOUS_CODING gCc/gGc A/G 12.5% 4 GG GG GC GG +chr1:319087 [C/A] chr1 319087 Cc01_g00330:2184 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA +chr1:319073 [G/A] chr1 319073 Cc01_g00330:2198 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 GG GG GG GA +chr1:319033 [A/G] chr1 319033 Cc01_g00330:2238 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA +chr1:317552 [C/T] chr1 317552 Cc01_g00330:2468 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 CC CC CT CC +chr1:315675 [A/T] chr1 315675 Cc01_g00330:2530 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT AT +chr1:315443 [G/A] chr1 315443 Cc01_g00330:2691 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:315404 [C/T] chr1 315404 Cc01_g00330:2730 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT TT CT +chr1:315126 [A/G] chr1 315126 Cc01_g00330:2787 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 AA GG GG GG +chr1:315087 [C/G] chr1 315087 Cc01_g00330:2826 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CC CG +chr1:312979 [T/C] chr1 312979 Cc01_g00330:3198 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT +chr1:312964 [C/T] chr1 312964 Cc01_g00330:3213 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC TT TT CT +chr1:312879 [G/A] chr1 312879 Cc01_g00330:3298 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 37.5% 4 GG AA AA GA +chr1:312680 [G/A] chr1 312680 Cc01_g00330:3393 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA AA GA +chr1:312672 [T/A] chr1 312672 Cc01_g00330:3401 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 37.5% 4 TT AA AA TA +chr1:312546 [A/G] chr1 312546 Cc01_g00330:3527 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:312321 [G/C] chr1 312321 Cc01_g00330:3752 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GG GG GC +chr1:312307 [C/G] chr1 312307 Cc01_g00330:3766 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 50.0% 4 CC GG CG GC +chr1:312213 [G/A] chr1 312213 Cc01_g00330:3860 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG GA +chr1:312086 [T/C] chr1 312086 Cc01_g00330:3987 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT CC TC TC +chr1:311898 [T/C] chr1 311898 Cc01_g00330:4175 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:311859 [C/T] chr1 311859 Cc01_g00330:4214 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 4 CC TT CT CT +chr1:311729 [T/C] chr1 311729 Cc01_g00330:4344 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TC TT +chr1:311665 [C/T] chr1 311665 Cc01_g00330:4408 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 CC TT CC CT +chr1:311522 [T/C] chr1 311522 Cc01_g00330:4551 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:311476 [T/G] chr1 311476 Cc01_g00330:4597 exon NON_SYNONYMOUS_CODING Act/Cct T/P 12.5% 4 TT TT GT TT +chr1:311457 [C/A] chr1 311457 Cc01_g00330:4616 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 37.5% 4 CC AA AA CA +chr1:311357 [G/C] chr1 311357 Cc01_g00330:4716 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC +chr1:311161 [A/G] chr1 311161 Cc01_g00330:4912 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA GG AG AG +chr1:311057 [G/A] chr1 311057 Cc01_g00330:5016 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:311024 [T/C] chr1 311024 Cc01_g00330:5049 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TC TT +chr1:310991 [A/G] chr1 310991 Cc01_g00330:5082 exon SYNONYMOUS_CODING ggT/ggC G/G 37.5% 4 AA GG AA AG +chr1:310760 [T/C] chr1 310760 Cc01_g00330:5229 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT +chr1:331033 [C/T] chr1 331033 Cc01_g00340:332 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 33.3% 3 CC TT NN TT +chr1:339763 [C/T] chr1 339763 Cc01_g00350:9 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC CT CT +chr1:339901 [G/C] chr1 339901 Cc01_g00350:147 exon SYNONYMOUS_CODING acG/acC T/T 12.5% 4 GG GG GG GC +chr1:339988 [A/G] chr1 339988 Cc01_g00350:234 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:346095 [A/G] chr1 346095 Cc01_g00350:384 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:346128 [C/G] chr1 346128 Cc01_g00350:417 exon NON_SYNONYMOUS_CODING atC/atG I/M 25.0% 4 CC CC GG CC +chr1:346300 [T/C] chr1 346300 Cc01_g00350:489 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT +chr1:346330 [A/G] chr1 346330 Cc01_g00350:519 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA GG AA AA +chr1:346342 [T/C] chr1 346342 Cc01_g00350:531 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC TT TT +chr1:349895 [T/C] chr1 349895 Cc01_g00360:87 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT CC NN NN +chr1:350036 [C/G] chr1 350036 Cc01_g00360:228 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 2 CC CG NN NN +chr1:350043 [T/C] chr1 350043 Cc01_g00360:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 2 TT CC NN NN +chr1:350373 [G/A] chr1 350373 Cc01_g00360:565 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 16.7% 3 GG GA NN GG +chr1:350416 [A/G] chr1 350416 Cc01_g00360:608 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 50.0% 2 AA GG NN NN +chr1:350429 [T/C] chr1 350429 Cc01_g00360:621 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT TT NN CC +chr1:350537 [A/T] chr1 350537 Cc01_g00360:729 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 AA AA AA TT +chr1:350672 [G/A] chr1 350672 Cc01_g00360:864 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 2 GG GA NN NN +chr1:350729 [C/T] chr1 350729 Cc01_g00360:921 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC +chr1:350738 [A/C] chr1 350738 Cc01_g00360:930 exon SYNONYMOUS_CODING ccA/ccC P/P 25.0% 4 AA AA CC AA +chr1:351014 [T/C] chr1 351014 Cc01_g00360:1206 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 2 TT CC NN NN +chr1:351188 [G/C] chr1 351188 Cc01_g00360:1380 exon SYNONYMOUS_CODING ccG/ccC P/P 33.3% 3 GG CC NN CC +chr1:351329 [A/T] chr1 351329 Cc01_g00360:1521 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 3 AA TT NN AT +chr1:392985 [A/G] chr1 392985 Cc01_g00370:84 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA +chr1:393004 [C/T] chr1 393004 Cc01_g00370:103 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:393006 [G/C] chr1 393006 Cc01_g00370:105 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 GG GG CG GG +chr1:393015 [G/A] chr1 393015 Cc01_g00370:114 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 GG AA AA AG +chr1:393081 [C/A] chr1 393081 Cc01_g00370:180 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 3 CC NN AA CA +chr1:393089 [T/A] chr1 393089 Cc01_g00370:188 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 TT TT TT TA +chr1:393111 [C/T] chr1 393111 Cc01_g00370:210 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TT TT CT +chr1:393120 [C/T] chr1 393120 Cc01_g00370:219 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC TT TT CT +chr1:393139 [G/A] chr1 393139 Cc01_g00370:238 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 GG AA AA GG +chr1:393271 [G/A] chr1 393271 Cc01_g00370:370 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG +chr1:393315 [G/A] chr1 393315 Cc01_g00370:414 exon SYNONYMOUS_CODING ggG/ggA G/G 16.7% 3 GG GG NN GA +chr1:393339 [G/T] chr1 393339 Cc01_g00370:438 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 50.0% 3 GG TT NN GT +chr1:393342 [G/A] chr1 393342 Cc01_g00370:441 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 GG NN NN GA +chr1:397208 [G/C] chr1 397208 Cc01_g00380:63 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG CC CC GC +chr1:397217 [T/C] chr1 397217 Cc01_g00380:72 exon SYNONYMOUS_CODING acT/acC T/T 37.5% 4 TT CC CC TC +chr1:397228 [G/T] chr1 397228 Cc01_g00380:83 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG TT TT TT +chr1:397253 [T/C] chr1 397253 Cc01_g00380:108 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC TT TT +chr1:397269 [T/A] chr1 397269 Cc01_g00380:124 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 50.0% 4 TT AA AA TT +chr1:397270 [T/C] chr1 397270 Cc01_g00380:125 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 TT CC CC TT +chr1:397361 [G/T] chr1 397361 Cc01_g00380:216 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 GG GG TT TT +chr1:397547 [C/A] chr1 397547 Cc01_g00380:402 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC AA AA AA +chr1:397566 [T/G] chr1 397566 Cc01_g00380:421 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 TT TT TT TG +chr1:397576 [T/C] chr1 397576 Cc01_g00380:431 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:398909 [G/C] chr1 398909 Cc01_g00380:456 exon SYNONYMOUS_CODING ggG/ggC G/G 12.5% 4 GG GG GC GG +chr1:398940 [A/G] chr1 398940 Cc01_g00380:487 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG GA AA +chr1:398942 [C/T] chr1 398942 Cc01_g00380:489 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TC CC +chr1:398951 [C/T] chr1 398951 Cc01_g00380:498 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC TT TC CC +chr1:399320 [T/C] chr1 399320 Cc01_g00380:867 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:399344 [C/T] chr1 399344 Cc01_g00380:891 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC +chr1:399368 [C/T] chr1 399368 Cc01_g00380:915 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT TT TT +chr1:399404 [A/T] chr1 399404 Cc01_g00380:951 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA +chr1:399453 [T/G] chr1 399453 Cc01_g00380:1000 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 TT GG GG GG +chr1:399557 [C/T] chr1 399557 Cc01_g00380:1104 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:399739 [C/G] chr1 399739 Cc01_g00380:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC +chr1:399765 [C/T] chr1 399765 Cc01_g00380:1312 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:399795 [C/A] chr1 399795 Cc01_g00380:1342 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CC CC AC +chr1:399796 [A/G] chr1 399796 Cc01_g00380:1343 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 25.0% 4 AA AA AA GG +chr1:399801 [A/G] chr1 399801 Cc01_g00380:1348 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 4 AA GG AA GG +chr1:399809 [C/G] chr1 399809 Cc01_g00380:1356 exon SYNONYMOUS_CODING gtC/gtG V/V 37.5% 4 CC GG CC GC +chr1:420355 [T/C] chr1 420355 Cc01_g00390:538 exon SYNONYMOUS_CODING Tta/Cta L/L 50.0% 2 TT NN NN CC +chr1:421363 [C/T] chr1 421363 Cc01_g00390:1546 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 CC NN NN TT +chr1:421532 [A/C] chr1 421532 Cc01_g00390:1715 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 37.5% 4 AA CC CC AC +chr1:421534 [A/G] chr1 421534 Cc01_g00390:1717 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA AG AG AA +chr1:421540 [G/A] chr1 421540 Cc01_g00390:1723 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 GG AG AG GA +chr1:421556 [T/A] chr1 421556 Cc01_g00390:1739 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 TT TT TA TT +chr1:421570 [T/C] chr1 421570 Cc01_g00390:1753 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 TT TC TT TT +chr1:421572 [C/T] chr1 421572 Cc01_g00390:1755 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT +chr1:421577 [C/T] chr1 421577 Cc01_g00390:1760 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 CC CC CC CT +chr1:421612 [A/G] chr1 421612 Cc01_g00390:1795 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 AA AA AG AA +chr1:422090 [G/C] chr1 422090 Cc01_g00390:2123 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 33.3% 3 GG NN CC GG +chr1:422353 [G/A] chr1 422353 Cc01_g00390:2386 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN NN GA +chr1:422467 [C/G] chr1 422467 Cc01_g00390:2500 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 33.3% 3 CC NN CC GG +chr1:422483 [C/A] chr1 422483 Cc01_g00390:2516 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 CC NN AA CC +chr1:422740 [G/T] chr1 422740 Cc01_g00390:2686 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 25.0% 2 GG NN NN GT +chr1:422742 [T/G] chr1 422742 Cc01_g00390:2688 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 2 TT NN NN TG +chr1:422746 [A/T] chr1 422746 Cc01_g00390:2692 exon STOP_GAINED Aaa/Taa K/8 25.0% 2 AA NN NN AT +chr1:422747 [A/C] chr1 422747 Cc01_g00390:2693 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 25.0% 2 AA NN NN AC +chr1:422885 [A/C] chr1 422885 Cc01_g00390:2831 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 33.3% 3 AA CC NN AA +chr1:445244 [A/G] chr1 445244 Cc01_g00410:59 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:445214 [A/T] chr1 445214 Cc01_g00410:89 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 37.5% 4 AA TT AT AA +chr1:445148 [T/G] chr1 445148 Cc01_g00410:155 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 16.7% 3 TT TG NN TT +chr1:445013 [T/C] chr1 445013 Cc01_g00410:185 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TC TT TT +chr1:444990 [C/T] chr1 444990 Cc01_g00410:208 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:444968 [G/A] chr1 444968 Cc01_g00410:230 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 GG GG GA GG +chr1:444952 [A/G] chr1 444952 Cc01_g00410:246 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG +chr1:444930 [G/A] chr1 444930 Cc01_g00410:268 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA +chr1:444929 [T/C] chr1 444929 Cc01_g00410:269 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC +chr1:444921 [T/C] chr1 444921 Cc01_g00410:277 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT TC TT CT +chr1:444904 [G/A] chr1 444904 Cc01_g00410:294 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:444879 [G/A] chr1 444879 Cc01_g00410:319 exon STOP_GAINED Cag/Tag Q/7 12.5% 4 GG GG GG GA +chr1:561287 [C/G] chr1 561287 Cc01_g00420:1568 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 2 CC NN NN GG +chr1:562257 [A/G] chr1 562257 Cc01_g00420:2449 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA GG NN AA +chr1:562260 [A/G] chr1 562260 Cc01_g00420:2452 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA GG NN AA +chr1:562358 [T/C] chr1 562358 Cc01_g00420:2550 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 2 TT NN NN TC +chr1:563082 [G/C] chr1 563082 Cc01_g00420:3274 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 33.3% 3 GG CC NN GG +chr1:563087 [A/G] chr1 563087 Cc01_g00420:3279 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA GG NN AA +chr1:563172 [C/T] chr1 563172 Cc01_g00420:3364 exon SYNONYMOUS_CODING Ctg/Ttg L/L 16.7% 3 CC CC NN CT +chr1:563178 [G/A] chr1 563178 Cc01_g00420:3370 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 16.7% 3 GG GG NN GA +chr1:563217 [A/G] chr1 563217 Cc01_g00420:3409 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 33.3% 3 AA NN GG AA +chr1:563316 [A/G] chr1 563316 Cc01_g00420:3439 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 AA NN AA GG +chr1:563359 [C/A] chr1 563359 Cc01_g00420:3482 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 50.0% 2 CC NN AA NN +chr1:563503 [T/C] chr1 563503 Cc01_g00420:3626 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT TT TC TC +chr1:563700 [T/A] chr1 563700 Cc01_g00420:3784 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 2 TT NN NN AA +chr1:563763 [G/A] chr1 563763 Cc01_g00420:3847 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG +chr1:563764 [A/T] chr1 563764 Cc01_g00420:3848 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 25.0% 4 AA TT AA AA +chr1:563780 [G/C] chr1 563780 Cc01_g00420:3864 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG GG GG CC +chr1:563788 [G/A] chr1 563788 Cc01_g00420:3872 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG AA GG GG +chr1:563836 [T/C] chr1 563836 Cc01_g00420:3920 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN +chr1:564119 [C/T] chr1 564119 Cc01_g00420:4122 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC NN TT NN +chr1:564245 [G/A] chr1 564245 Cc01_g00420:4248 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN AA NN +chr1:564250 [A/C] chr1 564250 Cc01_g00420:4253 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 50.0% 2 AA NN CC NN +chr1:564302 [A/G] chr1 564302 Cc01_g00420:4305 exon SYNONYMOUS_CODING tcA/tcG S/S 50.0% 4 AA GG GG AA +chr1:564307 [C/T] chr1 564307 Cc01_g00420:4310 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 33.3% 3 CC NN TT CC +chr1:564313 [T/A] chr1 564313 Cc01_g00420:4316 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TT TT AA +chr1:564315 [G/T] chr1 564315 Cc01_g00420:4318 exon NON_SYNONYMOUS_CODING Gac/Tac D/Y 12.5% 4 GG GG GG GT +chr1:564335 [C/G] chr1 564335 Cc01_g00420:4338 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC +chr1:564360 [T/G] chr1 564360 Cc01_g00420:4363 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 33.3% 3 TT GG NN GG +chr1:564391 [G/T] chr1 564391 Cc01_g00420:4394 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 33.3% 3 GG GG NN TT +chr1:564393 [C/G] chr1 564393 Cc01_g00420:4396 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 16.7% 3 CC CG NN CC +chr1:564416 [T/C] chr1 564416 Cc01_g00420:4419 exon SYNONYMOUS_CODING tcT/tcC S/S 33.3% 3 TT CC NN CC +chr1:564424 [C/A] chr1 564424 Cc01_g00420:4427 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 2 CC CA NN NN +chr1:564550 [T/A] chr1 564550 Cc01_g00420:4553 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 TT AA AA NN +chr1:624837 [T/G] chr1 624837 Cc01_g00430:60 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG +chr1:624841 [C/G] chr1 624841 Cc01_g00430:64 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 2 CC NN NN GG +chr1:625917 [T/G] chr1 625917 Cc01_g00430:987 exon SYNONYMOUS_CODING ctT/ctG L/L 50.0% 2 TT NN NN GG +chr1:625940 [G/C] chr1 625940 Cc01_g00430:1010 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 50.0% 2 GG NN NN CC +chr1:626077 [A/C] chr1 626077 Cc01_g00430:1147 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 50.0% 2 AA CC NN NN +chr1:626259 [G/A] chr1 626259 Cc01_g00430:1329 exon SYNONYMOUS_CODING ctG/ctA L/L 25.0% 2 GG NN NN GA +chr1:626317 [G/C] chr1 626317 Cc01_g00430:1387 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG NN NN GC +chr1:626491 [A/G] chr1 626491 Cc01_g00430:1561 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG +chr1:626499 [A/T] chr1 626499 Cc01_g00430:1569 exon SYNONYMOUS_CODING ccA/ccT P/P 50.0% 2 AA NN NN TT +chr1:626536 [C/T] chr1 626536 Cc01_g00430:1606 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC NN TT NN +chr1:626555 [C/G] chr1 626555 Cc01_g00430:1625 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN +chr1:626820 [T/C] chr1 626820 Cc01_g00430:1857 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TT TC +chr1:626826 [A/T] chr1 626826 Cc01_g00430:1863 exon SYNONYMOUS_CODING ccA/ccT P/P 16.7% 3 AA NN AA AT +chr1:626895 [G/A] chr1 626895 Cc01_g00430:1932 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN AA NN +chr1:626907 [G/A] chr1 626907 Cc01_g00430:1944 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:626917 [T/C] chr1 626917 Cc01_g00430:1954 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TC TT +chr1:626930 [G/C] chr1 626930 Cc01_g00430:1967 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 GG GG GG GC +chr1:626944 [G/A] chr1 626944 Cc01_g00430:1981 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG GA AG GG +chr1:626953 [G/A] chr1 626953 Cc01_g00430:1990 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA AA AG +chr1:626958 [A/C] chr1 626958 Cc01_g00430:1995 exon NON_SYNONYMOUS_CODING ttA/ttC L/F 12.5% 4 AA AA AC AA +chr1:626960 [T/G] chr1 626960 Cc01_g00430:1997 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 25.0% 4 TT TG GT TT +chr1:626962 [A/G] chr1 626962 Cc01_g00430:1999 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA GA AA AG +chr1:626990 [T/A] chr1 626990 Cc01_g00430:2027 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 12.5% 4 TT TT TT TA +chr1:626992 [G/A] chr1 626992 Cc01_g00430:2029 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 GG GA GG AG +chr1:627002 [G/A] chr1 627002 Cc01_g00430:2039 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG +chr1:627009 [C/T] chr1 627009 Cc01_g00430:2046 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC +chr1:627032 [G/T] chr1 627032 Cc01_g00430:2069 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GT GG GT +chr1:627051 [A/G] chr1 627051 Cc01_g00430:2088 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:627058 [G/C] chr1 627058 Cc01_g00430:2095 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG CC CC GC +chr1:627068 [C/T] chr1 627068 Cc01_g00430:2105 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC TT TT CT +chr1:627110 [C/T] chr1 627110 Cc01_g00430:2147 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CC CT +chr1:627131 [C/T] chr1 627131 Cc01_g00430:2168 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT +chr1:627366 [G/T] chr1 627366 Cc01_g00430:2307 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG TT NN NN +chr1:627379 [T/G] chr1 627379 Cc01_g00430:2320 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 2 TT GG NN NN +chr1:627697 [G/A] chr1 627697 Cc01_g00430:2548 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 2 GG NN AA NN +chr1:627713 [A/T] chr1 627713 Cc01_g00430:2564 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 50.0% 2 AA NN TT NN +chr1:627715 [G/C] chr1 627715 Cc01_g00430:2566 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN CC NN +chr1:627727 [T/C] chr1 627727 Cc01_g00430:2578 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 TT NN CC NN +chr1:627753 [T/G] chr1 627753 Cc01_g00430:2604 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 2 TT NN GG NN +chr1:627759 [C/A] chr1 627759 Cc01_g00430:2610 exon NON_SYNONYMOUS_CODING caC/caA H/Q 50.0% 2 CC NN AA NN +chr1:627760 [G/A] chr1 627760 Cc01_g00430:2611 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN GA NN +chr1:627858 [C/T] chr1 627858 Cc01_g00430:2709 exon SYNONYMOUS_CODING ccC/ccT P/P 50.0% 2 CC NN NN TT +chr1:694337 [T/C] chr1 694337 Cc01_g00440:1131 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT CC NN NN +chr1:694724 [A/C] chr1 694724 Cc01_g00440:1518 exon SYNONYMOUS_CODING gtA/gtC V/V 50.0% 2 AA NN NN CC +chr1:694734 [G/A] chr1 694734 Cc01_g00440:1528 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA +chr1:695273 [C/G] chr1 695273 Cc01_g00440:2067 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 2 CC NN NN CG +chr1:695280 [A/G] chr1 695280 Cc01_g00440:2074 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG +chr1:695301 [T/A] chr1 695301 Cc01_g00440:2095 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 25.0% 2 TT NN NN TA +chr1:695306 [A/G] chr1 695306 Cc01_g00440:2100 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 2 AA NN NN AG +chr1:695389 [A/C] chr1 695389 Cc01_g00440:2183 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AC AC +chr1:695751 [A/G] chr1 695751 Cc01_g00440:2506 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 50.0% 4 AA GG AA GG +chr1:696170 [A/G] chr1 696170 Cc01_g00440:2790 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG +chr1:696187 [A/T] chr1 696187 Cc01_g00440:2807 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 50.0% 2 AA NN NN TT +chr1:696190 [T/C] chr1 696190 Cc01_g00440:2810 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 TT NN NN CC +chr1:696193 [C/A] chr1 696193 Cc01_g00440:2813 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 50.0% 2 CC NN NN AA +chr1:696194 [A/G] chr1 696194 Cc01_g00440:2814 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 2 AA NN NN GG +chr1:696282 [A/T] chr1 696282 Cc01_g00440:2902 exon NON_SYNONYMOUS_CODING Act/Tct T/S 50.0% 2 AA NN NN TT +chr1:696283 [C/T] chr1 696283 Cc01_g00440:2903 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 CC NN NN TT +chr1:696299 [T/A] chr1 696299 Cc01_g00440:2919 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 2 TT NN NN TA +chr1:696368 [T/G] chr1 696368 Cc01_g00440:2988 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG +chr1:696565 [A/G] chr1 696565 Cc01_g00440:3131 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN GG AA +chr1:696569 [C/T] chr1 696569 Cc01_g00440:3135 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC NN TT CC +chr1:696578 [G/A] chr1 696578 Cc01_g00440:3144 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG NN AA GG +chr1:696580 [A/G] chr1 696580 Cc01_g00440:3146 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 33.3% 3 AA NN GG AA +chr1:696589 [A/T] chr1 696589 Cc01_g00440:3155 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA NN TT AA +chr1:696664 [C/A] chr1 696664 Cc01_g00440:3230 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC AA CC NN +chr1:698121 [T/A] chr1 698121 Cc01_g00450:9 exon STOP_GAINED taT/taA Y3* 25.0% 4 TT TA TT TA +chr1:698290 [C/A] chr1 698290 Cc01_g00450:59 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 12.5% 4 CC CC CC CA +chr1:698302 [A/G] chr1 698302 Cc01_g00450:71 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AG AG AA +chr1:698316 [G/T] chr1 698316 Cc01_g00450:85 exon STOP_GAINED Gga/Tga G/9 37.5% 4 GG TG TG TG +chr1:698328 [G/A] chr1 698328 Cc01_g00450:97 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AG GA GA +chr1:698331 [A/G] chr1 698331 Cc01_g00450:100 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 37.5% 4 AA GA AG AG +chr1:698332 [G/A] chr1 698332 Cc01_g00450:101 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 37.5% 4 GG GA AG AG +chr1:698333 [A/G] chr1 698333 Cc01_g00450:102 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG +chr1:698339 [A/G] chr1 698339 Cc01_g00450:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG GG GG +chr1:698350 [C/T] chr1 698350 Cc01_g00450:119 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 37.5% 4 CC TC CT CT +chr1:698355 [A/G] chr1 698355 Cc01_g00450:124 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG +chr1:698372 [C/G] chr1 698372 Cc01_g00450:141 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG +chr1:698398 [T/G] chr1 698398 Cc01_g00450:167 exon STOP_GAINED tTa/tGa L/6 33.3% 3 TT TT NN GG +chr1:698411 [T/C] chr1 698411 Cc01_g00450:180 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC TT TT +chr1:698426 [G/A] chr1 698426 Cc01_g00450:195 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG GA GG GA +chr1:698432 [G/A] chr1 698432 Cc01_g00450:201 exon STOP_GAINED tgG/tgA W/7 50.0% 4 GG AA GA GA +chr1:698434 [A/G] chr1 698434 Cc01_g00450:203 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 AA GG GG AG +chr1:714525 [A/G] chr1 714525 Cc01_g00470:91 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN GG NN +chr1:714606 [C/A] chr1 714606 Cc01_g00470:172 exon NON_SYNONYMOUS_CODING Cgt/Agt R/S 50.0% 4 CC AA CC AA +chr1:714611 [G/A] chr1 714611 Cc01_g00470:177 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG +chr1:714616 [T/A] chr1 714616 Cc01_g00470:182 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 33.3% 3 TT NN TT AA +chr1:714635 [G/A] chr1 714635 Cc01_g00470:201 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG NN AA AA +chr1:714636 [C/G] chr1 714636 Cc01_g00470:202 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 33.3% 3 CC NN GG GG +chr1:715733 [C/G] chr1 715733 Cc01_g00470:1198 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 4 CC GG GG CC +chr1:715736 [T/G] chr1 715736 Cc01_g00470:1201 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 TT TT TT TG +chr1:715743 [C/A] chr1 715743 Cc01_g00470:1208 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 50.0% 4 CC AA AA CC +chr1:715749 [G/T] chr1 715749 Cc01_g00470:1214 exon NON_SYNONYMOUS_CODING cGc/cTc R/L 50.0% 4 GG TT TT GG +chr1:715750 [C/T] chr1 715750 Cc01_g00470:1215 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CC CC TC +chr1:715751 [G/A] chr1 715751 Cc01_g00470:1216 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA +chr1:715769 [G/A] chr1 715769 Cc01_g00470:1234 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 2 GG NN NN GA +chr1:715779 [A/G] chr1 715779 Cc01_g00470:1244 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA NN NN GG +chr1:715853 [G/C] chr1 715853 Cc01_g00470:1318 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN NN CC +chr1:716060 [A/C] chr1 716060 Cc01_g00470:1525 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 50.0% 2 AA NN CC NN +chr1:716123 [G/A] chr1 716123 Cc01_g00470:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG NN AA NN +chr1:716482 [G/A] chr1 716482 Cc01_g00470:1836 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA GG +chr1:716498 [G/C] chr1 716498 Cc01_g00470:1852 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC +chr1:716510 [G/A] chr1 716510 Cc01_g00470:1864 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA +chr1:716535 [A/G] chr1 716535 Cc01_g00470:1889 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG AA AA +chr1:716594 [T/C] chr1 716594 Cc01_g00470:1948 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT CC TC CC +chr1:716622 [A/G] chr1 716622 Cc01_g00470:1976 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 12.5% 4 AA AA AA AG +chr1:716696 [C/T] chr1 716696 Cc01_g00470:2050 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 33.3% 3 CC NN TT CC +chr1:716714 [G/C] chr1 716714 Cc01_g00470:2068 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC +chr1:716724 [A/G] chr1 716724 Cc01_g00470:2078 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 3 AA NN GG AG +chr1:716729 [G/C] chr1 716729 Cc01_g00470:2083 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 33.3% 3 GG NN CC GG +chr1:716741 [G/A] chr1 716741 Cc01_g00470:2095 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 2 GG NN NN AA +chr1:716770 [C/T] chr1 716770 Cc01_g00470:2124 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 2 CC NN NN TT +chr1:716789 [C/A] chr1 716789 Cc01_g00470:2143 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 50.0% 2 CC NN NN AA +chr1:716793 [C/A] chr1 716793 Cc01_g00470:2147 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 2 CC NN NN CA +chr1:716863 [T/C] chr1 716863 Cc01_g00470:2217 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT NN CC TT +chr1:716867 [G/C] chr1 716867 Cc01_g00470:2221 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG NN CC GG +chr1:716879 [A/T] chr1 716879 Cc01_g00470:2233 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA NN AA AT +chr1:716880 [A/T] chr1 716880 Cc01_g00470:2234 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 33.3% 3 AA NN TT AA +chr1:717010 [T/C] chr1 717010 Cc01_g00470:2364 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC +chr1:717382 [A/G] chr1 717382 Cc01_g00470:2502 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA NN AA AG +chr1:717405 [A/G] chr1 717405 Cc01_g00470:2525 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AA AA AG +chr1:718555 [G/T] chr1 718555 Cc01_g00480:7 exon STOP_GAINED Gga/Tga G3* 50.0% 4 GG TT GT GT +chr1:718570 [A/G] chr1 718570 Cc01_g00480:22 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 25.0% 4 AA GG GG GG +chr1:718578 [A/G] chr1 718578 Cc01_g00480:30 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG +chr1:718579 [A/G] chr1 718579 Cc01_g00480:31 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG +chr1:718589 [T/C] chr1 718589 Cc01_g00480:41 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 TT TC CT CT +chr1:718602 [A/G] chr1 718602 Cc01_g00480:54 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:718616 [A/G] chr1 718616 Cc01_g00480:68 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA GA AG AG +chr1:718623 [A/G] chr1 718623 Cc01_g00480:75 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GA AG AG +chr1:718626 [A/C] chr1 718626 Cc01_g00480:78 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 37.5% 4 AA AC CA CA +chr1:718632 [A/G] chr1 718632 Cc01_g00480:84 exon SYNONYMOUS_CODING ggA/ggG G/G 37.5% 4 AA GG GG GA +chr1:718633 [C/T] chr1 718633 Cc01_g00480:85 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT +chr1:718636 [G/A] chr1 718636 Cc01_g00480:88 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG AG GA GA +chr1:718676 [A/G] chr1 718676 Cc01_g00480:128 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA GA AA AA +chr1:719091 [T/A] chr1 719091 Cc01_g00480:135 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA AT TT +chr1:720709 [G/A] chr1 720709 Cc01_g00490:200 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 33.3% 3 GG NN AA AA +chr1:757845 [A/T] chr1 757845 Cc01_g00500:54 exon SYNONYMOUS_CODING acT/acA T/T 50.0% 3 AA TT AT NN +chr1:757827 [A/T] chr1 757827 Cc01_g00500:72 exon SYNONYMOUS_CODING acT/acA T/T 37.5% 4 AA TT AT TT +chr1:757176 [T/A] chr1 757176 Cc01_g00500:160 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 TT TT TT TA +chr1:757171 [A/C] chr1 757171 Cc01_g00500:165 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 AA AC AC CA +chr1:757169 [C/G] chr1 757169 Cc01_g00500:167 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC GC CC +chr1:757141 [T/C] chr1 757141 Cc01_g00500:195 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:756891 [T/C] chr1 756891 Cc01_g00500:213 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT CT TT TT +chr1:756475 [G/A] chr1 756475 Cc01_g00500:399 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA +chr1:756448 [T/C] chr1 756448 Cc01_g00500:426 exon SYNONYMOUS_CODING tcA/tcG S/S 33.3% 3 TT NN TT CC +chr1:763230 [A/C] chr1 763230 Cc01_g00510:245 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 50.0% 2 AA NN NN CC +chr1:765710 [A/G] chr1 765710 Cc01_g00520:150 exon SYNONYMOUS_CODING acA/acG T/T 50.0% 3 AA NN AG GG +chr1:765774 [C/G] chr1 765774 Cc01_g00520:214 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 50.0% 2 CC NN NN GG +chr1:767708 [C/T] chr1 767708 Cc01_g00520:2019 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 3 CC TT NN CT +chr1:767754 [T/C] chr1 767754 Cc01_g00520:2065 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT +chr1:767773 [T/C] chr1 767773 Cc01_g00520:2084 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 TT TC TT TT +chr1:767784 [A/G] chr1 767784 Cc01_g00520:2095 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG AA AG +chr1:768089 [T/G] chr1 768089 Cc01_g00520:2142 exon NON_SYNONYMOUS_CODING agT/agG S/R 16.7% 3 TT NN TG TT +chr1:768095 [G/T] chr1 768095 Cc01_g00520:2148 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 16.7% 3 GG NN GT GG +chr1:768097 [G/T] chr1 768097 Cc01_g00520:2150 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 16.7% 3 GG NN GT GG +chr1:768140 [A/T] chr1 768140 Cc01_g00520:2193 exon SYNONYMOUS_CODING ctA/ctT L/L 50.0% 3 AA NN AT TT +chr1:768149 [G/T] chr1 768149 Cc01_g00520:2202 exon SYNONYMOUS_CODING gcG/gcT A/A 50.0% 3 GG NN GT TT +chr1:768210 [A/G] chr1 768210 Cc01_g00520:2263 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 3 AA NN AG GG +chr1:768322 [G/A] chr1 768322 Cc01_g00520:2375 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG NN GA GG +chr1:768476 [T/G] chr1 768476 Cc01_g00520:2529 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 25.0% 4 TT GG TT TT +chr1:768570 [G/A] chr1 768570 Cc01_g00520:2623 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 GG NN GA AA +chr1:768621 [A/C] chr1 768621 Cc01_g00520:2674 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 33.3% 3 AA NN CC AA +chr1:768623 [G/C] chr1 768623 Cc01_g00520:2676 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 50.0% 3 GG NN GC CC +chr1:768653 [C/T] chr1 768653 Cc01_g00520:2706 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC NN TT CC +chr1:768703 [C/T] chr1 768703 Cc01_g00520:2756 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 16.7% 3 CC NN CC CT +chr1:768709 [T/G] chr1 768709 Cc01_g00520:2762 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 16.7% 3 TT NN TT TG +chr1:768710 [T/G] chr1 768710 Cc01_g00520:2763 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 16.7% 3 TT NN TT TG +chr1:768718 [G/C] chr1 768718 Cc01_g00520:2771 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 33.3% 3 GG NN CC CC +chr1:768724 [C/T] chr1 768724 Cc01_g00520:2777 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 16.7% 3 CC NN CC CT +chr1:768748 [A/G] chr1 768748 Cc01_g00520:2801 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN AA GG +chr1:768806 [A/G] chr1 768806 Cc01_g00520:2859 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 3 AA NN AG GG +chr1:768948 [G/A] chr1 768948 Cc01_g00520:2917 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA AA GG +chr1:768971 [T/C] chr1 768971 Cc01_g00520:2940 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC NN TT +chr1:772576 [A/T] chr1 772576 Cc01_g00530:220 exon STOP_GAINED Aaa/Taa K/4 37.5% 4 AA TT TT AT +chr1:772604 [A/G] chr1 772604 Cc01_g00530:248 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 3 AA NN GG AG +chr1:787097 [G/A] chr1 787097 Cc01_g00550:1089 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 3 GG NN AA GA +chr1:787673 [T/G] chr1 787673 Cc01_g00550:1596 exon NON_SYNONYMOUS_CODING caT/caG H/Q 33.3% 3 TT GG NN GG +chr1:788087 [C/T] chr1 788087 Cc01_g00550:1680 exon SYNONYMOUS_CODING ctC/ctT L/L 16.7% 3 CC NN CC CT +chr1:788159 [G/A] chr1 788159 Cc01_g00550:1752 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GA GG GG +chr1:788273 [C/A] chr1 788273 Cc01_g00550:1866 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 25.0% 4 CC AA CC CC +chr1:788275 [C/T] chr1 788275 Cc01_g00550:1868 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC TT CT CT +chr1:788383 [C/G] chr1 788383 Cc01_g00550:1886 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN +chr1:788482 [C/T] chr1 788482 Cc01_g00550:1985 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:788491 [G/A] chr1 788491 Cc01_g00550:1994 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 GG GG GA GG +chr1:788516 [A/G] chr1 788516 Cc01_g00550:2019 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG +chr1:788558 [A/G] chr1 788558 Cc01_g00550:2061 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA GG AA AA +chr1:788560 [T/C] chr1 788560 Cc01_g00550:2063 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 TT CC TT TT +chr1:788561 [C/G] chr1 788561 Cc01_g00550:2064 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG CC CC +chr1:788694 [G/A] chr1 788694 Cc01_g00550:2197 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 GG AA GG GA +chr1:788708 [G/A] chr1 788708 Cc01_g00550:2211 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG +chr1:788716 [A/C] chr1 788716 Cc01_g00550:2219 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 AA AC AA AA +chr1:836275 [A/G] chr1 836275 Cc01_g00570:39 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 2 AA NN NN AG +chr1:836319 [C/T] chr1 836319 Cc01_g00570:83 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:836362 [T/A] chr1 836362 Cc01_g00570:126 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TA TT TT +chr1:837674 [G/C] chr1 837674 Cc01_g00570:1378 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 50.0% 2 GG NN NN CC +chr1:837956 [A/G] chr1 837956 Cc01_g00570:1660 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 AA GG NN AA +chr1:837958 [T/A] chr1 837958 Cc01_g00570:1662 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 TT AA NN TT +chr1:837989 [A/G] chr1 837989 Cc01_g00570:1693 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN +chr1:838599 [A/T] chr1 838599 Cc01_g00570:2303 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 16.7% 3 AA AA NN AT +chr1:838628 [T/C] chr1 838628 Cc01_g00570:2332 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 33.3% 3 TT CC NN CC +chr1:838667 [T/A] chr1 838667 Cc01_g00570:2338 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 2 TT TA NN NN +chr1:838670 [A/G] chr1 838670 Cc01_g00570:2341 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 AA GA NN NN +chr1:838676 [A/G] chr1 838676 Cc01_g00570:2347 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN +chr1:838683 [C/G] chr1 838683 Cc01_g00570:2354 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC GG NN NN +chr1:838689 [C/T] chr1 838689 Cc01_g00570:2360 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 33.3% 3 CC TT CC NN +chr1:838705 [C/T] chr1 838705 Cc01_g00570:2376 exon SYNONYMOUS_CODING ctC/ctT L/L 33.3% 3 CC CC TT NN +chr1:838717 [T/A] chr1 838717 Cc01_g00570:2388 exon SYNONYMOUS_CODING tcT/tcA S/S 50.0% 2 TT AA NN NN +chr1:839122 [G/A] chr1 839122 Cc01_g00570:2689 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 50.0% 2 GG AA NN NN +chr1:839352 [G/A] chr1 839352 Cc01_g00570:2919 exon SYNONYMOUS_CODING agG/agA R/R 50.0% 2 GG NN NN AA +chr1:839601 [A/T] chr1 839601 Cc01_g00570:3168 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA NN NN TT +chr1:839786 [G/A] chr1 839786 Cc01_g00570:3353 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 GG NN NN AA +chr1:839932 [G/A] chr1 839932 Cc01_g00570:3499 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA +chr1:928733 [T/C] chr1 928733 Cc01_g00580:26 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 TT NN TT TC +chr1:928809 [A/G] chr1 928809 Cc01_g00580:102 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 2 AA NN NN GG +chr1:928827 [A/G] chr1 928827 Cc01_g00580:120 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 2 AA NN NN AG +chr1:928836 [A/G] chr1 928836 Cc01_g00580:129 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 2 AA NN NN GA +chr1:928904 [A/G] chr1 928904 Cc01_g00580:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 2 AA NN NN GA +chr1:966451 [A/G] chr1 966451 Cc01_g00590:185 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 2 AA NN NN GG +chr1:966652 [A/G] chr1 966652 Cc01_g00590:386 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG +chr1:966654 [A/G] chr1 966654 Cc01_g00590:388 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN NN GG +chr1:966661 [A/C] chr1 966661 Cc01_g00590:395 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 50.0% 2 AA NN NN CC +chr1:966719 [A/G] chr1 966719 Cc01_g00590:453 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG +chr1:966803 [T/C] chr1 966803 Cc01_g00590:486 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC +chr1:966831 [G/C] chr1 966831 Cc01_g00590:514 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GG GG GC +chr1:966834 [A/G] chr1 966834 Cc01_g00590:517 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG +chr1:966846 [G/A] chr1 966846 Cc01_g00590:529 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 GG AA AA AG +chr1:966866 [C/T] chr1 966866 Cc01_g00590:549 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 2 CC NN NN TT +chr1:967049 [G/T] chr1 967049 Cc01_g00590:732 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG NN NN TT +chr1:967059 [G/A] chr1 967059 Cc01_g00590:742 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG NN NN AA +chr1:967062 [A/G] chr1 967062 Cc01_g00590:745 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA NN NN GG +chr1:967063 [A/T] chr1 967063 Cc01_g00590:746 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 50.0% 2 AA NN NN TT +chr1:967183 [C/G] chr1 967183 Cc01_g00590:866 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 33.3% 3 CC CC NN GG +chr1:967752 [G/T] chr1 967752 Cc01_g00590:1435 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 3 GG TT NN GT +chr1:967768 [C/G] chr1 967768 Cc01_g00590:1451 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 CC GG NN GG +chr1:967992 [G/A] chr1 967992 Cc01_g00590:1675 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG NN AA AA +chr1:986447 [C/A] chr1 986447 Cc01_g00610:57 exon SYNONYMOUS_CODING cgC/cgA R/R 12.5% 4 CC CC CC CA +chr1:986448 [G/A] chr1 986448 Cc01_g00610:58 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GA GG AG +chr1:986456 [A/G] chr1 986456 Cc01_g00610:66 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG +chr1:986518 [T/G] chr1 986518 Cc01_g00610:128 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 25.0% 4 TT TG TG TT +chr1:986525 [G/T] chr1 986525 Cc01_g00610:135 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GG TG +chr1:986546 [G/A] chr1 986546 Cc01_g00610:156 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 2 GG NN NN GA +chr1:986690 [G/A] chr1 986690 Cc01_g00610:300 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA +chr1:986709 [G/A] chr1 986709 Cc01_g00610:319 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA +chr1:986710 [A/T] chr1 986710 Cc01_g00610:320 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 AA AA AA AT +chr1:986736 [C/G] chr1 986736 Cc01_g00610:346 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 CC CG CC GG +chr1:987100 [C/T] chr1 987100 Cc01_g00610:546 exon SYNONYMOUS_CODING tcC/tcT S/S 16.7% 3 CC NN CC CT +chr1:987154 [T/A] chr1 987154 Cc01_g00610:600 exon NON_SYNONYMOUS_CODING agT/agA S/R 50.0% 4 TT AA TA TA +chr1:987159 [A/T] chr1 987159 Cc01_g00610:605 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA TA +chr1:987178 [A/G] chr1 987178 Cc01_g00610:624 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 4 AA GG AG AG +chr1:987200 [G/A] chr1 987200 Cc01_g00610:646 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG +chr1:987232 [T/G] chr1 987232 Cc01_g00610:678 exon SYNONYMOUS_CODING tcT/tcG S/S 50.0% 4 TT GG TG TG +chr1:987567 [A/T] chr1 987567 Cc01_g00610:1013 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 25.0% 4 AA AA AA TT +chr1:987582 [A/C] chr1 987582 Cc01_g00610:1028 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AA CC +chr1:987606 [G/A] chr1 987606 Cc01_g00610:1052 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA +chr1:987613 [T/C] chr1 987613 Cc01_g00610:1059 exon SYNONYMOUS_CODING acT/acC T/T 33.3% 3 TT NN TT CC +chr1:987648 [T/C] chr1 987648 Cc01_g00610:1094 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 16.7% 3 TT NN TT TC +chr1:987704 [A/C] chr1 987704 Cc01_g00610:1150 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 16.7% 3 AA NN AA AC +chr1:987875 [C/G] chr1 987875 Cc01_g00610:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 33.3% 3 CC NN GG GG +chr1:988107 [A/G] chr1 988107 Cc01_g00610:1518 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG +chr1:988121 [A/G] chr1 988121 Cc01_g00610:1532 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 12.5% 4 AA AA AA AG +chr1:988128 [T/A] chr1 988128 Cc01_g00610:1539 exon NON_SYNONYMOUS_CODING agT/agA S/R 12.5% 4 TT TT TA TT +chr1:988129 [C/T] chr1 988129 Cc01_g00610:1540 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC TC CC TC +chr1:988136 [C/G] chr1 988136 Cc01_g00610:1547 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 CC CC CC GC +chr1:988162 [G/C] chr1 988162 Cc01_g00610:1573 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GG GC GC +chr1:997411 [A/G] chr1 997411 Cc01_g00620:25 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA NN AG AG +chr1:997409 [G/A] chr1 997409 Cc01_g00620:27 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 GG NN AA AA +chr1:997392 [T/C] chr1 997392 Cc01_g00620:44 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 TT NN TT CT +chr1:997300 [C/G] chr1 997300 Cc01_g00620:60 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC +chr1:997296 [G/A] chr1 997296 Cc01_g00620:64 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG +chr1:997213 [G/A] chr1 997213 Cc01_g00620:147 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 GG AA AA AA +chr1:997200 [C/A] chr1 997200 Cc01_g00620:160 exon NON_SYNONYMOUS_CODING Gcg/Tcg A/S 50.0% 3 CC AA NN CA +chr1:997185 [T/G] chr1 997185 Cc01_g00620:175 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT NN NN GG +chr1:997169 [A/G] chr1 997169 Cc01_g00620:191 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 25.0% 2 AA NN NN AG +chr1:997094 [A/G] chr1 997094 Cc01_g00620:266 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 2 AA NN NN AG +chr1:997051 [G/C] chr1 997051 Cc01_g00620:309 exon SYNONYMOUS_CODING tcC/tcG S/S 50.0% 2 GG NN NN CC +chr1:995391 [A/G] chr1 995391 Cc01_g00620:348 exon SYNONYMOUS_CODING ctT/ctC L/L 16.7% 3 AA AG NN AA +chr1:995363 [T/C] chr1 995363 Cc01_g00620:376 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 TT TC NN NN +chr1:994056 [G/T] chr1 994056 Cc01_g00620:1180 exon SYNONYMOUS_CODING Cgg/Agg R/R 50.0% 2 GG NN NN TT +chr1:994012 [A/C] chr1 994012 Cc01_g00620:1224 exon SYNONYMOUS_CODING cgT/cgG R/R 50.0% 2 AA NN NN CC +chr1:1105670 [T/C] chr1 1105670 Cc01_g00630:393 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:1105722 [A/G] chr1 1105722 Cc01_g00630:445 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG +chr1:1124006 [T/C] chr1 1124006 Cc01_g00640:198 exon SYNONYMOUS_CODING atT/atC I/I 33.3% 3 TT CC NN TT +chr1:1124349 [T/C] chr1 1124349 Cc01_g00640:426 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT CC TT +chr1:1125855 [G/A] chr1 1125855 Cc01_g00640:1414 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GA NN GG +chr1:1125920 [T/A] chr1 1125920 Cc01_g00640:1479 exon SYNONYMOUS_CODING acT/acA T/T 33.3% 3 TT AA NN TT +chr1:1125966 [A/T] chr1 1125966 Cc01_g00640:1525 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA TT NN AA +chr1:1126013 [A/G] chr1 1126013 Cc01_g00640:1572 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA GG NN NN +chr1:1151834 [G/C] chr1 1151834 Cc01_g00670:239 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 GG GC GG GG +chr1:1153859 [G/A] chr1 1153859 Cc01_g00670:410 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GG GA +chr1:1153862 [A/G] chr1 1153862 Cc01_g00670:413 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 AA GG AG GG +chr1:1153873 [A/C] chr1 1153873 Cc01_g00670:424 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA AC +chr1:1154467 [T/G] chr1 1154467 Cc01_g00670:486 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT TG TG +chr1:1154473 [T/C] chr1 1154473 Cc01_g00670:492 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TT TC +chr1:1154482 [T/G] chr1 1154482 Cc01_g00670:501 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 TT TT TG TG +chr1:1154490 [C/G] chr1 1154490 Cc01_g00670:509 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC CC CG CG +chr1:1154495 [A/G] chr1 1154495 Cc01_g00670:514 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA +chr1:1154499 [T/C] chr1 1154499 Cc01_g00670:518 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1154515 [C/G] chr1 1154515 Cc01_g00670:534 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CG CC CC +chr1:1154527 [G/T] chr1 1154527 Cc01_g00670:546 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GT GG GG +chr1:1154549 [A/G] chr1 1154549 Cc01_g00670:568 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA GA AA +chr1:1154550 [A/T] chr1 1154550 Cc01_g00670:569 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 AA AT TA AT +chr1:1154579 [A/G] chr1 1154579 Cc01_g00670:598 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:1154582 [T/G] chr1 1154582 Cc01_g00670:601 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT +chr1:1154588 [A/C] chr1 1154588 Cc01_g00670:607 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA +chr1:1154849 [G/A] chr1 1154849 Cc01_g00670:711 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GA AA +chr1:1154858 [G/A] chr1 1154858 Cc01_g00670:720 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG +chr1:1154868 [A/G] chr1 1154868 Cc01_g00670:730 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA +chr1:1154885 [G/A] chr1 1154885 Cc01_g00670:747 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG AG GG GG +chr1:1154894 [A/G] chr1 1154894 Cc01_g00670:756 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA GA AA AA +chr1:1154916 [T/A] chr1 1154916 Cc01_g00670:778 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT AT TT TT +chr1:1154924 [T/C] chr1 1154924 Cc01_g00670:786 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT CT TT TT +chr1:1154929 [C/G] chr1 1154929 Cc01_g00670:791 exon STOP_GAINED tCa/tGa S/4 12.5% 4 CC GC CC CC +chr1:1154930 [A/G] chr1 1154930 Cc01_g00670:792 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:1154936 [G/C] chr1 1154936 Cc01_g00670:798 exon NON_SYNONYMOUS_CODING agG/agC R/S 12.5% 4 GG CG GG GG +chr1:1154941 [T/C] chr1 1154941 Cc01_g00670:803 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT CT TT TT +chr1:1154946 [G/A] chr1 1154946 Cc01_g00670:808 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG +chr1:1154952 [A/T] chr1 1154952 Cc01_g00670:814 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 25.0% 4 AA TT AA AA +chr1:1154976 [A/G] chr1 1154976 Cc01_g00670:838 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA +chr1:1154985 [C/G] chr1 1154985 Cc01_g00670:847 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 CC GC CC CC +chr1:1155000 [G/A] chr1 1155000 Cc01_g00670:862 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG +chr1:1155003 [C/A] chr1 1155003 Cc01_g00670:865 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 12.5% 4 CC AC CC CC +chr1:1155015 [T/A] chr1 1155015 Cc01_g00670:877 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 TT AT TT TT +chr1:1155017 [A/G] chr1 1155017 Cc01_g00670:879 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA GA AA AA +chr1:1155021 [C/T] chr1 1155021 Cc01_g00670:883 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC TC CC CC +chr1:1155927 [G/A] chr1 1155927 Cc01_g00670:906 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1155945 [C/G] chr1 1155945 Cc01_g00670:924 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 CC CC CC CG +chr1:1155970 [G/A] chr1 1155970 Cc01_g00670:949 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG +chr1:1155978 [G/A] chr1 1155978 Cc01_g00670:957 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG AG GG GG +chr1:1156036 [C/G] chr1 1156036 Cc01_g00670:1015 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC GC CC CC +chr1:1156056 [G/T] chr1 1156056 Cc01_g00670:1035 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 12.5% 4 GG GG GG GT +chr1:1156075 [C/T] chr1 1156075 Cc01_g00670:1054 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 12.5% 4 CC CT CC CC +chr1:1156086 [A/T] chr1 1156086 Cc01_g00670:1065 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 AA TA AA AA +chr1:1156095 [A/G] chr1 1156095 Cc01_g00670:1074 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG +chr1:1156099 [A/C] chr1 1156099 Cc01_g00670:1078 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 12.5% 4 AA CA AA AA +chr1:1156677 [C/T] chr1 1156677 Cc01_g00670:1089 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CT CC CC +chr1:1156701 [T/G] chr1 1156701 Cc01_g00670:1113 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT GT TT TT +chr1:1156712 [T/A] chr1 1156712 Cc01_g00670:1124 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 12.5% 4 TT AT TT TT +chr1:1156733 [T/C] chr1 1156733 Cc01_g00670:1145 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 TT CC TC CC +chr1:1156813 [G/A] chr1 1156813 Cc01_g00670:1225 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 GG GA GG GG +chr1:1156819 [A/G] chr1 1156819 Cc01_g00670:1231 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 12.5% 4 AA AG AA AA +chr1:1156820 [G/A] chr1 1156820 Cc01_g00670:1232 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1156883 [T/C] chr1 1156883 Cc01_g00670:1295 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1156892 [A/G] chr1 1156892 Cc01_g00670:1304 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA +chr1:1156901 [T/A] chr1 1156901 Cc01_g00670:1313 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TA TT TT +chr1:1156908 [C/T] chr1 1156908 Cc01_g00670:1320 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT CT +chr1:1165679 [A/T] chr1 1165679 Cc01_g00680:45 exon STOP_GAINED tgT/tgA C/5 37.5% 4 AA TT AT TT +chr1:1165649 [C/T] chr1 1165649 Cc01_g00680:75 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT CT TT +chr1:1165641 [A/G] chr1 1165641 Cc01_g00680:83 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 AA AA AG AA +chr1:1165640 [G/A] chr1 1165640 Cc01_g00680:84 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG AA AA AA +chr1:1165637 [A/G] chr1 1165637 Cc01_g00680:87 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA GG GG GG +chr1:1165630 [G/T] chr1 1165630 Cc01_g00680:94 exon NON_SYNONYMOUS_CODING Ccc/Acc P/T 25.0% 4 GG TT TT TT +chr1:1166386 [C/A] chr1 1166386 Cc01_g00690:200 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 33.3% 3 CC NN CC AA +chr1:1166466 [A/C] chr1 1166466 Cc01_g00690:280 exon NON_SYNONYMOUS_CODING Act/Cct T/P 16.7% 3 AA NN AA AC +chr1:1166542 [T/G] chr1 1166542 Cc01_g00690:356 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 33.3% 3 TT NN TT GG +chr1:1166804 [C/A] chr1 1166804 Cc01_g00690:618 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC CC CC AA +chr1:1167034 [G/C] chr1 1167034 Cc01_g00700:60 exon NON_SYNONYMOUS_CODING agG/agC R/S 33.3% 3 GG NN GG CC +chr1:1167354 [A/G] chr1 1167354 Cc01_g00700:380 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 33.3% 3 AA NN AA GG +chr1:1167571 [G/T] chr1 1167571 Cc01_g00700:597 exon NON_SYNONYMOUS_CODING agG/agT R/S 33.3% 3 GG NN GG TT +chr1:1179790 [G/A] chr1 1179790 Cc01_g00710:105 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GG AA GG +chr1:1179828 [C/G] chr1 1179828 Cc01_g00710:143 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG GG GG +chr1:1179917 [A/T] chr1 1179917 Cc01_g00710:232 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 AA TT TT TT +chr1:1179943 [C/T] chr1 1179943 Cc01_g00710:258 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT +chr1:1179952 [T/C] chr1 1179952 Cc01_g00710:267 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC +chr1:1179953 [G/A] chr1 1179953 Cc01_g00710:268 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA +chr1:1179985 [C/T] chr1 1179985 Cc01_g00710:300 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT +chr1:1180012 [A/G] chr1 1180012 Cc01_g00710:327 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG GG GG +chr1:1180056 [T/C] chr1 1180056 Cc01_g00710:371 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC CC CC +chr1:1180061 [T/C] chr1 1180061 Cc01_g00710:376 exon STOP_LOST Tag/Cag 1/Q 25.0% 4 TT CC CC CC +chr1:1180063 [G/C] chr1 1180063 Cc01_g00710:378 exon STOP_LOST taG/taC 1/Y 33.3% 3 GG NN CC CC +chr1:1212493 [G/C] chr1 1212493 Cc01_g00720:7 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 33.3% 3 GG CC NN GG +chr1:1212477 [T/C] chr1 1212477 Cc01_g00720:23 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT CC TT TT +chr1:1212194 [A/T] chr1 1212194 Cc01_g00720:160 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 AA TT AA AA +chr1:1212184 [C/G] chr1 1212184 Cc01_g00720:170 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 12.5% 4 CC CG CC CC +chr1:1212161 [G/A] chr1 1212161 Cc01_g00720:193 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 GG AA GG GG +chr1:1212152 [A/G] chr1 1212152 Cc01_g00720:202 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG AA AA +chr1:1212124 [C/A] chr1 1212124 Cc01_g00720:230 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC +chr1:1211997 [A/T] chr1 1211997 Cc01_g00720:357 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT AA AA +chr1:1211930 [T/C] chr1 1211930 Cc01_g00720:424 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC TT TT +chr1:1211567 [A/G] chr1 1211567 Cc01_g00720:530 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG AA AA +chr1:1211520 [G/T] chr1 1211520 Cc01_g00720:577 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 GG TT GG GG +chr1:1211473 [C/A] chr1 1211473 Cc01_g00720:624 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC AA CC CC +chr1:1211425 [A/G] chr1 1211425 Cc01_g00720:672 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA +chr1:1211423 [A/C] chr1 1211423 Cc01_g00720:674 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 25.0% 4 AA CC AA AA +chr1:1211422 [G/C] chr1 1211422 Cc01_g00720:675 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG CC GG GG +chr1:1211398 [G/C] chr1 1211398 Cc01_g00720:699 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG CC GG GG +chr1:1211397 [G/T] chr1 1211397 Cc01_g00720:700 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 GG TT GG GG +chr1:1211383 [C/T] chr1 1211383 Cc01_g00720:714 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 CC TT CC CC +chr1:1211377 [C/T] chr1 1211377 Cc01_g00720:720 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 CC TT CT CC +chr1:1211364 [T/G] chr1 1211364 Cc01_g00720:733 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 25.0% 4 TT GG TT TT +chr1:1211349 [C/T] chr1 1211349 Cc01_g00720:748 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TT CT CC +chr1:1210891 [T/A] chr1 1210891 Cc01_g00720:758 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 TT AA TT TT +chr1:1210874 [A/G] chr1 1210874 Cc01_g00720:775 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG AA AA +chr1:1210869 [A/G] chr1 1210869 Cc01_g00720:780 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:1210831 [T/A] chr1 1210831 Cc01_g00720:818 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 TT TA TT TT +chr1:1210823 [G/A] chr1 1210823 Cc01_g00720:826 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 25.0% 4 GG AA GG GG +chr1:1210781 [C/T] chr1 1210781 Cc01_g00720:868 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC +chr1:1210772 [A/T] chr1 1210772 Cc01_g00720:877 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 25.0% 4 AA TT TT TT +chr1:1210770 [A/C] chr1 1210770 Cc01_g00720:879 exon STOP_GAINED taT/taG Y/3 25.0% 4 AA CC AA AA +chr1:1210745 [T/C] chr1 1210745 Cc01_g00720:904 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT TT CC +chr1:1210744 [A/G] chr1 1210744 Cc01_g00720:905 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 AA GG AA AA +chr1:1210728 [T/C] chr1 1210728 Cc01_g00720:921 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC TT TT +chr1:1210710 [A/T] chr1 1210710 Cc01_g00720:939 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 AA TT AA AA +chr1:1210708 [A/G] chr1 1210708 Cc01_g00720:941 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA GG AA AA +chr1:1210663 [A/G] chr1 1210663 Cc01_g00720:986 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 AA GG AA AA +chr1:1210651 [T/A] chr1 1210651 Cc01_g00720:998 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT AA TT TT +chr1:1210640 [G/C] chr1 1210640 Cc01_g00720:1009 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG CC GG GG +chr1:1210632 [A/G] chr1 1210632 Cc01_g00720:1017 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA AA AG GG +chr1:1210613 [A/T] chr1 1210613 Cc01_g00720:1036 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 AA TT AA AA +chr1:1210611 [T/C] chr1 1210611 Cc01_g00720:1038 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC TT TT +chr1:1210566 [G/A] chr1 1210566 Cc01_g00720:1083 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG AA GG GG +chr1:1210546 [T/A] chr1 1210546 Cc01_g00720:1103 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 TT AA TT TT +chr1:1210538 [C/T] chr1 1210538 Cc01_g00720:1111 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT CC CC +chr1:1210516 [T/A] chr1 1210516 Cc01_g00720:1133 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT TT AA +chr1:1210512 [C/T] chr1 1210512 Cc01_g00720:1137 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC +chr1:1210505 [C/A] chr1 1210505 Cc01_g00720:1144 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 25.0% 4 CC AA CC CC +chr1:1242676 [A/G] chr1 1242676 Cc01_g00730:1 exon START_LOST Atg/Gtg M/V 25.0% 4 AA GG AA AA +chr1:1242683 [C/T] chr1 1242683 Cc01_g00730:8 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CT CC CC +chr1:1242684 [A/G] chr1 1242684 Cc01_g00730:9 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG AA +chr1:1242698 [C/T] chr1 1242698 Cc01_g00730:23 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 12.5% 4 CC CC CT CC +chr1:1242721 [C/G] chr1 1242721 Cc01_g00730:46 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC GG CC CG +chr1:1242729 [T/G] chr1 1242729 Cc01_g00730:54 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 TT GG TT TG +chr1:1242731 [C/A] chr1 1242731 Cc01_g00730:56 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 12.5% 4 CC CA CC CC +chr1:1242744 [A/T] chr1 1242744 Cc01_g00730:69 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 4 AA TT AT AT +chr1:1242762 [T/C] chr1 1242762 Cc01_g00730:87 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 4 TT CC TC TC +chr1:1242783 [A/G] chr1 1242783 Cc01_g00730:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 50.0% 4 AA GG AG AG +chr1:1242791 [G/C] chr1 1242791 Cc01_g00730:116 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 12.5% 4 GG GC GG GG +chr1:1242950 [G/T] chr1 1242950 Cc01_g00730:275 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT GG GG +chr1:1243019 [G/C] chr1 1243019 Cc01_g00730:344 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 25.0% 4 GG CC GG GG +chr1:1243020 [T/A] chr1 1243020 Cc01_g00730:345 exon SYNONYMOUS_CODING cgT/cgA R/R 25.0% 4 TT AA TT TT +chr1:1244895 [G/T] chr1 1244895 Cc01_g00730:369 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 GG TT GG GG +chr1:1244933 [T/A] chr1 1244933 Cc01_g00730:407 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT AA TT TT +chr1:1245002 [C/A] chr1 1245002 Cc01_g00730:476 exon NON_SYNONYMOUS_CODING cCt/cAt P/H 25.0% 4 CC CC CC AA +chr1:1245030 [G/A] chr1 1245030 Cc01_g00730:504 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG AA GG GG +chr1:1245060 [T/A] chr1 1245060 Cc01_g00730:534 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TA TT TT +chr1:1245492 [A/G] chr1 1245492 Cc01_g00730:553 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AA AG AG +chr1:1245530 [A/G] chr1 1245530 Cc01_g00730:591 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG +chr1:1245533 [T/C] chr1 1245533 Cc01_g00730:594 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:1245549 [C/A] chr1 1245549 Cc01_g00730:610 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 CC CC CA CA +chr1:1245553 [A/G] chr1 1245553 Cc01_g00730:614 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG +chr1:1245566 [G/C] chr1 1245566 Cc01_g00730:627 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC GG GG +chr1:1253676 [T/C] chr1 1253676 Cc01_g00740:865 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC TC +chr1:1256457 [G/T] chr1 1256457 Cc01_g00750:100 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 2 GG NN NN GT +chr1:1262785 [G/T] chr1 1262785 Cc01_g00760:45 exon SYNONYMOUS_CODING tcC/tcA S/S 50.0% 2 GG NN NN TT +chr1:1269842 [C/T] chr1 1269842 Cc01_g00770:45 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC CC NN CT +chr1:1269935 [C/G] chr1 1269935 Cc01_g00770:138 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GG GG CG +chr1:1269943 [G/A] chr1 1269943 Cc01_g00770:146 exon STOP_GAINED tGg/tAg W/9 37.5% 4 GG AA AA GA +chr1:1269976 [T/C] chr1 1269976 Cc01_g00770:179 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 TT TT TC TT +chr1:1270017 [T/C] chr1 1270017 Cc01_g00770:220 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT +chr1:1270071 [A/C] chr1 1270071 Cc01_g00770:274 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 12.5% 4 AA AA AA AC +chr1:1270072 [G/A] chr1 1270072 Cc01_g00770:275 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG +chr1:1270081 [T/C] chr1 1270081 Cc01_g00770:284 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TT CT +chr1:1270085 [T/C] chr1 1270085 Cc01_g00770:288 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT CT +chr1:1270104 [A/T] chr1 1270104 Cc01_g00770:307 exon NON_SYNONYMOUS_CODING Agg/Tgg R/W 12.5% 4 AA AA AT AA +chr1:1276100 [G/T] chr1 1276100 Cc01_g00770:317 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT +chr1:1278052 [G/A] chr1 1278052 Cc01_g00780:52 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA +chr1:1278096 [A/T] chr1 1278096 Cc01_g00780:96 exon NON_SYNONYMOUS_CODING agA/agT R/S 50.0% 4 AA TT AT AT +chr1:1278097 [A/G] chr1 1278097 Cc01_g00780:97 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 4 AA GG AG AG +chr1:1278180 [T/C] chr1 1278180 Cc01_g00780:180 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT CC CC CC +chr1:1278211 [T/C] chr1 1278211 Cc01_g00780:211 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT CC TC TT +chr1:1279216 [A/G] chr1 1279216 Cc01_g00780:409 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA AA AG AG +chr1:1287721 [T/C] chr1 1287721 Cc01_g00790:16 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 3 TT TC NN CC +chr1:1287672 [C/T] chr1 1287672 Cc01_g00790:31 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC CC TT CC +chr1:1287643 [T/C] chr1 1287643 Cc01_g00790:60 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:1287637 [C/T] chr1 1287637 Cc01_g00790:66 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT +chr1:1286824 [G/A] chr1 1286824 Cc01_g00790:136 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA +chr1:1286808 [T/C] chr1 1286808 Cc01_g00790:152 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TC TT TT +chr1:1285473 [T/C] chr1 1285473 Cc01_g00790:246 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC TC CC +chr1:1285472 [G/A] chr1 1285472 Cc01_g00790:247 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG +chr1:1284801 [T/C] chr1 1284801 Cc01_g00790:399 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TC TT +chr1:1287857 [C/A] chr1 1287857 Cc01_g00800:142 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 CC NN NN AA +chr1:1287818 [C/G] chr1 1287818 Cc01_g00800:181 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 50.0% 2 CC GG NN NN +chr1:1291612 [T/C] chr1 1291612 Cc01_g00810:61 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT +chr1:1291633 [A/T] chr1 1291633 Cc01_g00810:82 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 25.0% 4 AA AA AA TT +chr1:1291665 [T/C] chr1 1291665 Cc01_g00810:114 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TT CC +chr1:1291715 [A/G] chr1 1291715 Cc01_g00810:164 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GG AG AA +chr1:1291716 [C/T] chr1 1291716 Cc01_g00810:165 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 CC CC CC TT +chr1:1291740 [G/T] chr1 1291740 Cc01_g00810:189 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG GG GG TT +chr1:1292034 [T/A] chr1 1292034 Cc01_g00810:396 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT AA AA AA +chr1:1292248 [A/G] chr1 1292248 Cc01_g00810:510 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:1293103 [C/T] chr1 1293103 Cc01_g00810:767 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC +chr1:1293122 [C/G] chr1 1293122 Cc01_g00810:786 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC CC GG +chr1:1293811 [T/C] chr1 1293811 Cc01_g00810:813 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC +chr1:1293815 [C/A] chr1 1293815 Cc01_g00810:817 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 CC AA AA CC +chr1:1293824 [C/T] chr1 1293824 Cc01_g00810:826 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC TT TT CC +chr1:1293825 [A/G] chr1 1293825 Cc01_g00810:827 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 4 AA GG GG AA +chr1:1293978 [A/T] chr1 1293978 Cc01_g00810:882 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AA AA TT +chr1:1294013 [G/A] chr1 1294013 Cc01_g00810:917 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 GG GG GG GA +chr1:1294044 [A/T] chr1 1294044 Cc01_g00810:948 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA AA AA TT +chr1:1294134 [C/T] chr1 1294134 Cc01_g00810:1038 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC CC TT +chr1:1294702 [C/T] chr1 1294702 Cc01_g00810:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CT CC +chr1:1294781 [G/C] chr1 1294781 Cc01_g00810:1300 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG +chr1:1294832 [A/T] chr1 1294832 Cc01_g00810:1351 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 4 AA TT TT AA +chr1:1294843 [G/T] chr1 1294843 Cc01_g00810:1362 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT +chr1:1294891 [T/G] chr1 1294891 Cc01_g00810:1410 exon NON_SYNONYMOUS_CODING atT/atG I/M 37.5% 4 TT GG TG GG +chr1:1294916 [G/T] chr1 1294916 Cc01_g00810:1435 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GT GG +chr1:1299931 [A/C] chr1 1299931 Cc01_g00820:42 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 AA AC AA AC +chr1:1299953 [G/A] chr1 1299953 Cc01_g00820:64 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:1300252 [C/T] chr1 1300252 Cc01_g00820:219 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC CC TT CC +chr1:1300382 [C/T] chr1 1300382 Cc01_g00820:349 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 CC CC TT CC +chr1:1300390 [T/C] chr1 1300390 Cc01_g00820:357 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TT CC TT +chr1:1300457 [T/C] chr1 1300457 Cc01_g00820:424 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT +chr1:1300540 [T/C] chr1 1300540 Cc01_g00820:507 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TT CC TT +chr1:1300948 [C/T] chr1 1300948 Cc01_g00820:915 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT +chr1:1301593 [T/C] chr1 1301593 Cc01_g00820:1152 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT +chr1:1302393 [T/C] chr1 1302393 Cc01_g00820:1332 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT +chr1:1304941 [C/T] chr1 1304941 Cc01_g00820:2055 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT TT CC +chr1:1306040 [A/T] chr1 1306040 Cc01_g00820:2256 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA TT AA +chr1:1306100 [A/G] chr1 1306100 Cc01_g00820:2316 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GG AA +chr1:1306364 [T/C] chr1 1306364 Cc01_g00820:2482 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT +chr1:1306387 [A/G] chr1 1306387 Cc01_g00820:2505 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA +chr1:1307153 [T/C] chr1 1307153 Cc01_g00820:2580 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT +chr1:1307312 [T/C] chr1 1307312 Cc01_g00820:2652 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT +chr1:1307738 [A/T] chr1 1307738 Cc01_g00820:2802 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA TT AA +chr1:1308482 [A/T] chr1 1308482 Cc01_g00820:2964 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AT AA AA +chr1:1308494 [G/A] chr1 1308494 Cc01_g00820:2976 exon SYNONYMOUS_CODING agG/agA R/R 16.7% 3 GG GA NN GG +chr1:1308608 [C/A] chr1 1308608 Cc01_g00830:24 exon STOP_GAINED tgC/tgA C8* 16.7% 3 CC CA NN CC +chr1:1309677 [C/G] chr1 1309677 Cc01_g00830:163 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CG CG CC +chr1:1314539 [G/A] chr1 1314539 Cc01_g00840:25 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 3 GG AA NN GA +chr1:1314673 [G/A] chr1 1314673 Cc01_g00840:159 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA +chr1:1314823 [C/G] chr1 1314823 Cc01_g00840:309 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 CC GG GG GG +chr1:1314984 [G/A] chr1 1314984 Cc01_g00840:470 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 37.5% 4 GG GG AA GA +chr1:1315015 [G/C] chr1 1315015 Cc01_g00840:501 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG GG CC GC +chr1:1315050 [A/G] chr1 1315050 Cc01_g00840:536 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 AA AG NN AA +chr1:1315120 [C/A] chr1 1315120 Cc01_g00840:606 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA +chr1:1315139 [T/A] chr1 1315139 Cc01_g00840:625 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 16.7% 3 TT TT NN TA +chr1:1315156 [T/G] chr1 1315156 Cc01_g00840:642 exon SYNONYMOUS_CODING tcT/tcG S/S 16.7% 3 TT TT NN TG +chr1:1315218 [T/C] chr1 1315218 Cc01_g00840:704 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 3 TT NN CC TC +chr1:1315234 [C/T] chr1 1315234 Cc01_g00840:720 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC CC NN TT +chr1:1315240 [C/T] chr1 1315240 Cc01_g00840:726 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC CC NN TT +chr1:1315338 [A/T] chr1 1315338 Cc01_g00840:824 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA TT NN AA +chr1:1324380 [G/A] chr1 1324380 Cc01_g00850:82 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA +chr1:1324392 [A/G] chr1 1324392 Cc01_g00850:94 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 37.5% 4 AA GG GG AG +chr1:1324409 [G/C] chr1 1324409 Cc01_g00850:111 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 GG GG GG CG +chr1:1326674 [T/C] chr1 1326674 Cc01_g00850:270 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC +chr1:1326698 [A/G] chr1 1326698 Cc01_g00850:294 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA +chr1:1327530 [G/C] chr1 1327530 Cc01_g00850:418 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 25.0% 4 GG CC CC CC +chr1:1327531 [A/G] chr1 1327531 Cc01_g00850:419 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA GG GG AG +chr1:1327575 [C/G] chr1 1327575 Cc01_g00850:463 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CC GC +chr1:1327581 [G/A] chr1 1327581 Cc01_g00850:469 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG +chr1:1327613 [C/T] chr1 1327613 Cc01_g00850:501 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC TT TT TT +chr1:1327618 [C/T] chr1 1327618 Cc01_g00850:506 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC TT TT TT +chr1:1327624 [C/A] chr1 1327624 Cc01_g00850:512 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 37.5% 4 CC AA AA CA +chr1:1327630 [G/T] chr1 1327630 Cc01_g00850:518 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 GG TT TT TT +chr1:1327639 [T/G] chr1 1327639 Cc01_g00850:527 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 TT GG GG GG +chr1:1327826 [T/C] chr1 1327826 Cc01_g00850:714 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT CC CC CC +chr1:1327904 [C/T] chr1 1327904 Cc01_g00850:792 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC TT CT CC +chr1:1328126 [A/G] chr1 1328126 Cc01_g00850:859 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AA AG +chr1:1328127 [A/T] chr1 1328127 Cc01_g00850:860 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 AA AA AA AT +chr1:1332539 [C/A] chr1 1332539 Cc01_g00860:529 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 37.5% 4 CC CA CA CA +chr1:1332405 [T/C] chr1 1332405 Cc01_g00860:663 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TC TT TT +chr1:1332138 [T/C] chr1 1332138 Cc01_g00860:930 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC +chr1:1331004 [A/G] chr1 1331004 Cc01_g00860:1047 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA +chr1:1330827 [G/A] chr1 1330827 Cc01_g00860:1224 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GA GG GG +chr1:1330803 [T/A] chr1 1330803 Cc01_g00860:1248 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 TT TA TT TT +chr1:1330755 [A/G] chr1 1330755 Cc01_g00860:1296 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AG AA AA +chr1:1349945 [T/C] chr1 1349945 Cc01_g00870:84 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TC TT +chr1:1349954 [T/C] chr1 1349954 Cc01_g00870:93 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:1350532 [C/T] chr1 1350532 Cc01_g00870:144 exon SYNONYMOUS_CODING ggC/ggT G/G 37.5% 4 CC CC TC TT +chr1:1350732 [C/T] chr1 1350732 Cc01_g00870:344 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 37.5% 4 CC CC CT TT +chr1:1400299 [A/G] chr1 1400299 Cc01_g00880:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG +chr1:1400306 [C/T] chr1 1400306 Cc01_g00880:30 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC CC TT +chr1:1400308 [A/G] chr1 1400308 Cc01_g00880:32 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG +chr1:1400337 [T/G] chr1 1400337 Cc01_g00880:61 exon NON_SYNONYMOUS_CODING Tgg/Ggg W/G 25.0% 4 TT GG GG GG +chr1:1400339 [G/A] chr1 1400339 Cc01_g00880:63 exon STOP_GAINED tgG/tgA W/1 25.0% 4 GG AA AA AA +chr1:1400381 [A/C] chr1 1400381 Cc01_g00880:105 exon SYNONYMOUS_CODING ccA/ccC P/P 33.3% 3 AA CC NN CC +chr1:1410529 [A/G] chr1 1410529 Cc01_g00890:10 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 AA NN NN GG +chr1:1410533 [C/T] chr1 1410533 Cc01_g00890:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 33.3% 3 CC CC NN TT +chr1:1410555 [T/C] chr1 1410555 Cc01_g00890:36 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT CC TT TT +chr1:1410556 [T/C] chr1 1410556 Cc01_g00890:37 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 50.0% 4 TT TT CC CC +chr1:1410561 [C/T] chr1 1410561 Cc01_g00890:42 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 CC CC TT TT +chr1:1410563 [A/G] chr1 1410563 Cc01_g00890:44 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA GG GG GG +chr1:1410566 [C/T] chr1 1410566 Cc01_g00890:47 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 4 CC CC TT TT +chr1:1410569 [A/C] chr1 1410569 Cc01_g00890:50 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 25.0% 4 AA CC CC CC +chr1:1410570 [G/A] chr1 1410570 Cc01_g00890:51 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 4 GG GG AA AA +chr1:1410580 [A/C] chr1 1410580 Cc01_g00890:61 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA +chr1:1410597 [C/G] chr1 1410597 Cc01_g00890:78 exon NON_SYNONYMOUS_CODING caC/caG H/Q 25.0% 4 CC GG GG GG +chr1:1427295 [C/G] chr1 1427295 Cc01_g00900:7 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 25.0% 4 CC CG CC CG +chr1:1427282 [G/A] chr1 1427282 Cc01_g00900:20 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG AA AA GA +chr1:1427281 [G/A] chr1 1427281 Cc01_g00900:21 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GA AG +chr1:1427279 [G/A] chr1 1427279 Cc01_g00900:23 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG +chr1:1427275 [A/T] chr1 1427275 Cc01_g00900:27 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 AA AA AA TA +chr1:1427274 [A/G] chr1 1427274 Cc01_g00900:28 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 AA AA AA GA +chr1:1427261 [C/A] chr1 1427261 Cc01_g00900:41 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 CC CC CC AC +chr1:1427118 [T/C] chr1 1427118 Cc01_g00900:66 exon SYNONYMOUS_CODING ttA/ttG L/L 16.7% 3 TT NN TT CT +chr1:1427056 [T/C] chr1 1427056 Cc01_g00900:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TC TC TT +chr1:1427054 [C/T] chr1 1427054 Cc01_g00900:130 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC +chr1:1427045 [G/A] chr1 1427045 Cc01_g00900:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA GA AG +chr1:1427039 [G/T] chr1 1427039 Cc01_g00900:145 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 GG TG TG GT +chr1:1427035 [G/A] chr1 1427035 Cc01_g00900:149 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG GA AG AG +chr1:1427030 [A/T] chr1 1427030 Cc01_g00900:154 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT AT TA +chr1:1427016 [T/C] chr1 1427016 Cc01_g00900:168 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC CT TC +chr1:1427004 [G/A] chr1 1427004 Cc01_g00900:180 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA +chr1:1427003 [C/T] chr1 1427003 Cc01_g00900:181 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 CC CC CT CT +chr1:1426994 [A/T] chr1 1426994 Cc01_g00900:190 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 25.0% 4 AA TA AA AT +chr1:1426981 [A/G] chr1 1426981 Cc01_g00900:203 exon NON_SYNONYMOUS_CODING cTc/cCc L/P 12.5% 4 AA AA AA AG +chr1:1426962 [T/C] chr1 1426962 Cc01_g00900:222 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CT CT TC +chr1:1426958 [C/T] chr1 1426958 Cc01_g00900:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TC CC CT +chr1:1426939 [A/T] chr1 1426939 Cc01_g00900:245 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA TA AA +chr1:1426936 [A/G] chr1 1426936 Cc01_g00900:248 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA AG AA GA +chr1:1426925 [A/G] chr1 1426925 Cc01_g00900:259 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA AA AG GA +chr1:1426907 [T/A] chr1 1426907 Cc01_g00900:277 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 25.0% 4 TT TA AT TT +chr1:1426905 [G/A] chr1 1426905 Cc01_g00900:279 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 GG AA AA AA +chr1:1433418 [A/G] chr1 1433418 Cc01_g00910:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:1433394 [G/A] chr1 1433394 Cc01_g00910:126 exon SYNONYMOUS_CODING ctC/ctT L/L 50.0% 4 GG GA AA GA +chr1:1433392 [C/T] chr1 1433392 Cc01_g00910:128 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT CC CT +chr1:1433373 [C/G] chr1 1433373 Cc01_g00910:147 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC +chr1:1432755 [C/T] chr1 1432755 Cc01_g00910:549 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 CC CC CT CC +chr1:1432742 [C/T] chr1 1432742 Cc01_g00910:562 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CT CC CC +chr1:1432732 [C/T] chr1 1432732 Cc01_g00910:572 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 CC TC CT CC +chr1:1432730 [T/C] chr1 1432730 Cc01_g00910:574 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CT TC TT +chr1:1432728 [T/G] chr1 1432728 Cc01_g00910:576 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GT TG TT +chr1:1432698 [A/G] chr1 1432698 Cc01_g00910:606 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA GA AA AA +chr1:1432697 [A/G] chr1 1432697 Cc01_g00910:607 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA GA AA AA +chr1:1432689 [G/C] chr1 1432689 Cc01_g00910:615 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GC GG GG +chr1:1432664 [C/A] chr1 1432664 Cc01_g00910:640 exon STOP_GAINED Gag/Tag E/4 12.5% 4 CC CA CC CC +chr1:1432663 [T/A] chr1 1432663 Cc01_g00910:641 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 TT TA TT TT +chr1:1432611 [A/G] chr1 1432611 Cc01_g00910:693 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA +chr1:1432605 [G/A] chr1 1432605 Cc01_g00910:699 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG GA AA GG +chr1:1432569 [C/T] chr1 1432569 Cc01_g00910:735 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 CC CC NN CT +chr1:1500031 [G/T] chr1 1500031 Cc01_g00920:49 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 37.5% 4 GG GT GG TT +chr1:1500013 [A/T] chr1 1500013 Cc01_g00920:67 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA TA AT AA +chr1:1499982 [C/T] chr1 1499982 Cc01_g00920:98 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC NN TT NN +chr1:1499966 [C/T] chr1 1499966 Cc01_g00920:114 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 2 CC NN TT NN +chr1:1499954 [T/C] chr1 1499954 Cc01_g00920:126 exon SYNONYMOUS_CODING gcA/gcG A/A 33.3% 3 TT CC CC NN +chr1:1499939 [C/T] chr1 1499939 Cc01_g00920:141 exon SYNONYMOUS_CODING ctG/ctA L/L 33.3% 3 CC TT TT NN +chr1:1499937 [T/A] chr1 1499937 Cc01_g00920:143 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 33.3% 3 TT AA AA NN +chr1:1499906 [T/C] chr1 1499906 Cc01_g00920:174 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC CC TT +chr1:1499782 [C/G] chr1 1499782 Cc01_g00920:298 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 2 CC NN CG NN +chr1:1499780 [C/G] chr1 1499780 Cc01_g00920:300 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 2 CC NN CG NN +chr1:1499449 [G/A] chr1 1499449 Cc01_g00920:631 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 GG NN AA NN +chr1:1500757 [A/G] chr1 1500757 Cc01_g00930:205 exon SYNONYMOUS_CODING Ttg/Ctg L/L 16.7% 3 AA NN AA AG +chr1:1500735 [C/G] chr1 1500735 Cc01_g00930:227 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 16.7% 3 CC NN CC CG +chr1:1500625 [A/G] chr1 1500625 Cc01_g00930:337 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 2 AA NN NN AG +chr1:1500270 [T/C] chr1 1500270 Cc01_g00930:605 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TC TT +chr1:1500265 [G/T] chr1 1500265 Cc01_g00930:610 exon NON_SYNONYMOUS_CODING Cgc/Agc R/S 12.5% 4 GG GG GT GG +chr1:1500257 [C/A] chr1 1500257 Cc01_g00930:618 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA +chr1:1527537 [A/C] chr1 1527537 Cc01_g00940:47 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 12.5% 4 AA AC AA AA +chr1:1527535 [G/C] chr1 1527535 Cc01_g00940:49 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG CG GC GC +chr1:1527534 [C/A] chr1 1527534 Cc01_g00940:50 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 12.5% 4 CC CC CA CC +chr1:1527525 [G/C] chr1 1527525 Cc01_g00940:59 exon STOP_GAINED tCa/tGa S/0 37.5% 4 GG CG GC GC +chr1:1527523 [C/T] chr1 1527523 Cc01_g00940:61 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 25.0% 4 CC CT CC CT +chr1:1527516 [A/G] chr1 1527516 Cc01_g00940:68 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 AA AG GA AA +chr1:1527513 [T/C] chr1 1527513 Cc01_g00940:71 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC CC CC +chr1:1527501 [T/C] chr1 1527501 Cc01_g00940:83 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT TT CT TC +chr1:1527490 [C/A] chr1 1527490 Cc01_g00940:94 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 CC CC AC CC +chr1:1527489 [A/G] chr1 1527489 Cc01_g00940:95 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:1527479 [A/T] chr1 1527479 Cc01_g00940:105 exon NON_SYNONYMOUS_CODING agT/agA S/R 37.5% 4 AA AT TT TT +chr1:1527475 [A/G] chr1 1527475 Cc01_g00940:109 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA AG GA AA +chr1:1527337 [T/C] chr1 1527337 Cc01_g00940:124 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC CT TC +chr1:1527336 [G/A] chr1 1527336 Cc01_g00940:125 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 12.5% 4 GG GA GG GG +chr1:1527333 [G/A] chr1 1527333 Cc01_g00940:128 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG +chr1:1527325 [C/T] chr1 1527325 Cc01_g00940:136 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 CC CT CC CC +chr1:1527324 [A/G] chr1 1527324 Cc01_g00940:137 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA +chr1:1527323 [C/T] chr1 1527323 Cc01_g00940:138 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC TC +chr1:1527310 [G/T] chr1 1527310 Cc01_g00940:151 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 GG GG GG TG +chr1:1527283 [G/A] chr1 1527283 Cc01_g00940:178 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA GA GA +chr1:1527277 [T/C] chr1 1527277 Cc01_g00940:184 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 TT TT TC TT +chr1:1527264 [C/A] chr1 1527264 Cc01_g00940:197 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 CC CA CC CC +chr1:1527261 [T/C] chr1 1527261 Cc01_g00940:200 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 TT CC CC CC +chr1:1527259 [G/A] chr1 1527259 Cc01_g00940:202 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 25.0% 4 GG AA AA AA +chr1:1527237 [G/A] chr1 1527237 Cc01_g00940:224 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG +chr1:1527236 [C/T] chr1 1527236 Cc01_g00940:225 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:1531686 [A/G] chr1 1531686 Cc01_g00950:645 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA GG NN GG +chr1:1531682 [A/G] chr1 1531682 Cc01_g00950:649 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 AA GG NN GG +chr1:1531673 [C/T] chr1 1531673 Cc01_g00950:658 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 CC TT CC CT +chr1:1531659 [A/G] chr1 1531659 Cc01_g00950:672 exon SYNONYMOUS_CODING atT/atC I/I 12.5% 4 AA AA AA AG +chr1:1531644 [A/T] chr1 1531644 Cc01_g00950:687 exon SYNONYMOUS_CODING cgT/cgA R/R 50.0% 4 AA TT TT AA +chr1:1531643 [A/T] chr1 1531643 Cc01_g00950:688 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT TA +chr1:1531641 [C/T] chr1 1531641 Cc01_g00950:690 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC +chr1:1531626 [C/G] chr1 1531626 Cc01_g00950:705 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 50.0% 4 CC GG GG CC +chr1:1531625 [A/G] chr1 1531625 Cc01_g00950:706 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 25.0% 4 AA AA GG AA +chr1:1531616 [T/C] chr1 1531616 Cc01_g00950:715 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT CC TT +chr1:1531606 [T/C] chr1 1531606 Cc01_g00950:725 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 33.3% 3 TT NN CC TT +chr1:1531575 [A/G] chr1 1531575 Cc01_g00950:756 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AG AG +chr1:1531524 [G/A] chr1 1531524 Cc01_g00950:807 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG +chr1:1531385 [A/C] chr1 1531385 Cc01_g00950:946 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 AA AA AA AC +chr1:1531373 [T/G] chr1 1531373 Cc01_g00950:958 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT +chr1:1531330 [C/T] chr1 1531330 Cc01_g00950:1001 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CC CT +chr1:1531324 [C/G] chr1 1531324 Cc01_g00950:1007 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG GG GC +chr1:1530921 [T/A] chr1 1530921 Cc01_g00950:1410 exon NON_SYNONYMOUS_CODING agA/agT R/S 33.3% 3 TT AA NN AA +chr1:1530898 [T/A] chr1 1530898 Cc01_g00950:1433 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 50.0% 3 TT AA NN TA +chr1:1530757 [C/T] chr1 1530757 Cc01_g00950:1574 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 CC TT NN NN +chr1:1530731 [T/G] chr1 1530731 Cc01_g00950:1600 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT GG NN NN +chr1:1530707 [G/A] chr1 1530707 Cc01_g00950:1624 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 2 GG AA NN NN +chr1:1530676 [G/C] chr1 1530676 Cc01_g00950:1655 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 3 GG GC NN CC +chr1:1530668 [T/C] chr1 1530668 Cc01_g00950:1663 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CC TT TT +chr1:1530661 [T/G] chr1 1530661 Cc01_g00950:1670 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 TT TG TT TT +chr1:1530629 [T/G] chr1 1530629 Cc01_g00950:1702 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT TT TT GG +chr1:1530627 [T/C] chr1 1530627 Cc01_g00950:1704 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT CT TT TT +chr1:1530607 [C/T] chr1 1530607 Cc01_g00950:1724 exon STOP_GAINED tGg/tAg W/5 16.7% 3 CC TC CC NN +chr1:1530606 [C/A] chr1 1530606 Cc01_g00950:1725 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 16.7% 3 CC AC CC NN +chr1:1530597 [T/G] chr1 1530597 Cc01_g00950:1734 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 16.7% 3 TT GT TT NN +chr1:1530532 [T/C] chr1 1530532 Cc01_g00950:1799 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 33.3% 3 TT CC TT NN +chr1:1530520 [T/G] chr1 1530520 Cc01_g00950:1811 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 16.7% 3 TT TG TT NN +chr1:1530290 [T/C] chr1 1530290 Cc01_g00950:2041 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 TT TT NN CC +chr1:1530289 [A/G] chr1 1530289 Cc01_g00950:2042 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 33.3% 3 AA AA NN GG +chr1:1530287 [C/A] chr1 1530287 Cc01_g00950:2044 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 33.3% 3 CC CC NN AA +chr1:1530286 [C/T] chr1 1530286 Cc01_g00950:2045 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC CC CC TT +chr1:1538660 [T/G] chr1 1538660 Cc01_g00960:57 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TG TT TT +chr1:1538676 [T/C] chr1 1538676 Cc01_g00960:73 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TC TT TT +chr1:1538690 [A/G] chr1 1538690 Cc01_g00960:87 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AG AA AA +chr1:1538747 [G/A] chr1 1538747 Cc01_g00960:144 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG GA GG GG +chr1:1538777 [T/C] chr1 1538777 Cc01_g00960:174 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:1538784 [G/T] chr1 1538784 Cc01_g00960:181 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG +chr1:1538792 [T/G] chr1 1538792 Cc01_g00960:189 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT +chr1:1538814 [G/C] chr1 1538814 Cc01_g00960:211 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 12.5% 4 GG GC GG GG +chr1:1538834 [T/C] chr1 1538834 Cc01_g00960:231 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:1538885 [C/T] chr1 1538885 Cc01_g00960:282 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:1539091 [G/A] chr1 1539091 Cc01_g00960:488 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA GG GG +chr1:1539183 [A/G] chr1 1539183 Cc01_g00960:580 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA +chr1:1539211 [C/G] chr1 1539211 Cc01_g00960:608 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CC CC CG +chr1:1539272 [G/T] chr1 1539272 Cc01_g00960:669 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 GG GT GG GG +chr1:1539343 [G/A] chr1 1539343 Cc01_g00960:740 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1539365 [A/G] chr1 1539365 Cc01_g00960:762 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AG AA AA +chr1:1539374 [T/G] chr1 1539374 Cc01_g00960:771 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT GT TT TT +chr1:1539408 [T/C] chr1 1539408 Cc01_g00960:805 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT CT TT TT +chr1:1539428 [C/T] chr1 1539428 Cc01_g00960:825 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CT CC CC +chr1:1539430 [G/T] chr1 1539430 Cc01_g00960:827 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GT GG GG +chr1:1539431 [G/T] chr1 1539431 Cc01_g00960:828 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 12.5% 4 GG GT GG GG +chr1:1539509 [A/T] chr1 1539509 Cc01_g00960:906 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA +chr1:1539636 [T/G] chr1 1539636 Cc01_g00960:1033 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 TT TG TT TT +chr1:1539709 [C/G] chr1 1539709 Cc01_g00960:1106 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC +chr1:1539758 [C/T] chr1 1539758 Cc01_g00960:1155 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:1539788 [A/G] chr1 1539788 Cc01_g00960:1185 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA GA AA AA +chr1:1539824 [A/G] chr1 1539824 Cc01_g00960:1221 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:1540980 [G/A] chr1 1540980 Cc01_g00960:1273 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG AG GG GG +chr1:1540985 [T/A] chr1 1540985 Cc01_g00960:1278 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 TT TA TT TT +chr1:1541027 [G/A] chr1 1541027 Cc01_g00960:1320 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA GG GG +chr1:1541065 [A/G] chr1 1541065 Cc01_g00960:1358 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AG AA AA +chr1:1542189 [G/A] chr1 1542189 Cc01_g00960:1460 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 GG GA GG GG +chr1:1542199 [C/A] chr1 1542199 Cc01_g00960:1470 exon SYNONYMOUS_CODING ggC/ggA G/G 37.5% 4 CC AA CA AA +chr1:1542239 [G/A] chr1 1542239 Cc01_g00960:1510 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 GG GA GG GG +chr1:1542286 [T/C] chr1 1542286 Cc01_g00960:1557 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:1542364 [A/G] chr1 1542364 Cc01_g00960:1635 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG +chr1:1542404 [T/G] chr1 1542404 Cc01_g00960:1675 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT +chr1:1542434 [A/C] chr1 1542434 Cc01_g00960:1705 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 12.5% 4 AA CA AA AA +chr1:1546352 [C/G] chr1 1546352 Cc01_g00970:32 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 4 CC GG CG CG +chr1:1546365 [A/G] chr1 1546365 Cc01_g00970:45 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA GG AG GG +chr1:1546409 [G/T] chr1 1546409 Cc01_g00970:89 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 50.0% 4 GG TT GT GT +chr1:1546414 [A/C] chr1 1546414 Cc01_g00970:94 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 4 AA CC AC AC +chr1:1546454 [G/C] chr1 1546454 Cc01_g00970:134 exon NON_SYNONYMOUS_CODING cGc/cCc R/P 50.0% 4 GG CC GC GC +chr1:1546477 [C/G] chr1 1546477 Cc01_g00970:157 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC GG CG GG +chr1:1546480 [A/G] chr1 1546480 Cc01_g00970:160 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG AG GG +chr1:1546484 [T/G] chr1 1546484 Cc01_g00970:164 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 50.0% 4 TT GG TG TG +chr1:1546521 [C/G] chr1 1546521 Cc01_g00970:201 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG +chr1:1546531 [A/T] chr1 1546531 Cc01_g00970:211 exon NON_SYNONYMOUS_CODING Acg/Tcg T/S 25.0% 4 AA TT AA AA +chr1:1546532 [C/G] chr1 1546532 Cc01_g00970:212 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 CC CG CC CC +chr1:1546549 [C/G] chr1 1546549 Cc01_g00970:229 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC GG CC CC +chr1:1546652 [C/A] chr1 1546652 Cc01_g00970:257 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 CC AA CA CC +chr1:1546674 [G/A] chr1 1546674 Cc01_g00970:279 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA +chr1:1546728 [A/G] chr1 1546728 Cc01_g00970:333 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG AG GG +chr1:1547036 [C/T] chr1 1547036 Cc01_g00970:641 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 25.0% 4 CC CT CT CC +chr1:1547145 [G/A] chr1 1547145 Cc01_g00970:750 exon SYNONYMOUS_CODING cgG/cgA R/R 37.5% 4 GG AA GA AA +chr1:1547237 [A/G] chr1 1547237 Cc01_g00970:842 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AG GG +chr1:1547280 [A/G] chr1 1547280 Cc01_g00970:885 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG +chr1:1547353 [T/A] chr1 1547353 Cc01_g00970:958 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 37.5% 4 TT AA TA TT +chr1:1547421 [G/A] chr1 1547421 Cc01_g00970:1026 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG +chr1:1547527 [G/A] chr1 1547527 Cc01_g00970:1132 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG +chr1:1547536 [T/A] chr1 1547536 Cc01_g00970:1141 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 TT TT TT AA +chr1:1547613 [T/C] chr1 1547613 Cc01_g00970:1218 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT +chr1:1547682 [G/A] chr1 1547682 Cc01_g00970:1287 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 GG GA GG GG +chr1:1547853 [C/G] chr1 1547853 Cc01_g00970:1458 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 CC CG CC CC +chr1:1547901 [A/G] chr1 1547901 Cc01_g00970:1506 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA GG AG GG +chr1:1547985 [C/T] chr1 1547985 Cc01_g00970:1590 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CT CC CC +chr1:1548006 [G/A] chr1 1548006 Cc01_g00970:1611 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GG GG AA +chr1:1548171 [A/C] chr1 1548171 Cc01_g00970:1776 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 AA AA AA CC +chr1:1548194 [C/A] chr1 1548194 Cc01_g00970:1799 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 37.5% 4 CC AA CA AA +chr1:1548347 [G/A] chr1 1548347 Cc01_g00970:1952 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG +chr1:1548414 [G/A] chr1 1548414 Cc01_g00970:2019 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG +chr1:1548432 [T/C] chr1 1548432 Cc01_g00970:2037 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:1548609 [A/G] chr1 1548609 Cc01_g00970:2214 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AA AG +chr1:1548632 [C/T] chr1 1548632 Cc01_g00970:2237 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 37.5% 4 CC TT CT TT +chr1:1548721 [A/C] chr1 1548721 Cc01_g00970:2326 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AC AA AC +chr1:1565335 [T/C] chr1 1565335 Cc01_g00980:2 exon START_LOST aTg/aCg M/T 12.5% 4 TT TC TT TT +chr1:1565363 [T/A] chr1 1565363 Cc01_g00980:30 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 TT TA TT TT +chr1:1566976 [A/G] chr1 1566976 Cc01_g00980:324 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:1567002 [G/A] chr1 1567002 Cc01_g00980:350 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1567012 [C/T] chr1 1567012 Cc01_g00980:360 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:1568715 [T/C] chr1 1568715 Cc01_g00980:465 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TT TC +chr1:1568812 [A/G] chr1 1568812 Cc01_g00980:562 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:1568822 [T/C] chr1 1568822 Cc01_g00980:572 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TC TT TT +chr1:1569214 [G/A] chr1 1569214 Cc01_g00980:702 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 GG GA GG GG +chr1:1570049 [T/G] chr1 1570049 Cc01_g00980:976 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 12.5% 4 TT TG TT TT +chr1:1570069 [G/C] chr1 1570069 Cc01_g00980:996 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 GG GC GG GG +chr1:1570255 [A/G] chr1 1570255 Cc01_g00980:1068 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA +chr1:1570279 [A/T] chr1 1570279 Cc01_g00980:1092 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT +chr1:1570408 [C/T] chr1 1570408 Cc01_g00980:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT +chr1:1578648 [G/A] chr1 1578648 Cc01_g00990:84 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG GG GG AA +chr1:1577422 [G/C] chr1 1577422 Cc01_g00990:216 exon SYNONYMOUS_CODING cgC/cgG R/R 12.5% 4 GG GC GG GG +chr1:1574681 [T/G] chr1 1574681 Cc01_g00990:474 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 TT TT TG TT +chr1:1589010 [G/A] chr1 1589010 Cc01_g01000:168 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GA GG +chr1:1588986 [T/A] chr1 1588986 Cc01_g01000:192 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TA TT TT +chr1:1588914 [T/G] chr1 1588914 Cc01_g01000:264 exon SYNONYMOUS_CODING ctA/ctC L/L 25.0% 4 TT GG TT TT +chr1:1588838 [G/A] chr1 1588838 Cc01_g01000:340 exon STOP_GAINED Cga/Tga R/4 25.0% 4 GG AA GG GG +chr1:1588837 [C/A] chr1 1588837 Cc01_g01000:341 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 CC AA CC CC +chr1:1588277 [T/C] chr1 1588277 Cc01_g01000:901 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT CC TT TT +chr1:1588220 [G/A] chr1 1588220 Cc01_g01000:958 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 GG GG GA GG +chr1:1588137 [G/A] chr1 1588137 Cc01_g01000:1041 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 GG AA GG GG +chr1:1588135 [A/G] chr1 1588135 Cc01_g01000:1043 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG +chr1:1587967 [G/A] chr1 1587967 Cc01_g01000:1211 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 25.0% 4 GG GG GA GA +chr1:1587921 [A/G] chr1 1587921 Cc01_g01000:1257 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AG AG +chr1:1587798 [C/T] chr1 1587798 Cc01_g01000:1380 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 CC TT CC CC +chr1:1587708 [C/T] chr1 1587708 Cc01_g01000:1470 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC +chr1:1587646 [G/C] chr1 1587646 Cc01_g01000:1532 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 25.0% 4 GG GC GC GG +chr1:1587588 [T/A] chr1 1587588 Cc01_g01000:1590 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 TT AA TT TT +chr1:1587577 [C/T] chr1 1587577 Cc01_g01000:1601 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:1587576 [A/T] chr1 1587576 Cc01_g01000:1602 exon NON_SYNONYMOUS_CODING agT/agA S/R 25.0% 4 AA TT AA AA +chr1:1587527 [G/T] chr1 1587527 Cc01_g01000:1651 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 GG TT GG GG +chr1:1587435 [G/T] chr1 1587435 Cc01_g01000:1743 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 GG TT GG GG +chr1:1595916 [A/T] chr1 1595916 Cc01_g01010:153 exon SYNONYMOUS_CODING gtT/gtA V/V 37.5% 4 AA AT AT AT +chr1:1595665 [A/C] chr1 1595665 Cc01_g01010:278 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 AA AC AC AA +chr1:1594252 [G/A] chr1 1594252 Cc01_g01010:651 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 GG GA GA GA +chr1:1594186 [T/C] chr1 1594186 Cc01_g01010:717 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC +chr1:1593925 [G/A] chr1 1593925 Cc01_g01010:858 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG GA GA GA +chr1:1593817 [T/G] chr1 1593817 Cc01_g01010:966 exon SYNONYMOUS_CODING cgA/cgC R/R 37.5% 4 TT TG TG TG +chr1:1593814 [T/C] chr1 1593814 Cc01_g01010:969 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT +chr1:1593634 [C/T] chr1 1593634 Cc01_g01010:1056 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:1593035 [T/A] chr1 1593035 Cc01_g01010:1221 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT +chr1:1593017 [G/A] chr1 1593017 Cc01_g01010:1239 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG AA GA AA +chr1:1592810 [A/G] chr1 1592810 Cc01_g01010:1341 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG +chr1:1591963 [T/C] chr1 1591963 Cc01_g01010:1515 exon SYNONYMOUS_CODING cgA/cgG R/R 37.5% 4 TT TC TC TC +chr1:1591951 [A/G] chr1 1591951 Cc01_g01010:1527 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG +chr1:1591930 [G/A] chr1 1591930 Cc01_g01010:1548 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG GG GA GA +chr1:1591377 [A/G] chr1 1591377 Cc01_g01010:1560 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AG AA +chr1:1590960 [G/A] chr1 1590960 Cc01_g01010:1788 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG GA GA GA +chr1:1590951 [A/G] chr1 1590951 Cc01_g01010:1797 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA +chr1:1605944 [G/T] chr1 1605944 Cc01_g01020:27 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 GG GT GG GG +chr1:1605987 [T/G] chr1 1605987 Cc01_g01020:70 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 TT TT TG TT +chr1:1606067 [C/G] chr1 1606067 Cc01_g01020:150 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG +chr1:1606163 [A/C] chr1 1606163 Cc01_g01020:246 exon SYNONYMOUS_CODING acA/acC T/T 12.5% 4 AA AA AA AC +chr1:1609099 [T/C] chr1 1609099 Cc01_g01020:536 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TC TT TT +chr1:1609547 [G/C] chr1 1609547 Cc01_g01020:822 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 GG GC GG GG +chr1:1609736 [C/A] chr1 1609736 Cc01_g01020:912 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC CA CC CA +chr1:1609752 [G/C] chr1 1609752 Cc01_g01020:928 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 37.5% 4 GG CC GC CC +chr1:1609769 [A/C] chr1 1609769 Cc01_g01020:945 exon SYNONYMOUS_CODING ctA/ctC L/L 12.5% 4 AA AA AC AA +chr1:1610622 [A/G] chr1 1610622 Cc01_g01020:1431 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 AA AG AA AA +chr1:1610842 [A/G] chr1 1610842 Cc01_g01020:1560 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:1612395 [C/A] chr1 1612395 Cc01_g01020:2229 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 CC CA CC CC +chr1:1613838 [C/T] chr1 1613838 Cc01_g01020:2532 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC TT CC TT +chr1:1613901 [C/T] chr1 1613901 Cc01_g01020:2595 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CC CT +chr1:1615545 [T/G] chr1 1615545 Cc01_g01030:18 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT TG TT TT +chr1:1615529 [T/C] chr1 1615529 Cc01_g01030:34 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT +chr1:1615508 [C/T] chr1 1615508 Cc01_g01030:55 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 37.5% 4 CC TT CT TT +chr1:1615506 [C/T] chr1 1615506 Cc01_g01030:57 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1615500 [T/G] chr1 1615500 Cc01_g01030:63 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 TT TT TT GT +chr1:1615496 [T/C] chr1 1615496 Cc01_g01030:67 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT CT +chr1:1615491 [C/T] chr1 1615491 Cc01_g01030:72 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 CC TT CT TT +chr1:1615477 [G/A] chr1 1615477 Cc01_g01030:86 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG AG +chr1:1615472 [T/G] chr1 1615472 Cc01_g01030:91 exon NON_SYNONYMOUS_CODING Atc/Ctc I/L 37.5% 4 TT GG TG GG +chr1:1615458 [C/T] chr1 1615458 Cc01_g01030:105 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC +chr1:1615440 [T/C] chr1 1615440 Cc01_g01030:123 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT CT +chr1:1615335 [C/T] chr1 1615335 Cc01_g01030:132 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT CT TT +chr1:1615256 [A/T] chr1 1615256 Cc01_g01030:211 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA AT +chr1:1620903 [A/T] chr1 1620903 Cc01_g01040:366 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AT AA AA +chr1:1619369 [G/A] chr1 1619369 Cc01_g01040:648 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA GA GA +chr1:1619341 [G/C] chr1 1619341 Cc01_g01040:676 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CC GC CC +chr1:1619334 [C/T] chr1 1619334 Cc01_g01040:683 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CT TT +chr1:1619270 [C/G] chr1 1619270 Cc01_g01040:747 exon SYNONYMOUS_CODING tcG/tcC S/S 37.5% 4 CC GG CG GG +chr1:1619124 [A/G] chr1 1619124 Cc01_g01040:893 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:1618988 [A/G] chr1 1618988 Cc01_g01040:1029 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG +chr1:1618984 [C/G] chr1 1618984 Cc01_g01040:1033 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CC CC CG +chr1:1618978 [C/G] chr1 1618978 Cc01_g01040:1039 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 CC CG CG CG +chr1:1618886 [A/G] chr1 1618886 Cc01_g01040:1131 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA AG +chr1:1618879 [T/A] chr1 1618879 Cc01_g01040:1138 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TT TA +chr1:1618858 [T/G] chr1 1618858 Cc01_g01040:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT GG TG GG +chr1:1618504 [G/A] chr1 1618504 Cc01_g01040:1396 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG GA +chr1:1618376 [T/G] chr1 1618376 Cc01_g01040:1524 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 TT TG TT TT +chr1:1618358 [G/C] chr1 1618358 Cc01_g01040:1542 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC GC +chr1:1618326 [C/T] chr1 1618326 Cc01_g01040:1574 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 CC CC CT CC +chr1:1618307 [G/C] chr1 1618307 Cc01_g01040:1593 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 GG GG GG CG +chr1:1618184 [A/G] chr1 1618184 Cc01_g01040:1716 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:1618117 [G/C] chr1 1618117 Cc01_g01040:1783 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CG GG CC +chr1:1618040 [C/G] chr1 1618040 Cc01_g01040:1860 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 CC CC CG CC +chr1:1618037 [G/A] chr1 1618037 Cc01_g01040:1863 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG GA GA GA +chr1:1618016 [T/C] chr1 1618016 Cc01_g01040:1884 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT +chr1:1617998 [G/C] chr1 1617998 Cc01_g01040:1902 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC CG +chr1:1617793 [C/T] chr1 1617793 Cc01_g01040:2107 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 37.5% 4 CC CT CT CT +chr1:1617773 [T/C] chr1 1617773 Cc01_g01040:2127 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC +chr1:1617769 [T/C] chr1 1617769 Cc01_g01040:2131 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT TC +chr1:1617757 [C/T] chr1 1617757 Cc01_g01040:2143 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:1617670 [C/T] chr1 1617670 Cc01_g01040:2230 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 CC CT CC TT +chr1:1617634 [C/T] chr1 1617634 Cc01_g01040:2266 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CC CT +chr1:1617479 [A/G] chr1 1617479 Cc01_g01040:2421 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG AA AA +chr1:1617238 [G/A] chr1 1617238 Cc01_g01040:2662 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG +chr1:1617119 [A/T] chr1 1617119 Cc01_g01040:2725 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA AT AT AA +chr1:1626903 [A/C] chr1 1626903 Cc01_g01050:132 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 AA CC AC CC +chr1:1626922 [C/G] chr1 1626922 Cc01_g01050:151 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 CC CG CG CC +chr1:1626973 [G/T] chr1 1626973 Cc01_g01050:202 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 GG GT GG TT +chr1:1627071 [T/C] chr1 1627071 Cc01_g01050:300 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TT CC +chr1:1627227 [T/C] chr1 1627227 Cc01_g01050:456 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TC TC TT +chr1:1628554 [A/G] chr1 1628554 Cc01_g01050:650 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA AG AG AA +chr1:1628584 [A/G] chr1 1628584 Cc01_g01050:680 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GA AA GG +chr1:1628763 [G/A] chr1 1628763 Cc01_g01050:859 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GG GA +chr1:1628787 [G/C] chr1 1628787 Cc01_g01050:883 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG GC GG CC +chr1:1628828 [A/G] chr1 1628828 Cc01_g01050:924 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA AG AA GG +chr1:1628942 [A/G] chr1 1628942 Cc01_g01050:1038 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 AA GG AG GG +chr1:1630053 [T/C] chr1 1630053 Cc01_g01050:1464 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TC TT +chr1:1633739 [A/G] chr1 1633739 Cc01_g01060:12 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG +chr1:1633649 [T/C] chr1 1633649 Cc01_g01060:102 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC +chr1:1633602 [T/C] chr1 1633602 Cc01_g01060:149 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT CT TT TT +chr1:1633503 [G/A] chr1 1633503 Cc01_g01060:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GA GG GG +chr1:1633430 [A/T] chr1 1633430 Cc01_g01060:321 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 AA AT AA AA +chr1:1633429 [G/T] chr1 1633429 Cc01_g01060:322 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GT GG GG +chr1:1633388 [A/T] chr1 1633388 Cc01_g01060:363 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 AA AA AT AA +chr1:1752682 [C/T] chr1 1752682 Cc01_g01120:21 exon SYNONYMOUS_CODING acG/acA T/T 33.3% 3 CC TT NN TT +chr1:1752654 [A/T] chr1 1752654 Cc01_g01120:49 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT TT AA +chr1:1752632 [G/T] chr1 1752632 Cc01_g01120:71 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 37.5% 4 GG GT TT GG +chr1:1752577 [C/A] chr1 1752577 Cc01_g01120:126 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC CA CA CC +chr1:1752535 [T/C] chr1 1752535 Cc01_g01120:168 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 TT TT CC TT +chr1:1752526 [C/T] chr1 1752526 Cc01_g01120:177 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 CC CC TT CC +chr1:1750532 [T/G] chr1 1750532 Cc01_g01120:970 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 50.0% 2 TT NN NN GG +chr1:1750461 [C/T] chr1 1750461 Cc01_g01120:1041 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 CC TT CT TT +chr1:1750442 [C/T] chr1 1750442 Cc01_g01120:1060 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 37.5% 4 CC TT CT TT +chr1:1760523 [C/A] chr1 1760523 Cc01_g01130:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC +chr1:1760522 [G/C] chr1 1760522 Cc01_g01130:136 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 GG GG GC GG +chr1:1760486 [A/C] chr1 1760486 Cc01_g01130:172 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 AA AA AA AC +chr1:1760383 [C/T] chr1 1760383 Cc01_g01130:275 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC +chr1:1760328 [T/A] chr1 1760328 Cc01_g01130:330 exon SYNONYMOUS_CODING atA/atT I/I 50.0% 4 TT AA TT AA +chr1:1760185 [T/A] chr1 1760185 Cc01_g01130:473 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT TA TA TT +chr1:1760173 [C/A] chr1 1760173 Cc01_g01130:485 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 CC CC CC CA +chr1:1760172 [T/G] chr1 1760172 Cc01_g01130:486 exon NON_SYNONYMOUS_CODING agA/agC R/S 12.5% 4 TT TT TT TG +chr1:1759408 [A/G] chr1 1759408 Cc01_g01130:603 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA +chr1:1759378 [G/A] chr1 1759378 Cc01_g01130:633 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GA GG +chr1:1759372 [A/G] chr1 1759372 Cc01_g01130:639 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA AG AG AA +chr1:1759371 [T/A] chr1 1759371 Cc01_g01130:640 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 TT TA TA TT +chr1:1759364 [T/G] chr1 1759364 Cc01_g01130:647 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 TT TG TT TT +chr1:1759335 [G/A] chr1 1759335 Cc01_g01130:676 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG GA GA GG +chr1:1758971 [A/G] chr1 1758971 Cc01_g01130:1040 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 3 AA GG AG NN +chr1:1758937 [G/A] chr1 1758937 Cc01_g01130:1074 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 3 GG AA GA NN +chr1:1758885 [C/G] chr1 1758885 Cc01_g01130:1126 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 33.3% 3 CC GG CC NN +chr1:1758882 [C/T] chr1 1758882 Cc01_g01130:1129 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 CC TT CT NN +chr1:1758778 [G/A] chr1 1758778 Cc01_g01130:1233 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG GA GG GG +chr1:1758772 [A/G] chr1 1758772 Cc01_g01130:1239 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AG AA AA +chr1:1758762 [T/C] chr1 1758762 Cc01_g01130:1249 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 TT TC TT TT +chr1:1768762 [G/C] chr1 1768762 Cc01_g01140:100 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GC GG GC +chr1:1768873 [T/C] chr1 1768873 Cc01_g01140:211 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TT TC +chr1:1768956 [T/A] chr1 1768956 Cc01_g01140:294 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TT TT TA +chr1:1768961 [C/A] chr1 1768961 Cc01_g01140:299 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CC CA +chr1:1768967 [C/G] chr1 1768967 Cc01_g01140:305 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 4 CC CG CG GG +chr1:1769000 [A/G] chr1 1769000 Cc01_g01140:338 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG +chr1:1769038 [T/C] chr1 1769038 Cc01_g01140:376 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TC TT TT +chr1:1769040 [T/G] chr1 1769040 Cc01_g01140:378 exon SYNONYMOUS_CODING tcT/tcG S/S 12.5% 4 TT TT TT TG +chr1:1769074 [T/C] chr1 1769074 Cc01_g01140:412 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TT TC +chr1:1769115 [T/C] chr1 1769115 Cc01_g01140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TT TT TC +chr1:1769145 [C/T] chr1 1769145 Cc01_g01140:483 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC CT CT TT +chr1:1769183 [C/T] chr1 1769183 Cc01_g01140:521 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC CT CC CT +chr1:1769193 [A/T] chr1 1769193 Cc01_g01140:531 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA +chr1:1769201 [C/T] chr1 1769201 Cc01_g01140:539 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 CC CT CC CT +chr1:1769253 [A/C] chr1 1769253 Cc01_g01140:591 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 AA AA AA AC +chr1:1769277 [T/A] chr1 1769277 Cc01_g01140:615 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 TT TA TT TA +chr1:1769279 [G/A] chr1 1769279 Cc01_g01140:617 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA +chr1:1769288 [A/C] chr1 1769288 Cc01_g01140:626 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AA CA +chr1:1769296 [A/G] chr1 1769296 Cc01_g01140:634 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 AA AG AA AG +chr1:1769367 [T/C] chr1 1769367 Cc01_g01140:705 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TT TC TC +chr1:1769374 [G/A] chr1 1769374 Cc01_g01140:712 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA +chr1:1769389 [C/T] chr1 1769389 Cc01_g01140:727 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT +chr1:1769398 [T/C] chr1 1769398 Cc01_g01140:736 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TT TC +chr1:1769433 [T/G] chr1 1769433 Cc01_g01140:771 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT +chr1:1769441 [C/T] chr1 1769441 Cc01_g01140:779 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC CT CT CT +chr1:1769448 [A/T] chr1 1769448 Cc01_g01140:786 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 37.5% 4 AA AT AT AT +chr1:1769482 [A/T] chr1 1769482 Cc01_g01140:820 exon STOP_GAINED Aga/Tga R/4 12.5% 4 AA AA AA TA +chr1:1769483 [G/T] chr1 1769483 Cc01_g01140:821 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 GG GG GG TG +chr1:1769501 [C/G] chr1 1769501 Cc01_g01140:839 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CG CC CC +chr1:1769639 [A/G] chr1 1769639 Cc01_g01140:977 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AA AA AG +chr1:1769671 [C/A] chr1 1769671 Cc01_g01140:1009 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 12.5% 4 CC CA CC CC +chr1:1769978 [A/G] chr1 1769978 Cc01_g01140:1256 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 4 AA AG AA AG +chr1:1769992 [A/G] chr1 1769992 Cc01_g01140:1270 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG +chr1:1770017 [G/T] chr1 1770017 Cc01_g01140:1295 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 37.5% 4 GG GT GT GT +chr1:1770029 [C/T] chr1 1770029 Cc01_g01140:1307 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 CC CT CT CT +chr1:1770045 [C/T] chr1 1770045 Cc01_g01140:1323 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT +chr1:1770067 [C/T] chr1 1770067 Cc01_g01140:1345 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 CC CC CT CT +chr1:1770389 [C/G] chr1 1770389 Cc01_g01140:1667 exon STOP_GAINED tCa/tGa S/6 12.5% 4 CC CG CC CC +chr1:1770417 [A/C] chr1 1770417 Cc01_g01140:1695 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 AA AC AA AA +chr1:1770420 [C/A] chr1 1770420 Cc01_g01140:1698 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CA CC CC +chr1:1770531 [A/G] chr1 1770531 Cc01_g01140:1809 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AG AA AA +chr1:1770535 [A/G] chr1 1770535 Cc01_g01140:1813 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA +chr1:1770536 [G/A] chr1 1770536 Cc01_g01140:1814 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA +chr1:1770538 [C/T] chr1 1770538 Cc01_g01140:1816 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:1770756 [G/A] chr1 1770756 Cc01_g01140:1972 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA GA AA +chr1:1770764 [A/G] chr1 1770764 Cc01_g01140:1980 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG +chr1:1770768 [A/T] chr1 1770768 Cc01_g01140:1984 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AA AT +chr1:1770781 [G/T] chr1 1770781 Cc01_g01140:1997 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GG GG GT +chr1:1770792 [C/G] chr1 1770792 Cc01_g01140:2008 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CC GC GC +chr1:1770794 [T/C] chr1 1770794 Cc01_g01140:2010 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC +chr1:1770795 [G/A] chr1 1770795 Cc01_g01140:2011 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG +chr1:1770797 [A/T] chr1 1770797 Cc01_g01140:2013 exon SYNONYMOUS_CODING gtA/gtT V/V 12.5% 4 AA AT AA AA +chr1:1770804 [G/C] chr1 1770804 Cc01_g01140:2020 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG +chr1:1770806 [A/G] chr1 1770806 Cc01_g01140:2022 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AG AA AA +chr1:1770807 [A/T] chr1 1770807 Cc01_g01140:2023 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AT AA AA +chr1:1771162 [C/T] chr1 1771162 Cc01_g01140:2032 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT TC TT +chr1:1771185 [T/A] chr1 1771185 Cc01_g01140:2055 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 TT AA AT AA +chr1:1771201 [C/A] chr1 1771201 Cc01_g01140:2071 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 37.5% 4 CC AA AC AA +chr1:1775047 [T/C] chr1 1775047 Cc01_g01150:43 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 2 TT TC NN NN +chr1:1774997 [A/G] chr1 1774997 Cc01_g01150:93 exon SYNONYMOUS_CODING gtT/gtC V/V 33.3% 3 AA AG NN AG +chr1:1774994 [A/G] chr1 1774994 Cc01_g01150:96 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA AG GG GA +chr1:1774991 [C/T] chr1 1774991 Cc01_g01150:99 exon SYNONYMOUS_CODING gtG/gtA V/V 25.0% 4 CC TT TT TT +chr1:1774981 [A/G] chr1 1774981 Cc01_g01150:109 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 AA AG AG AG +chr1:1774977 [C/T] chr1 1774977 Cc01_g01150:113 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT +chr1:1774975 [C/T] chr1 1774975 Cc01_g01150:115 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 CC TC TC TC +chr1:1774972 [T/G] chr1 1774972 Cc01_g01150:118 exon NON_SYNONYMOUS_CODING Act/Cct T/P 37.5% 4 TT TG TG TG +chr1:1774959 [A/G] chr1 1774959 Cc01_g01150:131 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 AA GA GA GA +chr1:1774957 [A/C] chr1 1774957 Cc01_g01150:133 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 37.5% 4 AA CC CC AC +chr1:1774955 [C/A] chr1 1774955 Cc01_g01150:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 37.5% 4 CC AA AA CA +chr1:1774925 [A/C] chr1 1774925 Cc01_g01150:165 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 37.5% 4 AA AC AC AC +chr1:1774919 [A/G] chr1 1774919 Cc01_g01150:171 exon SYNONYMOUS_CODING ccT/ccC P/P 37.5% 4 AA AG AG AG +chr1:1774915 [C/G] chr1 1774915 Cc01_g01150:175 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC +chr1:1774911 [C/T] chr1 1774911 Cc01_g01150:179 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT TT CT +chr1:1774901 [C/A] chr1 1774901 Cc01_g01150:189 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 CC AA AA AA +chr1:1774894 [G/A] chr1 1774894 Cc01_g01150:196 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 37.5% 4 GG GA GA GA +chr1:1800628 [A/T] chr1 1800628 Cc01_g01180:18 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 AA AT AA TT +chr1:1800604 [A/G] chr1 1800604 Cc01_g01180:42 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AA GG +chr1:1800591 [A/C] chr1 1800591 Cc01_g01180:55 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 AA CA AA AA +chr1:1800153 [G/A] chr1 1800153 Cc01_g01180:237 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 GG GG GA GG +chr1:1800141 [C/A] chr1 1800141 Cc01_g01180:249 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 CC CA CC CC +chr1:1800037 [A/T] chr1 1800037 Cc01_g01180:353 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 37.5% 4 AA TT AT TT +chr1:1799883 [A/G] chr1 1799883 Cc01_g01180:507 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 AA AG AA AA +chr1:1799858 [C/A] chr1 1799858 Cc01_g01180:532 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 CC AC CC CA +chr1:1799772 [C/T] chr1 1799772 Cc01_g01180:618 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1799746 [C/A] chr1 1799746 Cc01_g01180:644 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 25.0% 4 CC CA CC AC +chr1:1799703 [T/A] chr1 1799703 Cc01_g01180:687 exon SYNONYMOUS_CODING gcA/gcT A/A 37.5% 4 TT AT TA TA +chr1:1799683 [C/T] chr1 1799683 Cc01_g01180:707 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC +chr1:1799560 [G/A] chr1 1799560 Cc01_g01180:830 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GG GA +chr1:1799253 [G/A] chr1 1799253 Cc01_g01180:1137 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GG GA +chr1:1799138 [C/G] chr1 1799138 Cc01_g01180:1252 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 CC CC CC CG +chr1:1799114 [C/T] chr1 1799114 Cc01_g01180:1276 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT +chr1:1799096 [T/C] chr1 1799096 Cc01_g01180:1294 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TC TC TT +chr1:1798930 [C/T] chr1 1798930 Cc01_g01180:1460 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 37.5% 4 CC CT CT CT +chr1:1798825 [T/C] chr1 1798825 Cc01_g01180:1565 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TT TC +chr1:1798812 [A/C] chr1 1798812 Cc01_g01180:1578 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 AA AA AA AC +chr1:1798782 [T/C] chr1 1798782 Cc01_g01180:1608 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC +chr1:1798753 [T/A] chr1 1798753 Cc01_g01180:1637 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA +chr1:1798733 [T/C] chr1 1798733 Cc01_g01180:1657 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC TC TC +chr1:1798724 [G/A] chr1 1798724 Cc01_g01180:1666 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA +chr1:1798690 [C/A] chr1 1798690 Cc01_g01180:1700 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 12.5% 4 CC CC CC CA +chr1:1798665 [T/C] chr1 1798665 Cc01_g01180:1725 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT +chr1:1798471 [T/A] chr1 1798471 Cc01_g01180:1919 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 12.5% 4 TT TT TT TA +chr1:1798453 [A/G] chr1 1798453 Cc01_g01180:1937 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG +chr1:1798341 [G/A] chr1 1798341 Cc01_g01180:2049 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG AA GA AA +chr1:1798269 [T/C] chr1 1798269 Cc01_g01180:2121 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TT TC +chr1:1798206 [A/G] chr1 1798206 Cc01_g01180:2184 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG +chr1:1798185 [A/T] chr1 1798185 Cc01_g01180:2205 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AA AA AT +chr1:1798172 [G/A] chr1 1798172 Cc01_g01180:2218 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:1798019 [A/G] chr1 1798019 Cc01_g01180:2277 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG +chr1:1797997 [A/C] chr1 1797997 Cc01_g01180:2299 exon NON_SYNONYMOUS_CODING Tgc/Ggc C/G 12.5% 4 AA AA AC AA +chr1:1796639 [G/T] chr1 1796639 Cc01_g01180:2517 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 GG GG GG GT +chr1:1796548 [C/T] chr1 1796548 Cc01_g01180:2608 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC CT +chr1:1796523 [G/C] chr1 1796523 Cc01_g01180:2633 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 GG GG GG GC +chr1:1796504 [G/A] chr1 1796504 Cc01_g01180:2652 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:1796501 [C/T] chr1 1796501 Cc01_g01180:2655 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1796477 [A/G] chr1 1796477 Cc01_g01180:2679 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AA AA AG +chr1:1794530 [C/A] chr1 1794530 Cc01_g01180:2830 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 CC CC CC CA +chr1:1793183 [A/G] chr1 1793183 Cc01_g01180:2975 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AA AG +chr1:1793145 [G/T] chr1 1793145 Cc01_g01180:3013 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT +chr1:1793065 [C/T] chr1 1793065 Cc01_g01180:3093 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC CT CC CC +chr1:1793054 [A/G] chr1 1793054 Cc01_g01180:3104 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 AA AG AA AA +chr1:1793045 [G/T] chr1 1793045 Cc01_g01180:3113 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 12.5% 4 GG GT GG GG +chr1:1792939 [G/T] chr1 1792939 Cc01_g01180:3147 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 GG GT GG GG +chr1:1792909 [A/T] chr1 1792909 Cc01_g01180:3177 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA TA AA AA +chr1:1813729 [G/T] chr1 1813729 Cc01_g01190:306 exon SYNONYMOUS_CODING ccC/ccA P/P 16.7% 3 GG GT NN GG +chr1:1813726 [A/T] chr1 1813726 Cc01_g01190:309 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 AA AT NN AA +chr1:1813696 [T/G] chr1 1813696 Cc01_g01190:339 exon SYNONYMOUS_CODING atA/atC I/I 16.7% 3 TT TG NN TT +chr1:1818371 [T/C] chr1 1818371 Cc01_g01200:87 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 4 TT TC CC TC +chr1:1818296 [A/T] chr1 1818296 Cc01_g01200:162 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AA TT AA +chr1:1818188 [A/G] chr1 1818188 Cc01_g01200:270 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA +chr1:1818116 [A/C] chr1 1818116 Cc01_g01200:342 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 AA AC AA AA +chr1:1818035 [A/G] chr1 1818035 Cc01_g01200:423 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA AG AG GG +chr1:1818018 [T/A] chr1 1818018 Cc01_g01200:440 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 50.0% 4 TT TA TA AA +chr1:1818013 [T/G] chr1 1818013 Cc01_g01200:445 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 25.0% 4 TT TT TG TG +chr1:1822497 [A/G] chr1 1822497 Cc01_g01210:153 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA AG AA AG +chr1:1822491 [C/G] chr1 1822491 Cc01_g01210:159 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 CC CC CC CG +chr1:1822434 [C/T] chr1 1822434 Cc01_g01210:216 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CT CC CC +chr1:1822365 [A/G] chr1 1822365 Cc01_g01210:285 exon SYNONYMOUS_CODING ctT/ctC L/L 37.5% 4 AA GG AA AG +chr1:1822344 [G/C] chr1 1822344 Cc01_g01210:306 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC +chr1:1822311 [G/C] chr1 1822311 Cc01_g01210:339 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GG GC GG +chr1:1822251 [G/A] chr1 1822251 Cc01_g01210:399 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA AG GA +chr1:1822215 [G/T] chr1 1822215 Cc01_g01210:435 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 GG GG TG GG +chr1:1822206 [G/A] chr1 1822206 Cc01_g01210:444 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA AG AA +chr1:1871413 [G/T] chr1 1871413 Cc01_g01220:7 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT GT TT +chr1:1871774 [T/C] chr1 1871774 Cc01_g01220:65 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT TT TT TC +chr1:1871782 [G/C] chr1 1871782 Cc01_g01220:73 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GG GC +chr1:1871785 [G/T] chr1 1871785 Cc01_g01220:76 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GG GT +chr1:1871959 [C/T] chr1 1871959 Cc01_g01220:118 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 CC CT CC CC +chr1:1871977 [G/C] chr1 1871977 Cc01_g01220:136 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 25.0% 4 GG GC GC GG +chr1:1871980 [T/G] chr1 1871980 Cc01_g01220:139 exon NON_SYNONYMOUS_CODING Ttt/Gtt F/V 12.5% 4 TT TG TT TT +chr1:1871994 [C/A] chr1 1871994 Cc01_g01220:153 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 12.5% 4 CC AC CC CC +chr1:1872001 [T/C] chr1 1872001 Cc01_g01220:160 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 12.5% 4 TT CT TT TT +chr1:1872003 [C/T] chr1 1872003 Cc01_g01220:162 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC CT CT CT +chr1:1872004 [A/G] chr1 1872004 Cc01_g01220:163 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA AG AG AG +chr1:1872020 [G/A] chr1 1872020 Cc01_g01220:179 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:1872035 [G/A] chr1 1872035 Cc01_g01220:194 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA +chr1:1872037 [A/G] chr1 1872037 Cc01_g01220:196 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG +chr1:1872051 [A/G] chr1 1872051 Cc01_g01220:210 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG GA GG +chr1:1873065 [C/T] chr1 1873065 Cc01_g01220:247 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC CC CT +chr1:1873088 [T/C] chr1 1873088 Cc01_g01220:270 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TT TC +chr1:1874574 [C/T] chr1 1874574 Cc01_g01230:34 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CC CT +chr1:1874587 [T/G] chr1 1874587 Cc01_g01230:47 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 12.5% 4 TT TT TG TT +chr1:1874774 [C/G] chr1 1874774 Cc01_g01230:135 exon STOP_GAINED taC/taG Y/5 12.5% 4 CC CC CG CC +chr1:1874797 [T/A] chr1 1874797 Cc01_g01230:158 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 25.0% 4 TT TT TA TA +chr1:1874808 [G/T] chr1 1874808 Cc01_g01230:169 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT +chr1:1874816 [G/T] chr1 1874816 Cc01_g01230:177 exon NON_SYNONYMOUS_CODING agG/agT R/S 12.5% 4 GG GT GG GG +chr1:1874818 [G/T] chr1 1874818 Cc01_g01230:179 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG GG GT GT +chr1:1879776 [A/C] chr1 1879776 Cc01_g01240:27 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 4 AA AC AC CC +chr1:1879628 [G/C] chr1 1879628 Cc01_g01240:175 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG GC GG GC +chr1:1879623 [T/C] chr1 1879623 Cc01_g01240:180 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:1907384 [G/A] chr1 1907384 Cc01_g01250:29 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA +chr1:1907400 [C/G] chr1 1907400 Cc01_g01250:45 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC GG GG GG +chr1:1907401 [A/G] chr1 1907401 Cc01_g01250:46 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 AA AG AG GA +chr1:1907418 [G/A] chr1 1907418 Cc01_g01250:63 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GA GA AG +chr1:1907454 [A/C] chr1 1907454 Cc01_g01250:99 exon NON_SYNONYMOUS_CODING caA/caC Q/H 37.5% 4 AA AC AC CA +chr1:1907455 [A/G] chr1 1907455 Cc01_g01250:100 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AG AA +chr1:1907457 [C/G] chr1 1907457 Cc01_g01250:102 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG +chr1:1907460 [T/A] chr1 1907460 Cc01_g01250:105 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 25.0% 4 TT TT AT TA +chr1:1907483 [A/C] chr1 1907483 Cc01_g01250:128 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 AA AA AA CA +chr1:1907485 [G/A] chr1 1907485 Cc01_g01250:130 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA +chr1:1907487 [C/T] chr1 1907487 Cc01_g01250:132 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT TC +chr1:1907489 [T/G] chr1 1907489 Cc01_g01250:134 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 12.5% 4 TT TT TT GT +chr1:1907499 [G/A] chr1 1907499 Cc01_g01250:144 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 GG GG AG GA +chr1:1907514 [T/C] chr1 1907514 Cc01_g01250:159 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TC CT +chr1:1907532 [G/C] chr1 1907532 Cc01_g01250:177 exon SYNONYMOUS_CODING ggG/ggC G/G 25.0% 4 GG CC CC CC +chr1:1907552 [A/G] chr1 1907552 Cc01_g01250:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA AG AG GA +chr1:1907554 [G/A] chr1 1907554 Cc01_g01250:199 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AG GA +chr1:1907571 [A/G] chr1 1907571 Cc01_g01250:216 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG GA +chr1:1907577 [G/A] chr1 1907577 Cc01_g01250:222 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 GG GG GA GG +chr1:1907584 [A/G] chr1 1907584 Cc01_g01250:229 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 37.5% 4 AA AG AG GA +chr1:1907613 [C/T] chr1 1907613 Cc01_g01250:258 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC CT CT TC +chr1:1907628 [G/A] chr1 1907628 Cc01_g01250:273 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA AG +chr1:1907636 [C/G] chr1 1907636 Cc01_g01250:281 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 37.5% 4 CC CG CG GC +chr1:1907643 [A/G] chr1 1907643 Cc01_g01250:288 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG GA +chr1:1907649 [G/T] chr1 1907649 Cc01_g01250:294 exon SYNONYMOUS_CODING ctG/ctT L/L 37.5% 4 GG GT GT TG +chr1:1907663 [A/T] chr1 1907663 Cc01_g01250:308 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA TA AA +chr1:1907745 [T/G] chr1 1907745 Cc01_g01250:390 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 4 TT GG GG GG +chr1:1907751 [G/A] chr1 1907751 Cc01_g01250:396 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 GG GA GA GA +chr1:1907865 [G/A] chr1 1907865 Cc01_g01250:438 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA +chr1:1907867 [C/T] chr1 1907867 Cc01_g01250:440 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC CT TT CT +chr1:1907913 [G/A] chr1 1907913 Cc01_g01250:486 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG AG GG GG +chr1:1907925 [C/T] chr1 1907925 Cc01_g01250:498 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT CT CT +chr1:1907951 [T/A] chr1 1907951 Cc01_g01250:524 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 37.5% 4 TT TA TA TA +chr1:1907955 [C/T] chr1 1907955 Cc01_g01250:528 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC CT CT CT +chr1:1907970 [G/A] chr1 1907970 Cc01_g01250:543 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG AG GG +chr1:1907971 [G/C] chr1 1907971 Cc01_g01250:544 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 GG GG CG GG +chr1:1907976 [A/G] chr1 1907976 Cc01_g01250:549 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 AA GA AA GA +chr1:1907998 [G/A] chr1 1907998 Cc01_g01250:571 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG AG GG +chr1:1908013 [C/G] chr1 1908013 Cc01_g01250:586 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CC GC +chr1:1908043 [T/C] chr1 1908043 Cc01_g01250:616 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC TC TC +chr1:1908051 [G/C] chr1 1908051 Cc01_g01250:624 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG CG GG CG +chr1:1908071 [A/T] chr1 1908071 Cc01_g01250:644 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 AA TT TT TT +chr1:1908072 [A/T] chr1 1908072 Cc01_g01250:645 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA AT AT AT +chr1:1908080 [G/C] chr1 1908080 Cc01_g01250:653 exon NON_SYNONYMOUS_CODING gGc/gCc G/A 37.5% 4 GG GC GC GC +chr1:1908088 [A/G] chr1 1908088 Cc01_g01250:661 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG +chr1:1908103 [C/T] chr1 1908103 Cc01_g01250:676 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 CC CT CT CT +chr1:1908119 [G/A] chr1 1908119 Cc01_g01250:692 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG GG GA GA +chr1:1908120 [G/T] chr1 1908120 Cc01_g01250:693 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG GT GT +chr1:1908140 [A/G] chr1 1908140 Cc01_g01250:713 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AA GA +chr1:1908345 [G/C] chr1 1908345 Cc01_g01250:738 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 GG GC GG GC +chr1:1908360 [C/G] chr1 1908360 Cc01_g01250:753 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC CG GC +chr1:1908383 [A/T] chr1 1908383 Cc01_g01250:776 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 37.5% 4 AA TA AT TA +chr1:1908403 [C/G] chr1 1908403 Cc01_g01250:796 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 CC CC GC CC +chr1:1908407 [G/A] chr1 1908407 Cc01_g01250:800 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG +chr1:1908410 [G/A] chr1 1908410 Cc01_g01250:803 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG +chr1:1908447 [T/C] chr1 1908447 Cc01_g01250:840 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CT TC CT +chr1:1908449 [T/C] chr1 1908449 Cc01_g01250:842 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1908471 [C/G] chr1 1908471 Cc01_g01250:864 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GC CG GC +chr1:1908474 [C/T] chr1 1908474 Cc01_g01250:867 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TC CT TC +chr1:1908527 [T/C] chr1 1908527 Cc01_g01250:920 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT CC CC CC +chr1:1908549 [A/G] chr1 1908549 Cc01_g01250:942 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA +chr1:1908765 [G/A] chr1 1908765 Cc01_g01250:954 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1908789 [C/A] chr1 1908789 Cc01_g01250:978 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 CC CA CA CA +chr1:1908791 [A/C] chr1 1908791 Cc01_g01250:980 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 12.5% 4 AA CA AA AA +chr1:1908792 [G/A] chr1 1908792 Cc01_g01250:981 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 GG AA AA AA +chr1:1908828 [C/T] chr1 1908828 Cc01_g01250:1017 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 CC CT CT CT +chr1:1908831 [G/A] chr1 1908831 Cc01_g01250:1020 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 GG GA GA GA +chr1:1908907 [A/G] chr1 1908907 Cc01_g01250:1096 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG +chr1:1908909 [A/G] chr1 1908909 Cc01_g01250:1098 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG AG AG +chr1:1908915 [T/C] chr1 1908915 Cc01_g01250:1104 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT TC TC TC +chr1:1908942 [G/A] chr1 1908942 Cc01_g01250:1131 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA AA AA +chr1:1908962 [G/A] chr1 1908962 Cc01_g01250:1151 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG AG +chr1:1908976 [A/G] chr1 1908976 Cc01_g01250:1165 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA AA GA AA +chr1:1909020 [A/G] chr1 1909020 Cc01_g01250:1209 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AA AG AA +chr1:1909071 [A/C] chr1 1909071 Cc01_g01250:1260 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA AC NN AC +chr1:1909091 [G/A] chr1 1909091 Cc01_g01250:1280 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG +chr1:1909122 [G/A] chr1 1909122 Cc01_g01250:1311 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG AA AA AA +chr1:1909165 [C/A] chr1 1909165 Cc01_g01250:1354 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC +chr1:1909186 [G/A] chr1 1909186 Cc01_g01250:1375 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GA GG +chr1:1909203 [C/T] chr1 1909203 Cc01_g01250:1392 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC TC CC +chr1:1909210 [G/T] chr1 1909210 Cc01_g01250:1399 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GT GG GG +chr1:1909247 [G/C] chr1 1909247 Cc01_g01250:1436 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 25.0% 4 GG CC CC CC +chr1:1909284 [G/A] chr1 1909284 Cc01_g01250:1473 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA GA GA +chr1:1909294 [C/G] chr1 1909294 Cc01_g01250:1483 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC GG GG GG +chr1:1909302 [T/C] chr1 1909302 Cc01_g01250:1491 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT CC CC CC +chr1:1909308 [C/T] chr1 1909308 Cc01_g01250:1497 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT +chr1:1909332 [C/T] chr1 1909332 Cc01_g01250:1521 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC TC TC TC +chr1:1909361 [G/A] chr1 1909361 Cc01_g01250:1550 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 GG GA GA GA +chr1:1909447 [G/A] chr1 1909447 Cc01_g01250:1636 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG GA GA GA +chr1:1909475 [C/T] chr1 1909475 Cc01_g01250:1664 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 25.0% 4 CC TT TT TT +chr1:1909487 [A/G] chr1 1909487 Cc01_g01250:1676 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GA AA GA +chr1:1909530 [A/G] chr1 1909530 Cc01_g01250:1719 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG AG +chr1:1909566 [A/G] chr1 1909566 Cc01_g01250:1755 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:1909582 [C/T] chr1 1909582 Cc01_g01250:1771 exon STOP_GAINED Cga/Tga R/1 12.5% 4 CC CC CC CT +chr1:1909609 [G/A] chr1 1909609 Cc01_g01250:1798 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GG GG AG +chr1:1909635 [C/T] chr1 1909635 Cc01_g01250:1824 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT +chr1:1909662 [C/T] chr1 1909662 Cc01_g01250:1851 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC CT TT CT +chr1:1909686 [C/T] chr1 1909686 Cc01_g01250:1875 exon SYNONYMOUS_CODING ccC/ccT P/P 37.5% 4 CC CT CT CT +chr1:1909689 [A/T] chr1 1909689 Cc01_g01250:1878 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA TA AA +chr1:1909703 [A/G] chr1 1909703 Cc01_g01250:1892 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA +chr1:1909742 [G/T] chr1 1909742 Cc01_g01250:1931 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 37.5% 4 GG GT GT TG +chr1:1909746 [T/G] chr1 1909746 Cc01_g01250:1935 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 TT TG TG GT +chr1:1909748 [G/A] chr1 1909748 Cc01_g01250:1937 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 GG AA AA AA +chr1:1909805 [G/A] chr1 1909805 Cc01_g01250:1994 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 37.5% 4 GG GA GA AG +chr1:1909856 [C/T] chr1 1909856 Cc01_g01250:2045 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 25.0% 4 CC TC CC CT +chr1:1909857 [A/T] chr1 1909857 Cc01_g01250:2046 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT +chr1:1909887 [G/A] chr1 1909887 Cc01_g01250:2076 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1909896 [A/G] chr1 1909896 Cc01_g01250:2085 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG +chr1:1909917 [A/G] chr1 1909917 Cc01_g01250:2106 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG +chr1:1909941 [G/A] chr1 1909941 Cc01_g01250:2130 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GA GA +chr1:1909992 [C/G] chr1 1909992 Cc01_g01250:2181 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC +chr1:2012155 [G/A] chr1 2012155 Cc01_g01280:207 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 GG GA NN GG +chr1:2012138 [G/A] chr1 2012138 Cc01_g01280:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG AA AA AA +chr1:2012066 [A/G] chr1 2012066 Cc01_g01280:296 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 33.3% 3 AA GG GG NN +chr1:2011950 [C/G] chr1 2011950 Cc01_g01280:412 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG CC CC +chr1:2011879 [G/A] chr1 2011879 Cc01_g01280:483 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GA NN GG +chr1:2029017 [G/C] chr1 2029017 Cc01_g01300:239 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 37.5% 4 GG CC CC GC +chr1:2028341 [A/G] chr1 2028341 Cc01_g01300:366 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG GG AG +chr1:2028339 [G/A] chr1 2028339 Cc01_g01300:368 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 GG AG GG GG +chr1:2028335 [A/C] chr1 2028335 Cc01_g01300:372 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 AA CC CC CC +chr1:2028322 [C/T] chr1 2028322 Cc01_g01300:385 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC TC CC CC +chr1:2028306 [C/G] chr1 2028306 Cc01_g01300:401 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CG CC +chr1:2028289 [T/C] chr1 2028289 Cc01_g01300:418 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 TT CC NN CC +chr1:2084455 [A/G] chr1 2084455 Cc01_g01330:36 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 AA AG AG GG +chr1:2084476 [G/C] chr1 2084476 Cc01_g01330:57 exon NON_SYNONYMOUS_CODING atG/atC M/I 37.5% 4 GG CG CC CC +chr1:2084479 [C/T] chr1 2084479 Cc01_g01330:60 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC TC CC CC +chr1:2084490 [C/A] chr1 2084490 Cc01_g01330:71 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC AC CC CC +chr1:2084532 [A/G] chr1 2084532 Cc01_g01330:113 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 4 AA AG AG GG +chr1:2084551 [A/G] chr1 2084551 Cc01_g01330:132 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA GA AA AA +chr1:2084565 [C/G] chr1 2084565 Cc01_g01330:146 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 50.0% 4 CC CG CG GG +chr1:2084606 [G/T] chr1 2084606 Cc01_g01330:187 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 4 GG GT GT TT +chr1:2084666 [A/G] chr1 2084666 Cc01_g01330:247 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG AG GG +chr1:2084667 [C/T] chr1 2084667 Cc01_g01330:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 CC TT TT TT +chr1:2084687 [G/A] chr1 2084687 Cc01_g01330:268 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 4 GG GA GA AA +chr1:2084690 [C/G] chr1 2084690 Cc01_g01330:271 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC +chr1:2084692 [A/G] chr1 2084692 Cc01_g01330:273 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA +chr1:2084718 [C/T] chr1 2084718 Cc01_g01330:299 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 33.3% 3 CC TT TT NN +chr1:2084791 [T/A] chr1 2084791 Cc01_g01330:372 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TA TT +chr1:2084820 [A/G] chr1 2084820 Cc01_g01330:401 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AA GA AG +chr1:2084834 [G/A] chr1 2084834 Cc01_g01330:415 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG AG +chr1:2084842 [G/C] chr1 2084842 Cc01_g01330:423 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG GG GC CG +chr1:2084851 [A/G] chr1 2084851 Cc01_g01330:432 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GA AG +chr1:2084863 [C/T] chr1 2084863 Cc01_g01330:444 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC TC CC +chr1:2084924 [A/T] chr1 2084924 Cc01_g01330:505 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA AT AT NN +chr1:2085060 [T/C] chr1 2085060 Cc01_g01330:641 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN +chr1:2085102 [A/C] chr1 2085102 Cc01_g01330:683 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 25.0% 4 AA AA CC AA +chr1:2085109 [T/G] chr1 2085109 Cc01_g01330:690 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 TT TT GG TT +chr1:2085145 [G/A] chr1 2085145 Cc01_g01330:726 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG GG AA GG +chr1:2085162 [C/G] chr1 2085162 Cc01_g01330:743 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC CG GG CC +chr1:2085194 [G/A] chr1 2085194 Cc01_g01330:775 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GG GA +chr1:2085203 [C/A] chr1 2085203 Cc01_g01330:784 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 CC CA CA CA +chr1:2085208 [A/G] chr1 2085208 Cc01_g01330:789 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG +chr1:2085218 [G/C] chr1 2085218 Cc01_g01330:799 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 GG GC GG CC +chr1:2085227 [T/G] chr1 2085227 Cc01_g01330:808 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 37.5% 4 TT TG TT GG +chr1:2085271 [A/G] chr1 2085271 Cc01_g01330:852 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AG AA NN +chr1:2085356 [C/G] chr1 2085356 Cc01_g01330:937 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 16.7% 3 CC CC CG NN +chr1:2085358 [T/A] chr1 2085358 Cc01_g01330:939 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT TT TA NN +chr1:2086315 [G/T] chr1 2086315 Cc01_g01330:1073 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GG GT GT +chr1:2086354 [A/G] chr1 2086354 Cc01_g01330:1112 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GA AA +chr1:2086380 [C/A] chr1 2086380 Cc01_g01330:1138 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 CC CC CA AA +chr1:2086424 [A/G] chr1 2086424 Cc01_g01330:1182 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AA AG GG +chr1:2086438 [C/T] chr1 2086438 Cc01_g01330:1196 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 CC TT TT TT +chr1:2086581 [G/T] chr1 2086581 Cc01_g01330:1261 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG +chr1:2086594 [T/C] chr1 2086594 Cc01_g01330:1274 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT TT TC TC +chr1:2086608 [T/C] chr1 2086608 Cc01_g01330:1288 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 37.5% 4 TT TC TC TC +chr1:2086613 [T/C] chr1 2086613 Cc01_g01330:1293 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT TC TC TC +chr1:2086637 [C/A] chr1 2086637 Cc01_g01330:1317 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 CC CA CC AA +chr1:2086679 [G/A] chr1 2086679 Cc01_g01330:1359 exon SYNONYMOUS_CODING gaG/gaA E/E 12.5% 4 GG GG GG GA +chr1:2086682 [C/T] chr1 2086682 Cc01_g01330:1362 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CC CT CT +chr1:2086716 [G/A] chr1 2086716 Cc01_g01330:1396 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GG AA +chr1:2086756 [G/A] chr1 2086756 Cc01_g01330:1436 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG GA +chr1:2086758 [C/G] chr1 2086758 Cc01_g01330:1438 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC CC CG GC +chr1:2086789 [T/A] chr1 2086789 Cc01_g01330:1469 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 TT AA AA AA +chr1:2086811 [A/G] chr1 2086811 Cc01_g01330:1491 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA +chr1:2086840 [T/A] chr1 2086840 Cc01_g01330:1520 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT AA TT TT +chr1:2093852 [C/T] chr1 2093852 Cc01_g01340:4 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 CC CT NN CC +chr1:2093847 [C/A] chr1 2093847 Cc01_g01340:9 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 4 CC AC AA CA +chr1:2093810 [G/A] chr1 2093810 Cc01_g01340:46 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG AG GG GG +chr1:2093799 [A/G] chr1 2093799 Cc01_g01340:57 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GA GG AA +chr1:2093778 [A/G] chr1 2093778 Cc01_g01340:78 exon SYNONYMOUS_CODING gaT/gaC D/D 16.7% 3 AA AA NN GA +chr1:2093758 [G/A] chr1 2093758 Cc01_g01340:98 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 33.3% 3 GG GA NN GA +chr1:2093731 [C/A] chr1 2093731 Cc01_g01340:125 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 16.7% 3 CC CC NN CA +chr1:2093721 [C/G] chr1 2093721 Cc01_g01340:135 exon SYNONYMOUS_CODING tcG/tcC S/S 50.0% 4 CC CG GG CG +chr1:2093714 [A/C] chr1 2093714 Cc01_g01340:142 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 50.0% 4 AA AC CC AC +chr1:2093686 [A/G] chr1 2093686 Cc01_g01340:170 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 AA AG GG AG +chr1:2093684 [T/C] chr1 2093684 Cc01_g01340:172 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 TT TC CC TC +chr1:2093683 [G/C] chr1 2093683 Cc01_g01340:173 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 12.5% 4 GG GC GG GG +chr1:2093672 [C/A] chr1 2093672 Cc01_g01340:184 exon STOP_GAINED Gag/Tag E/2 37.5% 4 CC CA CA CA +chr1:2093663 [G/A] chr1 2093663 Cc01_g01340:193 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 GG GG GG AG +chr1:2093646 [A/G] chr1 2093646 Cc01_g01340:210 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA AG AG AA +chr1:2093644 [T/C] chr1 2093644 Cc01_g01340:212 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 TT TC TC TC +chr1:2093642 [C/T] chr1 2093642 Cc01_g01340:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TC TC TC +chr1:2093636 [T/G] chr1 2093636 Cc01_g01340:220 exon NON_SYNONYMOUS_CODING Acc/Ccc T/P 25.0% 4 TT TG TG TT +chr1:2093635 [G/T] chr1 2093635 Cc01_g01340:221 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 25.0% 4 GG GT GG GT +chr1:2093634 [G/A] chr1 2093634 Cc01_g01340:222 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GA GG GG +chr1:2093633 [C/T] chr1 2093633 Cc01_g01340:223 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 CC CC CC CT +chr1:2093602 [A/T] chr1 2093602 Cc01_g01340:254 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 33.3% 3 AA AT NN AT +chr1:2093600 [C/G] chr1 2093600 Cc01_g01340:256 exon NON_SYNONYMOUS_CODING Gga/Cga G/R 16.7% 3 CC CG NN CC +chr1:2093588 [T/G] chr1 2093588 Cc01_g01340:268 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 16.7% 3 TT TG NN TT +chr1:2093575 [A/G] chr1 2093575 Cc01_g01340:281 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 50.0% 3 AA GG NN AG +chr1:2093569 [G/A] chr1 2093569 Cc01_g01340:287 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 16.7% 3 GG GG NN GA +chr1:2093565 [G/A] chr1 2093565 Cc01_g01340:291 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GG NN GA +chr1:2093525 [C/G] chr1 2093525 Cc01_g01340:331 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 50.0% 3 CC GG NN CG +chr1:2093515 [T/C] chr1 2093515 Cc01_g01340:341 exon SYNONYMOUS_STOP tAa/tGa 1/1 33.3% 3 TT CC NN TT +chr1:2095269 [G/A] chr1 2095269 Cc01_g01350:16 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG +chr1:2095295 [A/G] chr1 2095295 Cc01_g01350:42 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA +chr1:2095321 [A/T] chr1 2095321 Cc01_g01350:68 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA +chr1:2095431 [C/A] chr1 2095431 Cc01_g01350:178 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CA CC CC +chr1:2095629 [C/T] chr1 2095629 Cc01_g01350:376 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC CC CT CT +chr1:2095745 [G/A] chr1 2095745 Cc01_g01350:492 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA AA GG +chr1:2095959 [C/G] chr1 2095959 Cc01_g01350:706 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CG CC +chr1:2095960 [A/G] chr1 2095960 Cc01_g01350:707 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG GA AA +chr1:2095964 [C/T] chr1 2095964 Cc01_g01350:711 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC TC CC +chr1:2095974 [C/T] chr1 2095974 Cc01_g01350:721 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC +chr1:2095975 [A/C] chr1 2095975 Cc01_g01350:722 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 AA AA CA AA +chr1:2095983 [A/C] chr1 2095983 Cc01_g01350:730 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 12.5% 4 AA AC AA AA +chr1:2096351 [T/A] chr1 2096351 Cc01_g01350:980 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT +chr1:2096710 [C/G] chr1 2096710 Cc01_g01350:1261 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CG CC +chr1:2100328 [A/C] chr1 2100328 Cc01_g01360:24 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 50.0% 3 AA NN AC CC +chr1:2100313 [T/A] chr1 2100313 Cc01_g01360:39 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA +chr1:2100304 [T/C] chr1 2100304 Cc01_g01360:48 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 TT CC CC TC +chr1:2100300 [C/T] chr1 2100300 Cc01_g01360:52 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC TT TT TT +chr1:2100299 [G/A] chr1 2100299 Cc01_g01360:53 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG AA AA GA +chr1:2100295 [A/G] chr1 2100295 Cc01_g01360:57 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA GG GG AG +chr1:2100286 [A/G] chr1 2100286 Cc01_g01360:66 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG GG AA +chr1:2100277 [C/T] chr1 2100277 Cc01_g01360:75 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT TT TT +chr1:2100255 [C/T] chr1 2100255 Cc01_g01360:97 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TT CT TT +chr1:2100252 [A/T] chr1 2100252 Cc01_g01360:100 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 37.5% 4 AA TT AT TT +chr1:2100249 [C/T] chr1 2100249 Cc01_g01360:103 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 CC TT CT TT +chr1:2100244 [A/T] chr1 2100244 Cc01_g01360:108 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA TT AT TT +chr1:2100237 [T/C] chr1 2100237 Cc01_g01360:115 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 37.5% 4 TT CC TC CC +chr1:2100226 [G/A] chr1 2100226 Cc01_g01360:126 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA +chr1:2100223 [A/C] chr1 2100223 Cc01_g01360:129 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 3 AA NN AC CC +chr1:2100218 [C/T] chr1 2100218 Cc01_g01360:134 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 2 CC NN CT NN +chr1:2100189 [T/C] chr1 2100189 Cc01_g01360:163 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 TT CC TT TC +chr1:2100184 [G/A] chr1 2100184 Cc01_g01360:168 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GA GG GA +chr1:2100164 [A/G] chr1 2100164 Cc01_g01360:188 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 3 AA GG NN AG +chr1:2100139 [A/G] chr1 2100139 Cc01_g01360:213 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 2 AA NN NN AG +chr1:2105898 [A/G] chr1 2105898 Cc01_g01370:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA AG AA AG +chr1:2105943 [C/G] chr1 2105943 Cc01_g01370:68 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC +chr1:2105974 [T/G] chr1 2105974 Cc01_g01370:99 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT TG TT TG +chr1:2105998 [T/C] chr1 2105998 Cc01_g01370:123 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT CT TT +chr1:2106006 [G/C] chr1 2106006 Cc01_g01370:131 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 50.0% 4 GG CC GC GC +chr1:2106086 [G/A] chr1 2106086 Cc01_g01370:211 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG +chr1:2106188 [G/C] chr1 2106188 Cc01_g01370:313 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 4 GG GC GG GC +chr1:2106190 [G/A] chr1 2106190 Cc01_g01370:315 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA +chr1:2106216 [C/G] chr1 2106216 Cc01_g01370:341 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC CG CC CG +chr1:2106220 [T/C] chr1 2106220 Cc01_g01370:345 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TC TT TC +chr1:2106236 [T/C] chr1 2106236 Cc01_g01370:361 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT TC TT TC +chr1:2106264 [G/A] chr1 2106264 Cc01_g01370:389 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG +chr1:2106271 [C/A] chr1 2106271 Cc01_g01370:396 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA +chr1:2106279 [G/A] chr1 2106279 Cc01_g01370:404 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 GG GG GA GA +chr1:2106291 [A/C] chr1 2106291 Cc01_g01370:416 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 37.5% 4 AA AC AC AC +chr1:2106302 [A/G] chr1 2106302 Cc01_g01370:427 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG GG AG +chr1:2106324 [T/G] chr1 2106324 Cc01_g01370:449 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 37.5% 4 TT TG TG TG +chr1:2106332 [C/G] chr1 2106332 Cc01_g01370:457 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:2106375 [A/G] chr1 2106375 Cc01_g01370:500 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 37.5% 4 AA AG AG AG +chr1:2106435 [A/T] chr1 2106435 Cc01_g01370:560 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 AA AT AA AT +chr1:2106441 [T/G] chr1 2106441 Cc01_g01370:566 exon NON_SYNONYMOUS_CODING aTg/aGg M/R 25.0% 4 TT TG TT TG +chr1:2106443 [C/G] chr1 2106443 Cc01_g01370:568 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC +chr1:2106602 [A/G] chr1 2106602 Cc01_g01370:633 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG +chr1:2106604 [T/G] chr1 2106604 Cc01_g01370:635 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 TT TG TG TG +chr1:2106695 [G/C] chr1 2106695 Cc01_g01370:726 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG CC GG GG +chr1:2106696 [A/G] chr1 2106696 Cc01_g01370:727 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 AA GG GG AA +chr1:2106708 [G/A] chr1 2106708 Cc01_g01370:739 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG +chr1:2106774 [A/G] chr1 2106774 Cc01_g01370:805 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AA AG +chr1:2106839 [T/C] chr1 2106839 Cc01_g01370:870 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TT TC +chr1:2106857 [T/A] chr1 2106857 Cc01_g01370:888 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 50.0% 4 TT AA TA TA +chr1:2106878 [G/A] chr1 2106878 Cc01_g01370:909 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA GA +chr1:2106908 [A/G] chr1 2106908 Cc01_g01370:939 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA +chr1:2107068 [C/A] chr1 2107068 Cc01_g01370:980 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC +chr1:2107109 [G/C] chr1 2107109 Cc01_g01370:1021 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GC GG +chr1:2107131 [A/C] chr1 2107131 Cc01_g01370:1043 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 25.0% 4 AA CA AA AC +chr1:2107150 [G/A] chr1 2107150 Cc01_g01370:1062 exon STOP_GAINED tgG/tgA W/4 12.5% 4 GG GA GG GG +chr1:2107161 [T/C] chr1 2107161 Cc01_g01370:1073 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT CT TT +chr1:2107171 [C/G] chr1 2107171 Cc01_g01370:1083 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 12.5% 4 CC CC GC CC +chr1:2107215 [G/A] chr1 2107215 Cc01_g01370:1127 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 50.0% 4 GG AA GA GA +chr1:2107325 [A/C] chr1 2107325 Cc01_g01370:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 AA AC AC AC +chr1:2107345 [A/G] chr1 2107345 Cc01_g01370:1179 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG AG +chr1:2107361 [T/A] chr1 2107361 Cc01_g01370:1195 exon NON_SYNONYMOUS_CODING Tct/Act S/T 37.5% 4 TT TA TA TA +chr1:2107390 [A/C] chr1 2107390 Cc01_g01370:1224 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA AC +chr1:2107405 [T/A] chr1 2107405 Cc01_g01370:1239 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA +chr1:2107431 [C/T] chr1 2107431 Cc01_g01370:1265 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 CC CT CT CT +chr1:2107467 [A/T] chr1 2107467 Cc01_g01370:1301 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA TA AA AA +chr1:2107472 [G/A] chr1 2107472 Cc01_g01370:1306 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG AG GG +chr1:2107516 [T/C] chr1 2107516 Cc01_g01370:1350 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TC TC +chr1:2107607 [C/T] chr1 2107607 Cc01_g01370:1441 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT +chr1:2117223 [A/G] chr1 2117223 Cc01_g01380:117 exon SYNONYMOUS_CODING cgT/cgC R/R 33.3% 3 AA GG NN GG +chr1:2117210 [T/G] chr1 2117210 Cc01_g01380:130 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 33.3% 3 TT GG NN GG +chr1:2117175 [C/G] chr1 2117175 Cc01_g01380:165 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 2 CC GG NN NN +chr1:2117171 [C/T] chr1 2117171 Cc01_g01380:169 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 CC TT NN NN +chr1:2116944 [A/G] chr1 2116944 Cc01_g01380:240 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 AA NN NN GG +chr1:2116934 [T/A] chr1 2116934 Cc01_g01380:250 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 TT NN NN AA +chr1:2116932 [C/G] chr1 2116932 Cc01_g01380:252 exon NON_SYNONYMOUS_CODING atG/atC M/I 50.0% 2 CC NN NN GG +chr1:2116917 [C/A] chr1 2116917 Cc01_g01380:267 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 CC NN NN AA +chr1:2116877 [T/A] chr1 2116877 Cc01_g01380:307 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 50.0% 2 TT NN NN AA +chr1:2116873 [T/C] chr1 2116873 Cc01_g01380:311 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 TT NN NN CC +chr1:2116861 [A/G] chr1 2116861 Cc01_g01380:323 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 2 AA NN NN GG +chr1:2169162 [C/G] chr1 2169162 Cc01_g01390:5 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC +chr1:2169167 [C/G] chr1 2169167 Cc01_g01390:10 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 37.5% 4 CC CG CG CG +chr1:2169279 [A/G] chr1 2169279 Cc01_g01390:122 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG +chr1:2169286 [A/T] chr1 2169286 Cc01_g01390:129 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA AA AT AA +chr1:2169346 [T/C] chr1 2169346 Cc01_g01390:189 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TC TC TT +chr1:2169353 [G/A] chr1 2169353 Cc01_g01390:196 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG +chr1:2169630 [T/A] chr1 2169630 Cc01_g01390:473 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT AA TA AA +chr1:2169828 [C/A] chr1 2169828 Cc01_g01390:671 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CA CA CC +chr1:2169829 [G/C] chr1 2169829 Cc01_g01390:672 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GC GG +chr1:2169862 [C/T] chr1 2169862 Cc01_g01390:705 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:2169958 [T/C] chr1 2169958 Cc01_g01390:801 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:2169967 [C/T] chr1 2169967 Cc01_g01390:810 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CC CT CC +chr1:2170037 [G/C] chr1 2170037 Cc01_g01390:880 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG +chr1:2170043 [G/A] chr1 2170043 Cc01_g01390:886 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG +chr1:2170057 [C/T] chr1 2170057 Cc01_g01390:900 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC TC CC +chr1:2170129 [T/C] chr1 2170129 Cc01_g01390:972 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TT TC TT +chr1:2170192 [G/T] chr1 2170192 Cc01_g01390:1035 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GT GG GG +chr1:2170204 [T/C] chr1 2170204 Cc01_g01390:1047 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:2170362 [A/T] chr1 2170362 Cc01_g01390:1080 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 AA AT AT AA +chr1:2170446 [T/C] chr1 2170446 Cc01_g01390:1164 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CC TC CC +chr1:2170635 [T/C] chr1 2170635 Cc01_g01390:1275 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 TT CC TT CC +chr1:2170650 [T/C] chr1 2170650 Cc01_g01390:1290 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT +chr1:2170761 [T/G] chr1 2170761 Cc01_g01390:1401 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 37.5% 4 TT GG TG GG +chr1:2170780 [C/T] chr1 2170780 Cc01_g01390:1420 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CT CC +chr1:2170800 [G/A] chr1 2170800 Cc01_g01390:1440 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG AA GG AA +chr1:2170865 [C/A] chr1 2170865 Cc01_g01390:1505 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CA CC +chr1:2170868 [A/C] chr1 2170868 Cc01_g01390:1508 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 4 AA CC AA CC +chr1:2170873 [A/G] chr1 2170873 Cc01_g01390:1513 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AG AA AA +chr1:2170884 [C/T] chr1 2170884 Cc01_g01390:1524 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC TT CC TT +chr1:2174798 [C/T] chr1 2174798 Cc01_g01400:21 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC CT CT TT +chr1:2174809 [A/G] chr1 2174809 Cc01_g01400:32 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AG AG +chr1:2174843 [G/A] chr1 2174843 Cc01_g01400:66 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG GG GA GA +chr1:2174851 [G/A] chr1 2174851 Cc01_g01400:74 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GG AG GG +chr1:2174873 [C/A] chr1 2174873 Cc01_g01400:96 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA +chr1:2174883 [T/C] chr1 2174883 Cc01_g01400:106 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT TT TC TC +chr1:2174888 [T/C] chr1 2174888 Cc01_g01400:111 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TC TC +chr1:2174899 [T/C] chr1 2174899 Cc01_g01400:122 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 TT TT TT CT +chr1:2174901 [C/T] chr1 2174901 Cc01_g01400:124 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 CC CC CT CT +chr1:2174903 [T/C] chr1 2174903 Cc01_g01400:126 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TT TC TC +chr1:2174906 [T/G] chr1 2174906 Cc01_g01400:129 exon SYNONYMOUS_CODING acT/acG T/T 25.0% 4 TT TT TG TG +chr1:2174908 [C/A] chr1 2174908 Cc01_g01400:131 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 25.0% 4 CC CC CA CA +chr1:2174912 [T/G] chr1 2174912 Cc01_g01400:135 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 12.5% 4 TT TG TT TT +chr1:2174940 [C/A] chr1 2174940 Cc01_g01400:163 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CC CA CA +chr1:2174949 [T/G] chr1 2174949 Cc01_g01400:172 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 25.0% 4 TT TT TG TG +chr1:2174958 [G/A] chr1 2174958 Cc01_g01400:181 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GG GA GA +chr1:2174961 [C/T] chr1 2174961 Cc01_g01400:184 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 37.5% 4 CC CC TT CT +chr1:2174991 [G/A] chr1 2174991 Cc01_g01400:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG +chr1:2174992 [A/G] chr1 2174992 Cc01_g01400:215 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA GA AA GA +chr1:2174997 [C/T] chr1 2174997 Cc01_g01400:220 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC CT CT TT +chr1:2174999 [T/C] chr1 2174999 Cc01_g01400:222 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC TC +chr1:2175021 [G/C] chr1 2175021 Cc01_g01400:244 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 25.0% 4 GG GG GC GC +chr1:2175025 [C/G] chr1 2175025 Cc01_g01400:248 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 25.0% 4 CC CC CG CG +chr1:2175026 [T/C] chr1 2175026 Cc01_g01400:249 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT TC TC +chr1:2175072 [A/C] chr1 2175072 Cc01_g01400:295 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AC AA AA +chr1:2175151 [T/G] chr1 2175151 Cc01_g01400:374 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 12.5% 4 TT TT TT TG +chr1:2175157 [C/A] chr1 2175157 Cc01_g01400:380 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CC AC +chr1:2175167 [C/T] chr1 2175167 Cc01_g01400:390 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:2175183 [A/G] chr1 2175183 Cc01_g01400:406 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA +chr1:2175248 [C/T] chr1 2175248 Cc01_g01400:471 exon SYNONYMOUS_CODING taC/taT Y/Y 33.3% 3 CC TT NN TT +chr1:2175317 [A/C] chr1 2175317 Cc01_g01400:540 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 AA AA AA AC +chr1:2175371 [T/C] chr1 2175371 Cc01_g01400:594 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC +chr1:2175512 [C/T] chr1 2175512 Cc01_g01400:735 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CC CT +chr1:2175561 [G/T] chr1 2175561 Cc01_g01400:784 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT GG GG +chr1:2175562 [C/G] chr1 2175562 Cc01_g01400:785 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG CC CC +chr1:2175613 [G/T] chr1 2175613 Cc01_g01400:836 exon NON_SYNONYMOUS_CODING cGt/cTt R/L 25.0% 4 GG GG GG TT +chr1:2175705 [T/A] chr1 2175705 Cc01_g01400:928 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT TT TA TT +chr1:2175977 [G/A] chr1 2175977 Cc01_g01400:1088 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 GG GG GG GA +chr1:2176009 [G/A] chr1 2176009 Cc01_g01400:1120 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG +chr1:2176010 [A/C] chr1 2176010 Cc01_g01400:1121 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AC AA AA +chr1:2176046 [C/A] chr1 2176046 Cc01_g01400:1157 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 CC CA CC CC +chr1:2176075 [G/C] chr1 2176075 Cc01_g01400:1186 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GC GG +chr1:2176085 [G/A] chr1 2176085 Cc01_g01400:1196 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 GG GG GA GG +chr1:2176089 [A/G] chr1 2176089 Cc01_g01400:1200 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AG AA +chr1:2176098 [C/T] chr1 2176098 Cc01_g01400:1209 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:2176099 [G/A] chr1 2176099 Cc01_g01400:1210 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG AG GG GG +chr1:2176255 [G/A] chr1 2176255 Cc01_g01400:1285 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG +chr1:2176279 [T/A] chr1 2176279 Cc01_g01400:1309 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TT TT TA +chr1:2176311 [C/A] chr1 2176311 Cc01_g01400:1341 exon SYNONYMOUS_CODING atC/atA I/I 12.5% 4 CC CA CC CC +chr1:2176321 [G/A] chr1 2176321 Cc01_g01400:1351 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA +chr1:2176345 [C/G] chr1 2176345 Cc01_g01400:1375 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 12.5% 4 CC CG CC CC +chr1:2176383 [A/G] chr1 2176383 Cc01_g01400:1413 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:2176387 [A/T] chr1 2176387 Cc01_g01400:1417 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AT AA AA +chr1:2177071 [T/G] chr1 2177071 Cc01_g01410:37 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT GG NN TT +chr1:2177072 [G/T] chr1 2177072 Cc01_g01410:38 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 33.3% 3 GG GG NN TT +chr1:2177953 [T/C] chr1 2177953 Cc01_g01410:198 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT NN NN CC +chr1:2185597 [C/A] chr1 2185597 Cc01_g01420:45 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 CC CA CC CA +chr1:2185587 [T/C] chr1 2185587 Cc01_g01420:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TC TT TT +chr1:2185534 [T/C] chr1 2185534 Cc01_g01420:108 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TC TT +chr1:2185452 [G/C] chr1 2185452 Cc01_g01420:190 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 12.5% 4 GG GG GC GG +chr1:2185431 [T/C] chr1 2185431 Cc01_g01420:211 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC +chr1:2185418 [T/C] chr1 2185418 Cc01_g01420:224 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 12.5% 4 TT TT CT TT +chr1:2185408 [C/T] chr1 2185408 Cc01_g01420:234 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT TT CT +chr1:2185315 [A/C] chr1 2185315 Cc01_g01420:327 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 AA AA AA AC +chr1:2185281 [A/G] chr1 2185281 Cc01_g01420:361 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA +chr1:2185274 [G/T] chr1 2185274 Cc01_g01420:368 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 4 GG GG TT GG +chr1:2185232 [C/T] chr1 2185232 Cc01_g01420:410 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CT CC +chr1:2185228 [A/T] chr1 2185228 Cc01_g01420:414 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA TA AA +chr1:2185186 [A/G] chr1 2185186 Cc01_g01420:456 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AG AA AA +chr1:2185185 [T/A] chr1 2185185 Cc01_g01420:457 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 25.0% 4 TT AT TT TA +chr1:2185150 [A/G] chr1 2185150 Cc01_g01420:492 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GA AA AG +chr1:2185136 [T/G] chr1 2185136 Cc01_g01420:506 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 12.5% 4 TT TG TT TT +chr1:2185131 [A/T] chr1 2185131 Cc01_g01420:511 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 4 AA TT AT AT +chr1:2185130 [C/G] chr1 2185130 Cc01_g01420:512 exon NON_SYNONYMOUS_CODING tGg/tCg W/S 50.0% 4 CC GG CG CG +chr1:2185056 [C/T] chr1 2185056 Cc01_g01420:586 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CT CC CC +chr1:2185024 [C/G] chr1 2185024 Cc01_g01420:618 exon SYNONYMOUS_CODING cgG/cgC R/R 12.5% 4 CC CC CG CC +chr1:2184985 [C/T] chr1 2184985 Cc01_g01420:657 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:2184978 [A/G] chr1 2184978 Cc01_g01420:664 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 AA AA AG AA +chr1:2184967 [C/T] chr1 2184967 Cc01_g01420:675 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 CC CC CT CC +chr1:2184923 [T/C] chr1 2184923 Cc01_g01420:719 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT +chr1:2184900 [G/A] chr1 2184900 Cc01_g01420:742 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 GG GG GA GG +chr1:2184858 [C/T] chr1 2184858 Cc01_g01420:784 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC +chr1:2184847 [T/G] chr1 2184847 Cc01_g01420:795 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 12.5% 4 TT TT TG TT +chr1:2184843 [A/G] chr1 2184843 Cc01_g01420:799 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG GG GG +chr1:2184715 [A/G] chr1 2184715 Cc01_g01420:927 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:2184631 [A/G] chr1 2184631 Cc01_g01420:1011 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AG AA AA +chr1:2184436 [C/T] chr1 2184436 Cc01_g01420:1087 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC TT CT TT +chr1:2184420 [C/T] chr1 2184420 Cc01_g01420:1103 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC TC CC +chr1:2184375 [A/C] chr1 2184375 Cc01_g01420:1148 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 25.0% 4 AA CC CC CC +chr1:2184365 [C/T] chr1 2184365 Cc01_g01420:1158 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT +chr1:2184361 [T/C] chr1 2184361 Cc01_g01420:1162 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 4 TT CC CC TT +chr1:2184164 [T/A] chr1 2184164 Cc01_g01420:1280 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 37.5% 4 TT AA AA AT +chr1:2184085 [C/T] chr1 2184085 Cc01_g01420:1359 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 CC CC TT CC +chr1:2184069 [A/G] chr1 2184069 Cc01_g01420:1375 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG GG GG +chr1:2184058 [T/A] chr1 2184058 Cc01_g01420:1386 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA +chr1:2184010 [T/C] chr1 2184010 Cc01_g01420:1434 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TT TC +chr1:2183902 [T/C] chr1 2183902 Cc01_g01420:1542 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC +chr1:2191614 [T/C] chr1 2191614 Cc01_g01430:14 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 TT TC TC TC +chr1:2190583 [G/T] chr1 2190583 Cc01_g01430:511 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG GT GG GT +chr1:2190560 [C/G] chr1 2190560 Cc01_g01430:534 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CC CC GC +chr1:2190508 [A/G] chr1 2190508 Cc01_g01430:586 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA +chr1:2190494 [A/G] chr1 2190494 Cc01_g01430:600 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA +chr1:2189807 [A/T] chr1 2189807 Cc01_g01430:897 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA AT AT AA +chr1:2189651 [T/C] chr1 2189651 Cc01_g01430:1053 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC +chr1:2189636 [A/G] chr1 2189636 Cc01_g01430:1068 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG +chr1:2189634 [A/T] chr1 2189634 Cc01_g01430:1070 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 AA AA TA AA +chr1:2188570 [T/C] chr1 2188570 Cc01_g01430:1166 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT +chr1:2188551 [A/G] chr1 2188551 Cc01_g01430:1185 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:2196422 [A/G] chr1 2196422 Cc01_g01440:36 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AG AA AG +chr1:2196341 [T/C] chr1 2196341 Cc01_g01440:117 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC TC TC +chr1:2196333 [G/C] chr1 2196333 Cc01_g01440:125 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG CG GG GG +chr1:2196286 [C/A] chr1 2196286 Cc01_g01440:172 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 37.5% 4 CC AA CC CA +chr1:2196284 [T/G] chr1 2196284 Cc01_g01440:174 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT GT TT TT +chr1:2196257 [A/G] chr1 2196257 Cc01_g01440:201 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:2196212 [A/G] chr1 2196212 Cc01_g01440:246 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA +chr1:2196172 [A/G] chr1 2196172 Cc01_g01440:286 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 AA AA GG AA +chr1:2196160 [A/G] chr1 2196160 Cc01_g01440:298 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 AA GG AA AG +chr1:2196140 [A/G] chr1 2196140 Cc01_g01440:318 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA AA GG AA +chr1:2196134 [G/C] chr1 2196134 Cc01_g01440:324 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GC GG GG +chr1:2196132 [C/T] chr1 2196132 Cc01_g01440:326 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC +chr1:2196068 [T/A] chr1 2196068 Cc01_g01440:390 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 37.5% 4 TT TA TA TA +chr1:2196065 [T/C] chr1 2196065 Cc01_g01440:393 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC +chr1:2195449 [A/G] chr1 2195449 Cc01_g01440:536 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 AA AA AA AG +chr1:2195438 [T/A] chr1 2195438 Cc01_g01440:547 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 37.5% 4 TT TA TA TA +chr1:2195424 [C/A] chr1 2195424 Cc01_g01440:561 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC CA CA CC +chr1:2195362 [G/A] chr1 2195362 Cc01_g01440:623 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 GG AG GG GA +chr1:2195350 [A/G] chr1 2195350 Cc01_g01440:635 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AA AG +chr1:2195327 [T/C] chr1 2195327 Cc01_g01440:658 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CT TT TC +chr1:2195242 [C/G] chr1 2195242 Cc01_g01440:743 exon NON_SYNONYMOUS_CODING gGa/gCa G/A 12.5% 4 CC CG CC CC +chr1:2195189 [A/G] chr1 2195189 Cc01_g01440:796 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA GA AA AA +chr1:2195153 [T/C] chr1 2195153 Cc01_g01440:832 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT TT TC CC +chr1:2195139 [A/G] chr1 2195139 Cc01_g01440:846 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:2194136 [C/T] chr1 2194136 Cc01_g01440:878 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC TC CC CC +chr1:2194114 [G/A] chr1 2194114 Cc01_g01440:900 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG AA AA AA +chr1:2194101 [G/T] chr1 2194101 Cc01_g01440:913 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG TG GG GG +chr1:2194096 [T/G] chr1 2194096 Cc01_g01440:918 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 TT TG TT TT +chr1:2194092 [C/T] chr1 2194092 Cc01_g01440:922 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC +chr1:2194052 [T/A] chr1 2194052 Cc01_g01440:962 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TA TT +chr1:2193981 [A/G] chr1 2193981 Cc01_g01440:1033 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 AA AG AA AA +chr1:2193975 [T/C] chr1 2193975 Cc01_g01440:1039 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT +chr1:2193955 [C/A] chr1 2193955 Cc01_g01440:1059 exon SYNONYMOUS_CODING gcG/gcT A/A 37.5% 4 CC AA CC CA +chr1:2209238 [C/T] chr1 2209238 Cc01_g01450:478 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 25.0% 4 CC CC CC TT +chr1:2209206 [G/T] chr1 2209206 Cc01_g01450:510 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG GG TT NN +chr1:2208545 [T/C] chr1 2208545 Cc01_g01450:868 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT +chr1:2208543 [G/T] chr1 2208543 Cc01_g01450:870 exon NON_SYNONYMOUS_CODING agC/agA S/R 12.5% 4 GG GT GG GG +chr1:2208524 [T/A] chr1 2208524 Cc01_g01450:889 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 12.5% 4 TT TA TT TT +chr1:2208480 [C/T] chr1 2208480 Cc01_g01450:933 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:2208471 [A/G] chr1 2208471 Cc01_g01450:942 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA GA AA AA +chr1:2208398 [C/T] chr1 2208398 Cc01_g01450:1015 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 33.3% 3 CC TT NN TT +chr1:2208295 [T/G] chr1 2208295 Cc01_g01450:1118 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 TT TG TT TT +chr1:2208265 [G/A] chr1 2208265 Cc01_g01450:1148 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GA GG GG +chr1:2208247 [G/T] chr1 2208247 Cc01_g01450:1166 exon NON_SYNONYMOUS_CODING cCa/cAa P/Q 25.0% 4 GG GT GG GT +chr1:2208199 [T/A] chr1 2208199 Cc01_g01450:1214 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 TT TT TA TT +chr1:2208185 [C/T] chr1 2208185 Cc01_g01450:1228 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC TC CC +chr1:2208178 [T/C] chr1 2208178 Cc01_g01450:1235 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT +chr1:2208133 [G/A] chr1 2208133 Cc01_g01450:1280 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 GG GA GG GG +chr1:2274354 [C/T] chr1 2274354 Cc01_g01460:831 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC TT NN TT +chr1:2274363 [T/C] chr1 2274363 Cc01_g01460:840 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT CC NN CC +chr1:2274385 [G/C] chr1 2274385 Cc01_g01460:862 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 33.3% 3 GG CC NN CC +chr1:2274390 [A/T] chr1 2274390 Cc01_g01460:867 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT +chr1:2274408 [A/C] chr1 2274408 Cc01_g01460:885 exon SYNONYMOUS_CODING atA/atC I/I 50.0% 2 AA NN NN CC +chr1:2274417 [C/T] chr1 2274417 Cc01_g01460:894 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 CC TT NN TT +chr1:2300221 [C/T] chr1 2300221 Cc01_g01470:1228 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 CC NN NN TT +chr1:2300215 [T/C] chr1 2300215 Cc01_g01470:1234 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 2 TT NN NN CC +chr1:2300214 [G/A] chr1 2300214 Cc01_g01470:1235 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 GG NN NN AA +chr1:2343380 [T/C] chr1 2343380 Cc01_g01490:11 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TT TT TC +chr1:2343353 [T/C] chr1 2343353 Cc01_g01490:38 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT CC CC CC +chr1:2343351 [G/C] chr1 2343351 Cc01_g01490:40 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 GG CC CC CC +chr1:2343348 [T/C] chr1 2343348 Cc01_g01490:43 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT CC CC CC +chr1:2343347 [A/G] chr1 2343347 Cc01_g01490:44 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 4 AA GG GG GG +chr1:2343346 [C/T] chr1 2343346 Cc01_g01490:45 exon NON_SYNONYMOUS_CODING atG/atA M/I 37.5% 4 CC CC TT TC +chr1:2343313 [A/G] chr1 2343313 Cc01_g01490:78 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 AA AA GG GA +chr1:2343300 [G/A] chr1 2343300 Cc01_g01490:91 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG AG +chr1:2343296 [C/T] chr1 2343296 Cc01_g01490:95 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 25.0% 4 CC TT TT TT +chr1:2343283 [A/G] chr1 2343283 Cc01_g01490:108 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG AG GG +chr1:2343280 [T/G] chr1 2343280 Cc01_g01490:111 exon SYNONYMOUS_CODING acA/acC T/T 50.0% 4 TT TG TG GG +chr1:2343274 [A/C] chr1 2343274 Cc01_g01490:117 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 AA AA AC CA +chr1:2343261 [C/A] chr1 2343261 Cc01_g01490:130 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 CC CA CC AA +chr1:2343259 [C/G] chr1 2343259 Cc01_g01490:132 exon SYNONYMOUS_CODING gtG/gtC V/V 37.5% 4 CC CG CC GG +chr1:2343244 [G/T] chr1 2343244 Cc01_g01490:147 exon NON_SYNONYMOUS_CODING caC/caA H/Q 25.0% 4 GG GG GG TT +chr1:2343241 [T/G] chr1 2343241 Cc01_g01490:150 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 TT TT TG GG +chr1:2343235 [G/C] chr1 2343235 Cc01_g01490:156 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG GC CC +chr1:2343232 [A/C] chr1 2343232 Cc01_g01490:159 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AA AC CC +chr1:2343229 [A/T] chr1 2343229 Cc01_g01490:162 exon SYNONYMOUS_CODING tcT/tcA S/S 37.5% 4 AA AA AT TT +chr1:2343225 [T/C] chr1 2343225 Cc01_g01490:166 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 TT TT TC CC +chr1:2343092 [T/C] chr1 2343092 Cc01_g01490:299 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT TT CC +chr1:2342875 [G/A] chr1 2342875 Cc01_g01490:516 exon SYNONYMOUS_CODING ttC/ttT F/F 33.3% 3 GG AA NN AA +chr1:2342772 [C/T] chr1 2342772 Cc01_g01490:619 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC +chr1:2342382 [C/T] chr1 2342382 Cc01_g01490:636 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC TT NN CC +chr1:2342352 [A/T] chr1 2342352 Cc01_g01490:666 exon SYNONYMOUS_CODING atT/atA I/I 37.5% 4 AA TT TT AT +chr1:2342154 [T/G] chr1 2342154 Cc01_g01490:774 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 TT TT TG GG +chr1:2342153 [A/G] chr1 2342153 Cc01_g01490:775 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 37.5% 4 AA AA AG GG +chr1:2342152 [C/T] chr1 2342152 Cc01_g01490:776 exon STOP_GAINED tGg/tAg W/9 37.5% 4 CC CC CT TT +chr1:2342133 [G/A] chr1 2342133 Cc01_g01490:795 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 GG GA GA AA +chr1:2342078 [G/A] chr1 2342078 Cc01_g01490:850 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA +chr1:2342048 [C/A] chr1 2342048 Cc01_g01490:880 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 25.0% 4 CC AA AA AA +chr1:2342034 [A/G] chr1 2342034 Cc01_g01490:894 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG GG GG +chr1:2342013 [T/G] chr1 2342013 Cc01_g01490:915 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT GG GG GG +chr1:2342007 [T/A] chr1 2342007 Cc01_g01490:921 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 TT TT TT TA +chr1:2342001 [G/T] chr1 2342001 Cc01_g01490:927 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 GG TT GT TT +chr1:2341971 [A/G] chr1 2341971 Cc01_g01490:957 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA +chr1:2341944 [T/C] chr1 2341944 Cc01_g01490:984 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC +chr1:2341934 [C/T] chr1 2341934 Cc01_g01490:994 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 50.0% 4 CC CT CT TT +chr1:2341930 [A/C] chr1 2341930 Cc01_g01490:998 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 AA AC AA CC +chr1:2341921 [C/T] chr1 2341921 Cc01_g01490:1007 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 CC CT CC TT +chr1:2341915 [G/A] chr1 2341915 Cc01_g01490:1013 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 37.5% 4 GG GA GG AA +chr1:2341914 [T/G] chr1 2341914 Cc01_g01490:1014 exon SYNONYMOUS_CODING acA/acC T/T 37.5% 4 TT TG TT GG +chr1:2341905 [G/A] chr1 2341905 Cc01_g01490:1023 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG GA GA AA +chr1:2341899 [A/G] chr1 2341899 Cc01_g01490:1029 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 AA AG AG GG +chr1:2341885 [G/A] chr1 2341885 Cc01_g01490:1043 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG AA AA AA +chr1:2341855 [C/T] chr1 2341855 Cc01_g01490:1073 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 CC TT TT TT +chr1:2341853 [A/G] chr1 2341853 Cc01_g01490:1075 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG +chr1:2341843 [T/G] chr1 2341843 Cc01_g01490:1085 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 25.0% 4 TT GG GG GG +chr1:2341816 [C/T] chr1 2341816 Cc01_g01490:1112 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT +chr1:2341814 [G/C] chr1 2341814 Cc01_g01490:1114 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 GG CC CC CC +chr1:2341761 [A/G] chr1 2341761 Cc01_g01490:1167 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG +chr1:2341752 [T/G] chr1 2341752 Cc01_g01490:1176 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GG GG GG +chr1:2341742 [G/A] chr1 2341742 Cc01_g01490:1186 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA +chr1:2341734 [T/C] chr1 2341734 Cc01_g01490:1194 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT TC TC CC +chr1:2341733 [G/T] chr1 2341733 Cc01_g01490:1195 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 GG GT GT TT +chr1:2341731 [A/C] chr1 2341731 Cc01_g01490:1197 exon NON_SYNONYMOUS_CODING caT/caG H/Q 50.0% 4 AA AC AC CC +chr1:2341728 [G/A] chr1 2341728 Cc01_g01490:1200 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 GG GA GA AA +chr1:2341719 [C/G] chr1 2341719 Cc01_g01490:1209 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 CC GG GG GG +chr1:2341697 [T/C] chr1 2341697 Cc01_g01490:1231 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TT TC +chr1:2341685 [C/G] chr1 2341685 Cc01_g01490:1243 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC +chr1:2340685 [G/A] chr1 2340685 Cc01_g01490:1261 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA +chr1:2340667 [T/C] chr1 2340667 Cc01_g01490:1279 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC CC CC +chr1:2334881 [A/G] chr1 2334881 Cc01_g01490:1362 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA +chr1:2334835 [T/C] chr1 2334835 Cc01_g01490:1408 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT CC CT CC +chr1:2334831 [G/T] chr1 2334831 Cc01_g01490:1412 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 50.0% 4 GG GT TG TT +chr1:2334799 [A/C] chr1 2334799 Cc01_g01490:1444 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 25.0% 4 AA AC AA AC +chr1:2334780 [A/T] chr1 2334780 Cc01_g01490:1463 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 12.5% 4 AA TA AA AA +chr1:2334662 [A/T] chr1 2334662 Cc01_g01490:1581 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AA AT AA +chr1:2334642 [G/T] chr1 2334642 Cc01_g01490:1601 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 GG TT GT TT +chr1:2334620 [A/C] chr1 2334620 Cc01_g01490:1623 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC +chr1:2334584 [G/A] chr1 2334584 Cc01_g01490:1659 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AA GA AA +chr1:2334185 [G/A] chr1 2334185 Cc01_g01490:1719 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:2334144 [C/G] chr1 2334144 Cc01_g01490:1760 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 50.0% 4 CC GG CC GG +chr1:2334140 [A/C] chr1 2334140 Cc01_g01490:1764 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AC AA AA +chr1:2334026 [T/C] chr1 2334026 Cc01_g01490:1878 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:2333864 [T/C] chr1 2333864 Cc01_g01490:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 TT CC TC TC +chr1:2360212 [G/A] chr1 2360212 Cc01_g01510:67 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 33.3% 3 GG AA NN GG +chr1:2360304 [G/T] chr1 2360304 Cc01_g01510:159 exon SYNONYMOUS_CODING ggG/ggT G/G 33.3% 3 GG TT NN GG +chr1:2360308 [C/T] chr1 2360308 Cc01_g01510:163 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 CC TT NN CC +chr1:2360310 [A/G] chr1 2360310 Cc01_g01510:165 exon SYNONYMOUS_CODING ctA/ctG L/L 33.3% 3 AA GG NN AA +chr1:2360316 [A/G] chr1 2360316 Cc01_g01510:171 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA AA NN GG +chr1:2360324 [G/A] chr1 2360324 Cc01_g01510:179 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 50.0% 2 GG AA NN NN +chr1:2360326 [G/A] chr1 2360326 Cc01_g01510:181 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN +chr1:2360328 [C/A] chr1 2360328 Cc01_g01510:183 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 50.0% 2 CC AA NN NN +chr1:2361074 [C/T] chr1 2361074 Cc01_g01510:929 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 16.7% 3 CC CC NN CT +chr1:2361629 [A/G] chr1 2361629 Cc01_g01510:1263 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 2 AA NN NN GG +chr1:2361636 [T/C] chr1 2361636 Cc01_g01510:1270 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT NN NN CC +chr1:2361659 [G/A] chr1 2361659 Cc01_g01510:1293 exon SYNONYMOUS_CODING gaG/gaA E/E 50.0% 2 GG NN NN AA +chr1:2361716 [G/A] chr1 2361716 Cc01_g01510:1350 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN NN AA +chr1:2383654 [G/A] chr1 2383654 Cc01_g01520:42 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG +chr1:2383674 [T/C] chr1 2383674 Cc01_g01520:62 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 25.0% 4 TT CC TT TT +chr1:2383681 [C/T] chr1 2383681 Cc01_g01520:69 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT CC CC +chr1:2383712 [G/A] chr1 2383712 Cc01_g01520:100 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GG GG GA +chr1:2383714 [T/C] chr1 2383714 Cc01_g01520:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:2383758 [T/C] chr1 2383758 Cc01_g01520:146 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 TT CC CC CC +chr1:2383785 [A/G] chr1 2383785 Cc01_g01520:173 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA GG AA AA +chr1:2383795 [C/A] chr1 2383795 Cc01_g01520:183 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 50.0% 4 CC AA CC AA +chr1:2383839 [G/A] chr1 2383839 Cc01_g01520:227 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GG AA GG +chr1:2383851 [A/T] chr1 2383851 Cc01_g01520:239 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AT AA AA +chr1:2383866 [C/T] chr1 2383866 Cc01_g01520:254 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC +chr1:2383874 [T/A] chr1 2383874 Cc01_g01520:262 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TA TT TT +chr1:2383920 [G/T] chr1 2383920 Cc01_g01520:308 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG GG TT GG +chr1:2383927 [T/C] chr1 2383927 Cc01_g01520:315 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT +chr1:2384077 [T/G] chr1 2384077 Cc01_g01520:465 exon NON_SYNONYMOUS_CODING agT/agG S/R 25.0% 4 TT TT TT GG +chr1:2384181 [A/G] chr1 2384181 Cc01_g01520:569 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 AA AA AA AG +chr1:2384200 [C/T] chr1 2384200 Cc01_g01520:588 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC TT CC +chr1:2384756 [T/G] chr1 2384756 Cc01_g01520:1041 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT TG TT TT +chr1:2385308 [T/C] chr1 2385308 Cc01_g01520:1470 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TC TT TT +chr1:2409054 [C/A] chr1 2409054 Cc01_g01530:78 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA CC CC +chr1:2409092 [T/C] chr1 2409092 Cc01_g01530:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC TT TT +chr1:2409231 [A/C] chr1 2409231 Cc01_g01530:255 exon SYNONYMOUS_CODING tcA/tcC S/S 16.7% 3 AA AC NN AA +chr1:2409249 [C/T] chr1 2409249 Cc01_g01530:273 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 3 CC CT NN TT +chr1:2409678 [A/G] chr1 2409678 Cc01_g01530:702 exon SYNONYMOUS_CODING ctA/ctG L/L 16.7% 3 AA NN AA AG +chr1:2409702 [T/C] chr1 2409702 Cc01_g01530:726 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 TT TC CC CC +chr1:2409721 [T/A] chr1 2409721 Cc01_g01530:745 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 TT TT TT TA +chr1:2409726 [C/T] chr1 2409726 Cc01_g01530:750 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT +chr1:2425980 [A/G] chr1 2425980 Cc01_g01540:231 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG AA +chr1:2426360 [G/A] chr1 2426360 Cc01_g01540:397 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG AA GA GG +chr1:2426489 [T/C] chr1 2426489 Cc01_g01540:526 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 12.5% 4 TT TC TT TT +chr1:2427186 [G/A] chr1 2427186 Cc01_g01540:843 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GA GG GG +chr1:2427440 [T/C] chr1 2427440 Cc01_g01540:936 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC TT +chr1:2428201 [A/G] chr1 2428201 Cc01_g01540:1375 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 AA GG AG AA +chr1:2428270 [A/G] chr1 2428270 Cc01_g01540:1444 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA AG AA +chr1:2429289 [T/A] chr1 2429289 Cc01_g01540:1547 exon NON_SYNONYMOUS_CODING aTg/aAg M/K 12.5% 4 TT TA TT TT +chr1:2431687 [G/A] chr1 2431687 Cc01_g01540:1638 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:2432530 [C/T] chr1 2432530 Cc01_g01540:1850 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC +chr1:2432737 [A/G] chr1 2432737 Cc01_g01540:1942 exon NON_SYNONYMOUS_CODING Act/Gct T/A 12.5% 4 AA AA AG AA +chr1:2433099 [T/C] chr1 2433099 Cc01_g01540:2141 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:2434119 [T/A] chr1 2434119 Cc01_g01540:2374 exon NON_SYNONYMOUS_CODING Tct/Act S/T 12.5% 4 TT TA TT TT +chr1:2434512 [A/G] chr1 2434512 Cc01_g01540:2553 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA +chr1:2436532 [A/G] chr1 2436532 Cc01_g01550:172 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AG AA AA +chr1:2436544 [G/A] chr1 2436544 Cc01_g01550:184 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG +chr1:2436558 [G/A] chr1 2436558 Cc01_g01550:198 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG +chr1:2436572 [G/A] chr1 2436572 Cc01_g01550:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG +chr1:2439858 [T/C] chr1 2439858 Cc01_g01550:505 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 TT TC TT TC +chr1:2440047 [T/C] chr1 2440047 Cc01_g01550:597 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:2440153 [C/G] chr1 2440153 Cc01_g01550:703 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CG CC CG +chr1:2440191 [A/G] chr1 2440191 Cc01_g01550:741 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:2440206 [A/G] chr1 2440206 Cc01_g01550:756 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AG AA AG +chr1:2444991 [C/G] chr1 2444991 Cc01_g01560:39 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC +chr1:2445037 [C/T] chr1 2445037 Cc01_g01560:85 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CC CT +chr1:2445130 [G/A] chr1 2445130 Cc01_g01560:178 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA +chr1:2445144 [G/C] chr1 2445144 Cc01_g01560:192 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC CC CC +chr1:2445153 [C/T] chr1 2445153 Cc01_g01560:201 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT CC TT +chr1:2445246 [G/A] chr1 2445246 Cc01_g01560:294 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GG AA +chr1:2445335 [G/T] chr1 2445335 Cc01_g01560:383 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 GG TT TT TT +chr1:2445435 [T/C] chr1 2445435 Cc01_g01560:483 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC CC CC +chr1:2445449 [C/G] chr1 2445449 Cc01_g01560:497 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 16.7% 3 CC CG CC NN +chr1:2445473 [A/G] chr1 2445473 Cc01_g01560:521 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 16.7% 3 AA AA AG NN +chr1:2445488 [G/A] chr1 2445488 Cc01_g01560:536 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 33.3% 3 GG GG AA NN +chr1:2445537 [A/T] chr1 2445537 Cc01_g01560:585 exon SYNONYMOUS_CODING atA/atT I/I 16.7% 3 AA AT AA NN +chr1:2445552 [C/G] chr1 2445552 Cc01_g01560:600 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC +chr1:2445610 [G/C] chr1 2445610 Cc01_g01560:658 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GC GG GG +chr1:2445684 [G/A] chr1 2445684 Cc01_g01560:732 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:2445697 [C/G] chr1 2445697 Cc01_g01560:745 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC CG CC GG +chr1:2445722 [T/G] chr1 2445722 Cc01_g01560:770 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 37.5% 4 TT TG TT GG +chr1:2445747 [A/T] chr1 2445747 Cc01_g01560:795 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA TA AA AA +chr1:2445750 [T/C] chr1 2445750 Cc01_g01560:798 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TT TT CC +chr1:2445796 [A/T] chr1 2445796 Cc01_g01560:844 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 AA AT AA TT +chr1:2445815 [A/G] chr1 2445815 Cc01_g01560:863 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA AG AA NN +chr1:2445816 [G/A] chr1 2445816 Cc01_g01560:864 exon SYNONYMOUS_CODING gaG/gaA E/E 16.7% 3 GG AG GG NN +chr1:2445827 [G/T] chr1 2445827 Cc01_g01560:875 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 16.7% 3 GG GT GG NN +chr1:2483851 [A/G] chr1 2483851 Cc01_g01570:110 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 AA GG NN NN +chr1:2483849 [A/G] chr1 2483849 Cc01_g01570:112 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 AA GG NN NN +chr1:2483845 [A/G] chr1 2483845 Cc01_g01570:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 2 AA GG NN NN +chr1:2524880 [C/T] chr1 2524880 Cc01_g01600:173 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 CC CT CC CC +chr1:2523795 [C/T] chr1 2523795 Cc01_g01600:1189 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC +chr1:2523742 [G/A] chr1 2523742 Cc01_g01600:1242 exon SYNONYMOUS_CODING ttC/ttT F/F 16.7% 3 GG NN GG GA +chr1:2522662 [T/C] chr1 2522662 Cc01_g01600:2133 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 TT TT CC TT +chr1:2522423 [T/A] chr1 2522423 Cc01_g01600:2279 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 TT TT TT TA +chr1:2522420 [A/G] chr1 2522420 Cc01_g01600:2282 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AG AA AA +chr1:2522274 [T/C] chr1 2522274 Cc01_g01600:2428 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 TT CC TT TC +chr1:2522265 [A/G] chr1 2522265 Cc01_g01600:2437 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 16.7% 3 AA NN AA GA +chr1:2522182 [G/C] chr1 2522182 Cc01_g01600:2439 exon SYNONYMOUS_CODING tcC/tcG S/S 33.3% 3 GG NN CC GG +chr1:2522124 [G/A] chr1 2522124 Cc01_g01600:2497 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA GG GG +chr1:2522105 [T/C] chr1 2522105 Cc01_g01600:2516 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC +chr1:2522103 [C/T] chr1 2522103 Cc01_g01600:2518 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC +chr1:2522070 [G/A] chr1 2522070 Cc01_g01600:2551 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG AA GG GG +chr1:2522006 [C/A] chr1 2522006 Cc01_g01600:2615 exon NON_SYNONYMOUS_CODING cGg/cTg R/L 12.5% 4 CC CC CC CA +chr1:2521969 [T/C] chr1 2521969 Cc01_g01600:2652 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TT TC +chr1:2521892 [T/C] chr1 2521892 Cc01_g01600:2729 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT +chr1:2521826 [G/A] chr1 2521826 Cc01_g01600:2795 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG GG AA GA +chr1:2521810 [G/C] chr1 2521810 Cc01_g01600:2811 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GG GC +chr1:2521773 [A/G] chr1 2521773 Cc01_g01600:2848 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA GG GG GG +chr1:2521725 [G/C] chr1 2521725 Cc01_g01600:2896 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 50.0% 4 GG CC GC GC +chr1:2521724 [T/A] chr1 2521724 Cc01_g01600:2897 exon NON_SYNONYMOUS_CODING cAg/cTg Q/L 12.5% 4 TT TA TT TT +chr1:2521694 [C/A] chr1 2521694 Cc01_g01600:2927 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 CC AC CC CC +chr1:2521672 [T/C] chr1 2521672 Cc01_g01600:2949 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT CT TT +chr1:2521665 [G/A] chr1 2521665 Cc01_g01600:2956 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 37.5% 4 GG GA GA GA +chr1:2521659 [T/C] chr1 2521659 Cc01_g01600:2962 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 TT TC TT TT +chr1:2521567 [C/T] chr1 2521567 Cc01_g01600:3054 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:2521560 [A/T] chr1 2521560 Cc01_g01600:3061 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT +chr1:2521545 [G/A] chr1 2521545 Cc01_g01600:3076 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GA GG GG +chr1:2521544 [C/G] chr1 2521544 Cc01_g01600:3077 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 12.5% 4 CC CC CG CC +chr1:2521538 [G/A] chr1 2521538 Cc01_g01600:3083 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GA GG +chr1:2521522 [G/A] chr1 2521522 Cc01_g01600:3099 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG AG GG +chr1:2521518 [G/A] chr1 2521518 Cc01_g01600:3103 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG AG GG +chr1:2521434 [C/T] chr1 2521434 Cc01_g01600:3187 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 12.5% 4 CC CC CC CT +chr1:2521424 [T/C] chr1 2521424 Cc01_g01600:3197 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:2521409 [A/C] chr1 2521409 Cc01_g01600:3212 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 37.5% 4 AA AA CC CA +chr1:2521377 [C/A] chr1 2521377 Cc01_g01600:3244 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 CC CA CC CA +chr1:2521375 [T/C] chr1 2521375 Cc01_g01600:3246 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT TC TT CT +chr1:2521230 [G/A] chr1 2521230 Cc01_g01600:3301 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA AA GG +chr1:2520587 [T/C] chr1 2520587 Cc01_g01600:3322 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 TT CC CC CC +chr1:2520583 [C/T] chr1 2520583 Cc01_g01600:3326 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CT CC CC +chr1:2520561 [A/G] chr1 2520561 Cc01_g01600:3348 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG +chr1:2520556 [G/T] chr1 2520556 Cc01_g01600:3353 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 25.0% 4 GG TT TT TT +chr1:2520547 [A/G] chr1 2520547 Cc01_g01600:3362 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG GG GG +chr1:2520537 [T/C] chr1 2520537 Cc01_g01600:3372 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC TC +chr1:2520525 [C/T] chr1 2520525 Cc01_g01600:3384 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CT CC +chr1:2520511 [A/G] chr1 2520511 Cc01_g01600:3398 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 AA GG GG GG +chr1:2526140 [A/T] chr1 2526140 Cc01_g01610:233 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 AA AA TT AA +chr1:2528701 [G/C] chr1 2528701 Cc01_g01610:265 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 33.3% 3 GG GG NN CC +chr1:2528783 [T/C] chr1 2528783 Cc01_g01610:347 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TT TT TC +chr1:2528803 [T/C] chr1 2528803 Cc01_g01610:367 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TT CC +chr1:2528813 [T/C] chr1 2528813 Cc01_g01610:377 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TC TT +chr1:2528941 [T/G] chr1 2528941 Cc01_g01610:433 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG +chr1:2528952 [C/G] chr1 2528952 Cc01_g01610:444 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC CG CC CG +chr1:2529568 [A/G] chr1 2529568 Cc01_g01610:557 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 2 AA NN NN GG +chr1:2530078 [A/G] chr1 2530078 Cc01_g01610:1067 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA AG AG AG +chr1:2551182 [G/A] chr1 2551182 Cc01_g01620:26 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG AA GG GG +chr1:2551151 [G/T] chr1 2551151 Cc01_g01620:57 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG TT NN GG +chr1:2551113 [C/T] chr1 2551113 Cc01_g01620:95 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CC CT +chr1:2551100 [G/A] chr1 2551100 Cc01_g01620:108 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 GG AA GG GG +chr1:2551069 [T/A] chr1 2551069 Cc01_g01620:139 exon NON_SYNONYMOUS_CODING Agc/Tgc S/C 25.0% 4 TT AA TT TT +chr1:2551068 [C/A] chr1 2551068 Cc01_g01620:140 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 25.0% 4 CC AA CC CC +chr1:2551000 [T/A] chr1 2551000 Cc01_g01620:208 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 12.5% 4 TT TT TT TA +chr1:2550995 [T/C] chr1 2550995 Cc01_g01620:213 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC +chr1:2550979 [G/A] chr1 2550979 Cc01_g01620:229 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:2550929 [G/C] chr1 2550929 Cc01_g01620:279 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GG CG +chr1:2550905 [G/A] chr1 2550905 Cc01_g01620:303 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG AA GG GA +chr1:2550878 [T/C] chr1 2550878 Cc01_g01620:330 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TT TT TC +chr1:2550853 [G/A] chr1 2550853 Cc01_g01620:355 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 GG AA NN AA +chr1:2550817 [C/T] chr1 2550817 Cc01_g01620:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT +chr1:2550788 [A/G] chr1 2550788 Cc01_g01620:420 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GG AA AG +chr1:2550718 [C/A] chr1 2550718 Cc01_g01620:490 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 33.3% 3 CC AA NN AA +chr1:2550703 [A/G] chr1 2550703 Cc01_g01620:505 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA AA NN GG +chr1:2550656 [A/C] chr1 2550656 Cc01_g01620:552 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 AA AC AA AA +chr1:2550608 [A/G] chr1 2550608 Cc01_g01620:600 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA GG NN AG +chr1:2550457 [A/C] chr1 2550457 Cc01_g01620:751 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 AA CC AA NN +chr1:2550455 [A/T] chr1 2550455 Cc01_g01620:753 exon STOP_GAINED tgT/tgA C/1 33.3% 3 AA TT AA NN +chr1:2550410 [G/A] chr1 2550410 Cc01_g01620:798 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 GG AA NN AA +chr1:2550352 [A/C] chr1 2550352 Cc01_g01620:856 exon STOP_LOST Taa/Gaa 2/E 33.3% 3 AA CC AA NN +chr1:2565722 [C/G] chr1 2565722 Cc01_g01630:400 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 CC CG CC CC +chr1:2565615 [C/T] chr1 2565615 Cc01_g01630:437 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC TC CC CC +chr1:2558672 [A/G] chr1 2558672 Cc01_g01630:759 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG +chr1:2558633 [T/C] chr1 2558633 Cc01_g01630:798 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC CT +chr1:2558434 [T/C] chr1 2558434 Cc01_g01630:859 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 37.5% 4 TT TC CT CT +chr1:2558347 [C/A] chr1 2558347 Cc01_g01630:946 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 12.5% 4 CC CA CC CC +chr1:2558280 [T/G] chr1 2558280 Cc01_g01630:1013 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TG TT TT +chr1:2558276 [G/A] chr1 2558276 Cc01_g01630:1017 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GA GG GG +chr1:2558203 [G/A] chr1 2558203 Cc01_g01630:1090 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG +chr1:2558132 [G/C] chr1 2558132 Cc01_g01630:1161 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG +chr1:2558129 [G/A] chr1 2558129 Cc01_g01630:1164 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:2558028 [G/A] chr1 2558028 Cc01_g01630:1265 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 12.5% 4 GG GA GG GG +chr1:2557954 [G/C] chr1 2557954 Cc01_g01630:1339 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 12.5% 4 GG GC GG GG +chr1:2557932 [A/T] chr1 2557932 Cc01_g01630:1361 exon NON_SYNONYMOUS_CODING aTa/aAa I/K 12.5% 4 AA AT AA AA +chr1:2557907 [G/A] chr1 2557907 Cc01_g01630:1386 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:2557619 [T/C] chr1 2557619 Cc01_g01630:1575 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TC TT TT +chr1:2557277 [T/C] chr1 2557277 Cc01_g01630:1917 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TC TT TT +chr1:2557173 [A/G] chr1 2557173 Cc01_g01630:2021 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AG AA AA +chr1:2557145 [T/C] chr1 2557145 Cc01_g01630:2049 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TC TT TT +chr1:2557074 [C/A] chr1 2557074 Cc01_g01630:2120 exon NON_SYNONYMOUS_CODING gGa/gTa G/V 12.5% 4 CC CA CC CC +chr1:2557055 [G/A] chr1 2557055 Cc01_g01630:2139 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GA GG GG +chr1:2557019 [T/C] chr1 2557019 Cc01_g01630:2175 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT +chr1:2557016 [A/G] chr1 2557016 Cc01_g01630:2178 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA +chr1:2610598 [G/T] chr1 2610598 Cc01_g01650:233 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GT GG GG +chr1:2611238 [T/C] chr1 2611238 Cc01_g01650:279 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT +chr1:2612873 [T/C] chr1 2612873 Cc01_g01650:375 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:2612964 [C/T] chr1 2612964 Cc01_g01650:466 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT +chr1:2613791 [G/C] chr1 2613791 Cc01_g01650:835 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GG GC +chr1:2613877 [G/A] chr1 2613877 Cc01_g01650:921 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA +chr1:2613943 [C/T] chr1 2613943 Cc01_g01650:987 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:2615356 [A/T] chr1 2615356 Cc01_g01650:1179 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 AA AA AT AA +chr1:2618568 [T/C] chr1 2618568 Cc01_g01650:1693 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT +chr1:2618665 [C/T] chr1 2618665 Cc01_g01650:1790 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:2618850 [C/T] chr1 2618850 Cc01_g01650:1886 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CC CT +chr1:2618880 [A/G] chr1 2618880 Cc01_g01650:1916 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AG AA +chr1:2619302 [A/G] chr1 2619302 Cc01_g01650:2224 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA +chr1:2619373 [C/T] chr1 2619373 Cc01_g01650:2295 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:2622083 [C/T] chr1 2622083 Cc01_g01650:2580 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CT CC CC +chr1:2622084 [A/C] chr1 2622084 Cc01_g01650:2581 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA +chr1:2622099 [C/G] chr1 2622099 Cc01_g01650:2596 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC GC CC CC +chr1:2623353 [A/C] chr1 2623353 Cc01_g01650:2974 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AA AA AC +chr1:2624213 [G/T] chr1 2624213 Cc01_g01650:3039 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 25.0% 4 GG GT GG TG +chr1:2624222 [T/A] chr1 2624222 Cc01_g01650:3048 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA TT AT +chr1:2624249 [T/C] chr1 2624249 Cc01_g01650:3075 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TC TT TT +chr1:2624263 [T/A] chr1 2624263 Cc01_g01650:3089 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT +chr1:2624270 [T/A] chr1 2624270 Cc01_g01650:3096 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 TT TA TT TT +chr1:2624289 [G/T] chr1 2624289 Cc01_g01650:3115 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG TG +chr1:2624433 [C/T] chr1 2624433 Cc01_g01650:3173 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC CT +chr1:2668103 [C/G] chr1 2668103 Cc01_g01670:315 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG GG GG +chr1:2668636 [A/G] chr1 2668636 Cc01_g01670:848 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 25.0% 4 AA AA AA GG +chr1:2668660 [G/A] chr1 2668660 Cc01_g01670:872 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG +chr1:2668692 [T/C] chr1 2668692 Cc01_g01670:904 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN TT +chr1:2668715 [T/G] chr1 2668715 Cc01_g01670:927 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT NN TT GG +chr1:2668739 [T/A] chr1 2668739 Cc01_g01670:951 exon SYNONYMOUS_CODING ccT/ccA P/P 50.0% 2 TT NN AA NN +chr1:2668764 [A/T] chr1 2668764 Cc01_g01670:976 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 AA NN TT NN +chr1:2668782 [C/T] chr1 2668782 Cc01_g01670:994 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC NN TT TT +chr1:2668811 [G/A] chr1 2668811 Cc01_g01670:1023 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA AA +chr1:2669258 [A/C] chr1 2669258 Cc01_g01670:1470 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA NN CC CC +chr1:2669279 [T/A] chr1 2669279 Cc01_g01670:1491 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 2 TT NN AA NN +chr1:2669349 [A/G] chr1 2669349 Cc01_g01670:1519 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN GG AA +chr1:2669357 [T/A] chr1 2669357 Cc01_g01670:1527 exon SYNONYMOUS_CODING cgT/cgA R/R 33.3% 3 TT NN AA AA +chr1:2669424 [A/G] chr1 2669424 Cc01_g01670:1594 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA NN GG GG +chr1:2669466 [G/T] chr1 2669466 Cc01_g01670:1636 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 33.3% 3 GG NN TT GG +chr1:2669497 [A/G] chr1 2669497 Cc01_g01670:1667 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 33.3% 3 AA NN GG AA +chr1:2669523 [T/C] chr1 2669523 Cc01_g01670:1693 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TC TT TT +chr1:2669527 [G/T] chr1 2669527 Cc01_g01670:1697 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG GG TT GG +chr1:2669572 [G/A] chr1 2669572 Cc01_g01670:1742 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG +chr1:2669581 [C/A] chr1 2669581 Cc01_g01670:1751 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CC AA CC +chr1:2669627 [T/C] chr1 2669627 Cc01_g01670:1797 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC CC CC +chr1:2669629 [A/G] chr1 2669629 Cc01_g01670:1799 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 50.0% 4 AA GG GG AA +chr1:2669742 [A/C] chr1 2669742 Cc01_g01670:1912 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 25.0% 4 AA CC CC CC +chr1:2669750 [T/C] chr1 2669750 Cc01_g01670:1920 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT CC TT TT +chr1:2669752 [A/T] chr1 2669752 Cc01_g01670:1922 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 25.0% 4 AA TT AA AA +chr1:2669754 [G/A] chr1 2669754 Cc01_g01670:1924 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA GG AA +chr1:2669766 [G/T] chr1 2669766 Cc01_g01670:1936 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 50.0% 4 GG GG TT TT +chr1:2669787 [A/G] chr1 2669787 Cc01_g01670:1957 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA GG AA AA +chr1:2669788 [T/C] chr1 2669788 Cc01_g01670:1958 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 TT CC CC CC +chr1:2669790 [C/A] chr1 2669790 Cc01_g01670:1960 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 33.3% 3 CC AA NN AA +chr1:2669868 [C/T] chr1 2669868 Cc01_g01670:2038 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 33.3% 3 CC TT NN CC +chr1:2670063 [C/T] chr1 2670063 Cc01_g01670:2233 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 33.3% 3 CC NN CC TT +chr1:2670072 [C/T] chr1 2670072 Cc01_g01670:2242 exon STOP_GAINED Cga/Tga R/8 25.0% 4 CC CC CC TT +chr1:2670078 [G/A] chr1 2670078 Cc01_g01670:2248 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG +chr1:2670084 [T/A] chr1 2670084 Cc01_g01670:2254 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 50.0% 4 TT AA AA TT +chr1:2670086 [A/G] chr1 2670086 Cc01_g01670:2256 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA GG GG NN +chr1:2672520 [A/G] chr1 2672520 Cc01_g01670:2295 exon SYNONYMOUS_CODING agA/agG R/R 33.3% 3 AA AA NN GG +chr1:2672522 [C/G] chr1 2672522 Cc01_g01670:2297 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 33.3% 3 CC CC NN GG +chr1:2672529 [A/T] chr1 2672529 Cc01_g01670:2304 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT +chr1:2672531 [T/C] chr1 2672531 Cc01_g01670:2306 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 33.3% 3 TT TT NN CC +chr1:2672554 [T/A] chr1 2672554 Cc01_g01670:2329 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 33.3% 3 TT TT NN AA +chr1:2672699 [C/T] chr1 2672699 Cc01_g01670:2474 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 25.0% 2 CC CT NN NN +chr1:2672995 [T/C] chr1 2672995 Cc01_g01670:2770 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT CC NN NN +chr1:2672999 [C/T] chr1 2672999 Cc01_g01670:2774 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 2 CC CT NN NN +chr1:2673033 [A/G] chr1 2673033 Cc01_g01670:2808 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG +chr1:2673073 [A/T] chr1 2673073 Cc01_g01670:2848 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 33.3% 3 AA TT TT NN +chr1:2673080 [T/C] chr1 2673080 Cc01_g01670:2855 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 TT CC TT NN +chr1:2673111 [G/T] chr1 2673111 Cc01_g01670:2886 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG TT GG +chr1:2673117 [A/T] chr1 2673117 Cc01_g01670:2892 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 AA AA AA TT +chr1:2673163 [T/G] chr1 2673163 Cc01_g01670:2938 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 25.0% 4 TT TT GG TT +chr1:2673186 [G/C] chr1 2673186 Cc01_g01670:2961 exon NON_SYNONYMOUS_CODING atG/atC M/I 33.3% 3 GG GG NN CC +chr1:2673191 [G/A] chr1 2673191 Cc01_g01670:2966 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 2 GG GA NN NN +chr1:2673238 [C/G] chr1 2673238 Cc01_g01670:3013 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 2 CC CG NN NN +chr1:2673525 [G/A] chr1 2673525 Cc01_g01670:3300 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA +chr1:2673526 [G/T] chr1 2673526 Cc01_g01670:3301 exon STOP_GAINED Gag/Tag E/1 25.0% 4 GG GT GG GT +chr1:2673538 [T/G] chr1 2673538 Cc01_g01670:3313 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GG TG +chr1:2673541 [C/T] chr1 2673541 Cc01_g01670:3316 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 25.0% 4 CC TC CC CT +chr1:2673542 [C/T] chr1 2673542 Cc01_g01670:3317 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 CC TC CC CT +chr1:2673543 [G/T] chr1 2673543 Cc01_g01670:3318 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG TG GG GT +chr1:2674163 [G/A] chr1 2674163 Cc01_g01670:3319 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 GG AG GA GA +chr1:2674174 [G/C] chr1 2674174 Cc01_g01670:3330 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 37.5% 4 GG CG GC GC +chr1:2674189 [A/C] chr1 2674189 Cc01_g01670:3345 exon SYNONYMOUS_CODING ggA/ggC G/G 25.0% 4 AA CA AA AC +chr1:2674276 [C/T] chr1 2674276 Cc01_g01680:15 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:2674294 [G/A] chr1 2674294 Cc01_g01680:33 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA AA AA +chr1:2674295 [C/G] chr1 2674295 Cc01_g01680:34 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 25.0% 4 CC GG GG GG +chr1:2674297 [G/T] chr1 2674297 Cc01_g01680:36 exon NON_SYNONYMOUS_CODING caG/caT Q/H 25.0% 4 GG GG GG TT +chr1:2674941 [A/G] chr1 2674941 Cc01_g01680:48 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA +chr1:2674945 [C/T] chr1 2674945 Cc01_g01680:52 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC TC CC +chr1:2674962 [G/A] chr1 2674962 Cc01_g01680:69 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG +chr1:2674964 [G/T] chr1 2674964 Cc01_g01680:71 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 37.5% 4 GG GT GG TT +chr1:2674973 [T/A] chr1 2674973 Cc01_g01680:80 exon STOP_GAINED tTg/tAg L/7 37.5% 4 TT TA AA AA +chr1:2674983 [G/T] chr1 2674983 Cc01_g01680:90 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 GG TT TT TT +chr1:2675001 [T/C] chr1 2675001 Cc01_g01680:108 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 2 TT TC NN NN +chr1:2675015 [T/A] chr1 2675015 Cc01_g01680:122 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 16.7% 3 TT TA NN TT +chr1:2675040 [T/A] chr1 2675040 Cc01_g01680:147 exon SYNONYMOUS_CODING ccT/ccA P/P 33.3% 3 TT AA NN AA +chr1:2675043 [C/T] chr1 2675043 Cc01_g01680:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT +chr1:2675048 [G/A] chr1 2675048 Cc01_g01680:155 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG AG NN GG +chr1:2675053 [A/T] chr1 2675053 Cc01_g01680:160 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 3 AA AT NN TT +chr1:2732265 [A/G] chr1 2732265 Cc01_g01700:720 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 2 AA NN NN AG +chr1:2836390 [A/T] chr1 2836390 Cc01_g01710:126 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA TT NN NN +chr1:2836415 [G/C] chr1 2836415 Cc01_g01710:151 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG GC NN NN +chr1:2836420 [G/C] chr1 2836420 Cc01_g01710:156 exon SYNONYMOUS_CODING gcG/gcC A/A 50.0% 2 GG CC NN NN +chr1:2836423 [C/T] chr1 2836423 Cc01_g01710:159 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 2 CC CT NN NN +chr1:2836441 [C/A] chr1 2836441 Cc01_g01710:177 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 CC AA CC NN +chr1:2836445 [G/A] chr1 2836445 Cc01_g01710:181 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN +chr1:2836460 [G/A] chr1 2836460 Cc01_g01710:196 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:2836484 [A/G] chr1 2836484 Cc01_g01710:220 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 16.7% 3 AA AG AA NN +chr1:2836488 [C/T] chr1 2836488 Cc01_g01710:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 CC CT CC NN +chr1:2836561 [A/G] chr1 2836561 Cc01_g01710:297 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 2 AA GG NN NN +chr1:2837031 [G/A] chr1 2837031 Cc01_g01720:58 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN +chr1:2837037 [A/G] chr1 2837037 Cc01_g01720:64 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA GG NN NN +chr1:2837164 [A/G] chr1 2837164 Cc01_g01720:191 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AA GG +chr1:2837166 [A/G] chr1 2837166 Cc01_g01720:193 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA GG AA AA +chr1:2837171 [A/G] chr1 2837171 Cc01_g01720:198 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG AA AA +chr1:2837187 [G/C] chr1 2837187 Cc01_g01720:214 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 50.0% 4 GG GG CC CC +chr1:2837200 [T/G] chr1 2837200 Cc01_g01720:227 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 37.5% 4 TT TT TG GG +chr1:2837207 [A/G] chr1 2837207 Cc01_g01720:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:2837244 [G/A] chr1 2837244 Cc01_g01720:271 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA +chr1:2837245 [A/G] chr1 2837245 Cc01_g01720:272 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 25.0% 4 AA GG GG GG +chr1:2837246 [T/C] chr1 2837246 Cc01_g01720:273 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TT CC TC +chr1:2837248 [G/A] chr1 2837248 Cc01_g01720:275 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 37.5% 4 GG GG AA GA +chr1:2837259 [T/C] chr1 2837259 Cc01_g01720:286 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 TT CC TT CT +chr1:2837266 [A/G] chr1 2837266 Cc01_g01720:293 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AA GA +chr1:2837271 [C/T] chr1 2837271 Cc01_g01720:298 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 CC CC TT CT +chr1:2837287 [G/T] chr1 2837287 Cc01_g01720:314 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 33.3% 3 GG TT NN GG +chr1:2837295 [T/C] chr1 2837295 Cc01_g01720:322 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN CC +chr1:2837310 [A/C] chr1 2837310 Cc01_g01720:337 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 50.0% 3 AA AC NN CC +chr1:2837316 [G/A] chr1 2837316 Cc01_g01720:343 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 50.0% 3 GG GA NN AA +chr1:2837318 [G/C] chr1 2837318 Cc01_g01720:345 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG GG NN CC +chr1:2837319 [G/C] chr1 2837319 Cc01_g01720:346 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG GG NN CC +chr1:2837348 [A/G] chr1 2837348 Cc01_g01720:375 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA AG NN AG +chr1:2837391 [G/A] chr1 2837391 Cc01_g01720:418 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 3 GG GA NN AA +chr1:2837393 [A/T] chr1 2837393 Cc01_g01720:420 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA TA NN AA +chr1:2837420 [C/T] chr1 2837420 Cc01_g01720:447 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT +chr1:2837423 [T/G] chr1 2837423 Cc01_g01720:450 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 TT GG NN GG +chr1:2837425 [T/G] chr1 2837425 Cc01_g01720:452 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 33.3% 3 TT GG NN GG +chr1:2837433 [A/G] chr1 2837433 Cc01_g01720:460 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 AA GG NN GG +chr1:2837480 [T/C] chr1 2837480 Cc01_g01720:507 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC +chr1:2837519 [G/A] chr1 2837519 Cc01_g01720:546 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG AA NN AA +chr1:2837526 [G/T] chr1 2837526 Cc01_g01720:553 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 33.3% 3 GG TT NN TT +chr1:2837537 [G/A] chr1 2837537 Cc01_g01720:564 exon SYNONYMOUS_CODING aaG/aaA K/K 33.3% 3 GG AA NN AA +chr1:2837615 [T/C] chr1 2837615 Cc01_g01720:642 exon SYNONYMOUS_CODING gcT/gcC A/A 50.0% 2 TT NN CC NN +chr1:2837629 [T/A] chr1 2837629 Cc01_g01720:656 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 50.0% 2 TT NN AA NN +chr1:2837640 [A/G] chr1 2837640 Cc01_g01720:667 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN GG NN +chr1:2901565 [C/A] chr1 2901565 Cc01_g01730:118 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CA CC CC +chr1:2901573 [A/T] chr1 2901573 Cc01_g01730:126 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA AT NN AA +chr1:2901666 [T/C] chr1 2901666 Cc01_g01730:219 exon SYNONYMOUS_CODING ttT/ttC F/F 16.7% 3 TT TC NN TT +chr1:2902604 [C/T] chr1 2902604 Cc01_g01730:618 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT +chr1:2902609 [A/G] chr1 2902609 Cc01_g01730:623 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 3 AA AG NN GG +chr1:2902632 [G/A] chr1 2902632 Cc01_g01730:646 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 33.3% 3 GG AA NN AA +chr1:2902646 [A/C] chr1 2902646 Cc01_g01730:660 exon NON_SYNONYMOUS_CODING caA/caC Q/H 33.3% 3 AA CC NN CC +chr1:2902650 [G/A] chr1 2902650 Cc01_g01730:664 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG AA NN AA +chr1:2902664 [T/C] chr1 2902664 Cc01_g01730:678 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC +chr1:2902673 [T/G] chr1 2902673 Cc01_g01730:687 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG NN GG +chr1:2902849 [T/G] chr1 2902849 Cc01_g01730:863 exon NON_SYNONYMOUS_CODING aTa/aGa I/R 25.0% 2 TT NN NN TG +chr1:2902856 [G/C] chr1 2902856 Cc01_g01730:870 exon SYNONYMOUS_CODING ggG/ggC G/G 50.0% 2 GG NN NN CC +chr1:2902865 [G/A] chr1 2902865 Cc01_g01730:879 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG GG NN AA +chr1:2902892 [A/G] chr1 2902892 Cc01_g01730:906 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 2 AA GG NN NN +chr1:2903083 [G/A] chr1 2903083 Cc01_g01730:1097 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG AA NN AA +chr1:2903094 [G/A] chr1 2903094 Cc01_g01730:1108 exon NON_SYNONYMOUS_CODING Gct/Act A/T 33.3% 3 GG AA NN AA +chr1:2903117 [A/G] chr1 2903117 Cc01_g01730:1131 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA AA GG AA +chr1:2903173 [T/G] chr1 2903173 Cc01_g01730:1187 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 TT GG GG GG +chr1:2903230 [C/G] chr1 2903230 Cc01_g01730:1244 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 16.7% 3 CC NN CC CG +chr1:2903240 [A/G] chr1 2903240 Cc01_g01730:1254 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:2903273 [A/G] chr1 2903273 Cc01_g01730:1287 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:2903283 [G/A] chr1 2903283 Cc01_g01730:1297 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG +chr1:2903292 [G/A] chr1 2903292 Cc01_g01730:1306 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG AG GG GG +chr1:2903341 [A/G] chr1 2903341 Cc01_g01730:1355 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA GG NN NN +chr1:2903558 [C/T] chr1 2903558 Cc01_g01730:1572 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN +chr1:2903571 [C/T] chr1 2903571 Cc01_g01730:1585 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC TT NN NN +chr1:2903610 [G/A] chr1 2903610 Cc01_g01730:1624 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG AA NN NN +chr1:2903621 [T/C] chr1 2903621 Cc01_g01730:1635 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 2 TT CC NN NN +chr1:2903627 [T/G] chr1 2903627 Cc01_g01730:1641 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG TT NN +chr1:2903770 [G/A] chr1 2903770 Cc01_g01730:1784 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 2 GG NN AA NN +chr1:2903814 [G/A] chr1 2903814 Cc01_g01730:1828 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG NN AA GG +chr1:2903816 [G/T] chr1 2903816 Cc01_g01730:1830 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 33.3% 3 GG NN GG TT +chr1:2903820 [G/T] chr1 2903820 Cc01_g01730:1834 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 33.3% 3 GG NN TT GG +chr1:2903823 [A/G] chr1 2903823 Cc01_g01730:1837 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN AA GG +chr1:2904055 [G/T] chr1 2904055 Cc01_g01730:1910 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN +chr1:2904064 [A/G] chr1 2904064 Cc01_g01730:1919 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 50.0% 2 AA GG NN NN +chr1:2904368 [T/C] chr1 2904368 Cc01_g01730:2163 exon SYNONYMOUS_CODING acT/acC T/T 50.0% 2 TT NN CC NN +chr1:2904423 [C/T] chr1 2904423 Cc01_g01730:2218 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 3 CC CT TT NN +chr1:2986926 [T/C] chr1 2986926 Cc01_g01750:549 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 2 TT CC NN NN +chr1:2986947 [A/C] chr1 2986947 Cc01_g01750:570 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 2 AA AC NN NN +chr1:2988225 [A/G] chr1 2988225 Cc01_g01750:1848 exon SYNONYMOUS_CODING cgA/cgG R/R 50.0% 2 AA GG NN NN +chr1:2988245 [A/G] chr1 2988245 Cc01_g01750:1868 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 2 AA GG NN NN +chr1:2989009 [G/A] chr1 2989009 Cc01_g01750:2542 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG AA NN NN +chr1:2989157 [G/T] chr1 2989157 Cc01_g01750:2690 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 50.0% 2 GG NN NN TT +chr1:2989172 [A/G] chr1 2989172 Cc01_g01750:2705 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG +chr1:2989569 [T/C] chr1 2989569 Cc01_g01750:3021 exon SYNONYMOUS_CODING taT/taC Y/Y 33.3% 3 TT NN CC CC +chr1:2989571 [T/G] chr1 2989571 Cc01_g01750:3023 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT GG GG GG +chr1:2989664 [A/G] chr1 2989664 Cc01_g01750:3116 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 33.3% 3 AA GG NN GG +chr1:2989678 [G/C] chr1 2989678 Cc01_g01750:3130 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC NN CC +chr1:2989702 [G/A] chr1 2989702 Cc01_g01750:3154 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GA NN GG +chr1:2989705 [A/G] chr1 2989705 Cc01_g01750:3157 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 AA GG GG AA +chr1:2989708 [G/A] chr1 2989708 Cc01_g01750:3160 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:2989742 [A/G] chr1 2989742 Cc01_g01750:3194 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA AG AG AG +chr1:2989743 [A/T] chr1 2989743 Cc01_g01750:3195 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA TA TA TA +chr1:2989751 [G/A] chr1 2989751 Cc01_g01750:3203 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 GG GG AG GG +chr1:2989752 [G/T] chr1 2989752 Cc01_g01750:3204 exon SYNONYMOUS_CODING cgG/cgT R/R 12.5% 4 GG GG TG GG +chr1:2989766 [G/A] chr1 2989766 Cc01_g01750:3218 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 4 GG AA GA AG +chr1:2989770 [A/G] chr1 2989770 Cc01_g01750:3222 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AA GA +chr1:2989771 [C/T] chr1 2989771 Cc01_g01750:3223 exon STOP_GAINED Cga/Tga R/5 12.5% 4 CC CC CT CC +chr1:2989797 [C/T] chr1 2989797 Cc01_g01750:3249 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT +chr1:2989804 [T/G] chr1 2989804 Cc01_g01750:3256 exon STOP_LOST Tag/Gag 1/E 50.0% 2 TT GG NN NN +chr1:2996368 [A/C] chr1 2996368 Cc01_g01760:9 exon SYNONYMOUS_CODING cgA/cgC R/R 33.3% 3 AA CC NN CC +chr1:2996399 [G/A] chr1 2996399 Cc01_g01760:40 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG GA NN GA +chr1:2996415 [G/A] chr1 2996415 Cc01_g01760:56 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG GG NN AG +chr1:2996419 [A/G] chr1 2996419 Cc01_g01760:60 exon SYNONYMOUS_CODING caA/caG Q/Q 16.7% 3 AA AA NN AG +chr1:2996421 [A/G] chr1 2996421 Cc01_g01760:62 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA GG NN GG +chr1:2996436 [G/T] chr1 2996436 Cc01_g01760:77 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG GG GG TT +chr1:2997079 [G/A] chr1 2997079 Cc01_g01760:118 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GA GG GA +chr1:2997084 [T/C] chr1 2997084 Cc01_g01760:123 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC TT CC +chr1:2997085 [A/C] chr1 2997085 Cc01_g01760:124 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 25.0% 4 AA AA CC AA +chr1:2997097 [G/C] chr1 2997097 Cc01_g01760:136 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG CG GG CG +chr1:2997102 [A/T] chr1 2997102 Cc01_g01760:141 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA AA AT +chr1:2997106 [A/G] chr1 2997106 Cc01_g01760:145 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:2997108 [T/C] chr1 2997108 Cc01_g01760:147 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 TT CC TT CC +chr1:2997111 [T/C] chr1 2997111 Cc01_g01760:150 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:2997112 [G/A] chr1 2997112 Cc01_g01760:151 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA +chr1:2997122 [T/A] chr1 2997122 Cc01_g01760:161 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT TA TT AT +chr1:2997125 [C/T] chr1 2997125 Cc01_g01760:164 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CT CC +chr1:2997133 [A/G] chr1 2997133 Cc01_g01760:172 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 AA AG GA AG +chr1:2997137 [G/A] chr1 2997137 Cc01_g01760:176 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:2997152 [T/C] chr1 2997152 Cc01_g01760:191 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT CT TT +chr1:2997154 [G/C] chr1 2997154 Cc01_g01760:193 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 GG CG GG GC +chr1:2997157 [A/G] chr1 2997157 Cc01_g01760:196 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 AA GA AA AG +chr1:2997163 [G/C] chr1 2997163 Cc01_g01760:202 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 GG CC CG GC +chr1:2997173 [C/T] chr1 2997173 Cc01_g01760:212 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC +chr1:2997174 [T/G] chr1 2997174 Cc01_g01760:213 exon SYNONYMOUS_CODING gcT/gcG A/A 12.5% 4 TT TT TG TT +chr1:2997191 [C/T] chr1 2997191 Cc01_g01760:230 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC TC +chr1:2997196 [T/C] chr1 2997196 Cc01_g01760:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC CT CT +chr1:2997204 [A/G] chr1 2997204 Cc01_g01760:243 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG GA AG +chr1:2997206 [G/A] chr1 2997206 Cc01_g01760:245 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA +chr1:2997213 [C/G] chr1 2997213 Cc01_g01760:252 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC GC CG +chr1:2997215 [C/T] chr1 2997215 Cc01_g01760:254 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC CT TC TC +chr1:2997227 [T/G] chr1 2997227 Cc01_g01760:266 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT TT TG GT +chr1:2997231 [C/T] chr1 2997231 Cc01_g01760:270 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 CC CT CC CC +chr1:2997233 [G/C] chr1 2997233 Cc01_g01760:272 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 25.0% 4 GG GG GC CG +chr1:2997243 [T/A] chr1 2997243 Cc01_g01760:282 exon SYNONYMOUS_CODING atT/atA I/I 25.0% 4 TT AA AA AA +chr1:2997247 [C/G] chr1 2997247 Cc01_g01760:286 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CG CC CC +chr1:2997250 [C/T] chr1 2997250 Cc01_g01760:289 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC +chr1:2997252 [T/C] chr1 2997252 Cc01_g01760:291 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC CT +chr1:2997275 [C/A] chr1 2997275 Cc01_g01760:314 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC +chr1:2997294 [G/T] chr1 2997294 Cc01_g01760:333 exon STOP_LOST taG/taT 1/Y 25.0% 4 GG GG GG TT +chr1:3052579 [G/A] chr1 3052579 Cc01_g01770:91 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 50.0% 2 GG NN NN AA +chr1:3052586 [C/T] chr1 3052586 Cc01_g01770:98 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT +chr1:3052603 [G/A] chr1 3052603 Cc01_g01770:115 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 2 GG NN NN AA +chr1:3052725 [G/A] chr1 3052725 Cc01_g01770:237 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GA GA +chr1:3052735 [C/A] chr1 3052735 Cc01_g01770:247 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 CC AA AA AA +chr1:3052737 [C/A] chr1 3052737 Cc01_g01770:249 exon NON_SYNONYMOUS_CODING caC/caA H/Q 12.5% 4 CC CC CC CA +chr1:3052781 [T/C] chr1 3052781 Cc01_g01770:293 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT +chr1:3052796 [G/A] chr1 3052796 Cc01_g01770:308 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 50.0% 2 GG NN AA NN +chr1:3052819 [G/A] chr1 3052819 Cc01_g01770:331 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GG GA NN +chr1:3052820 [C/A] chr1 3052820 Cc01_g01770:332 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 16.7% 3 CC CC CA NN +chr1:3052827 [T/C] chr1 3052827 Cc01_g01770:339 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC TT NN +chr1:3052878 [C/G] chr1 3052878 Cc01_g01770:390 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 33.3% 3 CC GG GG NN +chr1:3053184 [T/A] chr1 3053184 Cc01_g01770:696 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT NN TA TT +chr1:3053253 [T/C] chr1 3053253 Cc01_g01770:765 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC +chr1:3053284 [A/G] chr1 3053284 Cc01_g01770:796 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 4 AA AA GG GG +chr1:3053300 [A/G] chr1 3053300 Cc01_g01770:812 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 4 AA AA GG GG +chr1:3053448 [T/A] chr1 3053448 Cc01_g01770:886 exon NON_SYNONYMOUS_CODING Tct/Act S/T 50.0% 2 TT NN NN AA +chr1:3053505 [C/T] chr1 3053505 Cc01_g01770:943 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 CC TT TT NN +chr1:3053568 [T/C] chr1 3053568 Cc01_g01770:1006 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT +chr1:3053590 [A/C] chr1 3053590 Cc01_g01770:1028 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 50.0% 4 AA AC CA CC +chr1:3053591 [T/C] chr1 3053591 Cc01_g01770:1029 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT CT TT TT +chr1:3053592 [T/G] chr1 3053592 Cc01_g01770:1030 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GT GG +chr1:3053593 [A/G] chr1 3053593 Cc01_g01770:1031 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 4 AA AG GA GG +chr1:3053596 [A/C] chr1 3053596 Cc01_g01770:1034 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AC AA +chr1:3053597 [A/C] chr1 3053597 Cc01_g01770:1035 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 AA AA CA CC +chr1:3053608 [G/A] chr1 3053608 Cc01_g01770:1046 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:3053622 [A/C] chr1 3053622 Cc01_g01770:1060 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 16.7% 3 AA NN CA AA +chr1:3053627 [C/T] chr1 3053627 Cc01_g01770:1065 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC NN CC TT +chr1:3053887 [T/C] chr1 3053887 Cc01_g01770:1325 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 2 TT NN NN CC +chr1:3054011 [A/G] chr1 3054011 Cc01_g01770:1449 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AA AG NN +chr1:3054042 [G/A] chr1 3054042 Cc01_g01770:1480 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3054054 [G/T] chr1 3054054 Cc01_g01770:1492 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 GG TT GG GG +chr1:3054055 [T/A] chr1 3054055 Cc01_g01770:1493 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT TT TA AA +chr1:3054103 [C/T] chr1 3054103 Cc01_g01770:1541 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 4 CC CC TT CC +chr1:3054112 [T/G] chr1 3054112 Cc01_g01770:1550 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 33.3% 3 TT NN GG TT +chr1:3054118 [T/C] chr1 3054118 Cc01_g01770:1556 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 33.3% 3 TT NN CC TT +chr1:3054218 [G/T] chr1 3054218 Cc01_g01770:1605 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 GG NN NN TT +chr1:3054264 [C/T] chr1 3054264 Cc01_g01770:1651 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 2 CC TT NN NN +chr1:3054265 [G/A] chr1 3054265 Cc01_g01770:1652 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 50.0% 2 GG AA NN NN +chr1:3054271 [G/T] chr1 3054271 Cc01_g01770:1658 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN +chr1:3054274 [T/A] chr1 3054274 Cc01_g01770:1661 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 50.0% 2 TT AA NN NN +chr1:3054279 [G/A] chr1 3054279 Cc01_g01770:1666 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:3054354 [G/A] chr1 3054354 Cc01_g01770:1741 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GA GG +chr1:3054370 [A/G] chr1 3054370 Cc01_g01770:1757 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA GG AA NN +chr1:3054389 [G/A] chr1 3054389 Cc01_g01770:1776 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG AA GG NN +chr1:3054402 [C/G] chr1 3054402 Cc01_g01770:1789 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 33.3% 3 CC CC GG NN +chr1:3054406 [G/A] chr1 3054406 Cc01_g01770:1793 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 33.3% 3 GG GG AA NN +chr1:3054411 [T/G] chr1 3054411 Cc01_g01770:1798 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT TT GG NN +chr1:3054417 [A/T] chr1 3054417 Cc01_g01770:1804 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 33.3% 3 AA AA TT NN +chr1:3054423 [C/G] chr1 3054423 Cc01_g01770:1810 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 33.3% 3 CC CC NN GG +chr1:3054432 [A/T] chr1 3054432 Cc01_g01770:1819 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA AT NN AA +chr1:3054439 [A/G] chr1 3054439 Cc01_g01770:1826 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 AA AG NN AA +chr1:3054447 [A/T] chr1 3054447 Cc01_g01770:1834 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 33.3% 3 AA AA NN TT +chr1:3054480 [G/A] chr1 3054480 Cc01_g01770:1867 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 33.3% 3 GG AA NN GG +chr1:3054501 [C/T] chr1 3054501 Cc01_g01770:1888 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC TT NN CC +chr1:3054566 [C/G] chr1 3054566 Cc01_g01770:1953 exon SYNONYMOUS_CODING acC/acG T/T 33.3% 3 CC CC NN GG +chr1:3054570 [A/C] chr1 3054570 Cc01_g01770:1957 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 33.3% 3 AA AA NN CC +chr1:3054575 [G/C] chr1 3054575 Cc01_g01770:1962 exon NON_SYNONYMOUS_CODING agG/agC R/S 16.7% 3 GG GC NN GG +chr1:3054596 [A/G] chr1 3054596 Cc01_g01770:1983 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 3 AA AG NN GG +chr1:3054734 [C/G] chr1 3054734 Cc01_g01770:2121 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 CC CG CC CC +chr1:3054743 [A/G] chr1 3054743 Cc01_g01770:2130 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AG AA AA +chr1:3054746 [A/G] chr1 3054746 Cc01_g01770:2133 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA +chr1:3054764 [G/C] chr1 3054764 Cc01_g01770:2151 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 GG GG GG CC +chr1:3054783 [C/A] chr1 3054783 Cc01_g01770:2170 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CC CC AA +chr1:3054800 [A/T] chr1 3054800 Cc01_g01770:2187 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT +chr1:3054820 [A/G] chr1 3054820 Cc01_g01770:2207 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA +chr1:3054956 [A/C] chr1 3054956 Cc01_g01770:2238 exon SYNONYMOUS_CODING cgA/cgC R/R 50.0% 2 AA NN NN CC +chr1:3054966 [T/C] chr1 3054966 Cc01_g01770:2248 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN CC CC +chr1:3054968 [A/G] chr1 3054968 Cc01_g01770:2250 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA NN GG GG +chr1:3054987 [C/G] chr1 3054987 Cc01_g01770:2269 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 25.0% 4 CC CC CC GG +chr1:3055134 [T/C] chr1 3055134 Cc01_g01770:2416 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 TT TT CC TT +chr1:3055136 [C/T] chr1 3055136 Cc01_g01770:2418 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CT CC CC +chr1:3055137 [G/A] chr1 3055137 Cc01_g01770:2419 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3055144 [C/A] chr1 3055144 Cc01_g01770:2426 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 4 CC CC AA CC +chr1:3055154 [C/A] chr1 3055154 Cc01_g01770:2436 exon SYNONYMOUS_CODING cgC/cgA R/R 25.0% 4 CC CA CC CA +chr1:3055178 [A/G] chr1 3055178 Cc01_g01770:2460 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG GG AA +chr1:3055254 [T/G] chr1 3055254 Cc01_g01770:2470 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 25.0% 4 TT GT TG TT +chr1:3055255 [A/T] chr1 3055255 Cc01_g01770:2471 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 AA AT AA AA +chr1:3055257 [T/C] chr1 3055257 Cc01_g01770:2473 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TC TT +chr1:3055258 [T/C] chr1 3055258 Cc01_g01770:2474 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 25.0% 4 TT TC TC TT +chr1:3055259 [T/G] chr1 3055259 Cc01_g01770:2475 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 TT TT TG TT +chr1:3076176 [T/C] chr1 3076176 Cc01_g01770:2481 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT CT CC CC +chr1:3076177 [G/A] chr1 3076177 Cc01_g01770:2482 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG GA GG AA +chr1:3076201 [A/G] chr1 3076201 Cc01_g01770:2506 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA +chr1:3076211 [A/T] chr1 3076211 Cc01_g01770:2516 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA AT AA +chr1:3076217 [C/T] chr1 3076217 Cc01_g01770:2522 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC TC CT CT +chr1:3076219 [G/A] chr1 3076219 Cc01_g01770:2524 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG GA AG GG +chr1:3076221 [C/T] chr1 3076221 Cc01_g01770:2526 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 CC TT CT TT +chr1:3076224 [A/G] chr1 3076224 Cc01_g01770:2529 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG GA AA +chr1:3076239 [G/A] chr1 3076239 Cc01_g01770:2544 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GA GG GA +chr1:3076622 [T/G] chr1 3076622 Cc01_g01770:2572 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 12.5% 4 TT TT GT TT +chr1:3080563 [C/T] chr1 3080563 Cc01_g01780:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 CC TT NN NN +chr1:3080566 [T/A] chr1 3080566 Cc01_g01780:17 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 50.0% 2 TT AA NN NN +chr1:3080588 [T/C] chr1 3080588 Cc01_g01780:39 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT TT CC NN +chr1:3080607 [C/T] chr1 3080607 Cc01_g01780:58 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 37.5% 4 CC CT TT TT +chr1:3080619 [G/A] chr1 3080619 Cc01_g01780:70 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG GA AA AA +chr1:3080771 [T/C] chr1 3080771 Cc01_g01780:138 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TT CC +chr1:3080777 [A/G] chr1 3080777 Cc01_g01780:144 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:3080789 [T/C] chr1 3080789 Cc01_g01780:156 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TC TT TC +chr1:3080803 [T/A] chr1 3080803 Cc01_g01780:170 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 25.0% 4 TT TA TT TA +chr1:3080819 [C/A] chr1 3080819 Cc01_g01780:186 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CC CC AC +chr1:3080919 [C/A] chr1 3080919 Cc01_g01780:200 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA CC CC +chr1:3080921 [C/T] chr1 3080921 Cc01_g01780:202 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 37.5% 4 CC CC TT TC +chr1:3080927 [C/G] chr1 3080927 Cc01_g01780:208 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CC CG CG +chr1:3080944 [G/A] chr1 3080944 Cc01_g01780:225 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG AA AA GA +chr1:3080947 [A/G] chr1 3080947 Cc01_g01780:228 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA AA GG AG +chr1:3080956 [T/A] chr1 3080956 Cc01_g01780:237 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA +chr1:3081805 [A/T] chr1 3081805 Cc01_g01780:415 exon STOP_GAINED Aga/Tga R/9 50.0% 3 AA TT NN AT +chr1:3081884 [T/A] chr1 3081884 Cc01_g01780:494 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TA TA TT +chr1:3081885 [T/A] chr1 3081885 Cc01_g01780:495 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 37.5% 4 TT AT TT AA +chr1:3081886 [T/A] chr1 3081886 Cc01_g01780:496 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 TT TA TA TT +chr1:3081887 [T/A] chr1 3081887 Cc01_g01780:497 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TT TA +chr1:3081888 [T/A] chr1 3081888 Cc01_g01780:498 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 TT TA TT TT +chr1:3100066 [G/C] chr1 3100066 Cc01_g01790:442 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG GC GG CC +chr1:3100063 [C/T] chr1 3100063 Cc01_g01790:445 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC CT CC TT +chr1:3099861 [T/C] chr1 3099861 Cc01_g01790:647 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 TT TC TT NN +chr1:3099819 [A/G] chr1 3099819 Cc01_g01790:689 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 AA AG AA NN +chr1:3099817 [A/G] chr1 3099817 Cc01_g01790:691 exon SYNONYMOUS_CODING Tta/Cta L/L 16.7% 3 AA AG AA NN +chr1:3099361 [C/T] chr1 3099361 Cc01_g01790:921 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT +chr1:3099178 [C/T] chr1 3099178 Cc01_g01790:1104 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC +chr1:3098863 [C/T] chr1 3098863 Cc01_g01790:1419 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 CC NN TT NN +chr1:3098710 [T/G] chr1 3098710 Cc01_g01790:1572 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 33.3% 3 TT NN GG TT +chr1:3098694 [C/T] chr1 3098694 Cc01_g01790:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC TT CC +chr1:3098670 [C/T] chr1 3098670 Cc01_g01790:1612 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 25.0% 4 CC CC CC TT +chr1:3098669 [A/T] chr1 3098669 Cc01_g01790:1613 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 AA AA AA TT +chr1:3098646 [G/A] chr1 3098646 Cc01_g01790:1636 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 33.3% 3 GG NN GG AA +chr1:3098643 [C/T] chr1 3098643 Cc01_g01790:1639 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 CC NN TT CC +chr1:3098575 [T/A] chr1 3098575 Cc01_g01790:1707 exon SYNONYMOUS_CODING gtA/gtT V/V 33.3% 3 TT TT NN AA +chr1:3098545 [C/T] chr1 3098545 Cc01_g01790:1737 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 CC NN NN CT +chr1:3098445 [T/G] chr1 3098445 Cc01_g01790:1837 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 33.3% 3 TT GG TT NN +chr1:3098439 [A/C] chr1 3098439 Cc01_g01790:1843 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA AC AC NN +chr1:3098433 [C/T] chr1 3098433 Cc01_g01790:1849 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 CC CC TC NN +chr1:3098416 [A/G] chr1 3098416 Cc01_g01790:1866 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 AA AA GA NN +chr1:3098249 [T/G] chr1 3098249 Cc01_g01790:1982 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN GG NN +chr1:3098236 [T/G] chr1 3098236 Cc01_g01790:1995 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT TG TG TT +chr1:3098217 [T/C] chr1 3098217 Cc01_g01790:2014 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT TT TT CC +chr1:3098210 [C/A] chr1 3098210 Cc01_g01790:2021 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 CC AC AC CC +chr1:3098185 [G/T] chr1 3098185 Cc01_g01790:2046 exon SYNONYMOUS_CODING ccC/ccA P/P 25.0% 4 GG GG GG TT +chr1:3098182 [C/T] chr1 3098182 Cc01_g01790:2049 exon SYNONYMOUS_CODING caG/caA Q/Q 37.5% 4 CC CC TC TT +chr1:3098175 [C/T] chr1 3098175 Cc01_g01790:2056 exon NON_SYNONYMOUS_CODING Gct/Act A/T 25.0% 4 CC CC TC CT +chr1:3098148 [A/G] chr1 3098148 Cc01_g01790:2083 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 25.0% 4 AA GG GG GG +chr1:3098140 [C/G] chr1 3098140 Cc01_g01790:2091 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 CC CC GC CG +chr1:3098133 [C/A] chr1 3098133 Cc01_g01790:2098 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 37.5% 4 CC AA CA CC +chr1:3098100 [T/C] chr1 3098100 Cc01_g01790:2131 exon NON_SYNONYMOUS_CODING Act/Gct T/A 25.0% 4 TT TT TC TC +chr1:3098097 [C/T] chr1 3098097 Cc01_g01790:2134 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CC TC +chr1:3098083 [C/G] chr1 3098083 Cc01_g01790:2148 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CG CC +chr1:3098073 [G/C] chr1 3098073 Cc01_g01790:2158 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 GG CC CG GG +chr1:3098015 [T/C] chr1 3098015 Cc01_g01790:2216 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC +chr1:3097800 [C/T] chr1 3097800 Cc01_g01790:2431 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 50.0% 2 CC NN NN TT +chr1:3130398 [G/A] chr1 3130398 Cc01_g01800:5 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG GA GA GA +chr1:3130394 [G/A] chr1 3130394 Cc01_g01800:9 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG AG GG +chr1:3130389 [G/A] chr1 3130389 Cc01_g01800:14 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG +chr1:3130367 [A/G] chr1 3130367 Cc01_g01800:36 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA GA AG GA +chr1:3130332 [C/T] chr1 3130332 Cc01_g01800:71 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC CC TC CC +chr1:3130320 [A/G] chr1 3130320 Cc01_g01800:83 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA GA AA AA +chr1:3130313 [C/T] chr1 3130313 Cc01_g01800:90 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC TT TT TT +chr1:3130268 [G/C] chr1 3130268 Cc01_g01800:135 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG CC GC GG +chr1:3130244 [G/A] chr1 3130244 Cc01_g01800:159 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:3130238 [G/T] chr1 3130238 Cc01_g01800:165 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 GG TT GT GG +chr1:3130227 [T/C] chr1 3130227 Cc01_g01800:176 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 4 TT CC TC TC +chr1:3130205 [T/C] chr1 3130205 Cc01_g01800:198 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CC TC TT +chr1:3130073 [A/C] chr1 3130073 Cc01_g01800:276 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 AA CC CC NN +chr1:3130016 [G/T] chr1 3130016 Cc01_g01800:333 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 3 GG NN TT GT +chr1:3129989 [G/C] chr1 3129989 Cc01_g01800:360 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GC GG GG +chr1:3129968 [G/C] chr1 3129968 Cc01_g01800:381 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GC GG +chr1:3129955 [C/T] chr1 3129955 Cc01_g01800:394 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 37.5% 4 CC TT TC CC +chr1:3129939 [G/C] chr1 3129939 Cc01_g01800:410 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 GG GG GG GC +chr1:3129936 [G/A] chr1 3129936 Cc01_g01800:413 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GG GG GA +chr1:3129931 [T/G] chr1 3129931 Cc01_g01800:418 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG +chr1:3129930 [C/T] chr1 3129930 Cc01_g01800:419 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC CC TC +chr1:3129911 [A/G] chr1 3129911 Cc01_g01800:438 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AA GA +chr1:3129147 [T/C] chr1 3129147 Cc01_g01800:481 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 TT CC NN NN +chr1:3129110 [C/T] chr1 3129110 Cc01_g01800:518 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC TT NN NN +chr1:3129103 [G/A] chr1 3129103 Cc01_g01800:525 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 2 GG AA NN NN +chr1:3128596 [C/T] chr1 3128596 Cc01_g01800:1032 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC +chr1:3128592 [T/C] chr1 3128592 Cc01_g01800:1036 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 TT NN CC TT +chr1:3128555 [A/G] chr1 3128555 Cc01_g01800:1073 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 16.7% 3 AA NN AG AA +chr1:3128551 [T/C] chr1 3128551 Cc01_g01800:1077 exon SYNONYMOUS_CODING gcA/gcG A/A 16.7% 3 TT NN TC TT +chr1:3128512 [A/C] chr1 3128512 Cc01_g01800:1116 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 AA NN CC CC +chr1:3128013 [A/T] chr1 3128013 Cc01_g01800:1525 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN TT AA +chr1:3127995 [T/A] chr1 3127995 Cc01_g01800:1543 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 33.3% 3 TT NN TT AA +chr1:3127863 [C/T] chr1 3127863 Cc01_g01800:1675 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 CC NN TT CC +chr1:3127784 [G/T] chr1 3127784 Cc01_g01800:1754 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 33.3% 3 GG NN GG TT +chr1:3127444 [C/G] chr1 3127444 Cc01_g01800:2094 exon NON_SYNONYMOUS_CODING caG/caC Q/H 50.0% 2 CC NN NN GG +chr1:3127440 [C/A] chr1 3127440 Cc01_g01800:2098 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 33.3% 3 CC NN CC AA +chr1:3127337 [C/T] chr1 3127337 Cc01_g01800:2201 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 33.3% 3 CC TT CC NN +chr1:3127308 [G/A] chr1 3127308 Cc01_g01800:2230 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 GG GA AA NN +chr1:3127296 [T/C] chr1 3127296 Cc01_g01800:2242 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 33.3% 3 TT CC CC NN +chr1:3127276 [C/T] chr1 3127276 Cc01_g01800:2262 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC CC TT NN +chr1:3127267 [C/T] chr1 3127267 Cc01_g01800:2271 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 CC TT TT NN +chr1:3127260 [A/C] chr1 3127260 Cc01_g01800:2278 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA CC AA NN +chr1:3127254 [T/G] chr1 3127254 Cc01_g01800:2284 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 2 TT NN GG NN +chr1:3127253 [C/T] chr1 3127253 Cc01_g01800:2285 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 CC TT TT NN +chr1:3127252 [C/T] chr1 3127252 Cc01_g01800:2286 exon SYNONYMOUS_CODING agG/agA R/R 33.3% 3 CC TT TT NN +chr1:3127234 [G/A] chr1 3127234 Cc01_g01800:2304 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 2 GG NN GA NN +chr1:3127034 [G/A] chr1 3127034 Cc01_g01800:2411 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 GG AA NN NN +chr1:3127033 [T/A] chr1 3127033 Cc01_g01800:2412 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 TT AA NN NN +chr1:3126983 [A/G] chr1 3126983 Cc01_g01800:2462 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA AA AA GG +chr1:3126979 [A/G] chr1 3126979 Cc01_g01800:2466 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:3126953 [A/C] chr1 3126953 Cc01_g01800:2492 exon NON_SYNONYMOUS_CODING cTc/cGc L/R 33.3% 3 AA NN AA CC +chr1:3126937 [G/T] chr1 3126937 Cc01_g01800:2508 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG NN GG TT +chr1:3126913 [C/T] chr1 3126913 Cc01_g01800:2532 exon SYNONYMOUS_CODING tcG/tcA S/S 16.7% 3 CC NN CT CC +chr1:3126816 [G/A] chr1 3126816 Cc01_g01800:2569 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 33.3% 3 GG NN GG AA +chr1:3126795 [C/T] chr1 3126795 Cc01_g01800:2590 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC CC TT +chr1:3126780 [A/T] chr1 3126780 Cc01_g01800:2605 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 25.0% 4 AA AA AA TT +chr1:3126751 [G/A] chr1 3126751 Cc01_g01800:2634 exon SYNONYMOUS_CODING gaC/gaT D/D 33.3% 3 GG AA AA NN +chr1:3126700 [G/T] chr1 3126700 Cc01_g01800:2685 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT +chr1:3126699 [G/A] chr1 3126699 Cc01_g01800:2686 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 GG GA GG GA +chr1:3126690 [C/G] chr1 3126690 Cc01_g01800:2695 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 CC GG CC GG +chr1:3126637 [A/G] chr1 3126637 Cc01_g01800:2748 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG AA GG +chr1:3126626 [C/T] chr1 3126626 Cc01_g01800:2759 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 33.3% 3 CC TT CC NN +chr1:3126612 [G/A] chr1 3126612 Cc01_g01800:2773 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 GG AA GG NN +chr1:3126600 [A/T] chr1 3126600 Cc01_g01800:2785 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 33.3% 3 AA TT AA NN +chr1:3126553 [T/A] chr1 3126553 Cc01_g01800:2832 exon SYNONYMOUS_CODING ccA/ccT P/P 33.3% 3 TT TT AA NN +chr1:3126547 [G/T] chr1 3126547 Cc01_g01800:2838 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG GG TT NN +chr1:3126532 [T/A] chr1 3126532 Cc01_g01800:2853 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 33.3% 3 TT TT AA NN +chr1:3126528 [T/C] chr1 3126528 Cc01_g01800:2857 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT CC TT NN +chr1:3126526 [T/A] chr1 3126526 Cc01_g01800:2859 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 TT TT TT AA +chr1:3126503 [C/T] chr1 3126503 Cc01_g01800:2882 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CC CT CC +chr1:3126400 [T/C] chr1 3126400 Cc01_g01800:2985 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 TT CC TT NN +chr1:3126397 [C/T] chr1 3126397 Cc01_g01800:2988 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TT TT TT +chr1:3126364 [G/T] chr1 3126364 Cc01_g01800:3021 exon SYNONYMOUS_CODING cgC/cgA R/R 50.0% 4 GG TT GG TT +chr1:3126267 [A/G] chr1 3126267 Cc01_g01800:3118 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 33.3% 3 AA GG GG NN +chr1:3126189 [T/C] chr1 3126189 Cc01_g01800:3196 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 TT NN CC NN +chr1:3126120 [T/G] chr1 3126120 Cc01_g01800:3265 exon SYNONYMOUS_CODING Aga/Cga R/R 33.3% 3 TT GG GG NN +chr1:3148320 [G/C] chr1 3148320 Cc01_g01810:19 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 25.0% 4 GG CC CC CC +chr1:3148319 [T/G] chr1 3148319 Cc01_g01810:20 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TT TT TG +chr1:3148309 [A/T] chr1 3148309 Cc01_g01810:30 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT TT TT +chr1:3148308 [A/C] chr1 3148308 Cc01_g01810:31 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 AA CC CC CC +chr1:3148305 [G/A] chr1 3148305 Cc01_g01810:34 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG AA AA AA +chr1:3148268 [G/T] chr1 3148268 Cc01_g01810:71 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 GG GG GT GG +chr1:3148255 [A/T] chr1 3148255 Cc01_g01810:84 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AT AA +chr1:3148238 [A/G] chr1 3148238 Cc01_g01810:101 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 AA GG GA GG +chr1:3148222 [G/C] chr1 3148222 Cc01_g01810:117 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 12.5% 4 GG GG CG GG +chr1:3148212 [A/G] chr1 3148212 Cc01_g01810:127 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 12.5% 4 AA AG AA AA +chr1:3148211 [C/T] chr1 3148211 Cc01_g01810:128 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 37.5% 4 CC TT TC TT +chr1:3148184 [T/C] chr1 3148184 Cc01_g01810:155 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 TT CT TT TT +chr1:3148162 [G/A] chr1 3148162 Cc01_g01810:177 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 GG AG GG GG +chr1:3148147 [C/T] chr1 3148147 Cc01_g01810:192 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT +chr1:3148104 [T/C] chr1 3148104 Cc01_g01810:202 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TC TT +chr1:3148094 [G/T] chr1 3148094 Cc01_g01810:212 exon STOP_GAINED tCa/tAa S/1 12.5% 4 GG GG GG GT +chr1:3148091 [G/T] chr1 3148091 Cc01_g01810:215 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 GG GG GG GT +chr1:3191460 [A/G] chr1 3191460 Cc01_g01820:313 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG AA AA +chr1:3191468 [T/G] chr1 3191468 Cc01_g01820:321 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 TT TG TT TT +chr1:3191469 [G/A] chr1 3191469 Cc01_g01820:322 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG AA AA AA +chr1:3191497 [A/G] chr1 3191497 Cc01_g01820:350 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AA AA AG +chr1:3191499 [G/A] chr1 3191499 Cc01_g01820:352 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG GA +chr1:3191505 [C/G] chr1 3191505 Cc01_g01820:358 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC CC GG +chr1:3191507 [A/G] chr1 3191507 Cc01_g01820:360 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 AA GA AA GG +chr1:3191521 [C/A] chr1 3191521 Cc01_g01820:374 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CA CC +chr1:3191526 [G/T] chr1 3191526 Cc01_g01820:379 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GG GT GG +chr1:3191552 [T/C] chr1 3191552 Cc01_g01820:405 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC +chr1:3191561 [A/G] chr1 3191561 Cc01_g01820:414 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA GA +chr1:3191576 [T/C] chr1 3191576 Cc01_g01820:429 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TC TC +chr1:3191774 [T/C] chr1 3191774 Cc01_g01820:627 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT +chr1:3191801 [A/G] chr1 3191801 Cc01_g01820:654 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG +chr1:3191814 [A/G] chr1 3191814 Cc01_g01820:667 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG +chr1:3191835 [G/A] chr1 3191835 Cc01_g01820:688 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG AG +chr1:3191836 [G/A] chr1 3191836 Cc01_g01820:689 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GA GG +chr1:3191840 [A/G] chr1 3191840 Cc01_g01820:693 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:3191846 [A/C] chr1 3191846 Cc01_g01820:699 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 AA AA AC AA +chr1:3191856 [C/A] chr1 3191856 Cc01_g01820:709 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CA CC AC +chr1:3191872 [G/A] chr1 3191872 Cc01_g01820:725 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 GG GA GG AG +chr1:3191876 [A/C] chr1 3191876 Cc01_g01820:729 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA CA +chr1:3191881 [A/G] chr1 3191881 Cc01_g01820:734 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AG AG AA +chr1:3191888 [A/C] chr1 3191888 Cc01_g01820:741 exon NON_SYNONYMOUS_CODING caA/caC Q/H 12.5% 4 AA AA CA AA +chr1:3191897 [G/A] chr1 3191897 Cc01_g01820:750 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GG GA +chr1:3191902 [A/G] chr1 3191902 Cc01_g01820:755 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:3191903 [G/A] chr1 3191903 Cc01_g01820:756 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG GG GA +chr1:3191912 [T/A] chr1 3191912 Cc01_g01820:765 exon SYNONYMOUS_CODING ctT/ctA L/L 50.0% 4 TT TT AA AA +chr1:3192960 [A/G] chr1 3192960 Cc01_g01820:1688 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 2 AA NN GG NN +chr1:3192995 [G/T] chr1 3192995 Cc01_g01820:1723 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 25.0% 2 GG NN GT NN +chr1:3193034 [T/A] chr1 3193034 Cc01_g01820:1762 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 3 TT AA TA NN +chr1:3193036 [G/T] chr1 3193036 Cc01_g01820:1764 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 50.0% 3 GG TT GT NN +chr1:3193095 [A/G] chr1 3193095 Cc01_g01820:1823 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 2 AA NN NN AG +chr1:3193128 [G/A] chr1 3193128 Cc01_g01820:1856 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG AA GG NN +chr1:3193178 [T/C] chr1 3193178 Cc01_g01820:1906 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 TT CC TT NN +chr1:3193205 [G/A] chr1 3193205 Cc01_g01820:1933 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3193208 [C/G] chr1 3193208 Cc01_g01820:1936 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 33.3% 3 CC GG GG NN +chr1:3193232 [G/A] chr1 3193232 Cc01_g01820:1960 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3193249 [T/A] chr1 3193249 Cc01_g01820:1977 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 33.3% 3 TT AA TT NN +chr1:3193250 [A/G] chr1 3193250 Cc01_g01820:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 33.3% 3 AA GG AA NN +chr1:3193251 [G/A] chr1 3193251 Cc01_g01820:1979 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 GG AA GG NN +chr1:3193257 [A/T] chr1 3193257 Cc01_g01820:1985 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 33.3% 3 AA TT AA NN +chr1:3193258 [A/T] chr1 3193258 Cc01_g01820:1986 exon NON_SYNONYMOUS_CODING caA/caT Q/H 33.3% 3 AA TT AA NN +chr1:3193262 [G/A] chr1 3193262 Cc01_g01820:1990 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:3193330 [T/C] chr1 3193330 Cc01_g01820:2058 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 TT NN CC NN +chr1:3193551 [A/C] chr1 3193551 Cc01_g01820:2279 exon NON_SYNONYMOUS_CODING tAt/tCt Y/S 50.0% 4 AA CC AA CC +chr1:3193556 [A/G] chr1 3193556 Cc01_g01820:2284 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA AA AA GG +chr1:3193561 [T/C] chr1 3193561 Cc01_g01820:2289 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT TT TT CC +chr1:3193565 [C/A] chr1 3193565 Cc01_g01820:2293 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 CC AA CC CC +chr1:3193580 [A/T] chr1 3193580 Cc01_g01820:2308 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA AA AA TT +chr1:3193581 [C/T] chr1 3193581 Cc01_g01820:2309 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 CC CC CC TT +chr1:3193590 [G/A] chr1 3193590 Cc01_g01820:2318 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 GG AA GG GG +chr1:3193598 [G/A] chr1 3193598 Cc01_g01820:2326 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG AA GG GG +chr1:3193621 [A/G] chr1 3193621 Cc01_g01820:2349 exon SYNONYMOUS_CODING caA/caG Q/Q 33.3% 3 AA NN AA GG +chr1:3193623 [G/A] chr1 3193623 Cc01_g01820:2351 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA +chr1:3193638 [T/C] chr1 3193638 Cc01_g01820:2366 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 33.3% 3 TT NN TT CC +chr1:3193642 [G/T] chr1 3193642 Cc01_g01820:2370 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GT GG +chr1:3193647 [A/T] chr1 3193647 Cc01_g01820:2375 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 37.5% 4 AA TT AT AA +chr1:3193825 [G/T] chr1 3193825 Cc01_g01820:2553 exon SYNONYMOUS_CODING tcG/tcT S/S 16.7% 3 GG GG GT NN +chr1:3193843 [A/G] chr1 3193843 Cc01_g01820:2571 exon SYNONYMOUS_CODING gaA/gaG E/E 33.3% 3 AA GG AA NN +chr1:3193848 [A/G] chr1 3193848 Cc01_g01820:2576 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA AG AG NN +chr1:3193868 [G/A] chr1 3193868 Cc01_g01820:2596 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN +chr1:3193975 [T/C] chr1 3193975 Cc01_g01820:2703 exon SYNONYMOUS_CODING gcT/gcC A/A 33.3% 3 TT NN TT CC +chr1:3194001 [G/A] chr1 3194001 Cc01_g01820:2729 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG NN GG AA +chr1:3197392 [A/G] chr1 3197392 Cc01_g01830:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA +chr1:3197403 [C/T] chr1 3197403 Cc01_g01830:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT TT CC +chr1:3197417 [A/G] chr1 3197417 Cc01_g01830:153 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 AA AG GG AG +chr1:3197423 [A/G] chr1 3197423 Cc01_g01830:159 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AA AG +chr1:3197426 [A/G] chr1 3197426 Cc01_g01830:162 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG AA AG +chr1:3197433 [T/A] chr1 3197433 Cc01_g01830:169 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 50.0% 4 TT TA AA TA +chr1:3197457 [T/C] chr1 3197457 Cc01_g01830:193 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT CT TT CT +chr1:3197458 [C/T] chr1 3197458 Cc01_g01830:194 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:3197465 [T/G] chr1 3197465 Cc01_g01830:201 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 TT TT TG TG +chr1:3197474 [C/T] chr1 3197474 Cc01_g01830:210 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT TC CT +chr1:3197478 [T/C] chr1 3197478 Cc01_g01830:214 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 TT TT TC TT +chr1:3197482 [T/C] chr1 3197482 Cc01_g01830:218 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 37.5% 4 TT CT TC CT +chr1:3197490 [G/A] chr1 3197490 Cc01_g01830:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3197494 [T/C] chr1 3197494 Cc01_g01830:230 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 12.5% 4 TT CT TT TT +chr1:3197498 [C/T] chr1 3197498 Cc01_g01830:234 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC TC CC CC +chr1:3197500 [T/C] chr1 3197500 Cc01_g01830:236 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 TT CT TC TT +chr1:3197504 [C/T] chr1 3197504 Cc01_g01830:240 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC +chr1:3197513 [G/T] chr1 3197513 Cc01_g01830:249 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GG GT GG +chr1:3197514 [C/A] chr1 3197514 Cc01_g01830:250 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CA AC CC +chr1:3197516 [T/G] chr1 3197516 Cc01_g01830:252 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT GT TG TT +chr1:3197529 [G/A] chr1 3197529 Cc01_g01830:265 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 4 GG GA GA AA +chr1:3197531 [C/T] chr1 3197531 Cc01_g01830:267 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC CC CT +chr1:3197533 [A/T] chr1 3197533 Cc01_g01830:269 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA AT +chr1:3197544 [T/G] chr1 3197544 Cc01_g01830:280 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 12.5% 4 TT TT TT GT +chr1:3197558 [C/T] chr1 3197558 Cc01_g01830:294 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CT CC +chr1:3293623 [C/T] chr1 3293623 Cc01_g01840:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT +chr1:3293672 [A/C] chr1 3293672 Cc01_g01840:199 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AA AC AA +chr1:3293717 [G/A] chr1 3293717 Cc01_g01840:244 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3294121 [G/C] chr1 3294121 Cc01_g01840:555 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 25.0% 4 GG CC GG GG +chr1:3294122 [A/C] chr1 3294122 Cc01_g01840:556 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AA CC AA +chr1:3294138 [T/A] chr1 3294138 Cc01_g01840:572 exon NON_SYNONYMOUS_CODING cTc/cAc L/H 33.3% 3 TT TT AA NN +chr1:3294175 [A/G] chr1 3294175 Cc01_g01840:609 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA AA NN AG +chr1:3294278 [G/A] chr1 3294278 Cc01_g01840:655 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA NN AA +chr1:3294351 [C/T] chr1 3294351 Cc01_g01840:728 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 25.0% 4 CC CC TT CC +chr1:3294386 [A/G] chr1 3294386 Cc01_g01840:763 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 AA GG NN GG +chr1:3294489 [G/T] chr1 3294489 Cc01_g01840:866 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG TT TT TT +chr1:3294543 [C/T] chr1 3294543 Cc01_g01840:920 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CT CC CC +chr1:3295343 [G/C] chr1 3295343 Cc01_g01840:1501 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC GG NN +chr1:3295400 [G/A] chr1 3295400 Cc01_g01840:1558 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG GA GG AA +chr1:3295407 [C/A] chr1 3295407 Cc01_g01840:1565 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC CC AA CC +chr1:3295410 [T/A] chr1 3295410 Cc01_g01840:1568 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 25.0% 4 TT TT TT AA +chr1:3295411 [T/G] chr1 3295411 Cc01_g01840:1569 exon SYNONYMOUS_CODING gtT/gtG V/V 50.0% 4 TT GG TT GG +chr1:3295423 [G/T] chr1 3295423 Cc01_g01840:1581 exon SYNONYMOUS_CODING ccG/ccT P/P 12.5% 4 GG TG GG GG +chr1:3295466 [G/A] chr1 3295466 Cc01_g01840:1624 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA NN AA +chr1:3295709 [T/C] chr1 3295709 Cc01_g01840:1867 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 50.0% 2 TT NN NN CC +chr1:3295750 [A/G] chr1 3295750 Cc01_g01840:1908 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA NN NN GG +chr1:3295781 [G/A] chr1 3295781 Cc01_g01840:1939 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GG NN GA +chr1:3295793 [T/A] chr1 3295793 Cc01_g01840:1951 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 25.0% 4 TT TT TT AA +chr1:3295794 [G/A] chr1 3295794 Cc01_g01840:1952 exon STOP_GAINED tGg/tAg W/1 50.0% 4 GG AA GG AA +chr1:3295796 [T/G] chr1 3295796 Cc01_g01840:1954 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 TT TT NN GG +chr1:3295811 [C/G] chr1 3295811 Cc01_g01840:1969 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC CG CC GG +chr1:3295832 [G/C] chr1 3295832 Cc01_g01840:1990 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 50.0% 3 GG CC NN GC +chr1:3295834 [T/A] chr1 3295834 Cc01_g01840:1992 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 3 TT AA NN TA +chr1:3295846 [A/G] chr1 3295846 Cc01_g01840:2004 exon SYNONYMOUS_CODING acA/acG T/T 33.3% 3 AA AG NN GA +chr1:3295852 [T/C] chr1 3295852 Cc01_g01840:2010 exon SYNONYMOUS_CODING ccT/ccC P/P 33.3% 3 TT CC NN CC +chr1:3295877 [T/A] chr1 3295877 Cc01_g01840:2035 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 33.3% 3 TT TT AA NN +chr1:3295893 [G/A] chr1 3295893 Cc01_g01840:2051 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 33.3% 3 GG NN AA GG +chr1:3323377 [T/C] chr1 3323377 Cc01_g01850:669 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC +chr1:3323201 [C/T] chr1 3323201 Cc01_g01850:845 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 16.7% 3 CC CT NN CC +chr1:3337218 [C/A] chr1 3337218 Cc01_g01860:15 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 CC CA CC CC +chr1:3337216 [G/A] chr1 3337216 Cc01_g01860:17 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 GG GG GG GA +chr1:3337209 [G/C] chr1 3337209 Cc01_g01860:24 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG +chr1:3337191 [C/T] chr1 3337191 Cc01_g01860:42 exon SYNONYMOUS_CODING ctG/ctA L/L 37.5% 4 CC TT TC CC +chr1:3337176 [G/T] chr1 3337176 Cc01_g01860:57 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 4 GG TT TT GG +chr1:3337167 [C/T] chr1 3337167 Cc01_g01860:66 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 CC TT TC CC +chr1:3337129 [C/T] chr1 3337129 Cc01_g01860:104 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 CC TT TT TT +chr1:3336284 [G/A] chr1 3336284 Cc01_g01860:213 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GG GA GG +chr1:3336266 [G/A] chr1 3336266 Cc01_g01860:231 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 GG GA GA AA +chr1:3336239 [T/C] chr1 3336239 Cc01_g01860:258 exon SYNONYMOUS_CODING gaA/gaG E/E 50.0% 4 TT TC CC TC +chr1:3333450 [A/T] chr1 3333450 Cc01_g01860:400 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 AA AA AT AA +chr1:3333413 [G/C] chr1 3333413 Cc01_g01860:437 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GC GG GG +chr1:3333326 [G/A] chr1 3333326 Cc01_g01860:524 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 12.5% 4 GG GG GG GA +chr1:3333322 [T/C] chr1 3333322 Cc01_g01860:528 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TT TC TT +chr1:3333297 [C/T] chr1 3333297 Cc01_g01860:553 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC TC CC +chr1:3333229 [G/A] chr1 3333229 Cc01_g01860:621 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GG GA +chr1:3333223 [C/T] chr1 3333223 Cc01_g01860:627 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CT CC +chr1:3332599 [C/T] chr1 3332599 Cc01_g01860:669 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 CC CC CT CC +chr1:3332597 [C/G] chr1 3332597 Cc01_g01860:671 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 CC CC GC CC +chr1:3332395 [T/C] chr1 3332395 Cc01_g01860:775 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TC TT +chr1:3332371 [G/C] chr1 3332371 Cc01_g01860:799 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 GG GG CG GG +chr1:3332350 [T/C] chr1 3332350 Cc01_g01860:820 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC TT TT +chr1:3332348 [T/C] chr1 3332348 Cc01_g01860:822 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC CC TC +chr1:3332316 [A/G] chr1 3332316 Cc01_g01860:854 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 AA AG AA AA +chr1:3332250 [A/G] chr1 3332250 Cc01_g01860:920 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 12.5% 4 AA AA AA AG +chr1:3332219 [G/A] chr1 3332219 Cc01_g01860:951 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:3332209 [T/C] chr1 3332209 Cc01_g01860:961 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC CC TC +chr1:3338434 [G/T] chr1 3338434 Cc01_g01870:20 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 16.7% 3 GG GG GT NN +chr1:3338449 [A/G] chr1 3338449 Cc01_g01870:35 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 2 AA NN AG NN +chr1:3338455 [C/G] chr1 3338455 Cc01_g01870:41 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 50.0% 2 CC NN GG NN +chr1:3338489 [T/G] chr1 3338489 Cc01_g01870:75 exon SYNONYMOUS_CODING gcT/gcG A/A 16.7% 3 TT TT TG NN +chr1:3338523 [A/G] chr1 3338523 Cc01_g01870:109 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 2 AA NN AG NN +chr1:3338527 [C/G] chr1 3338527 Cc01_g01870:113 exon NON_SYNONYMOUS_CODING cCg/cGg P/R 25.0% 2 CC NN CG NN +chr1:3338584 [C/A] chr1 3338584 Cc01_g01870:170 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 25.0% 4 CC CC AA CC +chr1:3338618 [G/A] chr1 3338618 Cc01_g01870:204 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG GG AA GG +chr1:3338682 [A/G] chr1 3338682 Cc01_g01870:268 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA +chr1:3340569 [G/C] chr1 3340569 Cc01_g01870:341 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GC GG +chr1:3340586 [C/A] chr1 3340586 Cc01_g01870:358 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CA CA CC +chr1:3340636 [A/T] chr1 3340636 Cc01_g01870:408 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AT AT AA +chr1:3341154 [G/A] chr1 3341154 Cc01_g01870:609 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA GG GG +chr1:3341373 [A/G] chr1 3341373 Cc01_g01870:828 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AG AG AA +chr1:3341763 [C/A] chr1 3341763 Cc01_g01870:1039 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC CA CA CC +chr1:3341885 [T/G] chr1 3341885 Cc01_g01870:1161 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT GG TT +chr1:3341925 [G/T] chr1 3341925 Cc01_g01870:1201 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 25.0% 4 GG GG TT GG +chr1:3341957 [C/T] chr1 3341957 Cc01_g01870:1233 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CT CC +chr1:3342026 [A/G] chr1 3342026 Cc01_g01870:1302 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AA GG AA +chr1:3342047 [T/C] chr1 3342047 Cc01_g01870:1323 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:3342053 [G/A] chr1 3342053 Cc01_g01870:1329 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG GG AA GG +chr1:3342122 [T/G] chr1 3342122 Cc01_g01870:1398 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TG TG TT +chr1:3342260 [C/G] chr1 3342260 Cc01_g01870:1441 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:3342603 [G/A] chr1 3342603 Cc01_g01870:1728 exon SYNONYMOUS_CODING aaG/aaA K/K 16.7% 3 GG GG GA NN +chr1:3342762 [T/C] chr1 3342762 Cc01_g01870:1887 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 TT TC TC TT +chr1:3342780 [C/T] chr1 3342780 Cc01_g01870:1905 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC TC CC +chr1:3342870 [C/T] chr1 3342870 Cc01_g01870:1995 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CT CT CC +chr1:3342879 [T/C] chr1 3342879 Cc01_g01870:2004 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TC TT +chr1:3342996 [C/T] chr1 3342996 Cc01_g01870:2121 exon SYNONYMOUS_CODING gtC/gtT V/V 33.3% 3 CC CT CT NN +chr1:3342999 [A/T] chr1 3342999 Cc01_g01870:2124 exon SYNONYMOUS_CODING gcA/gcT A/A 33.3% 3 AA AT AT NN +chr1:3343053 [T/A] chr1 3343053 Cc01_g01870:2178 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 TT TT TA NN +chr1:3343056 [T/C] chr1 3343056 Cc01_g01870:2181 exon SYNONYMOUS_CODING gcT/gcC A/A 16.7% 3 TT TT TC NN +chr1:3343080 [C/T] chr1 3343080 Cc01_g01870:2205 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 CC NN CT CC +chr1:3343146 [T/C] chr1 3343146 Cc01_g01870:2271 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TC TT +chr1:3343149 [C/T] chr1 3343149 Cc01_g01870:2274 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC NN CT CC +chr1:3343251 [C/T] chr1 3343251 Cc01_g01870:2376 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC +chr1:3343348 [G/A] chr1 3343348 Cc01_g01870:2473 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GG AA GG +chr1:3343425 [A/T] chr1 3343425 Cc01_g01870:2550 exon SYNONYMOUS_CODING acA/acT T/T 16.7% 3 AA NN AT AA +chr1:3343449 [A/G] chr1 3343449 Cc01_g01870:2574 exon SYNONYMOUS_CODING tcA/tcG S/S 16.7% 3 AA NN AG AA +chr1:3343557 [G/A] chr1 3343557 Cc01_g01870:2682 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 2 GG NN GA NN +chr1:3343584 [G/C] chr1 3343584 Cc01_g01870:2709 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 12.5% 4 GG GG GC GG +chr1:3343605 [T/C] chr1 3343605 Cc01_g01870:2730 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3343713 [G/A] chr1 3343713 Cc01_g01870:2838 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GA GG +chr1:3343793 [A/G] chr1 3343793 Cc01_g01870:2918 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA NN GG AA +chr1:3343946 [T/A] chr1 3343946 Cc01_g01870:3071 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TA TT +chr1:3343980 [T/A] chr1 3343980 Cc01_g01870:3105 exon SYNONYMOUS_CODING ctT/ctA L/L 12.5% 4 TT TT TA TT +chr1:3344061 [T/C] chr1 3344061 Cc01_g01870:3186 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:3344094 [C/G] chr1 3344094 Cc01_g01870:3219 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC +chr1:3344225 [A/C] chr1 3344225 Cc01_g01870:3350 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 25.0% 4 AA AC AC AA +chr1:3344291 [A/G] chr1 3344291 Cc01_g01870:3416 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AG AA +chr1:3344304 [A/G] chr1 3344304 Cc01_g01870:3429 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AG AG AA +chr1:3344335 [A/T] chr1 3344335 Cc01_g01870:3460 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AA AT AA +chr1:3344340 [A/G] chr1 3344340 Cc01_g01870:3465 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AG AA +chr1:3344367 [G/A] chr1 3344367 Cc01_g01870:3492 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GA GG +chr1:3344610 [A/G] chr1 3344610 Cc01_g01870:3646 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AG AA +chr1:3344615 [C/T] chr1 3344615 Cc01_g01870:3651 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CT CT CC +chr1:3344705 [T/C] chr1 3344705 Cc01_g01870:3741 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC CC TT +chr1:3344765 [C/T] chr1 3344765 Cc01_g01870:3801 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC CT CT CC +chr1:3344998 [C/G] chr1 3344998 Cc01_g01870:3928 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC GG CC +chr1:3345023 [C/G] chr1 3345023 Cc01_g01870:3953 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC +chr1:3345239 [G/A] chr1 3345239 Cc01_g01870:4077 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 GG GA AA GG +chr1:3345251 [G/A] chr1 3345251 Cc01_g01870:4089 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG +chr1:3345257 [A/G] chr1 3345257 Cc01_g01870:4095 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AG AA +chr1:3345539 [A/G] chr1 3345539 Cc01_g01870:4290 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA GG AA +chr1:3346036 [G/A] chr1 3346036 Cc01_g01870:4488 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG +chr1:3346713 [T/C] chr1 3346713 Cc01_g01870:4716 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TC TC TT +chr1:3346848 [C/T] chr1 3346848 Cc01_g01870:4851 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CT CT CC +chr1:3346851 [T/G] chr1 3346851 Cc01_g01870:4854 exon SYNONYMOUS_CODING cgT/cgG R/R 12.5% 4 TT TT TG TT +chr1:3346917 [G/A] chr1 3346917 Cc01_g01870:4920 exon SYNONYMOUS_CODING gaG/gaA E/E 33.3% 3 GG GA GA NN +chr1:3346920 [T/G] chr1 3346920 Cc01_g01870:4923 exon SYNONYMOUS_CODING ctT/ctG L/L 16.7% 3 TT TT GT NN +chr1:3347106 [T/C] chr1 3347106 Cc01_g01870:5109 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TC TC TT +chr1:3347181 [C/A] chr1 3347181 Cc01_g01870:5184 exon SYNONYMOUS_CODING acC/acA T/T 25.0% 4 CC CA CA CC +chr1:3347198 [T/C] chr1 3347198 Cc01_g01870:5201 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:3347363 [C/T] chr1 3347363 Cc01_g01870:5280 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CT CT CC +chr1:3347553 [A/G] chr1 3347553 Cc01_g01870:5361 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AA AG AA +chr1:3347739 [C/T] chr1 3347739 Cc01_g01870:5547 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CT CC +chr1:3347754 [A/G] chr1 3347754 Cc01_g01870:5562 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AG AA +chr1:3347884 [T/C] chr1 3347884 Cc01_g01870:5616 exon SYNONYMOUS_CODING cgT/cgC R/R 12.5% 4 TT TT TC TT +chr1:3347890 [A/C] chr1 3347890 Cc01_g01870:5622 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 AA AA AC AA +chr1:3348120 [T/A] chr1 3348120 Cc01_g01870:5852 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 25.0% 4 TT AA AA AA +chr1:3348121 [C/A] chr1 3348121 Cc01_g01870:5853 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA AA AA +chr1:3348167 [A/G] chr1 3348167 Cc01_g01870:5899 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AA AG AA +chr1:3348225 [A/G] chr1 3348225 Cc01_g01870:5957 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA +chr1:3348593 [G/A] chr1 3348593 Cc01_g01870:6109 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GG GA +chr1:3348598 [C/T] chr1 3348598 Cc01_g01870:6114 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:3348607 [G/A] chr1 3348607 Cc01_g01870:6123 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GA GG +chr1:3348689 [G/T] chr1 3348689 Cc01_g01870:6205 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG +chr1:3348691 [T/C] chr1 3348691 Cc01_g01870:6207 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT +chr1:3348799 [C/T] chr1 3348799 Cc01_g01870:6219 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC CT CT CC +chr1:3348886 [T/C] chr1 3348886 Cc01_g01870:6306 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3348950 [T/C] chr1 3348950 Cc01_g01870:6370 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TT TC TT +chr1:3349098 [C/A] chr1 3349098 Cc01_g01870:6441 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CC CA CC +chr1:3349159 [A/T] chr1 3349159 Cc01_g01870:6502 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AT AA +chr1:3349258 [T/C] chr1 3349258 Cc01_g01870:6601 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT +chr1:3349275 [T/C] chr1 3349275 Cc01_g01870:6618 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TT TC TT +chr1:3349309 [A/G] chr1 3349309 Cc01_g01870:6652 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 AA AA AA GG +chr1:3349550 [A/G] chr1 3349550 Cc01_g01870:6731 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:3349635 [A/G] chr1 3349635 Cc01_g01870:6816 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG GG AA +chr1:3349684 [A/C] chr1 3349684 Cc01_g01870:6865 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 AA AC AC AA +chr1:3349692 [T/C] chr1 3349692 Cc01_g01870:6873 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3349701 [G/A] chr1 3349701 Cc01_g01870:6882 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 GG GG GA GA +chr1:3349725 [T/C] chr1 3349725 Cc01_g01870:6906 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT +chr1:3349872 [T/A] chr1 3349872 Cc01_g01870:6942 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT TA TA TT +chr1:3349938 [A/G] chr1 3349938 Cc01_g01870:7008 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AA AG AA +chr1:3349953 [T/G] chr1 3349953 Cc01_g01870:7023 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TT TG TT +chr1:3349955 [A/G] chr1 3349955 Cc01_g01870:7025 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AG AA +chr1:3349959 [C/G] chr1 3349959 Cc01_g01870:7029 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 CC GG GG GG +chr1:3349968 [T/C] chr1 3349968 Cc01_g01870:7038 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC TT TT +chr1:3350026 [A/G] chr1 3350026 Cc01_g01870:7096 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 AA AG GG AA +chr1:3350040 [C/T] chr1 3350040 Cc01_g01870:7110 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CT CC CC +chr1:3362501 [A/T] chr1 3362501 Cc01_g01900:15 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 AA NN TT TT +chr1:3362493 [G/C] chr1 3362493 Cc01_g01900:23 exon STOP_GAINED tCa/tGa S8* 25.0% 4 GG CC CC CC +chr1:3362488 [C/T] chr1 3362488 Cc01_g01900:28 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC TT TT TT +chr1:3362464 [C/G] chr1 3362464 Cc01_g01900:52 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 25.0% 4 CC GG GG GG +chr1:3362461 [C/G] chr1 3362461 Cc01_g01900:55 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG GG GG +chr1:3362423 [T/G] chr1 3362423 Cc01_g01900:93 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 50.0% 4 TT TT GG GG +chr1:3383330 [A/T] chr1 3383330 Cc01_g01910:149 exon NON_SYNONYMOUS_CODING aTc/aAc I/N 50.0% 2 AA TT NN NN +chr1:3383254 [C/T] chr1 3383254 Cc01_g01910:225 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT +chr1:3383250 [A/C] chr1 3383250 Cc01_g01910:229 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 50.0% 2 AA NN NN CC +chr1:3383240 [T/G] chr1 3383240 Cc01_g01910:239 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN NN GG +chr1:3543339 [T/C] chr1 3543339 Cc01_g01950:133 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 37.5% 4 TT CC TT TC +chr1:3543344 [T/C] chr1 3543344 Cc01_g01950:138 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TC TT TT +chr1:3543798 [C/T] chr1 3543798 Cc01_g01950:592 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CT CC CC +chr1:3544052 [T/C] chr1 3544052 Cc01_g01950:846 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TC TT TT +chr1:3563539 [T/A] chr1 3563539 Cc01_g01960:208 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 TT AA TT NN +chr1:3563667 [G/A] chr1 3563667 Cc01_g01960:336 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 GG GG NN GA +chr1:3563754 [G/C] chr1 3563754 Cc01_g01960:423 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GG GC +chr1:3563771 [A/G] chr1 3563771 Cc01_g01960:440 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 AA GG AG AG +chr1:3563793 [T/C] chr1 3563793 Cc01_g01960:462 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT +chr1:3574473 [G/C] chr1 3574473 Cc01_g01970:51 exon SYNONYMOUS_CODING gcC/gcG A/A 33.3% 3 GG NN CC GG +chr1:3574458 [A/G] chr1 3574458 Cc01_g01970:66 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 AA NN AA GG +chr1:3574326 [A/T] chr1 3574326 Cc01_g01970:198 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 33.3% 3 AA NN TT TT +chr1:3574296 [A/G] chr1 3574296 Cc01_g01970:228 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AA GG +chr1:3574115 [T/C] chr1 3574115 Cc01_g01970:409 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT NN CC CC +chr1:3574063 [G/A] chr1 3574063 Cc01_g01970:461 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG GG AA GG +chr1:3574027 [A/T] chr1 3574027 Cc01_g01970:497 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT +chr1:3573800 [C/T] chr1 3573800 Cc01_g01970:724 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC TT TT TT +chr1:3573759 [A/G] chr1 3573759 Cc01_g01970:765 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 AA NN AA GG +chr1:3573736 [C/T] chr1 3573736 Cc01_g01970:788 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 50.0% 4 CC TT CC TT +chr1:3573699 [G/C] chr1 3573699 Cc01_g01970:825 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG GG CC GG +chr1:3573693 [A/G] chr1 3573693 Cc01_g01970:831 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA GG AA GG +chr1:3573559 [A/T] chr1 3573559 Cc01_g01970:965 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT +chr1:3573509 [A/T] chr1 3573509 Cc01_g01970:1015 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN AA TT +chr1:3573370 [C/T] chr1 3573370 Cc01_g01970:1053 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 CC NN CC TT +chr1:3573336 [C/A] chr1 3573336 Cc01_g01970:1087 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 CC AA CC AA +chr1:3573271 [C/G] chr1 3573271 Cc01_g01970:1152 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 CC NN GG CC +chr1:3573239 [G/C] chr1 3573239 Cc01_g01970:1184 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 GG NN CC CC +chr1:3573098 [G/T] chr1 3573098 Cc01_g01970:1251 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT +chr1:3573097 [T/G] chr1 3573097 Cc01_g01970:1252 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 50.0% 4 TT GG TT GG +chr1:3572965 [G/A] chr1 3572965 Cc01_g01970:1384 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 33.3% 3 GG NN AA AA +chr1:3572931 [A/G] chr1 3572931 Cc01_g01970:1418 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 AA NN GG GG +chr1:3572899 [T/C] chr1 3572899 Cc01_g01970:1450 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT CC CC CC +chr1:3572885 [C/G] chr1 3572885 Cc01_g01970:1464 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC GG GG GG +chr1:3572859 [C/T] chr1 3572859 Cc01_g01970:1490 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT +chr1:3572854 [G/T] chr1 3572854 Cc01_g01970:1495 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG TT TT TT +chr1:3572835 [T/A] chr1 3572835 Cc01_g01970:1514 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT AA TT +chr1:3649364 [A/T] chr1 3649364 Cc01_g01980:156 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AA AA AT +chr1:3649391 [C/T] chr1 3649391 Cc01_g01980:183 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC CT +chr1:3649422 [C/G] chr1 3649422 Cc01_g01980:214 exon NON_SYNONYMOUS_CODING Cgc/Ggc R/G 25.0% 4 CC GG CC CC +chr1:3649490 [G/A] chr1 3649490 Cc01_g01980:282 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG +chr1:3649502 [T/C] chr1 3649502 Cc01_g01980:294 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC CC +chr1:3649727 [T/C] chr1 3649727 Cc01_g01980:519 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT +chr1:3649746 [G/T] chr1 3649746 Cc01_g01980:538 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT TT TT +chr1:3661555 [G/C] chr1 3661555 Cc01_g01990:23 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 33.3% 3 GG CC GG NN +chr1:3661523 [T/C] chr1 3661523 Cc01_g01990:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 TT CC CC NN +chr1:3661511 [C/G] chr1 3661511 Cc01_g01990:67 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 33.3% 3 CC GG NN CC +chr1:3661507 [A/C] chr1 3661507 Cc01_g01990:71 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 33.3% 3 AA CC NN AA +chr1:3661453 [T/C] chr1 3661453 Cc01_g01990:125 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT +chr1:3661403 [A/T] chr1 3661403 Cc01_g01990:175 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 AA TT AA NN +chr1:3661345 [G/T] chr1 3661345 Cc01_g01990:233 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 GG GG NN TT +chr1:3661344 [A/G] chr1 3661344 Cc01_g01990:234 exon SYNONYMOUS_CODING tcT/tcC S/S 16.7% 3 AA AG NN AA +chr1:3660894 [T/C] chr1 3660894 Cc01_g01990:273 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 TT CC NN TT +chr1:3660770 [C/T] chr1 3660770 Cc01_g01990:319 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 33.3% 3 CC NN TT CC +chr1:3660756 [A/C] chr1 3660756 Cc01_g01990:333 exon NON_SYNONYMOUS_CODING caT/caG H/Q 25.0% 4 AA CC AA AA +chr1:3660584 [T/C] chr1 3660584 Cc01_g01990:379 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TT TT CC +chr1:3660566 [G/A] chr1 3660566 Cc01_g01990:397 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA AA GG +chr1:3660548 [C/T] chr1 3660548 Cc01_g01990:415 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC CT TT CC +chr1:3660530 [C/T] chr1 3660530 Cc01_g01990:433 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 CC TT TT TT +chr1:3660529 [C/A] chr1 3660529 Cc01_g01990:434 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 50.0% 4 CC AA AA CC +chr1:3660523 [C/T] chr1 3660523 Cc01_g01990:440 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 50.0% 4 CC TT TT CC +chr1:3660509 [T/C] chr1 3660509 Cc01_g01990:454 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 TT CC TT TT +chr1:3660489 [T/G] chr1 3660489 Cc01_g01990:474 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 4 TT GG GG TT +chr1:3660392 [T/G] chr1 3660392 Cc01_g01990:571 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT GG GG GG +chr1:3660382 [T/A] chr1 3660382 Cc01_g01990:581 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 TT AA TT TT +chr1:3660368 [T/C] chr1 3660368 Cc01_g01990:595 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 TT CC CC CC +chr1:3663378 [T/A] chr1 3663378 Cc01_g02000:123 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT +chr1:3663363 [C/T] chr1 3663363 Cc01_g02000:138 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC +chr1:3663324 [G/A] chr1 3663324 Cc01_g02000:177 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG AG GG GG +chr1:3663323 [C/T] chr1 3663323 Cc01_g02000:178 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC CT CC +chr1:3663308 [A/T] chr1 3663308 Cc01_g02000:193 exon STOP_LOST Tag/Aag 6/K 37.5% 4 AA TT AT AA +chr1:3704574 [A/T] chr1 3704574 Cc01_g02010:179 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 AA TT TT TT +chr1:3704558 [T/A] chr1 3704558 Cc01_g02010:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT +chr1:3704537 [A/G] chr1 3704537 Cc01_g02010:216 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AG AA +chr1:3704524 [A/T] chr1 3704524 Cc01_g02010:229 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT +chr1:3704520 [G/C] chr1 3704520 Cc01_g02010:233 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG +chr1:3704494 [C/T] chr1 3704494 Cc01_g02010:259 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 25.0% 4 CC TT TT TT +chr1:3702641 [A/T] chr1 3702641 Cc01_g02010:350 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 AA AT AA AA +chr1:3702616 [T/A] chr1 3702616 Cc01_g02010:375 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TA TT TT +chr1:3702601 [T/C] chr1 3702601 Cc01_g02010:390 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:3702599 [T/A] chr1 3702599 Cc01_g02010:392 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 TT TT TT AT +chr1:3702582 [C/T] chr1 3702582 Cc01_g02010:409 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC +chr1:3702367 [T/C] chr1 3702367 Cc01_g02010:534 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT TT CC +chr1:3702346 [A/T] chr1 3702346 Cc01_g02010:555 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 AA AA AT AA +chr1:3702331 [G/A] chr1 3702331 Cc01_g02010:570 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA AA GG +chr1:3702283 [G/A] chr1 3702283 Cc01_g02010:618 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG AA AA AA +chr1:3702270 [A/G] chr1 3702270 Cc01_g02010:631 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA AG AA AA +chr1:3702235 [A/G] chr1 3702235 Cc01_g02010:666 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA GA AA AA +chr1:3702233 [T/C] chr1 3702233 Cc01_g02010:668 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT TC CC TT +chr1:3702222 [T/G] chr1 3702222 Cc01_g02010:679 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG +chr1:3702218 [T/C] chr1 3702218 Cc01_g02010:683 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TT CT +chr1:3701396 [C/T] chr1 3701396 Cc01_g02010:708 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT +chr1:3701386 [A/G] chr1 3701386 Cc01_g02010:718 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA AA AA GG +chr1:3701243 [T/C] chr1 3701243 Cc01_g02010:861 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT +chr1:3701240 [G/A] chr1 3701240 Cc01_g02010:864 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GG AA +chr1:3701237 [C/T] chr1 3701237 Cc01_g02010:867 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:3700510 [C/T] chr1 3700510 Cc01_g02010:931 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 16.7% 3 CC CC CT NN +chr1:3699429 [C/T] chr1 3699429 Cc01_g02010:1020 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC CC CC TT +chr1:3699397 [G/C] chr1 3699397 Cc01_g02010:1052 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 16.7% 3 GG GG GC NN +chr1:3699002 [C/A] chr1 3699002 Cc01_g02010:1192 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 CC CA CC AA +chr1:3698979 [A/G] chr1 3698979 Cc01_g02010:1215 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG +chr1:3698964 [T/C] chr1 3698964 Cc01_g02010:1230 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 TT TT TC TT +chr1:3698934 [C/T] chr1 3698934 Cc01_g02010:1260 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC CT CT TT +chr1:3698922 [C/T] chr1 3698922 Cc01_g02010:1272 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC CC CC TT +chr1:3698901 [C/T] chr1 3698901 Cc01_g02010:1293 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC CC CT TT +chr1:3698886 [A/G] chr1 3698886 Cc01_g02010:1308 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 AA AA AG AA +chr1:3698880 [T/C] chr1 3698880 Cc01_g02010:1314 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:3698871 [T/A] chr1 3698871 Cc01_g02010:1323 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 TT TT TT AA +chr1:3698841 [T/A] chr1 3698841 Cc01_g02010:1353 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 TT AA AA AA +chr1:3698450 [C/T] chr1 3698450 Cc01_g02010:1477 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CT CC +chr1:3698412 [G/A] chr1 3698412 Cc01_g02010:1515 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GG GG AA +chr1:3698398 [T/A] chr1 3698398 Cc01_g02010:1529 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 12.5% 4 TT TA TT TT +chr1:3698247 [A/G] chr1 3698247 Cc01_g02010:1680 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 AA AA AA GG +chr1:3697989 [T/C] chr1 3697989 Cc01_g02010:1692 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT +chr1:3696904 [A/T] chr1 3696904 Cc01_g02010:1866 exon NON_SYNONYMOUS_CODING caT/caA H/Q 50.0% 2 AA NN TT NN +chr1:3696445 [A/G] chr1 3696445 Cc01_g02010:1945 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 AA AA AA GG +chr1:3696441 [C/T] chr1 3696441 Cc01_g02010:1949 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT +chr1:3696389 [C/T] chr1 3696389 Cc01_g02010:2001 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 CC CC CT TT +chr1:3696380 [C/T] chr1 3696380 Cc01_g02010:2010 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT +chr1:3696362 [T/C] chr1 3696362 Cc01_g02010:2028 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TT TT CC +chr1:3696314 [T/G] chr1 3696314 Cc01_g02010:2076 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 TT TT TT GG +chr1:3696312 [C/G] chr1 3696312 Cc01_g02010:2078 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG CG CC +chr1:3695395 [A/G] chr1 3695395 Cc01_g02010:2114 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:3695358 [T/C] chr1 3695358 Cc01_g02010:2151 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT CT +chr1:3695350 [T/C] chr1 3695350 Cc01_g02010:2159 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 TT CC CC TT +chr1:3695299 [G/A] chr1 3695299 Cc01_g02010:2210 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG GG GG AA +chr1:3725796 [T/C] chr1 3725796 Cc01_g02020:642 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 TT NN TT TC +chr1:3725964 [A/G] chr1 3725964 Cc01_g02020:810 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA NN GG GG +chr1:3727454 [C/T] chr1 3727454 Cc01_g02020:1724 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT +chr1:3727458 [A/T] chr1 3727458 Cc01_g02020:1728 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 2 AA NN NN TT +chr1:3727501 [G/A] chr1 3727501 Cc01_g02020:1771 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AA AA GA +chr1:3727517 [T/C] chr1 3727517 Cc01_g02020:1787 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TT TC +chr1:3727787 [T/A] chr1 3727787 Cc01_g02020:2057 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN AA TT +chr1:3727789 [A/G] chr1 3727789 Cc01_g02020:2059 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 AA NN NN GG +chr1:3727802 [T/G] chr1 3727802 Cc01_g02020:2072 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 50.0% 2 TT NN NN GG +chr1:3727809 [C/T] chr1 3727809 Cc01_g02020:2079 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 2 CC NN NN TT +chr1:3727827 [T/C] chr1 3727827 Cc01_g02020:2097 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT NN NN CC +chr1:3727876 [T/G] chr1 3727876 Cc01_g02020:2146 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG +chr1:3727959 [G/A] chr1 3727959 Cc01_g02020:2229 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 2 GG NN NN GA +chr1:3727969 [T/C] chr1 3727969 Cc01_g02020:2239 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 33.3% 3 TT TT NN CC +chr1:3728011 [C/T] chr1 3728011 Cc01_g02020:2281 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 2 CC NN NN CT +chr1:3728022 [C/T] chr1 3728022 Cc01_g02020:2292 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 2 CC NN NN CT +chr1:3728064 [G/A] chr1 3728064 Cc01_g02020:2334 exon SYNONYMOUS_CODING gcG/gcA A/A 50.0% 2 GG NN NN AA +chr1:3728080 [T/A] chr1 3728080 Cc01_g02020:2350 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 50.0% 2 TT NN NN AA +chr1:3740570 [G/A] chr1 3740570 Cc01_g02030:19 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA AA NN +chr1:3740594 [G/A] chr1 3740594 Cc01_g02030:43 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA GG NN +chr1:3740608 [G/T] chr1 3740608 Cc01_g02030:57 exon SYNONYMOUS_CODING tcG/tcT S/S 50.0% 2 GG TT NN NN +chr1:3740686 [G/A] chr1 3740686 Cc01_g02030:135 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA GG GG +chr1:3740718 [C/T] chr1 3740718 Cc01_g02030:167 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:3740764 [C/T] chr1 3740764 Cc01_g02030:213 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC NN TT CC +chr1:3740817 [C/A] chr1 3740817 Cc01_g02030:266 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC NN AA CC +chr1:3750735 [C/T] chr1 3750735 Cc01_g02040:6 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CT CC CT +chr1:3750711 [C/G] chr1 3750711 Cc01_g02040:30 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CG CC CC +chr1:3750587 [C/T] chr1 3750587 Cc01_g02040:154 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 CC CC CC CT +chr1:3750577 [C/T] chr1 3750577 Cc01_g02040:164 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CT CC CC +chr1:3750569 [T/C] chr1 3750569 Cc01_g02040:172 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TT TC +chr1:3750546 [T/A] chr1 3750546 Cc01_g02040:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT +chr1:3750522 [A/G] chr1 3750522 Cc01_g02040:219 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 4 AA AA GG GG +chr1:3750505 [G/C] chr1 3750505 Cc01_g02040:236 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG +chr1:3748656 [T/C] chr1 3748656 Cc01_g02040:302 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC +chr1:3748610 [C/T] chr1 3748610 Cc01_g02040:348 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CC CC CT +chr1:3748546 [C/T] chr1 3748546 Cc01_g02040:412 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC +chr1:3748306 [A/G] chr1 3748306 Cc01_g02040:562 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AA AA AG +chr1:3748282 [C/T] chr1 3748282 Cc01_g02040:586 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT TT TT +chr1:3748213 [T/C] chr1 3748213 Cc01_g02040:655 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT TT TT CC +chr1:3748170 [A/C] chr1 3748170 Cc01_g02040:698 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 12.5% 4 AA AA AA AC +chr1:3747303 [G/A] chr1 3747303 Cc01_g02040:777 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG +chr1:3747255 [G/A] chr1 3747255 Cc01_g02040:825 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG AA AA AA +chr1:3747226 [T/G] chr1 3747226 Cc01_g02040:854 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG +chr1:3745743 [G/A] chr1 3745743 Cc01_g02040:1024 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 4 GG GG AA AA +chr1:3745742 [C/T] chr1 3745742 Cc01_g02040:1025 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC TT CC CC +chr1:3745322 [A/T] chr1 3745322 Cc01_g02040:1191 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:3745225 [G/T] chr1 3745225 Cc01_g02040:1288 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT +chr1:3745223 [G/A] chr1 3745223 Cc01_g02040:1290 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG AG +chr1:3745208 [T/C] chr1 3745208 Cc01_g02040:1305 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC TT CC +chr1:3745196 [T/C] chr1 3745196 Cc01_g02040:1317 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 TT TT TC CT +chr1:3745187 [T/A] chr1 3745187 Cc01_g02040:1326 exon SYNONYMOUS_CODING ctA/ctT L/L 12.5% 4 TT TT TT TA +chr1:3745165 [G/A] chr1 3745165 Cc01_g02040:1348 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG AG +chr1:3745164 [C/T] chr1 3745164 Cc01_g02040:1349 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 CC CC CT CC +chr1:3744647 [G/C] chr1 3744647 Cc01_g02040:1598 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC +chr1:3744596 [C/T] chr1 3744596 Cc01_g02040:1649 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CC CT +chr1:3744575 [T/C] chr1 3744575 Cc01_g02040:1670 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT +chr1:3744299 [T/A] chr1 3744299 Cc01_g02040:1698 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TA TT +chr1:3742967 [T/C] chr1 3742967 Cc01_g02040:1935 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TC TT +chr1:3742922 [G/A] chr1 3742922 Cc01_g02040:1980 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG AA GG GA +chr1:3742793 [C/T] chr1 3742793 Cc01_g02040:2109 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC +chr1:3741865 [T/G] chr1 3741865 Cc01_g02040:2131 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TG TT TT +chr1:3741857 [A/G] chr1 3741857 Cc01_g02040:2139 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 AA AA AA AG +chr1:3741842 [T/C] chr1 3741842 Cc01_g02040:2154 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC +chr1:3741793 [C/T] chr1 3741793 Cc01_g02040:2203 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:3759622 [T/A] chr1 3759622 Cc01_g02050:54 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT TT TA TA +chr1:3762484 [A/G] chr1 3762484 Cc01_g02050:82 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 AA AA AA AG +chr1:3762723 [A/G] chr1 3762723 Cc01_g02050:202 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AA AG +chr1:3762755 [A/G] chr1 3762755 Cc01_g02050:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG GG GG +chr1:3762781 [A/C] chr1 3762781 Cc01_g02050:260 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA +chr1:3762848 [G/A] chr1 3762848 Cc01_g02050:327 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA +chr1:3763034 [A/G] chr1 3763034 Cc01_g02050:411 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:3763038 [C/A] chr1 3763038 Cc01_g02050:415 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC AA CC CC +chr1:3763049 [G/A] chr1 3763049 Cc01_g02050:426 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG AA GG GG +chr1:3763055 [A/T] chr1 3763055 Cc01_g02050:432 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT +chr1:3763064 [A/G] chr1 3763064 Cc01_g02050:441 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA GG AA AA +chr1:3763079 [G/A] chr1 3763079 Cc01_g02050:456 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GG AA GA +chr1:3766634 [T/G] chr1 3766634 Cc01_g02060:471 exon SYNONYMOUS_CODING ccT/ccG P/P 33.3% 3 TT GG NN TT +chr1:3766695 [T/C] chr1 3766695 Cc01_g02060:532 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN TT CC +chr1:3920385 [G/T] chr1 3920385 Cc01_g02110:211 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 GG NN TT NN +chr1:3920402 [T/C] chr1 3920402 Cc01_g02110:228 exon SYNONYMOUS_CODING tcT/tcC S/S 50.0% 2 TT NN CC NN +chr1:3923592 [A/T] chr1 3923592 Cc01_g02120:176 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AA AA AT +chr1:3923713 [C/T] chr1 3923713 Cc01_g02120:207 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC +chr1:3923759 [C/T] chr1 3923759 Cc01_g02120:253 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC +chr1:3923905 [C/T] chr1 3923905 Cc01_g02120:399 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT CT CT +chr1:3923938 [T/A] chr1 3923938 Cc01_g02120:432 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 TT TA TT TT +chr1:3923947 [C/T] chr1 3923947 Cc01_g02120:441 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC TT CT CT +chr1:3924037 [G/A] chr1 3924037 Cc01_g02120:531 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:3924086 [C/T] chr1 3924086 Cc01_g02120:580 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CT CC CC +chr1:3924307 [T/C] chr1 3924307 Cc01_g02120:801 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:3924337 [G/A] chr1 3924337 Cc01_g02120:831 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA AA AA +chr1:3924341 [C/G] chr1 3924341 Cc01_g02120:835 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:3924368 [C/A] chr1 3924368 Cc01_g02120:862 exon NON_SYNONYMOUS_CODING Cct/Act P/T 12.5% 4 CC AC CC CC +chr1:3924378 [A/G] chr1 3924378 Cc01_g02120:872 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA +chr1:3924397 [G/A] chr1 3924397 Cc01_g02120:891 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG +chr1:3924554 [A/C] chr1 3924554 Cc01_g02120:1048 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA +chr1:3924566 [T/C] chr1 3924566 Cc01_g02120:1060 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TT TT TC +chr1:3924571 [C/A] chr1 3924571 Cc01_g02120:1065 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC +chr1:3924632 [G/T] chr1 3924632 Cc01_g02120:1126 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG TG GG GG +chr1:3924644 [G/A] chr1 3924644 Cc01_g02120:1138 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG +chr1:3924648 [A/C] chr1 3924648 Cc01_g02120:1142 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA +chr1:3924703 [A/G] chr1 3924703 Cc01_g02120:1197 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:3924857 [G/C] chr1 3924857 Cc01_g02120:1351 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GC GG GG +chr1:3924860 [G/A] chr1 3924860 Cc01_g02120:1354 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG +chr1:3924877 [A/C] chr1 3924877 Cc01_g02120:1371 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 AA CA AA AA +chr1:3925027 [T/C] chr1 3925027 Cc01_g02120:1521 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:3925086 [C/T] chr1 3925086 Cc01_g02120:1580 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 CC TC CC CC +chr1:3925308 [G/A] chr1 3925308 Cc01_g02120:1650 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GA GA GA +chr1:3925317 [T/C] chr1 3925317 Cc01_g02120:1659 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TC TC TC +chr1:3925320 [G/T] chr1 3925320 Cc01_g02120:1662 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 37.5% 4 GG GT GT GT +chr1:3925346 [A/G] chr1 3925346 Cc01_g02120:1688 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AG AA AG +chr1:3930848 [G/T] chr1 3930848 Cc01_g02130:14 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 GG GT GG GG +chr1:3930877 [G/T] chr1 3930877 Cc01_g02130:43 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 12.5% 4 GG GG GG GT +chr1:3930883 [G/T] chr1 3930883 Cc01_g02130:49 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 50.0% 4 GG TT GT GT +chr1:3930897 [T/A] chr1 3930897 Cc01_g02130:63 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT +chr1:3931056 [C/T] chr1 3931056 Cc01_g02130:222 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CT CT CC +chr1:3931087 [C/A] chr1 3931087 Cc01_g02130:253 exon SYNONYMOUS_CODING Cga/Aga R/R 37.5% 4 CC AA CA CC +chr1:3931218 [A/G] chr1 3931218 Cc01_g02130:267 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GA AA AG +chr1:3931281 [T/C] chr1 3931281 Cc01_g02130:330 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 4 TT CC TC CT +chr1:3931307 [C/T] chr1 3931307 Cc01_g02130:356 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 50.0% 4 CC TT CT TC +chr1:3932233 [C/T] chr1 3932233 Cc01_g02130:381 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CT CT CT +chr1:3932286 [G/A] chr1 3932286 Cc01_g02130:434 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 37.5% 4 GG GA GA GA +chr1:3932490 [A/G] chr1 3932490 Cc01_g02130:492 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AA GA +chr1:3933113 [G/T] chr1 3933113 Cc01_g02130:592 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GT GG GG +chr1:3933131 [G/A] chr1 3933131 Cc01_g02130:610 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GG GA GA +chr1:3933913 [C/T] chr1 3933913 Cc01_g02130:645 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 CC TT CT CT +chr1:3933970 [T/C] chr1 3933970 Cc01_g02130:702 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT TC TC TT +chr1:3933994 [C/T] chr1 3933994 Cc01_g02130:726 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT +chr1:3934095 [A/G] chr1 3934095 Cc01_g02130:733 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 AA AG AG AA +chr1:3934103 [C/T] chr1 3934103 Cc01_g02130:741 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:3934155 [G/A] chr1 3934155 Cc01_g02130:793 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AG GG GA +chr1:3935070 [A/G] chr1 3935070 Cc01_g02130:858 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AG AG AA +chr1:3935127 [A/G] chr1 3935127 Cc01_g02130:915 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA GG AG GG +chr1:3935145 [A/T] chr1 3935145 Cc01_g02130:933 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 AA AT AT AA +chr1:3935149 [G/C] chr1 3935149 Cc01_g02130:937 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 12.5% 4 GG GG GG GC +chr1:3935722 [A/C] chr1 3935722 Cc01_g02130:949 exon SYNONYMOUS_CODING Aga/Cga R/R 25.0% 4 AA AC AC AA +chr1:3935742 [A/G] chr1 3935742 Cc01_g02130:969 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA +chr1:3935757 [G/A] chr1 3935757 Cc01_g02130:984 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG AG +chr1:3935791 [T/G] chr1 3935791 Cc01_g02130:1018 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 37.5% 4 TT GG TG GG +chr1:3935805 [T/G] chr1 3935805 Cc01_g02130:1032 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT TT TT TG +chr1:3935956 [A/C] chr1 3935956 Cc01_g02130:1061 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AA AA AC +chr1:3935975 [G/A] chr1 3935975 Cc01_g02130:1080 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG GA +chr1:3936792 [A/G] chr1 3936792 Cc01_g02130:1125 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA AG +chr1:3936831 [A/G] chr1 3936831 Cc01_g02130:1164 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 4 AA AG AG GG +chr1:3936971 [G/C] chr1 3936971 Cc01_g02130:1222 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 37.5% 4 GG CC GC CC +chr1:3942733 [G/A] chr1 3942733 Cc01_g02140:62 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 GG AA GG GG +chr1:3942723 [T/A] chr1 3942723 Cc01_g02140:72 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA TT TT +chr1:3940926 [G/A] chr1 3940926 Cc01_g02140:213 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG +chr1:3940777 [C/A] chr1 3940777 Cc01_g02140:362 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC +chr1:3940686 [A/G] chr1 3940686 Cc01_g02140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA +chr1:3940475 [A/G] chr1 3940475 Cc01_g02140:664 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA AA AA AG +chr1:3940287 [C/T] chr1 3940287 Cc01_g02140:852 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT CC CC +chr1:3940278 [G/A] chr1 3940278 Cc01_g02140:861 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG +chr1:3940190 [T/C] chr1 3940190 Cc01_g02140:949 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT +chr1:3940062 [G/A] chr1 3940062 Cc01_g02140:1077 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG AA GA AA +chr1:3939962 [C/A] chr1 3939962 Cc01_g02140:1177 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 12.5% 4 CC CA CC CC +chr1:3939959 [G/T] chr1 3939959 Cc01_g02140:1180 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 GG TT GG GG +chr1:3939916 [C/T] chr1 3939916 Cc01_g02140:1223 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:3938977 [G/C] chr1 3938977 Cc01_g02140:1335 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GC GG GG +chr1:3938798 [T/G] chr1 3938798 Cc01_g02140:1369 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 37.5% 4 TT GG TG TT +chr1:3938797 [C/G] chr1 3938797 Cc01_g02140:1370 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC CC CG +chr1:3938792 [G/A] chr1 3938792 Cc01_g02140:1375 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 GG GG GG AG +chr1:3938784 [C/T] chr1 3938784 Cc01_g02140:1383 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TC CT CC +chr1:3938738 [C/T] chr1 3938738 Cc01_g02140:1429 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC +chr1:3938734 [T/C] chr1 3938734 Cc01_g02140:1433 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 TT TT TC CT +chr1:3938731 [A/G] chr1 3938731 Cc01_g02140:1436 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA +chr1:3938674 [C/T] chr1 3938674 Cc01_g02140:1493 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC +chr1:3950327 [A/C] chr1 3950327 Cc01_g02150:300 exon NON_SYNONYMOUS_CODING caT/caG H/Q 37.5% 4 AA CC AC AA +chr1:3949508 [G/T] chr1 3949508 Cc01_g02150:438 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 GG GT GG GG +chr1:3949500 [T/C] chr1 3949500 Cc01_g02150:446 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 TT TT TC TT +chr1:3949478 [G/A] chr1 3949478 Cc01_g02150:468 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 GG GG GA GG +chr1:3949470 [C/T] chr1 3949470 Cc01_g02150:476 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 CC TT CC CC +chr1:3949465 [C/G] chr1 3949465 Cc01_g02150:481 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 37.5% 4 CC GG CG CC +chr1:3949086 [C/T] chr1 3949086 Cc01_g02150:541 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC CT CC +chr1:3967535 [C/T] chr1 3967535 Cc01_g02160:57 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CT CC CC +chr1:3967530 [A/T] chr1 3967530 Cc01_g02160:62 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA AA AT +chr1:3967524 [G/A] chr1 3967524 Cc01_g02160:68 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 37.5% 4 GG AG GA AG +chr1:3967512 [A/G] chr1 3967512 Cc01_g02160:80 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AG AA +chr1:3967435 [A/G] chr1 3967435 Cc01_g02160:157 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 AA AG AA AG +chr1:3967421 [G/A] chr1 3967421 Cc01_g02160:171 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG AG GG GG +chr1:3967412 [A/C] chr1 3967412 Cc01_g02160:180 exon STOP_GAINED taT/taG Y/0 37.5% 4 AA AC AC AC +chr1:3967382 [A/G] chr1 3967382 Cc01_g02160:210 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA GA GA AA +chr1:3967354 [G/T] chr1 3967354 Cc01_g02160:238 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG GG GG GT +chr1:3967352 [T/C] chr1 3967352 Cc01_g02160:240 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT CC CT CC +chr1:3967310 [G/C] chr1 3967310 Cc01_g02160:282 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG GC GC GC +chr1:3967300 [C/T] chr1 3967300 Cc01_g02160:292 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC TC +chr1:3967295 [G/A] chr1 3967295 Cc01_g02160:297 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:3966909 [T/A] chr1 3966909 Cc01_g02160:683 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 TT TA TT TT +chr1:3966784 [G/A] chr1 3966784 Cc01_g02160:808 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 16.7% 3 GG NN GA GG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/.svn/text-base/result.txt.svn-base Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,21 @@ +Chromosome Position SNPs +chr1 200000 355 +chr1 400000 228 +chr1 600000 63 +chr1 800000 191 +chr1 1000000 88 +chr1 1200000 90 +chr1 1400000 190 +chr1 1600000 267 +chr1 1800000 226 +chr1 2000000 163 +chr1 2200000 357 +chr1 2400000 132 +chr1 2600000 158 +chr1 2800000 104 +chr1 3000000 146 +chr1 3200000 331 +chr1 3400000 181 +chr1 3600000 36 +chr1 3800000 167 +chr1 4000000 110
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/.svn/text-base/result_bysample.txt.svn-base Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,21 @@ +Chromosome BA58 BA59 BD54 +chr1 220 197 225 +chr1 130 119 133 +chr1 43 43 40 +chr1 139 167 141 +chr1 62 72 78 +chr1 35 76 38 +chr1 98 123 82 +chr1 133 205 135 +chr1 94 141 151 +chr1 112 116 117 +chr1 228 238 204 +chr1 86 95 96 +chr1 60 106 82 +chr1 60 74 64 +chr1 106 112 115 +chr1 199 220 228 +chr1 151 94 64 +chr1 18 32 27 +chr1 87 90 100 +chr1 54 75 47
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/hapmap Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,3584 @@ +rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 +chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT +chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA +chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC +chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG +chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG +chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT +chr1:1398 [T/G] chr1 1398 Cc01_g00010:369 exon SYNONYMOUS_CODING gcA/gcC A/A 16.7% 3 TT TT NN TG +chr1:1394 [G/C] chr1 1394 Cc01_g00010:373 exon NON_SYNONYMOUS_CODING Cgt/Ggt R/G 16.7% 3 GG GG NN GC +chr1:1379 [A/T] chr1 1379 Cc01_g00010:388 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 16.7% 3 AA AA NN AT +chr1:1352 [T/C] chr1 1352 Cc01_g00010:415 exon NON_SYNONYMOUS_CODING Act/Gct T/A 33.3% 3 TT CC NN CC +chr1:1252 [T/A] chr1 1252 Cc01_g00010:515 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA +chr1:17176 [T/G] chr1 17176 Cc01_g00030:504 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TT TG TT +chr1:18041 [A/G] chr1 18041 Cc01_g00030:661 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 AA AA GG AG +chr1:18442 [C/A] chr1 18442 Cc01_g00030:929 exon NON_SYNONYMOUS_CODING tCc/tAc S/Y 25.0% 4 CC CC CA CA +chr1:18478 [T/C] chr1 18478 Cc01_g00030:965 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 25.0% 4 TT TT TC TC +chr1:18554 [T/G] chr1 18554 Cc01_g00030:1041 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT TT TG TG +chr1:19062 [T/A] chr1 19062 Cc01_g00030:1151 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN TT AA +chr1:19078 [A/G] chr1 19078 Cc01_g00030:1167 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:19138 [T/C] chr1 19138 Cc01_g00030:1227 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT CT TC +chr1:22125 [C/T] chr1 22125 Cc01_g00030:1773 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC CT CT +chr1:22212 [T/C] chr1 22212 Cc01_g00030:1860 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:22342 [T/A] chr1 22342 Cc01_g00030:1990 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 4 TT TT TA TA +chr1:22404 [C/T] chr1 22404 Cc01_g00030:2052 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC CT CT +chr1:22478 [C/G] chr1 22478 Cc01_g00030:2126 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC GG CC CC +chr1:22613 [C/T] chr1 22613 Cc01_g00030:2261 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 CC TT CC CC +chr1:22657 [C/T] chr1 22657 Cc01_g00030:2305 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC +chr1:22758 [A/G] chr1 22758 Cc01_g00030:2406 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AA AG AG +chr1:22903 [C/A] chr1 22903 Cc01_g00030:2551 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CC CA CA +chr1:22965 [G/T] chr1 22965 Cc01_g00030:2613 exon NON_SYNONYMOUS_CODING atG/atT M/I 12.5% 4 GG GG TG GG +chr1:23037 [A/G] chr1 23037 Cc01_g00030:2685 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA AA AG AG +chr1:24151 [A/G] chr1 24151 Cc01_g00030:3063 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA AG AG +chr1:24436 [T/C] chr1 24436 Cc01_g00030:3240 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT TC TC +chr1:25763 [G/C] chr1 25763 Cc01_g00030:3610 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 25.0% 4 GG GG GC GC +chr1:26910 [T/G] chr1 26910 Cc01_g00030:3889 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 25.0% 4 TT TT TG TG +chr1:26996 [C/T] chr1 26996 Cc01_g00030:3975 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 CC CC CT CT +chr1:27095 [A/T] chr1 27095 Cc01_g00030:4074 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT +chr1:27755 [C/T] chr1 27755 Cc01_g00030:4734 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC CT CT +chr1:30493 [C/T] chr1 30493 Cc01_g00030:4992 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:30505 [C/T] chr1 30505 Cc01_g00030:5004 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CC TT CT +chr1:30560 [A/G] chr1 30560 Cc01_g00030:5059 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AG AA +chr1:30592 [T/C] chr1 30592 Cc01_g00030:5091 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:32950 [A/G] chr1 32950 Cc01_g00030:5337 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AA AG AG +chr1:32968 [A/C] chr1 32968 Cc01_g00030:5355 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 4 AA CC AA AA +chr1:33022 [A/T] chr1 33022 Cc01_g00030:5409 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TT AA AA +chr1:33025 [T/A] chr1 33025 Cc01_g00030:5412 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT AA TT TT +chr1:33167 [T/C] chr1 33167 Cc01_g00030:5554 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 25.0% 4 TT CC TT TT +chr1:33196 [C/T] chr1 33196 Cc01_g00030:5583 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 CC TT CC CC +chr1:33467 [T/C] chr1 33467 Cc01_g00030:5854 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TC TC +chr1:37303 [G/A] chr1 37303 Cc01_g00040:129 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 GG NN NN AA +chr1:37602 [C/G] chr1 37602 Cc01_g00040:428 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC GG GG CG +chr1:37607 [T/G] chr1 37607 Cc01_g00040:433 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 50.0% 3 TT GG NN TG +chr1:38519 [A/C] chr1 38519 Cc01_g00040:507 exon SYNONYMOUS_CODING gcA/gcC A/A 33.3% 3 AA NN CC CC +chr1:38606 [G/A] chr1 38606 Cc01_g00040:594 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 4 GG AA GA GA +chr1:38657 [C/T] chr1 38657 Cc01_g00040:645 exon SYNONYMOUS_CODING caC/caT H/H 37.5% 4 CC TT TT CT +chr1:38927 [G/A] chr1 38927 Cc01_g00040:915 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN NN AA +chr1:38942 [G/C] chr1 38942 Cc01_g00040:930 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG NN CC CC +chr1:38952 [C/T] chr1 38952 Cc01_g00040:940 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 CC NN TT CT +chr1:38956 [T/C] chr1 38956 Cc01_g00040:944 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 3 TT NN CC TC +chr1:39103 [C/T] chr1 39103 Cc01_g00040:1091 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT +chr1:39113 [C/T] chr1 39113 Cc01_g00040:1101 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TT CT +chr1:39164 [T/G] chr1 39164 Cc01_g00040:1152 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TG TT TT +chr1:39389 [T/C] chr1 39389 Cc01_g00040:1377 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 2 TT NN NN TC +chr1:77092 [C/G] chr1 77092 Cc01_g00050:8 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 25.0% 4 CC GG GG GG +chr1:77069 [C/A] chr1 77069 Cc01_g00050:31 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 12.5% 4 CC CA CC CC +chr1:77040 [A/C] chr1 77040 Cc01_g00050:60 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 AA CC CC CC +chr1:77030 [T/C] chr1 77030 Cc01_g00050:70 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC CC CC +chr1:76998 [C/A] chr1 76998 Cc01_g00050:102 exon SYNONYMOUS_CODING ccG/ccT P/P 50.0% 4 CC AA CA CA +chr1:76995 [T/C] chr1 76995 Cc01_g00050:105 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC +chr1:83837 [G/A] chr1 83837 Cc01_g00060:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:84858 [A/C] chr1 84858 Cc01_g00060:392 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 37.5% 4 AA CC AA AC +chr1:84868 [C/T] chr1 84868 Cc01_g00060:402 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 4 CC TT CC TT +chr1:84880 [G/A] chr1 84880 Cc01_g00060:414 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GG AA +chr1:84991 [C/G] chr1 84991 Cc01_g00060:525 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 CC CC CG CC +chr1:105491 [C/A] chr1 105491 Cc01_g00070:36 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA +chr1:100754 [G/C] chr1 100754 Cc01_g00070:660 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 GG GC GG GG +chr1:100458 [A/C] chr1 100458 Cc01_g00070:720 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 37.5% 4 AA CC AA AC +chr1:100367 [C/A] chr1 100367 Cc01_g00070:811 exon STOP_GAINED Gga/Tga G/1 12.5% 4 CC CC CA CC +chr1:99870 [T/C] chr1 99870 Cc01_g00070:1068 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC +chr1:99742 [C/G] chr1 99742 Cc01_g00070:1196 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CC CG +chr1:99729 [G/A] chr1 99729 Cc01_g00070:1209 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GG GA +chr1:99727 [G/C] chr1 99727 Cc01_g00070:1211 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC +chr1:99642 [C/T] chr1 99642 Cc01_g00070:1296 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT +chr1:99567 [T/G] chr1 99567 Cc01_g00070:1371 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 TT TT TT TG +chr1:99549 [T/C] chr1 99549 Cc01_g00070:1389 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT CC TT TT +chr1:99448 [T/G] chr1 99448 Cc01_g00070:1490 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG +chr1:99354 [T/C] chr1 99354 Cc01_g00070:1584 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC +chr1:99162 [T/C] chr1 99162 Cc01_g00070:1776 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:98368 [C/G] chr1 98368 Cc01_g00070:2112 exon NON_SYNONYMOUS_CODING agG/agC R/S 50.0% 2 CC NN NN GG +chr1:97071 [A/C] chr1 97071 Cc01_g00070:2285 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 AA CC CC CC +chr1:96611 [C/T] chr1 96611 Cc01_g00070:2292 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CT CC CC +chr1:95183 [T/C] chr1 95183 Cc01_g00070:2748 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC +chr1:95134 [T/C] chr1 95134 Cc01_g00070:2797 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC TT TC +chr1:95116 [G/A] chr1 95116 Cc01_g00070:2815 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:94898 [G/A] chr1 94898 Cc01_g00070:2895 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA +chr1:94841 [A/T] chr1 94841 Cc01_g00070:2952 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:94700 [C/T] chr1 94700 Cc01_g00070:2994 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:94679 [A/G] chr1 94679 Cc01_g00070:3015 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AA AG +chr1:93879 [T/C] chr1 93879 Cc01_g00070:3411 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 TT CC TT TC +chr1:93873 [C/T] chr1 93873 Cc01_g00070:3417 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CC CT +chr1:92117 [A/T] chr1 92117 Cc01_g00070:3663 exon SYNONYMOUS_CODING ctT/ctA L/L 25.0% 4 AA TT AA AA +chr1:92011 [A/C] chr1 92011 Cc01_g00070:3769 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC +chr1:91347 [G/A] chr1 91347 Cc01_g00070:4194 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG +chr1:90731 [A/C] chr1 90731 Cc01_g00070:4545 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AC AC AC +chr1:90332 [T/A] chr1 90332 Cc01_g00070:4746 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TT TA +chr1:90303 [A/G] chr1 90303 Cc01_g00070:4775 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 25.0% 4 AA GG AA AA +chr1:90289 [C/T] chr1 90289 Cc01_g00070:4789 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 CC TT CC CT +chr1:90161 [A/G] chr1 90161 Cc01_g00070:4917 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:90128 [G/A] chr1 90128 Cc01_g00070:4950 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA +chr1:89792 [G/A] chr1 89792 Cc01_g00070:5127 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA GG GA +chr1:89745 [A/G] chr1 89745 Cc01_g00070:5174 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 37.5% 4 AA GG AA AG +chr1:89720 [T/C] chr1 89720 Cc01_g00070:5199 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC CC CC +chr1:89493 [A/G] chr1 89493 Cc01_g00070:5304 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG +chr1:89423 [A/C] chr1 89423 Cc01_g00070:5374 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC +chr1:89418 [A/T] chr1 89418 Cc01_g00070:5379 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 AA AA AA TA +chr1:88516 [T/G] chr1 88516 Cc01_g00070:5910 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 TT TT TT TG +chr1:87964 [T/C] chr1 87964 Cc01_g00070:6237 exon SYNONYMOUS_CODING agA/agG R/R 37.5% 4 TT CC TT TC +chr1:112990 [T/C] chr1 112990 Cc01_g00080:4 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 50.0% 4 TT TT CC CC +chr1:112983 [A/G] chr1 112983 Cc01_g00080:11 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 4 AA AA GG GG +chr1:112926 [A/T] chr1 112926 Cc01_g00080:68 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 50.0% 4 AA AA TT TT +chr1:112910 [T/C] chr1 112910 Cc01_g00080:84 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:112909 [A/C] chr1 112909 Cc01_g00080:85 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC +chr1:112875 [C/A] chr1 112875 Cc01_g00080:119 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 12.5% 4 CC CC CA CC +chr1:112874 [G/A] chr1 112874 Cc01_g00080:120 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG GG GA GA +chr1:112792 [A/G] chr1 112792 Cc01_g00080:202 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA AA GG GG +chr1:112070 [T/C] chr1 112070 Cc01_g00080:274 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 TT TT TC CC +chr1:111976 [T/C] chr1 111976 Cc01_g00080:368 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TC TT +chr1:111966 [G/C] chr1 111966 Cc01_g00080:378 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG +chr1:111413 [T/C] chr1 111413 Cc01_g00080:741 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 TT CC TT TT +chr1:111011 [T/A] chr1 111011 Cc01_g00080:879 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TT TA TT +chr1:111002 [G/A] chr1 111002 Cc01_g00080:888 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG AA AA AA +chr1:110176 [A/G] chr1 110176 Cc01_g00080:1233 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AA AG AA +chr1:127984 [A/G] chr1 127984 Cc01_g00090:15 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:128022 [T/A] chr1 128022 Cc01_g00090:53 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 TT AA AA AA +chr1:128047 [A/G] chr1 128047 Cc01_g00090:78 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:128072 [A/T] chr1 128072 Cc01_g00090:103 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA TT TT TT +chr1:128252 [T/C] chr1 128252 Cc01_g00090:283 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT CC CC CC +chr1:133985 [C/T] chr1 133985 Cc01_g00100:165 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC TT CC +chr1:133990 [T/G] chr1 133990 Cc01_g00100:170 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 12.5% 4 TT TT TT TG +chr1:134007 [G/T] chr1 134007 Cc01_g00100:187 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT TT GT +chr1:134174 [T/A] chr1 134174 Cc01_g00100:354 exon SYNONYMOUS_CODING gtT/gtA V/V 25.0% 4 TT TT TA TA +chr1:134262 [G/A] chr1 134262 Cc01_g00100:442 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GA GG +chr1:134333 [T/C] chr1 134333 Cc01_g00100:513 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT TC TC +chr1:134393 [C/A] chr1 134393 Cc01_g00100:573 exon SYNONYMOUS_CODING acC/acA T/T 37.5% 4 CC AA CC AC +chr1:134403 [C/T] chr1 134403 Cc01_g00100:583 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC CC TC CC +chr1:134481 [C/A] chr1 134481 Cc01_g00100:661 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC +chr1:134514 [T/C] chr1 134514 Cc01_g00100:694 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT TC TC TC +chr1:134570 [T/C] chr1 134570 Cc01_g00100:750 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TT CC TC +chr1:134580 [C/T] chr1 134580 Cc01_g00100:760 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT +chr1:134592 [C/G] chr1 134592 Cc01_g00100:772 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC GG CC CC +chr1:134603 [G/T] chr1 134603 Cc01_g00100:783 exon SYNONYMOUS_CODING acG/acT T/T 25.0% 4 GG GG TT GG +chr1:134957 [T/G] chr1 134957 Cc01_g00100:1137 exon SYNONYMOUS_CODING ccT/ccG P/P 37.5% 4 TT GG TT TG +chr1:135249 [C/A] chr1 135249 Cc01_g00100:1429 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 12.5% 4 CC CC CC CA +chr1:135260 [G/A] chr1 135260 Cc01_g00100:1440 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GG AA GA +chr1:135922 [T/C] chr1 135922 Cc01_g00110:53 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 37.5% 4 TT CC TT TC +chr1:135925 [A/G] chr1 135925 Cc01_g00110:56 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AA AG +chr1:136539 [G/A] chr1 136539 Cc01_g00120:13 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AA GG +chr1:136654 [A/T] chr1 136654 Cc01_g00120:128 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 AA AA TT AA +chr1:136658 [A/G] chr1 136658 Cc01_g00120:132 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG +chr1:136898 [A/G] chr1 136898 Cc01_g00120:372 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG +chr1:136996 [A/G] chr1 136996 Cc01_g00120:470 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GG AG +chr1:137035 [T/C] chr1 137035 Cc01_g00120:509 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT +chr1:137064 [G/A] chr1 137064 Cc01_g00120:538 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG AA AA GA +chr1:137153 [A/G] chr1 137153 Cc01_g00120:627 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AA AG +chr1:137300 [C/T] chr1 137300 Cc01_g00120:774 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC TT CC +chr1:137483 [G/A] chr1 137483 Cc01_g00120:957 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GG GA +chr1:137525 [A/G] chr1 137525 Cc01_g00120:999 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA GG AA +chr1:137571 [A/G] chr1 137571 Cc01_g00120:1045 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG GG AG +chr1:137669 [C/T] chr1 137669 Cc01_g00120:1143 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT +chr1:137725 [T/C] chr1 137725 Cc01_g00120:1199 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 TT TT TT TC +chr1:137873 [T/C] chr1 137873 Cc01_g00120:1347 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC +chr1:137891 [C/T] chr1 137891 Cc01_g00120:1365 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:138059 [T/C] chr1 138059 Cc01_g00120:1533 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC TT TT +chr1:138108 [C/T] chr1 138108 Cc01_g00120:1582 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT CC CT +chr1:138227 [C/T] chr1 138227 Cc01_g00120:1701 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC TT CC +chr1:138383 [C/T] chr1 138383 Cc01_g00120:1857 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT +chr1:138386 [T/C] chr1 138386 Cc01_g00120:1860 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC +chr1:138497 [G/A] chr1 138497 Cc01_g00120:1971 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG +chr1:144606 [G/C] chr1 144606 Cc01_g00130:45 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG CC GC +chr1:144576 [C/G] chr1 144576 Cc01_g00130:75 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 CC GG GG GG +chr1:144519 [A/G] chr1 144519 Cc01_g00130:132 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA AA GG AA +chr1:144434 [T/A] chr1 144434 Cc01_g00130:217 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 37.5% 4 TT AA TT TA +chr1:144286 [C/G] chr1 144286 Cc01_g00130:365 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 50.0% 4 CC GG GG CC +chr1:147816 [C/T] chr1 147816 Cc01_g00140:18 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC TT NN NN +chr1:147821 [G/T] chr1 147821 Cc01_g00140:23 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 33.3% 3 GG TT NN GG +chr1:147823 [G/A] chr1 147823 Cc01_g00140:25 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG +chr1:147861 [G/A] chr1 147861 Cc01_g00140:63 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 GG GG NN AA +chr1:147863 [G/C] chr1 147863 Cc01_g00140:65 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 33.3% 3 GG GG NN CC +chr1:147872 [C/T] chr1 147872 Cc01_g00140:74 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 33.3% 3 CC TT NN CC +chr1:147974 [G/T] chr1 147974 Cc01_g00140:176 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT TT TT +chr1:148011 [T/G] chr1 148011 Cc01_g00140:213 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT GG TT TT +chr1:148050 [T/C] chr1 148050 Cc01_g00140:252 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT CC TT +chr1:148062 [G/A] chr1 148062 Cc01_g00140:264 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA +chr1:148150 [A/G] chr1 148150 Cc01_g00140:352 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 AA AG AA AA +chr1:148165 [C/G] chr1 148165 Cc01_g00140:367 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 CC CC GG CC +chr1:148179 [C/G] chr1 148179 Cc01_g00140:381 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC +chr1:148184 [A/G] chr1 148184 Cc01_g00140:386 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG +chr1:148230 [C/T] chr1 148230 Cc01_g00140:432 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC TT CC CC +chr1:148933 [G/T] chr1 148933 Cc01_g00140:447 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT +chr1:148935 [G/T] chr1 148935 Cc01_g00140:449 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT +chr1:148943 [G/A] chr1 148943 Cc01_g00140:457 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA AA AA +chr1:148945 [A/G] chr1 148945 Cc01_g00140:459 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA GG GG GG +chr1:149174 [A/G] chr1 149174 Cc01_g00140:492 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 4 AA AG GG AG +chr1:149185 [A/G] chr1 149185 Cc01_g00140:503 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AA GG AA +chr1:149253 [C/T] chr1 149253 Cc01_g00140:571 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT +chr1:149279 [G/A] chr1 149279 Cc01_g00140:597 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG GA AA GA +chr1:150025 [G/C] chr1 150025 Cc01_g00140:698 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 12.5% 4 GG GG GG GC +chr1:150045 [G/A] chr1 150045 Cc01_g00140:718 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG +chr1:150080 [A/T] chr1 150080 Cc01_g00140:753 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA +chr1:150083 [G/A] chr1 150083 Cc01_g00140:756 exon SYNONYMOUS_CODING gtG/gtA V/V 50.0% 4 GG AG AA AG +chr1:151272 [C/T] chr1 151272 Cc01_g00140:847 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:151277 [G/C] chr1 151277 Cc01_g00140:852 exon SYNONYMOUS_CODING ccG/ccC P/P 50.0% 4 GG GC CC CG +chr1:152592 [T/C] chr1 152592 Cc01_g00140:903 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TT TC +chr1:157051 [C/T] chr1 157051 Cc01_g00140:960 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC TT TT TT +chr1:160171 [C/A] chr1 160171 Cc01_g00140:1088 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA AA AA +chr1:160217 [A/G] chr1 160217 Cc01_g00140:1134 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA AG AA AG +chr1:160786 [C/T] chr1 160786 Cc01_g00140:1194 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC TC +chr1:161276 [A/G] chr1 161276 Cc01_g00140:1312 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA +chr1:161769 [A/T] chr1 161769 Cc01_g00140:1461 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 4 AA AT TT AT +chr1:161789 [A/C] chr1 161789 Cc01_g00140:1481 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA CA AA AA +chr1:161808 [A/T] chr1 161808 Cc01_g00140:1500 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA TA AA AA +chr1:161819 [G/A] chr1 161819 Cc01_g00140:1511 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 12.5% 4 GG GA GG GG +chr1:161837 [T/C] chr1 161837 Cc01_g00140:1529 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT +chr1:162050 [C/T] chr1 162050 Cc01_g00140:1545 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC CT CC +chr1:162069 [C/A] chr1 162069 Cc01_g00140:1564 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 12.5% 4 CC CC CC AC +chr1:162112 [A/T] chr1 162112 Cc01_g00140:1607 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 12.5% 4 AA AT AA AA +chr1:162135 [A/C] chr1 162135 Cc01_g00140:1630 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA CA +chr1:162634 [C/G] chr1 162634 Cc01_g00140:1650 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 CC CC CC GC +chr1:163489 [A/T] chr1 163489 Cc01_g00140:1854 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AT AA AA +chr1:168498 [C/T] chr1 168498 Cc01_g00150:90 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC TT CC +chr1:168595 [G/A] chr1 168595 Cc01_g00150:187 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:168747 [A/T] chr1 168747 Cc01_g00150:339 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA AA TT +chr1:174617 [C/G] chr1 174617 Cc01_g00160:6 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC CC GG CC +chr1:174616 [C/T] chr1 174616 Cc01_g00160:7 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC CC TT CC +chr1:174601 [G/C] chr1 174601 Cc01_g00160:22 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 GG GC GG GG +chr1:174600 [A/G] chr1 174600 Cc01_g00160:23 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AA AG AA +chr1:174590 [C/A] chr1 174590 Cc01_g00160:33 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC +chr1:174580 [C/T] chr1 174580 Cc01_g00160:43 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TC TC CT +chr1:174572 [C/T] chr1 174572 Cc01_g00160:51 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TC TC CT +chr1:174565 [T/C] chr1 174565 Cc01_g00160:58 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CT TC TC +chr1:174562 [A/G] chr1 174562 Cc01_g00160:61 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA GA AA AG +chr1:174533 [C/G] chr1 174533 Cc01_g00160:90 exon SYNONYMOUS_CODING ctG/ctC L/L 25.0% 4 CC GG GG GG +chr1:174501 [C/T] chr1 174501 Cc01_g00160:122 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 37.5% 4 CC TC TT CC +chr1:174490 [C/T] chr1 174490 Cc01_g00160:133 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 4 CC TC TT TC +chr1:174472 [C/T] chr1 174472 Cc01_g00160:151 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 CC TC CC CC +chr1:174446 [T/C] chr1 174446 Cc01_g00160:177 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:174440 [G/A] chr1 174440 Cc01_g00160:183 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 GG AG AA GG +chr1:174419 [C/T] chr1 174419 Cc01_g00160:204 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TC CT CC +chr1:174413 [G/C] chr1 174413 Cc01_g00160:210 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG +chr1:174411 [C/T] chr1 174411 Cc01_g00160:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 CC TC CT CC +chr1:174403 [T/C] chr1 174403 Cc01_g00160:220 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT CT TT TT +chr1:174401 [G/A] chr1 174401 Cc01_g00160:222 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GA AG GG +chr1:174374 [G/A] chr1 174374 Cc01_g00160:249 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG GG AA GG +chr1:174353 [G/A] chr1 174353 Cc01_g00160:270 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG +chr1:174324 [G/A] chr1 174324 Cc01_g00160:299 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 37.5% 4 GG GA GA GA +chr1:174310 [C/T] chr1 174310 Cc01_g00160:313 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 CC CT TT CT +chr1:174297 [C/T] chr1 174297 Cc01_g00160:326 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC CT +chr1:174295 [G/A] chr1 174295 Cc01_g00160:328 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GA GG GA +chr1:174280 [G/T] chr1 174280 Cc01_g00160:343 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 GG GT GT GG +chr1:174257 [G/A] chr1 174257 Cc01_g00160:366 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG GA GG +chr1:174251 [C/T] chr1 174251 Cc01_g00160:372 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CC CT CC +chr1:174248 [G/A] chr1 174248 Cc01_g00160:375 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:174242 [A/T] chr1 174242 Cc01_g00160:381 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:174232 [C/T] chr1 174232 Cc01_g00160:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CT CC +chr1:174225 [G/C] chr1 174225 Cc01_g00160:398 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GC GG GG +chr1:174208 [C/G] chr1 174208 Cc01_g00160:415 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 CC CG CC CC +chr1:174205 [G/A] chr1 174205 Cc01_g00160:418 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG GA AG GG +chr1:174192 [G/A] chr1 174192 Cc01_g00160:431 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG GA GA GG +chr1:174190 [G/A] chr1 174190 Cc01_g00160:433 exon STOP_GAINED Cag/Tag Q/5 25.0% 4 GG GA AG GG +chr1:174185 [A/T] chr1 174185 Cc01_g00160:438 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AT TA AA +chr1:174174 [C/T] chr1 174174 Cc01_g00160:449 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT TC CC +chr1:174172 [T/C] chr1 174172 Cc01_g00160:451 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT +chr1:174068 [G/C] chr1 174068 Cc01_g00160:555 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 16.7% 3 GG GC NN GG +chr1:174026 [G/T] chr1 174026 Cc01_g00160:597 exon NON_SYNONYMOUS_CODING agC/agA S/R 33.3% 3 GG TT NN GG +chr1:173945 [C/G] chr1 173945 Cc01_g00160:678 exon SYNONYMOUS_CODING gcG/gcC A/A 12.5% 4 CC CG CC CC +chr1:173942 [C/T] chr1 173942 Cc01_g00160:681 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT TT CT +chr1:173921 [G/A] chr1 173921 Cc01_g00160:702 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG AA AA GA +chr1:173846 [G/A] chr1 173846 Cc01_g00160:777 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 3 GG AA NN GA +chr1:173642 [A/T] chr1 173642 Cc01_g00160:981 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA TT AA AA +chr1:173627 [A/G] chr1 173627 Cc01_g00160:996 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA GG AA AA +chr1:173596 [C/A] chr1 173596 Cc01_g00160:1027 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 CC CA CC CC +chr1:173585 [G/A] chr1 173585 Cc01_g00160:1038 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AG AA AA +chr1:173444 [G/T] chr1 173444 Cc01_g00160:1179 exon SYNONYMOUS_CODING atC/atA I/I 25.0% 2 GG NN NN GT +chr1:173410 [C/T] chr1 173410 Cc01_g00160:1213 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 16.7% 3 CC CC NN CT +chr1:173230 [T/C] chr1 173230 Cc01_g00160:1393 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 16.7% 3 TT TT NN TC +chr1:173180 [C/T] chr1 173180 Cc01_g00160:1443 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 CC TT NN CC +chr1:173126 [A/G] chr1 173126 Cc01_g00160:1497 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA GG AA AA +chr1:172613 [G/C] chr1 172613 Cc01_g00160:2010 exon SYNONYMOUS_CODING ctC/ctG L/L 50.0% 3 GG CC NN GC +chr1:172589 [G/T] chr1 172589 Cc01_g00160:2034 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 16.7% 3 GG GG NN TG +chr1:172499 [A/G] chr1 172499 Cc01_g00160:2124 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA NN GG AG +chr1:172355 [T/C] chr1 172355 Cc01_g00160:2268 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TC NN TT +chr1:172314 [T/C] chr1 172314 Cc01_g00160:2309 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 TT TC NN TT +chr1:172303 [G/A] chr1 172303 Cc01_g00160:2320 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 GG AA NN GG +chr1:172265 [T/C] chr1 172265 Cc01_g00160:2358 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TT NN TC +chr1:172206 [G/A] chr1 172206 Cc01_g00160:2417 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 GG GA NN GG +chr1:172178 [T/C] chr1 172178 Cc01_g00160:2445 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 2 TT NN NN TC +chr1:172150 [T/C] chr1 172150 Cc01_g00160:2473 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 2 TT NN NN TC +chr1:181949 [A/C] chr1 181949 Cc01_g00170:492 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 2 AA NN NN CC +chr1:182195 [C/A] chr1 182195 Cc01_g00170:738 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 2 CC NN NN AA +chr1:182231 [G/A] chr1 182231 Cc01_g00170:774 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA +chr1:182291 [A/G] chr1 182291 Cc01_g00170:834 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 3 AA NN AG GG +chr1:182424 [G/A] chr1 182424 Cc01_g00170:861 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA +chr1:182456 [A/G] chr1 182456 Cc01_g00170:893 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA NN AA AG +chr1:182483 [A/G] chr1 182483 Cc01_g00170:920 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:182874 [A/G] chr1 182874 Cc01_g00170:1113 exon SYNONYMOUS_CODING ccA/ccG P/P 33.3% 3 AA NN AA GG +chr1:183107 [T/C] chr1 183107 Cc01_g00170:1346 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT +chr1:188621 [G/A] chr1 188621 Cc01_g00180:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:188690 [C/A] chr1 188690 Cc01_g00180:81 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC +chr1:189264 [A/G] chr1 189264 Cc01_g00180:254 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AA AG AG +chr1:189346 [C/G] chr1 189346 Cc01_g00180:336 exon SYNONYMOUS_CODING cgC/cgG R/R 25.0% 4 CC GG GG GG +chr1:189357 [G/A] chr1 189357 Cc01_g00180:347 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA +chr1:189499 [G/C] chr1 189499 Cc01_g00180:489 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 4 GG CC CC GG +chr1:189586 [C/T] chr1 189586 Cc01_g00180:576 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT TT CC +chr1:190066 [A/G] chr1 190066 Cc01_g00180:780 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA +chr1:190127 [T/G] chr1 190127 Cc01_g00180:841 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 TT GG GG GG +chr1:190494 [C/T] chr1 190494 Cc01_g00180:1023 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 CC TT TT TT +chr1:190503 [A/G] chr1 190503 Cc01_g00180:1032 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:190584 [T/C] chr1 190584 Cc01_g00180:1113 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT +chr1:190662 [A/G] chr1 190662 Cc01_g00180:1191 exon SYNONYMOUS_STOP taA/taG 3/3 25.0% 4 AA AA GG AA +chr1:193899 [T/C] chr1 193899 Cc01_g00190:67 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 TT CC TT TT +chr1:193871 [T/C] chr1 193871 Cc01_g00190:95 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 TT TT CC TC +chr1:193809 [A/T] chr1 193809 Cc01_g00190:157 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA TA +chr1:193801 [G/C] chr1 193801 Cc01_g00190:165 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 GG GG GG CG +chr1:193793 [C/T] chr1 193793 Cc01_g00190:173 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC TC +chr1:193735 [C/T] chr1 193735 Cc01_g00190:231 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CT CT TC +chr1:193681 [G/C] chr1 193681 Cc01_g00190:240 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG GC GG GC +chr1:193649 [T/G] chr1 193649 Cc01_g00190:272 exon NON_SYNONYMOUS_CODING gAc/gCc D/A 12.5% 4 TT TT TT TG +chr1:193584 [G/A] chr1 193584 Cc01_g00190:337 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 25.0% 4 GG GG AA GG +chr1:193551 [T/A] chr1 193551 Cc01_g00190:370 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 TT AA TT TA +chr1:193129 [T/A] chr1 193129 Cc01_g00190:445 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 25.0% 4 TT TT AA TT +chr1:192625 [A/G] chr1 192625 Cc01_g00190:654 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AA GG AA +chr1:191959 [T/C] chr1 191959 Cc01_g00190:689 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT CC TT +chr1:191385 [T/A] chr1 191385 Cc01_g00190:915 exon SYNONYMOUS_CODING tcA/tcT S/S 25.0% 4 TT AA AA AA +chr1:191370 [A/G] chr1 191370 Cc01_g00190:930 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AA GG AA +chr1:191325 [C/T] chr1 191325 Cc01_g00190:975 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT +chr1:199253 [T/C] chr1 199253 Cc01_g00200:6 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT CC TT +chr1:199193 [G/A] chr1 199193 Cc01_g00200:66 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GG GA +chr1:199148 [T/A] chr1 199148 Cc01_g00200:111 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 12.5% 4 TT TT TT AT +chr1:199134 [G/A] chr1 199134 Cc01_g00200:125 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG AG +chr1:199093 [A/C] chr1 199093 Cc01_g00200:166 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 37.5% 4 AA CC AA CA +chr1:199078 [T/C] chr1 199078 Cc01_g00200:181 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CC TT TT +chr1:198900 [A/T] chr1 198900 Cc01_g00200:262 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 12.5% 4 AA AA AA AT +chr1:198850 [G/A] chr1 198850 Cc01_g00200:312 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA +chr1:198811 [A/G] chr1 198811 Cc01_g00200:351 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 AA GG AA AA +chr1:198805 [A/G] chr1 198805 Cc01_g00200:357 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA AA GG AA +chr1:198802 [C/G] chr1 198802 Cc01_g00200:360 exon SYNONYMOUS_CODING gtG/gtC V/V 25.0% 4 CC CC GG CC +chr1:197996 [A/G] chr1 197996 Cc01_g00200:615 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG +chr1:197551 [A/G] chr1 197551 Cc01_g00200:963 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG AA AA +chr1:197200 [C/T] chr1 197200 Cc01_g00200:1207 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 CC TT CT CT +chr1:197177 [C/T] chr1 197177 Cc01_g00200:1230 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC TT TT TT +chr1:196815 [C/T] chr1 196815 Cc01_g00200:1344 exon SYNONYMOUS_CODING acG/acA T/T 50.0% 4 CC CT TT CT +chr1:196570 [A/T] chr1 196570 Cc01_g00200:1485 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AA AT +chr1:196315 [G/A] chr1 196315 Cc01_g00200:1584 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GG AA GG +chr1:196047 [G/C] chr1 196047 Cc01_g00200:1668 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 GG GG CC GG +chr1:195875 [A/G] chr1 195875 Cc01_g00200:1698 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GG AA AA +chr1:195821 [A/G] chr1 195821 Cc01_g00200:1752 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:208818 [T/C] chr1 208818 Cc01_g00220:430 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TC TT TC +chr1:207744 [G/A] chr1 207744 Cc01_g00220:618 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG GA GG GA +chr1:207027 [T/C] chr1 207027 Cc01_g00220:756 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TC TT TT +chr1:206648 [A/G] chr1 206648 Cc01_g00220:891 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:206440 [T/C] chr1 206440 Cc01_g00220:1099 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC +chr1:206402 [A/G] chr1 206402 Cc01_g00220:1137 exon SYNONYMOUS_CODING ccT/ccC P/P 50.0% 4 AA AA GG GG +chr1:216024 [C/T] chr1 216024 Cc01_g00230:429 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN +chr1:218860 [T/C] chr1 218860 Cc01_g00230:1338 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TT CC +chr1:218862 [G/A] chr1 218862 Cc01_g00230:1340 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 GG GG AA GG +chr1:219273 [C/T] chr1 219273 Cc01_g00230:1566 exon SYNONYMOUS_CODING tcC/tcT S/S 33.3% 3 CC NN TT TT +chr1:219413 [G/A] chr1 219413 Cc01_g00230:1605 exon SYNONYMOUS_CODING ccG/ccA P/P 50.0% 3 GG NN GA AA +chr1:219545 [T/C] chr1 219545 Cc01_g00230:1737 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC +chr1:220134 [A/G] chr1 220134 Cc01_g00230:2126 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA GG GG GG +chr1:220340 [A/G] chr1 220340 Cc01_g00230:2332 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG +chr1:221669 [G/T] chr1 221669 Cc01_g00240:79 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 GG TT TT GG +chr1:221674 [T/C] chr1 221674 Cc01_g00240:84 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT TC +chr1:221714 [G/T] chr1 221714 Cc01_g00240:124 exon NON_SYNONYMOUS_CODING Ggg/Tgg G/W 25.0% 4 GG TT GG GG +chr1:221718 [G/A] chr1 221718 Cc01_g00240:128 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GG AG +chr1:221746 [A/T] chr1 221746 Cc01_g00240:156 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 AA AT AA AA +chr1:221763 [A/T] chr1 221763 Cc01_g00240:173 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA +chr1:221788 [C/T] chr1 221788 Cc01_g00240:198 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 CC CT CC CC +chr1:221833 [T/C] chr1 221833 Cc01_g00240:243 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT CT TT TT +chr1:221852 [C/T] chr1 221852 Cc01_g00240:262 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 CC CC CC CT +chr1:221853 [G/A] chr1 221853 Cc01_g00240:263 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 GG GG GG AA +chr1:221866 [A/T] chr1 221866 Cc01_g00240:276 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT +chr1:222383 [T/C] chr1 222383 Cc01_g00240:354 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT +chr1:222633 [T/C] chr1 222633 Cc01_g00240:417 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:222951 [T/C] chr1 222951 Cc01_g00240:534 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:224386 [T/A] chr1 224386 Cc01_g00240:726 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT +chr1:224660 [A/T] chr1 224660 Cc01_g00240:825 exon SYNONYMOUS_CODING ggA/ggT G/G 37.5% 4 AA TT AA AT +chr1:224706 [G/C] chr1 224706 Cc01_g00240:871 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 GG GG GC GG +chr1:225032 [G/A] chr1 225032 Cc01_g00240:933 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG +chr1:225065 [C/T] chr1 225065 Cc01_g00240:966 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC TC CC CC +chr1:225194 [C/T] chr1 225194 Cc01_g00240:1008 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC TT CC CT +chr1:226501 [T/C] chr1 226501 Cc01_g00240:1072 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC CT +chr1:226539 [C/A] chr1 226539 Cc01_g00240:1110 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA +chr1:226575 [T/C] chr1 226575 Cc01_g00240:1146 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 TT TC TT TT +chr1:226694 [C/G] chr1 226694 Cc01_g00240:1181 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC +chr1:232340 [C/T] chr1 232340 Cc01_g00250:33 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CC TT CC +chr1:232292 [G/A] chr1 232292 Cc01_g00250:81 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA AA AA +chr1:229696 [A/G] chr1 229696 Cc01_g00250:380 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AA AG +chr1:228604 [A/G] chr1 228604 Cc01_g00250:468 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA +chr1:250535 [A/C] chr1 250535 Cc01_g00260:69 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC +chr1:250487 [T/A] chr1 250487 Cc01_g00260:117 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 TT TA TT TT +chr1:250388 [G/A] chr1 250388 Cc01_g00260:216 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA GG GG +chr1:246857 [G/A] chr1 246857 Cc01_g00260:529 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG GA GG +chr1:246722 [T/C] chr1 246722 Cc01_g00260:584 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT CC TT TC +chr1:246700 [A/G] chr1 246700 Cc01_g00260:606 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA GA +chr1:246674 [G/C] chr1 246674 Cc01_g00260:632 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GG GG GC +chr1:244939 [T/C] chr1 244939 Cc01_g00260:648 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TC TC TT +chr1:244750 [T/C] chr1 244750 Cc01_g00260:726 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TT TC +chr1:254013 [C/T] chr1 254013 Cc01_g00270:80 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:254369 [A/G] chr1 254369 Cc01_g00270:114 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AG AA +chr1:254414 [C/T] chr1 254414 Cc01_g00270:159 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:254486 [C/T] chr1 254486 Cc01_g00270:231 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CT CC CC +chr1:256173 [C/T] chr1 256173 Cc01_g00270:426 exon SYNONYMOUS_CODING ggC/ggT G/G 50.0% 4 CC CT TT CT +chr1:256269 [T/A] chr1 256269 Cc01_g00270:522 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 TT TT TT TA +chr1:256296 [C/G] chr1 256296 Cc01_g00270:549 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CC CG CC +chr1:256351 [G/C] chr1 256351 Cc01_g00270:604 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG +chr1:269489 [G/A] chr1 269489 Cc01_g00280:101 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GG GA +chr1:269514 [T/C] chr1 269514 Cc01_g00280:126 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC CC CC +chr1:269516 [T/C] chr1 269516 Cc01_g00280:128 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT TC +chr1:269724 [T/C] chr1 269724 Cc01_g00280:336 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC CC CC +chr1:269781 [G/A] chr1 269781 Cc01_g00280:393 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA +chr1:269793 [T/C] chr1 269793 Cc01_g00280:405 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TT TC +chr1:269833 [G/T] chr1 269833 Cc01_g00280:445 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT +chr1:269843 [T/C] chr1 269843 Cc01_g00280:455 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 TT TT TT CT +chr1:269847 [C/T] chr1 269847 Cc01_g00280:459 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC CT +chr1:269904 [T/C] chr1 269904 Cc01_g00280:516 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:269928 [C/T] chr1 269928 Cc01_g00280:540 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT +chr1:270027 [G/T] chr1 270027 Cc01_g00280:639 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT +chr1:270312 [A/C] chr1 270312 Cc01_g00280:924 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 AA AA CC AA +chr1:270383 [G/C] chr1 270383 Cc01_g00280:995 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GG GC +chr1:270395 [G/T] chr1 270395 Cc01_g00280:1007 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GG GT GG +chr1:270483 [T/C] chr1 270483 Cc01_g00280:1095 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TT TT TC +chr1:276780 [A/C] chr1 276780 Cc01_g00290:10 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 AA CC CC CC +chr1:274650 [T/G] chr1 274650 Cc01_g00290:196 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT +chr1:274413 [T/A] chr1 274413 Cc01_g00290:433 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TA TT +chr1:274345 [A/G] chr1 274345 Cc01_g00290:501 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA +chr1:273652 [G/A] chr1 273652 Cc01_g00290:639 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA GG GA +chr1:273576 [C/T] chr1 273576 Cc01_g00290:715 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC CC TT CC +chr1:273394 [C/T] chr1 273394 Cc01_g00290:897 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CC TT CT +chr1:273220 [G/A] chr1 273220 Cc01_g00290:1071 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GG GA GG +chr1:273180 [C/G] chr1 273180 Cc01_g00290:1111 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 37.5% 4 CC CC GG CG +chr1:273178 [G/A] chr1 273178 Cc01_g00290:1113 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GG AA GA +chr1:288461 [C/T] chr1 288461 Cc01_g00300:50 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:288120 [G/A] chr1 288120 Cc01_g00300:228 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 GG GG GA GG +chr1:287468 [G/A] chr1 287468 Cc01_g00300:469 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GG AA GG +chr1:287403 [A/G] chr1 287403 Cc01_g00300:534 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG GG GG +chr1:287370 [C/T] chr1 287370 Cc01_g00300:567 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT +chr1:286545 [A/G] chr1 286545 Cc01_g00300:774 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA AA GG AA +chr1:286507 [G/A] chr1 286507 Cc01_g00300:812 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG GA +chr1:286482 [G/C] chr1 286482 Cc01_g00300:837 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GG GG CG +chr1:285910 [C/A] chr1 285910 Cc01_g00300:942 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 CC AA CC AA +chr1:285897 [A/G] chr1 285897 Cc01_g00300:955 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG +chr1:285722 [T/G] chr1 285722 Cc01_g00300:1031 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 25.0% 4 TT TT GG TT +chr1:283896 [T/C] chr1 283896 Cc01_g00300:1335 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TT TC +chr1:283878 [G/A] chr1 283878 Cc01_g00300:1353 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG AA AA AA +chr1:283455 [A/T] chr1 283455 Cc01_g00300:1569 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AT AA AA +chr1:283107 [T/C] chr1 283107 Cc01_g00300:1682 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TC TT TT +chr1:280180 [T/C] chr1 280180 Cc01_g00300:1872 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC CC CC +chr1:293608 [T/C] chr1 293608 Cc01_g00310:9 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:293593 [G/A] chr1 293593 Cc01_g00310:24 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA GA GA +chr1:293581 [A/T] chr1 293581 Cc01_g00310:36 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA AT AT AT +chr1:293556 [G/A] chr1 293556 Cc01_g00310:61 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 GG GA GA GA +chr1:293548 [G/A] chr1 293548 Cc01_g00310:69 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 GG GG GA GG +chr1:293524 [A/G] chr1 293524 Cc01_g00310:93 exon SYNONYMOUS_CODING aaT/aaC N/N 37.5% 4 AA GG GG AG +chr1:290571 [T/C] chr1 290571 Cc01_g00310:310 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT +chr1:300689 [C/A] chr1 300689 Cc01_g00320:60 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 CC CC CC CA +chr1:300911 [G/T] chr1 300911 Cc01_g00320:111 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT +chr1:301164 [A/C] chr1 301164 Cc01_g00320:219 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA +chr1:301180 [G/T] chr1 301180 Cc01_g00320:235 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG +chr1:304719 [T/A] chr1 304719 Cc01_g00320:558 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TT TA +chr1:304779 [A/C] chr1 304779 Cc01_g00320:618 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA +chr1:329247 [C/A] chr1 329247 Cc01_g00330:270 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC AA CC CC +chr1:329217 [G/A] chr1 329217 Cc01_g00330:300 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG AA GA GA +chr1:329108 [G/A] chr1 329108 Cc01_g00330:409 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GA GG GG +chr1:329088 [A/G] chr1 329088 Cc01_g00330:429 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA +chr1:328149 [A/G] chr1 328149 Cc01_g00330:456 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA GA AA +chr1:328065 [T/G] chr1 328065 Cc01_g00330:540 exon SYNONYMOUS_CODING tcA/tcC S/S 50.0% 4 TT GG TG TG +chr1:327708 [A/C] chr1 327708 Cc01_g00330:644 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 12.5% 4 AA AC AA AA +chr1:327632 [C/T] chr1 327632 Cc01_g00330:720 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT CC CT +chr1:327519 [A/C] chr1 327519 Cc01_g00330:760 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC +chr1:327109 [T/C] chr1 327109 Cc01_g00330:833 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT TT TT TC +chr1:320096 [C/G] chr1 320096 Cc01_g00330:1285 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 37.5% 4 CC GG GG CG +chr1:319913 [T/C] chr1 319913 Cc01_g00330:1358 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:319903 [G/C] chr1 319903 Cc01_g00330:1368 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 GG GG GC GG +chr1:319887 [G/T] chr1 319887 Cc01_g00330:1384 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 GG TT GG GT +chr1:319879 [C/A] chr1 319879 Cc01_g00330:1392 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA +chr1:319682 [T/A] chr1 319682 Cc01_g00330:1589 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 TT AA AA TA +chr1:319581 [C/T] chr1 319581 Cc01_g00330:1690 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 CC CC CT CC +chr1:319379 [A/G] chr1 319379 Cc01_g00330:1892 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:319299 [A/C] chr1 319299 Cc01_g00330:1972 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 AA AA AC AA +chr1:319123 [G/A] chr1 319123 Cc01_g00330:2148 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:319112 [G/C] chr1 319112 Cc01_g00330:2159 exon NON_SYNONYMOUS_CODING gCc/gGc A/G 12.5% 4 GG GG GC GG +chr1:319087 [C/A] chr1 319087 Cc01_g00330:2184 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA +chr1:319073 [G/A] chr1 319073 Cc01_g00330:2198 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 GG GG GG GA +chr1:319033 [A/G] chr1 319033 Cc01_g00330:2238 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA +chr1:317552 [C/T] chr1 317552 Cc01_g00330:2468 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 CC CC CT CC +chr1:315675 [A/T] chr1 315675 Cc01_g00330:2530 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT AT +chr1:315443 [G/A] chr1 315443 Cc01_g00330:2691 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:315404 [C/T] chr1 315404 Cc01_g00330:2730 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT TT CT +chr1:315126 [A/G] chr1 315126 Cc01_g00330:2787 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 AA GG GG GG +chr1:315087 [C/G] chr1 315087 Cc01_g00330:2826 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CC CG +chr1:312979 [T/C] chr1 312979 Cc01_g00330:3198 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT +chr1:312964 [C/T] chr1 312964 Cc01_g00330:3213 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC TT TT CT +chr1:312879 [G/A] chr1 312879 Cc01_g00330:3298 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 37.5% 4 GG AA AA GA +chr1:312680 [G/A] chr1 312680 Cc01_g00330:3393 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA AA GA +chr1:312672 [T/A] chr1 312672 Cc01_g00330:3401 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 37.5% 4 TT AA AA TA +chr1:312546 [A/G] chr1 312546 Cc01_g00330:3527 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:312321 [G/C] chr1 312321 Cc01_g00330:3752 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GG GG GC +chr1:312307 [C/G] chr1 312307 Cc01_g00330:3766 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 50.0% 4 CC GG CG GC +chr1:312213 [G/A] chr1 312213 Cc01_g00330:3860 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG GA +chr1:312086 [T/C] chr1 312086 Cc01_g00330:3987 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT CC TC TC +chr1:311898 [T/C] chr1 311898 Cc01_g00330:4175 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:311859 [C/T] chr1 311859 Cc01_g00330:4214 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 4 CC TT CT CT +chr1:311729 [T/C] chr1 311729 Cc01_g00330:4344 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TC TT +chr1:311665 [C/T] chr1 311665 Cc01_g00330:4408 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 CC TT CC CT +chr1:311522 [T/C] chr1 311522 Cc01_g00330:4551 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:311476 [T/G] chr1 311476 Cc01_g00330:4597 exon NON_SYNONYMOUS_CODING Act/Cct T/P 12.5% 4 TT TT GT TT +chr1:311457 [C/A] chr1 311457 Cc01_g00330:4616 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 37.5% 4 CC AA AA CA +chr1:311357 [G/C] chr1 311357 Cc01_g00330:4716 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC +chr1:311161 [A/G] chr1 311161 Cc01_g00330:4912 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA GG AG AG +chr1:311057 [G/A] chr1 311057 Cc01_g00330:5016 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG +chr1:311024 [T/C] chr1 311024 Cc01_g00330:5049 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TC TT +chr1:310991 [A/G] chr1 310991 Cc01_g00330:5082 exon SYNONYMOUS_CODING ggT/ggC G/G 37.5% 4 AA GG AA AG +chr1:310760 [T/C] chr1 310760 Cc01_g00330:5229 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT +chr1:331033 [C/T] chr1 331033 Cc01_g00340:332 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 33.3% 3 CC TT NN TT +chr1:339763 [C/T] chr1 339763 Cc01_g00350:9 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC CT CT +chr1:339901 [G/C] chr1 339901 Cc01_g00350:147 exon SYNONYMOUS_CODING acG/acC T/T 12.5% 4 GG GG GG GC +chr1:339988 [A/G] chr1 339988 Cc01_g00350:234 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:346095 [A/G] chr1 346095 Cc01_g00350:384 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:346128 [C/G] chr1 346128 Cc01_g00350:417 exon NON_SYNONYMOUS_CODING atC/atG I/M 25.0% 4 CC CC GG CC +chr1:346300 [T/C] chr1 346300 Cc01_g00350:489 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT +chr1:346330 [A/G] chr1 346330 Cc01_g00350:519 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA GG AA AA +chr1:346342 [T/C] chr1 346342 Cc01_g00350:531 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC TT TT +chr1:349895 [T/C] chr1 349895 Cc01_g00360:87 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT CC NN NN +chr1:350036 [C/G] chr1 350036 Cc01_g00360:228 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 2 CC CG NN NN +chr1:350043 [T/C] chr1 350043 Cc01_g00360:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 2 TT CC NN NN +chr1:350373 [G/A] chr1 350373 Cc01_g00360:565 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 16.7% 3 GG GA NN GG +chr1:350416 [A/G] chr1 350416 Cc01_g00360:608 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 50.0% 2 AA GG NN NN +chr1:350429 [T/C] chr1 350429 Cc01_g00360:621 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT TT NN CC +chr1:350537 [A/T] chr1 350537 Cc01_g00360:729 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 AA AA AA TT +chr1:350672 [G/A] chr1 350672 Cc01_g00360:864 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 2 GG GA NN NN +chr1:350729 [C/T] chr1 350729 Cc01_g00360:921 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC +chr1:350738 [A/C] chr1 350738 Cc01_g00360:930 exon SYNONYMOUS_CODING ccA/ccC P/P 25.0% 4 AA AA CC AA +chr1:351014 [T/C] chr1 351014 Cc01_g00360:1206 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 2 TT CC NN NN +chr1:351188 [G/C] chr1 351188 Cc01_g00360:1380 exon SYNONYMOUS_CODING ccG/ccC P/P 33.3% 3 GG CC NN CC +chr1:351329 [A/T] chr1 351329 Cc01_g00360:1521 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 3 AA TT NN AT +chr1:392985 [A/G] chr1 392985 Cc01_g00370:84 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA +chr1:393004 [C/T] chr1 393004 Cc01_g00370:103 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:393006 [G/C] chr1 393006 Cc01_g00370:105 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 GG GG CG GG +chr1:393015 [G/A] chr1 393015 Cc01_g00370:114 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 GG AA AA AG +chr1:393081 [C/A] chr1 393081 Cc01_g00370:180 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 3 CC NN AA CA +chr1:393089 [T/A] chr1 393089 Cc01_g00370:188 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 TT TT TT TA +chr1:393111 [C/T] chr1 393111 Cc01_g00370:210 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TT TT CT +chr1:393120 [C/T] chr1 393120 Cc01_g00370:219 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC TT TT CT +chr1:393139 [G/A] chr1 393139 Cc01_g00370:238 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 GG AA AA GG +chr1:393271 [G/A] chr1 393271 Cc01_g00370:370 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG +chr1:393315 [G/A] chr1 393315 Cc01_g00370:414 exon SYNONYMOUS_CODING ggG/ggA G/G 16.7% 3 GG GG NN GA +chr1:393339 [G/T] chr1 393339 Cc01_g00370:438 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 50.0% 3 GG TT NN GT +chr1:393342 [G/A] chr1 393342 Cc01_g00370:441 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 GG NN NN GA +chr1:397208 [G/C] chr1 397208 Cc01_g00380:63 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG CC CC GC +chr1:397217 [T/C] chr1 397217 Cc01_g00380:72 exon SYNONYMOUS_CODING acT/acC T/T 37.5% 4 TT CC CC TC +chr1:397228 [G/T] chr1 397228 Cc01_g00380:83 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG TT TT TT +chr1:397253 [T/C] chr1 397253 Cc01_g00380:108 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC TT TT +chr1:397269 [T/A] chr1 397269 Cc01_g00380:124 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 50.0% 4 TT AA AA TT +chr1:397270 [T/C] chr1 397270 Cc01_g00380:125 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 TT CC CC TT +chr1:397361 [G/T] chr1 397361 Cc01_g00380:216 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 GG GG TT TT +chr1:397547 [C/A] chr1 397547 Cc01_g00380:402 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC AA AA AA +chr1:397566 [T/G] chr1 397566 Cc01_g00380:421 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 TT TT TT TG +chr1:397576 [T/C] chr1 397576 Cc01_g00380:431 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:398909 [G/C] chr1 398909 Cc01_g00380:456 exon SYNONYMOUS_CODING ggG/ggC G/G 12.5% 4 GG GG GC GG +chr1:398940 [A/G] chr1 398940 Cc01_g00380:487 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG GA AA +chr1:398942 [C/T] chr1 398942 Cc01_g00380:489 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TC CC +chr1:398951 [C/T] chr1 398951 Cc01_g00380:498 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC TT TC CC +chr1:399320 [T/C] chr1 399320 Cc01_g00380:867 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:399344 [C/T] chr1 399344 Cc01_g00380:891 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC +chr1:399368 [C/T] chr1 399368 Cc01_g00380:915 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT TT TT +chr1:399404 [A/T] chr1 399404 Cc01_g00380:951 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA +chr1:399453 [T/G] chr1 399453 Cc01_g00380:1000 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 TT GG GG GG +chr1:399557 [C/T] chr1 399557 Cc01_g00380:1104 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:399739 [C/G] chr1 399739 Cc01_g00380:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC +chr1:399765 [C/T] chr1 399765 Cc01_g00380:1312 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:399795 [C/A] chr1 399795 Cc01_g00380:1342 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CC CC AC +chr1:399796 [A/G] chr1 399796 Cc01_g00380:1343 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 25.0% 4 AA AA AA GG +chr1:399801 [A/G] chr1 399801 Cc01_g00380:1348 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 4 AA GG AA GG +chr1:399809 [C/G] chr1 399809 Cc01_g00380:1356 exon SYNONYMOUS_CODING gtC/gtG V/V 37.5% 4 CC GG CC GC +chr1:420355 [T/C] chr1 420355 Cc01_g00390:538 exon SYNONYMOUS_CODING Tta/Cta L/L 50.0% 2 TT NN NN CC +chr1:421363 [C/T] chr1 421363 Cc01_g00390:1546 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 CC NN NN TT +chr1:421532 [A/C] chr1 421532 Cc01_g00390:1715 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 37.5% 4 AA CC CC AC +chr1:421534 [A/G] chr1 421534 Cc01_g00390:1717 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA AG AG AA +chr1:421540 [G/A] chr1 421540 Cc01_g00390:1723 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 GG AG AG GA +chr1:421556 [T/A] chr1 421556 Cc01_g00390:1739 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 TT TT TA TT +chr1:421570 [T/C] chr1 421570 Cc01_g00390:1753 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 TT TC TT TT +chr1:421572 [C/T] chr1 421572 Cc01_g00390:1755 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT +chr1:421577 [C/T] chr1 421577 Cc01_g00390:1760 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 CC CC CC CT +chr1:421612 [A/G] chr1 421612 Cc01_g00390:1795 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 AA AA AG AA +chr1:422090 [G/C] chr1 422090 Cc01_g00390:2123 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 33.3% 3 GG NN CC GG +chr1:422353 [G/A] chr1 422353 Cc01_g00390:2386 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN NN GA +chr1:422467 [C/G] chr1 422467 Cc01_g00390:2500 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 33.3% 3 CC NN CC GG +chr1:422483 [C/A] chr1 422483 Cc01_g00390:2516 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 CC NN AA CC +chr1:422740 [G/T] chr1 422740 Cc01_g00390:2686 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 25.0% 2 GG NN NN GT +chr1:422742 [T/G] chr1 422742 Cc01_g00390:2688 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 2 TT NN NN TG +chr1:422746 [A/T] chr1 422746 Cc01_g00390:2692 exon STOP_GAINED Aaa/Taa K/8 25.0% 2 AA NN NN AT +chr1:422747 [A/C] chr1 422747 Cc01_g00390:2693 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 25.0% 2 AA NN NN AC +chr1:422885 [A/C] chr1 422885 Cc01_g00390:2831 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 33.3% 3 AA CC NN AA +chr1:445244 [A/G] chr1 445244 Cc01_g00410:59 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:445214 [A/T] chr1 445214 Cc01_g00410:89 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 37.5% 4 AA TT AT AA +chr1:445148 [T/G] chr1 445148 Cc01_g00410:155 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 16.7% 3 TT TG NN TT +chr1:445013 [T/C] chr1 445013 Cc01_g00410:185 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TC TT TT +chr1:444990 [C/T] chr1 444990 Cc01_g00410:208 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:444968 [G/A] chr1 444968 Cc01_g00410:230 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 GG GG GA GG +chr1:444952 [A/G] chr1 444952 Cc01_g00410:246 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG +chr1:444930 [G/A] chr1 444930 Cc01_g00410:268 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA +chr1:444929 [T/C] chr1 444929 Cc01_g00410:269 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC +chr1:444921 [T/C] chr1 444921 Cc01_g00410:277 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT TC TT CT +chr1:444904 [G/A] chr1 444904 Cc01_g00410:294 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:444879 [G/A] chr1 444879 Cc01_g00410:319 exon STOP_GAINED Cag/Tag Q/7 12.5% 4 GG GG GG GA +chr1:561287 [C/G] chr1 561287 Cc01_g00420:1568 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 2 CC NN NN GG +chr1:562257 [A/G] chr1 562257 Cc01_g00420:2449 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA GG NN AA +chr1:562260 [A/G] chr1 562260 Cc01_g00420:2452 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA GG NN AA +chr1:562358 [T/C] chr1 562358 Cc01_g00420:2550 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 2 TT NN NN TC +chr1:563082 [G/C] chr1 563082 Cc01_g00420:3274 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 33.3% 3 GG CC NN GG +chr1:563087 [A/G] chr1 563087 Cc01_g00420:3279 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA GG NN AA +chr1:563172 [C/T] chr1 563172 Cc01_g00420:3364 exon SYNONYMOUS_CODING Ctg/Ttg L/L 16.7% 3 CC CC NN CT +chr1:563178 [G/A] chr1 563178 Cc01_g00420:3370 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 16.7% 3 GG GG NN GA +chr1:563217 [A/G] chr1 563217 Cc01_g00420:3409 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 33.3% 3 AA NN GG AA +chr1:563316 [A/G] chr1 563316 Cc01_g00420:3439 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 AA NN AA GG +chr1:563359 [C/A] chr1 563359 Cc01_g00420:3482 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 50.0% 2 CC NN AA NN +chr1:563503 [T/C] chr1 563503 Cc01_g00420:3626 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT TT TC TC +chr1:563700 [T/A] chr1 563700 Cc01_g00420:3784 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 2 TT NN NN AA +chr1:563763 [G/A] chr1 563763 Cc01_g00420:3847 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG +chr1:563764 [A/T] chr1 563764 Cc01_g00420:3848 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 25.0% 4 AA TT AA AA +chr1:563780 [G/C] chr1 563780 Cc01_g00420:3864 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG GG GG CC +chr1:563788 [G/A] chr1 563788 Cc01_g00420:3872 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG AA GG GG +chr1:563836 [T/C] chr1 563836 Cc01_g00420:3920 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN +chr1:564119 [C/T] chr1 564119 Cc01_g00420:4122 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC NN TT NN +chr1:564245 [G/A] chr1 564245 Cc01_g00420:4248 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN AA NN +chr1:564250 [A/C] chr1 564250 Cc01_g00420:4253 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 50.0% 2 AA NN CC NN +chr1:564302 [A/G] chr1 564302 Cc01_g00420:4305 exon SYNONYMOUS_CODING tcA/tcG S/S 50.0% 4 AA GG GG AA +chr1:564307 [C/T] chr1 564307 Cc01_g00420:4310 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 33.3% 3 CC NN TT CC +chr1:564313 [T/A] chr1 564313 Cc01_g00420:4316 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TT TT AA +chr1:564315 [G/T] chr1 564315 Cc01_g00420:4318 exon NON_SYNONYMOUS_CODING Gac/Tac D/Y 12.5% 4 GG GG GG GT +chr1:564335 [C/G] chr1 564335 Cc01_g00420:4338 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC +chr1:564360 [T/G] chr1 564360 Cc01_g00420:4363 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 33.3% 3 TT GG NN GG +chr1:564391 [G/T] chr1 564391 Cc01_g00420:4394 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 33.3% 3 GG GG NN TT +chr1:564393 [C/G] chr1 564393 Cc01_g00420:4396 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 16.7% 3 CC CG NN CC +chr1:564416 [T/C] chr1 564416 Cc01_g00420:4419 exon SYNONYMOUS_CODING tcT/tcC S/S 33.3% 3 TT CC NN CC +chr1:564424 [C/A] chr1 564424 Cc01_g00420:4427 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 2 CC CA NN NN +chr1:564550 [T/A] chr1 564550 Cc01_g00420:4553 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 TT AA AA NN +chr1:624837 [T/G] chr1 624837 Cc01_g00430:60 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG +chr1:624841 [C/G] chr1 624841 Cc01_g00430:64 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 2 CC NN NN GG +chr1:625917 [T/G] chr1 625917 Cc01_g00430:987 exon SYNONYMOUS_CODING ctT/ctG L/L 50.0% 2 TT NN NN GG +chr1:625940 [G/C] chr1 625940 Cc01_g00430:1010 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 50.0% 2 GG NN NN CC +chr1:626077 [A/C] chr1 626077 Cc01_g00430:1147 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 50.0% 2 AA CC NN NN +chr1:626259 [G/A] chr1 626259 Cc01_g00430:1329 exon SYNONYMOUS_CODING ctG/ctA L/L 25.0% 2 GG NN NN GA +chr1:626317 [G/C] chr1 626317 Cc01_g00430:1387 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG NN NN GC +chr1:626491 [A/G] chr1 626491 Cc01_g00430:1561 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG +chr1:626499 [A/T] chr1 626499 Cc01_g00430:1569 exon SYNONYMOUS_CODING ccA/ccT P/P 50.0% 2 AA NN NN TT +chr1:626536 [C/T] chr1 626536 Cc01_g00430:1606 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC NN TT NN +chr1:626555 [C/G] chr1 626555 Cc01_g00430:1625 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN +chr1:626820 [T/C] chr1 626820 Cc01_g00430:1857 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TT TC +chr1:626826 [A/T] chr1 626826 Cc01_g00430:1863 exon SYNONYMOUS_CODING ccA/ccT P/P 16.7% 3 AA NN AA AT +chr1:626895 [G/A] chr1 626895 Cc01_g00430:1932 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN AA NN +chr1:626907 [G/A] chr1 626907 Cc01_g00430:1944 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:626917 [T/C] chr1 626917 Cc01_g00430:1954 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TC TT +chr1:626930 [G/C] chr1 626930 Cc01_g00430:1967 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 GG GG GG GC +chr1:626944 [G/A] chr1 626944 Cc01_g00430:1981 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG GA AG GG +chr1:626953 [G/A] chr1 626953 Cc01_g00430:1990 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA AA AG +chr1:626958 [A/C] chr1 626958 Cc01_g00430:1995 exon NON_SYNONYMOUS_CODING ttA/ttC L/F 12.5% 4 AA AA AC AA +chr1:626960 [T/G] chr1 626960 Cc01_g00430:1997 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 25.0% 4 TT TG GT TT +chr1:626962 [A/G] chr1 626962 Cc01_g00430:1999 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA GA AA AG +chr1:626990 [T/A] chr1 626990 Cc01_g00430:2027 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 12.5% 4 TT TT TT TA +chr1:626992 [G/A] chr1 626992 Cc01_g00430:2029 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 GG GA GG AG +chr1:627002 [G/A] chr1 627002 Cc01_g00430:2039 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG +chr1:627009 [C/T] chr1 627009 Cc01_g00430:2046 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC +chr1:627032 [G/T] chr1 627032 Cc01_g00430:2069 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GT GG GT +chr1:627051 [A/G] chr1 627051 Cc01_g00430:2088 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG +chr1:627058 [G/C] chr1 627058 Cc01_g00430:2095 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG CC CC GC +chr1:627068 [C/T] chr1 627068 Cc01_g00430:2105 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC TT TT CT +chr1:627110 [C/T] chr1 627110 Cc01_g00430:2147 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CC CT +chr1:627131 [C/T] chr1 627131 Cc01_g00430:2168 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT +chr1:627366 [G/T] chr1 627366 Cc01_g00430:2307 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG TT NN NN +chr1:627379 [T/G] chr1 627379 Cc01_g00430:2320 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 2 TT GG NN NN +chr1:627697 [G/A] chr1 627697 Cc01_g00430:2548 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 2 GG NN AA NN +chr1:627713 [A/T] chr1 627713 Cc01_g00430:2564 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 50.0% 2 AA NN TT NN +chr1:627715 [G/C] chr1 627715 Cc01_g00430:2566 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN CC NN +chr1:627727 [T/C] chr1 627727 Cc01_g00430:2578 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 TT NN CC NN +chr1:627753 [T/G] chr1 627753 Cc01_g00430:2604 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 2 TT NN GG NN +chr1:627759 [C/A] chr1 627759 Cc01_g00430:2610 exon NON_SYNONYMOUS_CODING caC/caA H/Q 50.0% 2 CC NN AA NN +chr1:627760 [G/A] chr1 627760 Cc01_g00430:2611 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN GA NN +chr1:627858 [C/T] chr1 627858 Cc01_g00430:2709 exon SYNONYMOUS_CODING ccC/ccT P/P 50.0% 2 CC NN NN TT +chr1:694337 [T/C] chr1 694337 Cc01_g00440:1131 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT CC NN NN +chr1:694724 [A/C] chr1 694724 Cc01_g00440:1518 exon SYNONYMOUS_CODING gtA/gtC V/V 50.0% 2 AA NN NN CC +chr1:694734 [G/A] chr1 694734 Cc01_g00440:1528 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA +chr1:695273 [C/G] chr1 695273 Cc01_g00440:2067 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 2 CC NN NN CG +chr1:695280 [A/G] chr1 695280 Cc01_g00440:2074 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG +chr1:695301 [T/A] chr1 695301 Cc01_g00440:2095 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 25.0% 2 TT NN NN TA +chr1:695306 [A/G] chr1 695306 Cc01_g00440:2100 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 2 AA NN NN AG +chr1:695389 [A/C] chr1 695389 Cc01_g00440:2183 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AC AC +chr1:695751 [A/G] chr1 695751 Cc01_g00440:2506 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 50.0% 4 AA GG AA GG +chr1:696170 [A/G] chr1 696170 Cc01_g00440:2790 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG +chr1:696187 [A/T] chr1 696187 Cc01_g00440:2807 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 50.0% 2 AA NN NN TT +chr1:696190 [T/C] chr1 696190 Cc01_g00440:2810 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 TT NN NN CC +chr1:696193 [C/A] chr1 696193 Cc01_g00440:2813 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 50.0% 2 CC NN NN AA +chr1:696194 [A/G] chr1 696194 Cc01_g00440:2814 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 2 AA NN NN GG +chr1:696282 [A/T] chr1 696282 Cc01_g00440:2902 exon NON_SYNONYMOUS_CODING Act/Tct T/S 50.0% 2 AA NN NN TT +chr1:696283 [C/T] chr1 696283 Cc01_g00440:2903 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 CC NN NN TT +chr1:696299 [T/A] chr1 696299 Cc01_g00440:2919 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 2 TT NN NN TA +chr1:696368 [T/G] chr1 696368 Cc01_g00440:2988 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG +chr1:696565 [A/G] chr1 696565 Cc01_g00440:3131 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN GG AA +chr1:696569 [C/T] chr1 696569 Cc01_g00440:3135 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC NN TT CC +chr1:696578 [G/A] chr1 696578 Cc01_g00440:3144 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG NN AA GG +chr1:696580 [A/G] chr1 696580 Cc01_g00440:3146 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 33.3% 3 AA NN GG AA +chr1:696589 [A/T] chr1 696589 Cc01_g00440:3155 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA NN TT AA +chr1:696664 [C/A] chr1 696664 Cc01_g00440:3230 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC AA CC NN +chr1:698121 [T/A] chr1 698121 Cc01_g00450:9 exon STOP_GAINED taT/taA Y3* 25.0% 4 TT TA TT TA +chr1:698290 [C/A] chr1 698290 Cc01_g00450:59 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 12.5% 4 CC CC CC CA +chr1:698302 [A/G] chr1 698302 Cc01_g00450:71 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AG AG AA +chr1:698316 [G/T] chr1 698316 Cc01_g00450:85 exon STOP_GAINED Gga/Tga G/9 37.5% 4 GG TG TG TG +chr1:698328 [G/A] chr1 698328 Cc01_g00450:97 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AG GA GA +chr1:698331 [A/G] chr1 698331 Cc01_g00450:100 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 37.5% 4 AA GA AG AG +chr1:698332 [G/A] chr1 698332 Cc01_g00450:101 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 37.5% 4 GG GA AG AG +chr1:698333 [A/G] chr1 698333 Cc01_g00450:102 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG +chr1:698339 [A/G] chr1 698339 Cc01_g00450:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG GG GG +chr1:698350 [C/T] chr1 698350 Cc01_g00450:119 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 37.5% 4 CC TC CT CT +chr1:698355 [A/G] chr1 698355 Cc01_g00450:124 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG +chr1:698372 [C/G] chr1 698372 Cc01_g00450:141 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG +chr1:698398 [T/G] chr1 698398 Cc01_g00450:167 exon STOP_GAINED tTa/tGa L/6 33.3% 3 TT TT NN GG +chr1:698411 [T/C] chr1 698411 Cc01_g00450:180 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC TT TT +chr1:698426 [G/A] chr1 698426 Cc01_g00450:195 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG GA GG GA +chr1:698432 [G/A] chr1 698432 Cc01_g00450:201 exon STOP_GAINED tgG/tgA W/7 50.0% 4 GG AA GA GA +chr1:698434 [A/G] chr1 698434 Cc01_g00450:203 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 AA GG GG AG +chr1:714525 [A/G] chr1 714525 Cc01_g00470:91 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN GG NN +chr1:714606 [C/A] chr1 714606 Cc01_g00470:172 exon NON_SYNONYMOUS_CODING Cgt/Agt R/S 50.0% 4 CC AA CC AA +chr1:714611 [G/A] chr1 714611 Cc01_g00470:177 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG +chr1:714616 [T/A] chr1 714616 Cc01_g00470:182 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 33.3% 3 TT NN TT AA +chr1:714635 [G/A] chr1 714635 Cc01_g00470:201 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG NN AA AA +chr1:714636 [C/G] chr1 714636 Cc01_g00470:202 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 33.3% 3 CC NN GG GG +chr1:715733 [C/G] chr1 715733 Cc01_g00470:1198 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 4 CC GG GG CC +chr1:715736 [T/G] chr1 715736 Cc01_g00470:1201 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 TT TT TT TG +chr1:715743 [C/A] chr1 715743 Cc01_g00470:1208 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 50.0% 4 CC AA AA CC +chr1:715749 [G/T] chr1 715749 Cc01_g00470:1214 exon NON_SYNONYMOUS_CODING cGc/cTc R/L 50.0% 4 GG TT TT GG +chr1:715750 [C/T] chr1 715750 Cc01_g00470:1215 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CC CC TC +chr1:715751 [G/A] chr1 715751 Cc01_g00470:1216 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA +chr1:715769 [G/A] chr1 715769 Cc01_g00470:1234 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 2 GG NN NN GA +chr1:715779 [A/G] chr1 715779 Cc01_g00470:1244 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA NN NN GG +chr1:715853 [G/C] chr1 715853 Cc01_g00470:1318 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN NN CC +chr1:716060 [A/C] chr1 716060 Cc01_g00470:1525 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 50.0% 2 AA NN CC NN +chr1:716123 [G/A] chr1 716123 Cc01_g00470:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG NN AA NN +chr1:716482 [G/A] chr1 716482 Cc01_g00470:1836 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA GG +chr1:716498 [G/C] chr1 716498 Cc01_g00470:1852 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC +chr1:716510 [G/A] chr1 716510 Cc01_g00470:1864 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA +chr1:716535 [A/G] chr1 716535 Cc01_g00470:1889 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG AA AA +chr1:716594 [T/C] chr1 716594 Cc01_g00470:1948 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT CC TC CC +chr1:716622 [A/G] chr1 716622 Cc01_g00470:1976 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 12.5% 4 AA AA AA AG +chr1:716696 [C/T] chr1 716696 Cc01_g00470:2050 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 33.3% 3 CC NN TT CC +chr1:716714 [G/C] chr1 716714 Cc01_g00470:2068 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC +chr1:716724 [A/G] chr1 716724 Cc01_g00470:2078 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 3 AA NN GG AG +chr1:716729 [G/C] chr1 716729 Cc01_g00470:2083 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 33.3% 3 GG NN CC GG +chr1:716741 [G/A] chr1 716741 Cc01_g00470:2095 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 2 GG NN NN AA +chr1:716770 [C/T] chr1 716770 Cc01_g00470:2124 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 2 CC NN NN TT +chr1:716789 [C/A] chr1 716789 Cc01_g00470:2143 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 50.0% 2 CC NN NN AA +chr1:716793 [C/A] chr1 716793 Cc01_g00470:2147 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 2 CC NN NN CA +chr1:716863 [T/C] chr1 716863 Cc01_g00470:2217 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT NN CC TT +chr1:716867 [G/C] chr1 716867 Cc01_g00470:2221 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG NN CC GG +chr1:716879 [A/T] chr1 716879 Cc01_g00470:2233 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA NN AA AT +chr1:716880 [A/T] chr1 716880 Cc01_g00470:2234 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 33.3% 3 AA NN TT AA +chr1:717010 [T/C] chr1 717010 Cc01_g00470:2364 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC +chr1:717382 [A/G] chr1 717382 Cc01_g00470:2502 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA NN AA AG +chr1:717405 [A/G] chr1 717405 Cc01_g00470:2525 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AA AA AG +chr1:718555 [G/T] chr1 718555 Cc01_g00480:7 exon STOP_GAINED Gga/Tga G3* 50.0% 4 GG TT GT GT +chr1:718570 [A/G] chr1 718570 Cc01_g00480:22 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 25.0% 4 AA GG GG GG +chr1:718578 [A/G] chr1 718578 Cc01_g00480:30 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG +chr1:718579 [A/G] chr1 718579 Cc01_g00480:31 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG +chr1:718589 [T/C] chr1 718589 Cc01_g00480:41 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 TT TC CT CT +chr1:718602 [A/G] chr1 718602 Cc01_g00480:54 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:718616 [A/G] chr1 718616 Cc01_g00480:68 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA GA AG AG +chr1:718623 [A/G] chr1 718623 Cc01_g00480:75 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GA AG AG +chr1:718626 [A/C] chr1 718626 Cc01_g00480:78 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 37.5% 4 AA AC CA CA +chr1:718632 [A/G] chr1 718632 Cc01_g00480:84 exon SYNONYMOUS_CODING ggA/ggG G/G 37.5% 4 AA GG GG GA +chr1:718633 [C/T] chr1 718633 Cc01_g00480:85 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT +chr1:718636 [G/A] chr1 718636 Cc01_g00480:88 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG AG GA GA +chr1:718676 [A/G] chr1 718676 Cc01_g00480:128 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA GA AA AA +chr1:719091 [T/A] chr1 719091 Cc01_g00480:135 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA AT TT +chr1:720709 [G/A] chr1 720709 Cc01_g00490:200 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 33.3% 3 GG NN AA AA +chr1:757845 [A/T] chr1 757845 Cc01_g00500:54 exon SYNONYMOUS_CODING acT/acA T/T 50.0% 3 AA TT AT NN +chr1:757827 [A/T] chr1 757827 Cc01_g00500:72 exon SYNONYMOUS_CODING acT/acA T/T 37.5% 4 AA TT AT TT +chr1:757176 [T/A] chr1 757176 Cc01_g00500:160 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 TT TT TT TA +chr1:757171 [A/C] chr1 757171 Cc01_g00500:165 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 AA AC AC CA +chr1:757169 [C/G] chr1 757169 Cc01_g00500:167 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC GC CC +chr1:757141 [T/C] chr1 757141 Cc01_g00500:195 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:756891 [T/C] chr1 756891 Cc01_g00500:213 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT CT TT TT +chr1:756475 [G/A] chr1 756475 Cc01_g00500:399 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA +chr1:756448 [T/C] chr1 756448 Cc01_g00500:426 exon SYNONYMOUS_CODING tcA/tcG S/S 33.3% 3 TT NN TT CC +chr1:763230 [A/C] chr1 763230 Cc01_g00510:245 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 50.0% 2 AA NN NN CC +chr1:765710 [A/G] chr1 765710 Cc01_g00520:150 exon SYNONYMOUS_CODING acA/acG T/T 50.0% 3 AA NN AG GG +chr1:765774 [C/G] chr1 765774 Cc01_g00520:214 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 50.0% 2 CC NN NN GG +chr1:767708 [C/T] chr1 767708 Cc01_g00520:2019 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 3 CC TT NN CT +chr1:767754 [T/C] chr1 767754 Cc01_g00520:2065 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT +chr1:767773 [T/C] chr1 767773 Cc01_g00520:2084 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 TT TC TT TT +chr1:767784 [A/G] chr1 767784 Cc01_g00520:2095 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG AA AG +chr1:768089 [T/G] chr1 768089 Cc01_g00520:2142 exon NON_SYNONYMOUS_CODING agT/agG S/R 16.7% 3 TT NN TG TT +chr1:768095 [G/T] chr1 768095 Cc01_g00520:2148 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 16.7% 3 GG NN GT GG +chr1:768097 [G/T] chr1 768097 Cc01_g00520:2150 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 16.7% 3 GG NN GT GG +chr1:768140 [A/T] chr1 768140 Cc01_g00520:2193 exon SYNONYMOUS_CODING ctA/ctT L/L 50.0% 3 AA NN AT TT +chr1:768149 [G/T] chr1 768149 Cc01_g00520:2202 exon SYNONYMOUS_CODING gcG/gcT A/A 50.0% 3 GG NN GT TT +chr1:768210 [A/G] chr1 768210 Cc01_g00520:2263 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 3 AA NN AG GG +chr1:768322 [G/A] chr1 768322 Cc01_g00520:2375 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG NN GA GG +chr1:768476 [T/G] chr1 768476 Cc01_g00520:2529 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 25.0% 4 TT GG TT TT +chr1:768570 [G/A] chr1 768570 Cc01_g00520:2623 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 GG NN GA AA +chr1:768621 [A/C] chr1 768621 Cc01_g00520:2674 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 33.3% 3 AA NN CC AA +chr1:768623 [G/C] chr1 768623 Cc01_g00520:2676 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 50.0% 3 GG NN GC CC +chr1:768653 [C/T] chr1 768653 Cc01_g00520:2706 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC NN TT CC +chr1:768703 [C/T] chr1 768703 Cc01_g00520:2756 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 16.7% 3 CC NN CC CT +chr1:768709 [T/G] chr1 768709 Cc01_g00520:2762 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 16.7% 3 TT NN TT TG +chr1:768710 [T/G] chr1 768710 Cc01_g00520:2763 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 16.7% 3 TT NN TT TG +chr1:768718 [G/C] chr1 768718 Cc01_g00520:2771 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 33.3% 3 GG NN CC CC +chr1:768724 [C/T] chr1 768724 Cc01_g00520:2777 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 16.7% 3 CC NN CC CT +chr1:768748 [A/G] chr1 768748 Cc01_g00520:2801 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN AA GG +chr1:768806 [A/G] chr1 768806 Cc01_g00520:2859 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 3 AA NN AG GG +chr1:768948 [G/A] chr1 768948 Cc01_g00520:2917 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA AA GG +chr1:768971 [T/C] chr1 768971 Cc01_g00520:2940 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC NN TT +chr1:772576 [A/T] chr1 772576 Cc01_g00530:220 exon STOP_GAINED Aaa/Taa K/4 37.5% 4 AA TT TT AT +chr1:772604 [A/G] chr1 772604 Cc01_g00530:248 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 3 AA NN GG AG +chr1:787097 [G/A] chr1 787097 Cc01_g00550:1089 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 3 GG NN AA GA +chr1:787673 [T/G] chr1 787673 Cc01_g00550:1596 exon NON_SYNONYMOUS_CODING caT/caG H/Q 33.3% 3 TT GG NN GG +chr1:788087 [C/T] chr1 788087 Cc01_g00550:1680 exon SYNONYMOUS_CODING ctC/ctT L/L 16.7% 3 CC NN CC CT +chr1:788159 [G/A] chr1 788159 Cc01_g00550:1752 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GA GG GG +chr1:788273 [C/A] chr1 788273 Cc01_g00550:1866 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 25.0% 4 CC AA CC CC +chr1:788275 [C/T] chr1 788275 Cc01_g00550:1868 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC TT CT CT +chr1:788383 [C/G] chr1 788383 Cc01_g00550:1886 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN +chr1:788482 [C/T] chr1 788482 Cc01_g00550:1985 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:788491 [G/A] chr1 788491 Cc01_g00550:1994 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 GG GG GA GG +chr1:788516 [A/G] chr1 788516 Cc01_g00550:2019 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG +chr1:788558 [A/G] chr1 788558 Cc01_g00550:2061 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA GG AA AA +chr1:788560 [T/C] chr1 788560 Cc01_g00550:2063 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 TT CC TT TT +chr1:788561 [C/G] chr1 788561 Cc01_g00550:2064 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG CC CC +chr1:788694 [G/A] chr1 788694 Cc01_g00550:2197 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 GG AA GG GA +chr1:788708 [G/A] chr1 788708 Cc01_g00550:2211 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG +chr1:788716 [A/C] chr1 788716 Cc01_g00550:2219 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 AA AC AA AA +chr1:836275 [A/G] chr1 836275 Cc01_g00570:39 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 2 AA NN NN AG +chr1:836319 [C/T] chr1 836319 Cc01_g00570:83 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:836362 [T/A] chr1 836362 Cc01_g00570:126 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TA TT TT +chr1:837674 [G/C] chr1 837674 Cc01_g00570:1378 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 50.0% 2 GG NN NN CC +chr1:837956 [A/G] chr1 837956 Cc01_g00570:1660 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 AA GG NN AA +chr1:837958 [T/A] chr1 837958 Cc01_g00570:1662 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 TT AA NN TT +chr1:837989 [A/G] chr1 837989 Cc01_g00570:1693 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN +chr1:838599 [A/T] chr1 838599 Cc01_g00570:2303 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 16.7% 3 AA AA NN AT +chr1:838628 [T/C] chr1 838628 Cc01_g00570:2332 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 33.3% 3 TT CC NN CC +chr1:838667 [T/A] chr1 838667 Cc01_g00570:2338 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 2 TT TA NN NN +chr1:838670 [A/G] chr1 838670 Cc01_g00570:2341 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 AA GA NN NN +chr1:838676 [A/G] chr1 838676 Cc01_g00570:2347 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN +chr1:838683 [C/G] chr1 838683 Cc01_g00570:2354 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC GG NN NN +chr1:838689 [C/T] chr1 838689 Cc01_g00570:2360 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 33.3% 3 CC TT CC NN +chr1:838705 [C/T] chr1 838705 Cc01_g00570:2376 exon SYNONYMOUS_CODING ctC/ctT L/L 33.3% 3 CC CC TT NN +chr1:838717 [T/A] chr1 838717 Cc01_g00570:2388 exon SYNONYMOUS_CODING tcT/tcA S/S 50.0% 2 TT AA NN NN +chr1:839122 [G/A] chr1 839122 Cc01_g00570:2689 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 50.0% 2 GG AA NN NN +chr1:839352 [G/A] chr1 839352 Cc01_g00570:2919 exon SYNONYMOUS_CODING agG/agA R/R 50.0% 2 GG NN NN AA +chr1:839601 [A/T] chr1 839601 Cc01_g00570:3168 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA NN NN TT +chr1:839786 [G/A] chr1 839786 Cc01_g00570:3353 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 GG NN NN AA +chr1:839932 [G/A] chr1 839932 Cc01_g00570:3499 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA +chr1:928733 [T/C] chr1 928733 Cc01_g00580:26 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 TT NN TT TC +chr1:928809 [A/G] chr1 928809 Cc01_g00580:102 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 2 AA NN NN GG +chr1:928827 [A/G] chr1 928827 Cc01_g00580:120 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 2 AA NN NN AG +chr1:928836 [A/G] chr1 928836 Cc01_g00580:129 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 2 AA NN NN GA +chr1:928904 [A/G] chr1 928904 Cc01_g00580:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 2 AA NN NN GA +chr1:966451 [A/G] chr1 966451 Cc01_g00590:185 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 2 AA NN NN GG +chr1:966652 [A/G] chr1 966652 Cc01_g00590:386 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG +chr1:966654 [A/G] chr1 966654 Cc01_g00590:388 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN NN GG +chr1:966661 [A/C] chr1 966661 Cc01_g00590:395 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 50.0% 2 AA NN NN CC +chr1:966719 [A/G] chr1 966719 Cc01_g00590:453 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG +chr1:966803 [T/C] chr1 966803 Cc01_g00590:486 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC +chr1:966831 [G/C] chr1 966831 Cc01_g00590:514 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GG GG GC +chr1:966834 [A/G] chr1 966834 Cc01_g00590:517 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG +chr1:966846 [G/A] chr1 966846 Cc01_g00590:529 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 GG AA AA AG +chr1:966866 [C/T] chr1 966866 Cc01_g00590:549 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 2 CC NN NN TT +chr1:967049 [G/T] chr1 967049 Cc01_g00590:732 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG NN NN TT +chr1:967059 [G/A] chr1 967059 Cc01_g00590:742 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG NN NN AA +chr1:967062 [A/G] chr1 967062 Cc01_g00590:745 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA NN NN GG +chr1:967063 [A/T] chr1 967063 Cc01_g00590:746 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 50.0% 2 AA NN NN TT +chr1:967183 [C/G] chr1 967183 Cc01_g00590:866 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 33.3% 3 CC CC NN GG +chr1:967752 [G/T] chr1 967752 Cc01_g00590:1435 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 3 GG TT NN GT +chr1:967768 [C/G] chr1 967768 Cc01_g00590:1451 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 CC GG NN GG +chr1:967992 [G/A] chr1 967992 Cc01_g00590:1675 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG NN AA AA +chr1:986447 [C/A] chr1 986447 Cc01_g00610:57 exon SYNONYMOUS_CODING cgC/cgA R/R 12.5% 4 CC CC CC CA +chr1:986448 [G/A] chr1 986448 Cc01_g00610:58 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GA GG AG +chr1:986456 [A/G] chr1 986456 Cc01_g00610:66 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG +chr1:986518 [T/G] chr1 986518 Cc01_g00610:128 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 25.0% 4 TT TG TG TT +chr1:986525 [G/T] chr1 986525 Cc01_g00610:135 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GG TG +chr1:986546 [G/A] chr1 986546 Cc01_g00610:156 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 2 GG NN NN GA +chr1:986690 [G/A] chr1 986690 Cc01_g00610:300 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA +chr1:986709 [G/A] chr1 986709 Cc01_g00610:319 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA +chr1:986710 [A/T] chr1 986710 Cc01_g00610:320 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 AA AA AA AT +chr1:986736 [C/G] chr1 986736 Cc01_g00610:346 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 CC CG CC GG +chr1:987100 [C/T] chr1 987100 Cc01_g00610:546 exon SYNONYMOUS_CODING tcC/tcT S/S 16.7% 3 CC NN CC CT +chr1:987154 [T/A] chr1 987154 Cc01_g00610:600 exon NON_SYNONYMOUS_CODING agT/agA S/R 50.0% 4 TT AA TA TA +chr1:987159 [A/T] chr1 987159 Cc01_g00610:605 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA TA +chr1:987178 [A/G] chr1 987178 Cc01_g00610:624 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 4 AA GG AG AG +chr1:987200 [G/A] chr1 987200 Cc01_g00610:646 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG +chr1:987232 [T/G] chr1 987232 Cc01_g00610:678 exon SYNONYMOUS_CODING tcT/tcG S/S 50.0% 4 TT GG TG TG +chr1:987567 [A/T] chr1 987567 Cc01_g00610:1013 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 25.0% 4 AA AA AA TT +chr1:987582 [A/C] chr1 987582 Cc01_g00610:1028 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AA CC +chr1:987606 [G/A] chr1 987606 Cc01_g00610:1052 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA +chr1:987613 [T/C] chr1 987613 Cc01_g00610:1059 exon SYNONYMOUS_CODING acT/acC T/T 33.3% 3 TT NN TT CC +chr1:987648 [T/C] chr1 987648 Cc01_g00610:1094 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 16.7% 3 TT NN TT TC +chr1:987704 [A/C] chr1 987704 Cc01_g00610:1150 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 16.7% 3 AA NN AA AC +chr1:987875 [C/G] chr1 987875 Cc01_g00610:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 33.3% 3 CC NN GG GG +chr1:988107 [A/G] chr1 988107 Cc01_g00610:1518 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG +chr1:988121 [A/G] chr1 988121 Cc01_g00610:1532 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 12.5% 4 AA AA AA AG +chr1:988128 [T/A] chr1 988128 Cc01_g00610:1539 exon NON_SYNONYMOUS_CODING agT/agA S/R 12.5% 4 TT TT TA TT +chr1:988129 [C/T] chr1 988129 Cc01_g00610:1540 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC TC CC TC +chr1:988136 [C/G] chr1 988136 Cc01_g00610:1547 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 CC CC CC GC +chr1:988162 [G/C] chr1 988162 Cc01_g00610:1573 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GG GC GC +chr1:997411 [A/G] chr1 997411 Cc01_g00620:25 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA NN AG AG +chr1:997409 [G/A] chr1 997409 Cc01_g00620:27 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 GG NN AA AA +chr1:997392 [T/C] chr1 997392 Cc01_g00620:44 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 TT NN TT CT +chr1:997300 [C/G] chr1 997300 Cc01_g00620:60 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC +chr1:997296 [G/A] chr1 997296 Cc01_g00620:64 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG +chr1:997213 [G/A] chr1 997213 Cc01_g00620:147 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 GG AA AA AA +chr1:997200 [C/A] chr1 997200 Cc01_g00620:160 exon NON_SYNONYMOUS_CODING Gcg/Tcg A/S 50.0% 3 CC AA NN CA +chr1:997185 [T/G] chr1 997185 Cc01_g00620:175 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT NN NN GG +chr1:997169 [A/G] chr1 997169 Cc01_g00620:191 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 25.0% 2 AA NN NN AG +chr1:997094 [A/G] chr1 997094 Cc01_g00620:266 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 2 AA NN NN AG +chr1:997051 [G/C] chr1 997051 Cc01_g00620:309 exon SYNONYMOUS_CODING tcC/tcG S/S 50.0% 2 GG NN NN CC +chr1:995391 [A/G] chr1 995391 Cc01_g00620:348 exon SYNONYMOUS_CODING ctT/ctC L/L 16.7% 3 AA AG NN AA +chr1:995363 [T/C] chr1 995363 Cc01_g00620:376 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 TT TC NN NN +chr1:994056 [G/T] chr1 994056 Cc01_g00620:1180 exon SYNONYMOUS_CODING Cgg/Agg R/R 50.0% 2 GG NN NN TT +chr1:994012 [A/C] chr1 994012 Cc01_g00620:1224 exon SYNONYMOUS_CODING cgT/cgG R/R 50.0% 2 AA NN NN CC +chr1:1105670 [T/C] chr1 1105670 Cc01_g00630:393 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:1105722 [A/G] chr1 1105722 Cc01_g00630:445 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG +chr1:1124006 [T/C] chr1 1124006 Cc01_g00640:198 exon SYNONYMOUS_CODING atT/atC I/I 33.3% 3 TT CC NN TT +chr1:1124349 [T/C] chr1 1124349 Cc01_g00640:426 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT CC TT +chr1:1125855 [G/A] chr1 1125855 Cc01_g00640:1414 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GA NN GG +chr1:1125920 [T/A] chr1 1125920 Cc01_g00640:1479 exon SYNONYMOUS_CODING acT/acA T/T 33.3% 3 TT AA NN TT +chr1:1125966 [A/T] chr1 1125966 Cc01_g00640:1525 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA TT NN AA +chr1:1126013 [A/G] chr1 1126013 Cc01_g00640:1572 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA GG NN NN +chr1:1151834 [G/C] chr1 1151834 Cc01_g00670:239 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 GG GC GG GG +chr1:1153859 [G/A] chr1 1153859 Cc01_g00670:410 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GG GA +chr1:1153862 [A/G] chr1 1153862 Cc01_g00670:413 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 AA GG AG GG +chr1:1153873 [A/C] chr1 1153873 Cc01_g00670:424 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA AC +chr1:1154467 [T/G] chr1 1154467 Cc01_g00670:486 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT TG TG +chr1:1154473 [T/C] chr1 1154473 Cc01_g00670:492 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TT TC +chr1:1154482 [T/G] chr1 1154482 Cc01_g00670:501 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 TT TT TG TG +chr1:1154490 [C/G] chr1 1154490 Cc01_g00670:509 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC CC CG CG +chr1:1154495 [A/G] chr1 1154495 Cc01_g00670:514 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA +chr1:1154499 [T/C] chr1 1154499 Cc01_g00670:518 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1154515 [C/G] chr1 1154515 Cc01_g00670:534 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CG CC CC +chr1:1154527 [G/T] chr1 1154527 Cc01_g00670:546 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GT GG GG +chr1:1154549 [A/G] chr1 1154549 Cc01_g00670:568 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA GA AA +chr1:1154550 [A/T] chr1 1154550 Cc01_g00670:569 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 AA AT TA AT +chr1:1154579 [A/G] chr1 1154579 Cc01_g00670:598 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:1154582 [T/G] chr1 1154582 Cc01_g00670:601 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT +chr1:1154588 [A/C] chr1 1154588 Cc01_g00670:607 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA +chr1:1154849 [G/A] chr1 1154849 Cc01_g00670:711 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GA AA +chr1:1154858 [G/A] chr1 1154858 Cc01_g00670:720 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG +chr1:1154868 [A/G] chr1 1154868 Cc01_g00670:730 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA +chr1:1154885 [G/A] chr1 1154885 Cc01_g00670:747 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG AG GG GG +chr1:1154894 [A/G] chr1 1154894 Cc01_g00670:756 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA GA AA AA +chr1:1154916 [T/A] chr1 1154916 Cc01_g00670:778 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT AT TT TT +chr1:1154924 [T/C] chr1 1154924 Cc01_g00670:786 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT CT TT TT +chr1:1154929 [C/G] chr1 1154929 Cc01_g00670:791 exon STOP_GAINED tCa/tGa S/4 12.5% 4 CC GC CC CC +chr1:1154930 [A/G] chr1 1154930 Cc01_g00670:792 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:1154936 [G/C] chr1 1154936 Cc01_g00670:798 exon NON_SYNONYMOUS_CODING agG/agC R/S 12.5% 4 GG CG GG GG +chr1:1154941 [T/C] chr1 1154941 Cc01_g00670:803 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT CT TT TT +chr1:1154946 [G/A] chr1 1154946 Cc01_g00670:808 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG +chr1:1154952 [A/T] chr1 1154952 Cc01_g00670:814 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 25.0% 4 AA TT AA AA +chr1:1154976 [A/G] chr1 1154976 Cc01_g00670:838 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA +chr1:1154985 [C/G] chr1 1154985 Cc01_g00670:847 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 CC GC CC CC +chr1:1155000 [G/A] chr1 1155000 Cc01_g00670:862 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG +chr1:1155003 [C/A] chr1 1155003 Cc01_g00670:865 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 12.5% 4 CC AC CC CC +chr1:1155015 [T/A] chr1 1155015 Cc01_g00670:877 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 TT AT TT TT +chr1:1155017 [A/G] chr1 1155017 Cc01_g00670:879 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA GA AA AA +chr1:1155021 [C/T] chr1 1155021 Cc01_g00670:883 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC TC CC CC +chr1:1155927 [G/A] chr1 1155927 Cc01_g00670:906 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1155945 [C/G] chr1 1155945 Cc01_g00670:924 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 CC CC CC CG +chr1:1155970 [G/A] chr1 1155970 Cc01_g00670:949 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG +chr1:1155978 [G/A] chr1 1155978 Cc01_g00670:957 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG AG GG GG +chr1:1156036 [C/G] chr1 1156036 Cc01_g00670:1015 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC GC CC CC +chr1:1156056 [G/T] chr1 1156056 Cc01_g00670:1035 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 12.5% 4 GG GG GG GT +chr1:1156075 [C/T] chr1 1156075 Cc01_g00670:1054 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 12.5% 4 CC CT CC CC +chr1:1156086 [A/T] chr1 1156086 Cc01_g00670:1065 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 AA TA AA AA +chr1:1156095 [A/G] chr1 1156095 Cc01_g00670:1074 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG +chr1:1156099 [A/C] chr1 1156099 Cc01_g00670:1078 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 12.5% 4 AA CA AA AA +chr1:1156677 [C/T] chr1 1156677 Cc01_g00670:1089 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CT CC CC +chr1:1156701 [T/G] chr1 1156701 Cc01_g00670:1113 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT GT TT TT +chr1:1156712 [T/A] chr1 1156712 Cc01_g00670:1124 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 12.5% 4 TT AT TT TT +chr1:1156733 [T/C] chr1 1156733 Cc01_g00670:1145 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 TT CC TC CC +chr1:1156813 [G/A] chr1 1156813 Cc01_g00670:1225 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 GG GA GG GG +chr1:1156819 [A/G] chr1 1156819 Cc01_g00670:1231 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 12.5% 4 AA AG AA AA +chr1:1156820 [G/A] chr1 1156820 Cc01_g00670:1232 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1156883 [T/C] chr1 1156883 Cc01_g00670:1295 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1156892 [A/G] chr1 1156892 Cc01_g00670:1304 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA +chr1:1156901 [T/A] chr1 1156901 Cc01_g00670:1313 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TA TT TT +chr1:1156908 [C/T] chr1 1156908 Cc01_g00670:1320 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT CT +chr1:1165679 [A/T] chr1 1165679 Cc01_g00680:45 exon STOP_GAINED tgT/tgA C/5 37.5% 4 AA TT AT TT +chr1:1165649 [C/T] chr1 1165649 Cc01_g00680:75 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT CT TT +chr1:1165641 [A/G] chr1 1165641 Cc01_g00680:83 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 AA AA AG AA +chr1:1165640 [G/A] chr1 1165640 Cc01_g00680:84 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG AA AA AA +chr1:1165637 [A/G] chr1 1165637 Cc01_g00680:87 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA GG GG GG +chr1:1165630 [G/T] chr1 1165630 Cc01_g00680:94 exon NON_SYNONYMOUS_CODING Ccc/Acc P/T 25.0% 4 GG TT TT TT +chr1:1166386 [C/A] chr1 1166386 Cc01_g00690:200 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 33.3% 3 CC NN CC AA +chr1:1166466 [A/C] chr1 1166466 Cc01_g00690:280 exon NON_SYNONYMOUS_CODING Act/Cct T/P 16.7% 3 AA NN AA AC +chr1:1166542 [T/G] chr1 1166542 Cc01_g00690:356 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 33.3% 3 TT NN TT GG +chr1:1166804 [C/A] chr1 1166804 Cc01_g00690:618 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC CC CC AA +chr1:1167034 [G/C] chr1 1167034 Cc01_g00700:60 exon NON_SYNONYMOUS_CODING agG/agC R/S 33.3% 3 GG NN GG CC +chr1:1167354 [A/G] chr1 1167354 Cc01_g00700:380 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 33.3% 3 AA NN AA GG +chr1:1167571 [G/T] chr1 1167571 Cc01_g00700:597 exon NON_SYNONYMOUS_CODING agG/agT R/S 33.3% 3 GG NN GG TT +chr1:1179790 [G/A] chr1 1179790 Cc01_g00710:105 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GG AA GG +chr1:1179828 [C/G] chr1 1179828 Cc01_g00710:143 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG GG GG +chr1:1179917 [A/T] chr1 1179917 Cc01_g00710:232 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 AA TT TT TT +chr1:1179943 [C/T] chr1 1179943 Cc01_g00710:258 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT +chr1:1179952 [T/C] chr1 1179952 Cc01_g00710:267 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC +chr1:1179953 [G/A] chr1 1179953 Cc01_g00710:268 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA +chr1:1179985 [C/T] chr1 1179985 Cc01_g00710:300 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT +chr1:1180012 [A/G] chr1 1180012 Cc01_g00710:327 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG GG GG +chr1:1180056 [T/C] chr1 1180056 Cc01_g00710:371 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC CC CC +chr1:1180061 [T/C] chr1 1180061 Cc01_g00710:376 exon STOP_LOST Tag/Cag 1/Q 25.0% 4 TT CC CC CC +chr1:1180063 [G/C] chr1 1180063 Cc01_g00710:378 exon STOP_LOST taG/taC 1/Y 33.3% 3 GG NN CC CC +chr1:1212493 [G/C] chr1 1212493 Cc01_g00720:7 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 33.3% 3 GG CC NN GG +chr1:1212477 [T/C] chr1 1212477 Cc01_g00720:23 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT CC TT TT +chr1:1212194 [A/T] chr1 1212194 Cc01_g00720:160 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 AA TT AA AA +chr1:1212184 [C/G] chr1 1212184 Cc01_g00720:170 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 12.5% 4 CC CG CC CC +chr1:1212161 [G/A] chr1 1212161 Cc01_g00720:193 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 GG AA GG GG +chr1:1212152 [A/G] chr1 1212152 Cc01_g00720:202 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG AA AA +chr1:1212124 [C/A] chr1 1212124 Cc01_g00720:230 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC +chr1:1211997 [A/T] chr1 1211997 Cc01_g00720:357 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT AA AA +chr1:1211930 [T/C] chr1 1211930 Cc01_g00720:424 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC TT TT +chr1:1211567 [A/G] chr1 1211567 Cc01_g00720:530 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG AA AA +chr1:1211520 [G/T] chr1 1211520 Cc01_g00720:577 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 GG TT GG GG +chr1:1211473 [C/A] chr1 1211473 Cc01_g00720:624 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC AA CC CC +chr1:1211425 [A/G] chr1 1211425 Cc01_g00720:672 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA +chr1:1211423 [A/C] chr1 1211423 Cc01_g00720:674 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 25.0% 4 AA CC AA AA +chr1:1211422 [G/C] chr1 1211422 Cc01_g00720:675 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG CC GG GG +chr1:1211398 [G/C] chr1 1211398 Cc01_g00720:699 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG CC GG GG +chr1:1211397 [G/T] chr1 1211397 Cc01_g00720:700 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 GG TT GG GG +chr1:1211383 [C/T] chr1 1211383 Cc01_g00720:714 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 CC TT CC CC +chr1:1211377 [C/T] chr1 1211377 Cc01_g00720:720 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 CC TT CT CC +chr1:1211364 [T/G] chr1 1211364 Cc01_g00720:733 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 25.0% 4 TT GG TT TT +chr1:1211349 [C/T] chr1 1211349 Cc01_g00720:748 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TT CT CC +chr1:1210891 [T/A] chr1 1210891 Cc01_g00720:758 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 TT AA TT TT +chr1:1210874 [A/G] chr1 1210874 Cc01_g00720:775 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG AA AA +chr1:1210869 [A/G] chr1 1210869 Cc01_g00720:780 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:1210831 [T/A] chr1 1210831 Cc01_g00720:818 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 TT TA TT TT +chr1:1210823 [G/A] chr1 1210823 Cc01_g00720:826 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 25.0% 4 GG AA GG GG +chr1:1210781 [C/T] chr1 1210781 Cc01_g00720:868 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC +chr1:1210772 [A/T] chr1 1210772 Cc01_g00720:877 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 25.0% 4 AA TT TT TT +chr1:1210770 [A/C] chr1 1210770 Cc01_g00720:879 exon STOP_GAINED taT/taG Y/3 25.0% 4 AA CC AA AA +chr1:1210745 [T/C] chr1 1210745 Cc01_g00720:904 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT TT CC +chr1:1210744 [A/G] chr1 1210744 Cc01_g00720:905 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 AA GG AA AA +chr1:1210728 [T/C] chr1 1210728 Cc01_g00720:921 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC TT TT +chr1:1210710 [A/T] chr1 1210710 Cc01_g00720:939 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 AA TT AA AA +chr1:1210708 [A/G] chr1 1210708 Cc01_g00720:941 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA GG AA AA +chr1:1210663 [A/G] chr1 1210663 Cc01_g00720:986 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 AA GG AA AA +chr1:1210651 [T/A] chr1 1210651 Cc01_g00720:998 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT AA TT TT +chr1:1210640 [G/C] chr1 1210640 Cc01_g00720:1009 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG CC GG GG +chr1:1210632 [A/G] chr1 1210632 Cc01_g00720:1017 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA AA AG GG +chr1:1210613 [A/T] chr1 1210613 Cc01_g00720:1036 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 AA TT AA AA +chr1:1210611 [T/C] chr1 1210611 Cc01_g00720:1038 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC TT TT +chr1:1210566 [G/A] chr1 1210566 Cc01_g00720:1083 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG AA GG GG +chr1:1210546 [T/A] chr1 1210546 Cc01_g00720:1103 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 TT AA TT TT +chr1:1210538 [C/T] chr1 1210538 Cc01_g00720:1111 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT CC CC +chr1:1210516 [T/A] chr1 1210516 Cc01_g00720:1133 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT TT AA +chr1:1210512 [C/T] chr1 1210512 Cc01_g00720:1137 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC +chr1:1210505 [C/A] chr1 1210505 Cc01_g00720:1144 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 25.0% 4 CC AA CC CC +chr1:1242676 [A/G] chr1 1242676 Cc01_g00730:1 exon START_LOST Atg/Gtg M/V 25.0% 4 AA GG AA AA +chr1:1242683 [C/T] chr1 1242683 Cc01_g00730:8 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CT CC CC +chr1:1242684 [A/G] chr1 1242684 Cc01_g00730:9 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG AA +chr1:1242698 [C/T] chr1 1242698 Cc01_g00730:23 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 12.5% 4 CC CC CT CC +chr1:1242721 [C/G] chr1 1242721 Cc01_g00730:46 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC GG CC CG +chr1:1242729 [T/G] chr1 1242729 Cc01_g00730:54 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 TT GG TT TG +chr1:1242731 [C/A] chr1 1242731 Cc01_g00730:56 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 12.5% 4 CC CA CC CC +chr1:1242744 [A/T] chr1 1242744 Cc01_g00730:69 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 4 AA TT AT AT +chr1:1242762 [T/C] chr1 1242762 Cc01_g00730:87 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 4 TT CC TC TC +chr1:1242783 [A/G] chr1 1242783 Cc01_g00730:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 50.0% 4 AA GG AG AG +chr1:1242791 [G/C] chr1 1242791 Cc01_g00730:116 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 12.5% 4 GG GC GG GG +chr1:1242950 [G/T] chr1 1242950 Cc01_g00730:275 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT GG GG +chr1:1243019 [G/C] chr1 1243019 Cc01_g00730:344 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 25.0% 4 GG CC GG GG +chr1:1243020 [T/A] chr1 1243020 Cc01_g00730:345 exon SYNONYMOUS_CODING cgT/cgA R/R 25.0% 4 TT AA TT TT +chr1:1244895 [G/T] chr1 1244895 Cc01_g00730:369 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 GG TT GG GG +chr1:1244933 [T/A] chr1 1244933 Cc01_g00730:407 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT AA TT TT +chr1:1245002 [C/A] chr1 1245002 Cc01_g00730:476 exon NON_SYNONYMOUS_CODING cCt/cAt P/H 25.0% 4 CC CC CC AA +chr1:1245030 [G/A] chr1 1245030 Cc01_g00730:504 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG AA GG GG +chr1:1245060 [T/A] chr1 1245060 Cc01_g00730:534 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TA TT TT +chr1:1245492 [A/G] chr1 1245492 Cc01_g00730:553 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AA AG AG +chr1:1245530 [A/G] chr1 1245530 Cc01_g00730:591 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG +chr1:1245533 [T/C] chr1 1245533 Cc01_g00730:594 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:1245549 [C/A] chr1 1245549 Cc01_g00730:610 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 CC CC CA CA +chr1:1245553 [A/G] chr1 1245553 Cc01_g00730:614 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG +chr1:1245566 [G/C] chr1 1245566 Cc01_g00730:627 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC GG GG +chr1:1253676 [T/C] chr1 1253676 Cc01_g00740:865 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC TC +chr1:1256457 [G/T] chr1 1256457 Cc01_g00750:100 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 2 GG NN NN GT +chr1:1262785 [G/T] chr1 1262785 Cc01_g00760:45 exon SYNONYMOUS_CODING tcC/tcA S/S 50.0% 2 GG NN NN TT +chr1:1269842 [C/T] chr1 1269842 Cc01_g00770:45 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC CC NN CT +chr1:1269935 [C/G] chr1 1269935 Cc01_g00770:138 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GG GG CG +chr1:1269943 [G/A] chr1 1269943 Cc01_g00770:146 exon STOP_GAINED tGg/tAg W/9 37.5% 4 GG AA AA GA +chr1:1269976 [T/C] chr1 1269976 Cc01_g00770:179 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 TT TT TC TT +chr1:1270017 [T/C] chr1 1270017 Cc01_g00770:220 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT +chr1:1270071 [A/C] chr1 1270071 Cc01_g00770:274 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 12.5% 4 AA AA AA AC +chr1:1270072 [G/A] chr1 1270072 Cc01_g00770:275 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG +chr1:1270081 [T/C] chr1 1270081 Cc01_g00770:284 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TT CT +chr1:1270085 [T/C] chr1 1270085 Cc01_g00770:288 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT CT +chr1:1270104 [A/T] chr1 1270104 Cc01_g00770:307 exon NON_SYNONYMOUS_CODING Agg/Tgg R/W 12.5% 4 AA AA AT AA +chr1:1276100 [G/T] chr1 1276100 Cc01_g00770:317 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT +chr1:1278052 [G/A] chr1 1278052 Cc01_g00780:52 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA +chr1:1278096 [A/T] chr1 1278096 Cc01_g00780:96 exon NON_SYNONYMOUS_CODING agA/agT R/S 50.0% 4 AA TT AT AT +chr1:1278097 [A/G] chr1 1278097 Cc01_g00780:97 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 4 AA GG AG AG +chr1:1278180 [T/C] chr1 1278180 Cc01_g00780:180 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT CC CC CC +chr1:1278211 [T/C] chr1 1278211 Cc01_g00780:211 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT CC TC TT +chr1:1279216 [A/G] chr1 1279216 Cc01_g00780:409 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA AA AG AG +chr1:1287721 [T/C] chr1 1287721 Cc01_g00790:16 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 3 TT TC NN CC +chr1:1287672 [C/T] chr1 1287672 Cc01_g00790:31 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC CC TT CC +chr1:1287643 [T/C] chr1 1287643 Cc01_g00790:60 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:1287637 [C/T] chr1 1287637 Cc01_g00790:66 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT +chr1:1286824 [G/A] chr1 1286824 Cc01_g00790:136 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA +chr1:1286808 [T/C] chr1 1286808 Cc01_g00790:152 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TC TT TT +chr1:1285473 [T/C] chr1 1285473 Cc01_g00790:246 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC TC CC +chr1:1285472 [G/A] chr1 1285472 Cc01_g00790:247 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG +chr1:1284801 [T/C] chr1 1284801 Cc01_g00790:399 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TC TT +chr1:1287857 [C/A] chr1 1287857 Cc01_g00800:142 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 CC NN NN AA +chr1:1287818 [C/G] chr1 1287818 Cc01_g00800:181 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 50.0% 2 CC GG NN NN +chr1:1291612 [T/C] chr1 1291612 Cc01_g00810:61 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT +chr1:1291633 [A/T] chr1 1291633 Cc01_g00810:82 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 25.0% 4 AA AA AA TT +chr1:1291665 [T/C] chr1 1291665 Cc01_g00810:114 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TT CC +chr1:1291715 [A/G] chr1 1291715 Cc01_g00810:164 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GG AG AA +chr1:1291716 [C/T] chr1 1291716 Cc01_g00810:165 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 CC CC CC TT +chr1:1291740 [G/T] chr1 1291740 Cc01_g00810:189 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG GG GG TT +chr1:1292034 [T/A] chr1 1292034 Cc01_g00810:396 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT AA AA AA +chr1:1292248 [A/G] chr1 1292248 Cc01_g00810:510 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:1293103 [C/T] chr1 1293103 Cc01_g00810:767 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC +chr1:1293122 [C/G] chr1 1293122 Cc01_g00810:786 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC CC GG +chr1:1293811 [T/C] chr1 1293811 Cc01_g00810:813 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC +chr1:1293815 [C/A] chr1 1293815 Cc01_g00810:817 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 CC AA AA CC +chr1:1293824 [C/T] chr1 1293824 Cc01_g00810:826 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC TT TT CC +chr1:1293825 [A/G] chr1 1293825 Cc01_g00810:827 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 4 AA GG GG AA +chr1:1293978 [A/T] chr1 1293978 Cc01_g00810:882 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AA AA TT +chr1:1294013 [G/A] chr1 1294013 Cc01_g00810:917 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 GG GG GG GA +chr1:1294044 [A/T] chr1 1294044 Cc01_g00810:948 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA AA AA TT +chr1:1294134 [C/T] chr1 1294134 Cc01_g00810:1038 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC CC TT +chr1:1294702 [C/T] chr1 1294702 Cc01_g00810:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CT CC +chr1:1294781 [G/C] chr1 1294781 Cc01_g00810:1300 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG +chr1:1294832 [A/T] chr1 1294832 Cc01_g00810:1351 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 4 AA TT TT AA +chr1:1294843 [G/T] chr1 1294843 Cc01_g00810:1362 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT +chr1:1294891 [T/G] chr1 1294891 Cc01_g00810:1410 exon NON_SYNONYMOUS_CODING atT/atG I/M 37.5% 4 TT GG TG GG +chr1:1294916 [G/T] chr1 1294916 Cc01_g00810:1435 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GT GG +chr1:1299931 [A/C] chr1 1299931 Cc01_g00820:42 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 AA AC AA AC +chr1:1299953 [G/A] chr1 1299953 Cc01_g00820:64 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:1300252 [C/T] chr1 1300252 Cc01_g00820:219 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC CC TT CC +chr1:1300382 [C/T] chr1 1300382 Cc01_g00820:349 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 CC CC TT CC +chr1:1300390 [T/C] chr1 1300390 Cc01_g00820:357 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TT CC TT +chr1:1300457 [T/C] chr1 1300457 Cc01_g00820:424 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT +chr1:1300540 [T/C] chr1 1300540 Cc01_g00820:507 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TT CC TT +chr1:1300948 [C/T] chr1 1300948 Cc01_g00820:915 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT +chr1:1301593 [T/C] chr1 1301593 Cc01_g00820:1152 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT +chr1:1302393 [T/C] chr1 1302393 Cc01_g00820:1332 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT +chr1:1304941 [C/T] chr1 1304941 Cc01_g00820:2055 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT TT CC +chr1:1306040 [A/T] chr1 1306040 Cc01_g00820:2256 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA TT AA +chr1:1306100 [A/G] chr1 1306100 Cc01_g00820:2316 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GG AA +chr1:1306364 [T/C] chr1 1306364 Cc01_g00820:2482 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT +chr1:1306387 [A/G] chr1 1306387 Cc01_g00820:2505 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA +chr1:1307153 [T/C] chr1 1307153 Cc01_g00820:2580 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT +chr1:1307312 [T/C] chr1 1307312 Cc01_g00820:2652 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT +chr1:1307738 [A/T] chr1 1307738 Cc01_g00820:2802 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA TT AA +chr1:1308482 [A/T] chr1 1308482 Cc01_g00820:2964 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AT AA AA +chr1:1308494 [G/A] chr1 1308494 Cc01_g00820:2976 exon SYNONYMOUS_CODING agG/agA R/R 16.7% 3 GG GA NN GG +chr1:1308608 [C/A] chr1 1308608 Cc01_g00830:24 exon STOP_GAINED tgC/tgA C8* 16.7% 3 CC CA NN CC +chr1:1309677 [C/G] chr1 1309677 Cc01_g00830:163 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CG CG CC +chr1:1314539 [G/A] chr1 1314539 Cc01_g00840:25 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 3 GG AA NN GA +chr1:1314673 [G/A] chr1 1314673 Cc01_g00840:159 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA +chr1:1314823 [C/G] chr1 1314823 Cc01_g00840:309 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 CC GG GG GG +chr1:1314984 [G/A] chr1 1314984 Cc01_g00840:470 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 37.5% 4 GG GG AA GA +chr1:1315015 [G/C] chr1 1315015 Cc01_g00840:501 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG GG CC GC +chr1:1315050 [A/G] chr1 1315050 Cc01_g00840:536 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 AA AG NN AA +chr1:1315120 [C/A] chr1 1315120 Cc01_g00840:606 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA +chr1:1315139 [T/A] chr1 1315139 Cc01_g00840:625 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 16.7% 3 TT TT NN TA +chr1:1315156 [T/G] chr1 1315156 Cc01_g00840:642 exon SYNONYMOUS_CODING tcT/tcG S/S 16.7% 3 TT TT NN TG +chr1:1315218 [T/C] chr1 1315218 Cc01_g00840:704 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 3 TT NN CC TC +chr1:1315234 [C/T] chr1 1315234 Cc01_g00840:720 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC CC NN TT +chr1:1315240 [C/T] chr1 1315240 Cc01_g00840:726 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC CC NN TT +chr1:1315338 [A/T] chr1 1315338 Cc01_g00840:824 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA TT NN AA +chr1:1324380 [G/A] chr1 1324380 Cc01_g00850:82 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA +chr1:1324392 [A/G] chr1 1324392 Cc01_g00850:94 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 37.5% 4 AA GG GG AG +chr1:1324409 [G/C] chr1 1324409 Cc01_g00850:111 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 GG GG GG CG +chr1:1326674 [T/C] chr1 1326674 Cc01_g00850:270 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC +chr1:1326698 [A/G] chr1 1326698 Cc01_g00850:294 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA +chr1:1327530 [G/C] chr1 1327530 Cc01_g00850:418 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 25.0% 4 GG CC CC CC +chr1:1327531 [A/G] chr1 1327531 Cc01_g00850:419 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA GG GG AG +chr1:1327575 [C/G] chr1 1327575 Cc01_g00850:463 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CC GC +chr1:1327581 [G/A] chr1 1327581 Cc01_g00850:469 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG +chr1:1327613 [C/T] chr1 1327613 Cc01_g00850:501 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC TT TT TT +chr1:1327618 [C/T] chr1 1327618 Cc01_g00850:506 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC TT TT TT +chr1:1327624 [C/A] chr1 1327624 Cc01_g00850:512 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 37.5% 4 CC AA AA CA +chr1:1327630 [G/T] chr1 1327630 Cc01_g00850:518 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 GG TT TT TT +chr1:1327639 [T/G] chr1 1327639 Cc01_g00850:527 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 TT GG GG GG +chr1:1327826 [T/C] chr1 1327826 Cc01_g00850:714 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT CC CC CC +chr1:1327904 [C/T] chr1 1327904 Cc01_g00850:792 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC TT CT CC +chr1:1328126 [A/G] chr1 1328126 Cc01_g00850:859 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AA AG +chr1:1328127 [A/T] chr1 1328127 Cc01_g00850:860 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 AA AA AA AT +chr1:1332539 [C/A] chr1 1332539 Cc01_g00860:529 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 37.5% 4 CC CA CA CA +chr1:1332405 [T/C] chr1 1332405 Cc01_g00860:663 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TC TT TT +chr1:1332138 [T/C] chr1 1332138 Cc01_g00860:930 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC +chr1:1331004 [A/G] chr1 1331004 Cc01_g00860:1047 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA +chr1:1330827 [G/A] chr1 1330827 Cc01_g00860:1224 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GA GG GG +chr1:1330803 [T/A] chr1 1330803 Cc01_g00860:1248 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 TT TA TT TT +chr1:1330755 [A/G] chr1 1330755 Cc01_g00860:1296 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AG AA AA +chr1:1349945 [T/C] chr1 1349945 Cc01_g00870:84 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TC TT +chr1:1349954 [T/C] chr1 1349954 Cc01_g00870:93 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:1350532 [C/T] chr1 1350532 Cc01_g00870:144 exon SYNONYMOUS_CODING ggC/ggT G/G 37.5% 4 CC CC TC TT +chr1:1350732 [C/T] chr1 1350732 Cc01_g00870:344 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 37.5% 4 CC CC CT TT +chr1:1400299 [A/G] chr1 1400299 Cc01_g00880:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG +chr1:1400306 [C/T] chr1 1400306 Cc01_g00880:30 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC CC TT +chr1:1400308 [A/G] chr1 1400308 Cc01_g00880:32 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG +chr1:1400337 [T/G] chr1 1400337 Cc01_g00880:61 exon NON_SYNONYMOUS_CODING Tgg/Ggg W/G 25.0% 4 TT GG GG GG +chr1:1400339 [G/A] chr1 1400339 Cc01_g00880:63 exon STOP_GAINED tgG/tgA W/1 25.0% 4 GG AA AA AA +chr1:1400381 [A/C] chr1 1400381 Cc01_g00880:105 exon SYNONYMOUS_CODING ccA/ccC P/P 33.3% 3 AA CC NN CC +chr1:1410529 [A/G] chr1 1410529 Cc01_g00890:10 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 AA NN NN GG +chr1:1410533 [C/T] chr1 1410533 Cc01_g00890:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 33.3% 3 CC CC NN TT +chr1:1410555 [T/C] chr1 1410555 Cc01_g00890:36 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT CC TT TT +chr1:1410556 [T/C] chr1 1410556 Cc01_g00890:37 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 50.0% 4 TT TT CC CC +chr1:1410561 [C/T] chr1 1410561 Cc01_g00890:42 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 CC CC TT TT +chr1:1410563 [A/G] chr1 1410563 Cc01_g00890:44 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA GG GG GG +chr1:1410566 [C/T] chr1 1410566 Cc01_g00890:47 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 4 CC CC TT TT +chr1:1410569 [A/C] chr1 1410569 Cc01_g00890:50 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 25.0% 4 AA CC CC CC +chr1:1410570 [G/A] chr1 1410570 Cc01_g00890:51 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 4 GG GG AA AA +chr1:1410580 [A/C] chr1 1410580 Cc01_g00890:61 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA +chr1:1410597 [C/G] chr1 1410597 Cc01_g00890:78 exon NON_SYNONYMOUS_CODING caC/caG H/Q 25.0% 4 CC GG GG GG +chr1:1427295 [C/G] chr1 1427295 Cc01_g00900:7 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 25.0% 4 CC CG CC CG +chr1:1427282 [G/A] chr1 1427282 Cc01_g00900:20 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG AA AA GA +chr1:1427281 [G/A] chr1 1427281 Cc01_g00900:21 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GA AG +chr1:1427279 [G/A] chr1 1427279 Cc01_g00900:23 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG +chr1:1427275 [A/T] chr1 1427275 Cc01_g00900:27 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 AA AA AA TA +chr1:1427274 [A/G] chr1 1427274 Cc01_g00900:28 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 AA AA AA GA +chr1:1427261 [C/A] chr1 1427261 Cc01_g00900:41 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 CC CC CC AC +chr1:1427118 [T/C] chr1 1427118 Cc01_g00900:66 exon SYNONYMOUS_CODING ttA/ttG L/L 16.7% 3 TT NN TT CT +chr1:1427056 [T/C] chr1 1427056 Cc01_g00900:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TC TC TT +chr1:1427054 [C/T] chr1 1427054 Cc01_g00900:130 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC +chr1:1427045 [G/A] chr1 1427045 Cc01_g00900:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA GA AG +chr1:1427039 [G/T] chr1 1427039 Cc01_g00900:145 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 GG TG TG GT +chr1:1427035 [G/A] chr1 1427035 Cc01_g00900:149 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG GA AG AG +chr1:1427030 [A/T] chr1 1427030 Cc01_g00900:154 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT AT TA +chr1:1427016 [T/C] chr1 1427016 Cc01_g00900:168 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC CT TC +chr1:1427004 [G/A] chr1 1427004 Cc01_g00900:180 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA +chr1:1427003 [C/T] chr1 1427003 Cc01_g00900:181 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 CC CC CT CT +chr1:1426994 [A/T] chr1 1426994 Cc01_g00900:190 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 25.0% 4 AA TA AA AT +chr1:1426981 [A/G] chr1 1426981 Cc01_g00900:203 exon NON_SYNONYMOUS_CODING cTc/cCc L/P 12.5% 4 AA AA AA AG +chr1:1426962 [T/C] chr1 1426962 Cc01_g00900:222 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CT CT TC +chr1:1426958 [C/T] chr1 1426958 Cc01_g00900:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TC CC CT +chr1:1426939 [A/T] chr1 1426939 Cc01_g00900:245 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA TA AA +chr1:1426936 [A/G] chr1 1426936 Cc01_g00900:248 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA AG AA GA +chr1:1426925 [A/G] chr1 1426925 Cc01_g00900:259 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA AA AG GA +chr1:1426907 [T/A] chr1 1426907 Cc01_g00900:277 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 25.0% 4 TT TA AT TT +chr1:1426905 [G/A] chr1 1426905 Cc01_g00900:279 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 GG AA AA AA +chr1:1433418 [A/G] chr1 1433418 Cc01_g00910:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:1433394 [G/A] chr1 1433394 Cc01_g00910:126 exon SYNONYMOUS_CODING ctC/ctT L/L 50.0% 4 GG GA AA GA +chr1:1433392 [C/T] chr1 1433392 Cc01_g00910:128 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT CC CT +chr1:1433373 [C/G] chr1 1433373 Cc01_g00910:147 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC +chr1:1432755 [C/T] chr1 1432755 Cc01_g00910:549 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 CC CC CT CC +chr1:1432742 [C/T] chr1 1432742 Cc01_g00910:562 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CT CC CC +chr1:1432732 [C/T] chr1 1432732 Cc01_g00910:572 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 CC TC CT CC +chr1:1432730 [T/C] chr1 1432730 Cc01_g00910:574 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CT TC TT +chr1:1432728 [T/G] chr1 1432728 Cc01_g00910:576 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GT TG TT +chr1:1432698 [A/G] chr1 1432698 Cc01_g00910:606 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA GA AA AA +chr1:1432697 [A/G] chr1 1432697 Cc01_g00910:607 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA GA AA AA +chr1:1432689 [G/C] chr1 1432689 Cc01_g00910:615 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GC GG GG +chr1:1432664 [C/A] chr1 1432664 Cc01_g00910:640 exon STOP_GAINED Gag/Tag E/4 12.5% 4 CC CA CC CC +chr1:1432663 [T/A] chr1 1432663 Cc01_g00910:641 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 TT TA TT TT +chr1:1432611 [A/G] chr1 1432611 Cc01_g00910:693 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA +chr1:1432605 [G/A] chr1 1432605 Cc01_g00910:699 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG GA AA GG +chr1:1432569 [C/T] chr1 1432569 Cc01_g00910:735 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 CC CC NN CT +chr1:1500031 [G/T] chr1 1500031 Cc01_g00920:49 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 37.5% 4 GG GT GG TT +chr1:1500013 [A/T] chr1 1500013 Cc01_g00920:67 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA TA AT AA +chr1:1499982 [C/T] chr1 1499982 Cc01_g00920:98 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC NN TT NN +chr1:1499966 [C/T] chr1 1499966 Cc01_g00920:114 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 2 CC NN TT NN +chr1:1499954 [T/C] chr1 1499954 Cc01_g00920:126 exon SYNONYMOUS_CODING gcA/gcG A/A 33.3% 3 TT CC CC NN +chr1:1499939 [C/T] chr1 1499939 Cc01_g00920:141 exon SYNONYMOUS_CODING ctG/ctA L/L 33.3% 3 CC TT TT NN +chr1:1499937 [T/A] chr1 1499937 Cc01_g00920:143 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 33.3% 3 TT AA AA NN +chr1:1499906 [T/C] chr1 1499906 Cc01_g00920:174 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC CC TT +chr1:1499782 [C/G] chr1 1499782 Cc01_g00920:298 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 2 CC NN CG NN +chr1:1499780 [C/G] chr1 1499780 Cc01_g00920:300 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 2 CC NN CG NN +chr1:1499449 [G/A] chr1 1499449 Cc01_g00920:631 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 GG NN AA NN +chr1:1500757 [A/G] chr1 1500757 Cc01_g00930:205 exon SYNONYMOUS_CODING Ttg/Ctg L/L 16.7% 3 AA NN AA AG +chr1:1500735 [C/G] chr1 1500735 Cc01_g00930:227 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 16.7% 3 CC NN CC CG +chr1:1500625 [A/G] chr1 1500625 Cc01_g00930:337 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 2 AA NN NN AG +chr1:1500270 [T/C] chr1 1500270 Cc01_g00930:605 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TC TT +chr1:1500265 [G/T] chr1 1500265 Cc01_g00930:610 exon NON_SYNONYMOUS_CODING Cgc/Agc R/S 12.5% 4 GG GG GT GG +chr1:1500257 [C/A] chr1 1500257 Cc01_g00930:618 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA +chr1:1527537 [A/C] chr1 1527537 Cc01_g00940:47 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 12.5% 4 AA AC AA AA +chr1:1527535 [G/C] chr1 1527535 Cc01_g00940:49 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG CG GC GC +chr1:1527534 [C/A] chr1 1527534 Cc01_g00940:50 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 12.5% 4 CC CC CA CC +chr1:1527525 [G/C] chr1 1527525 Cc01_g00940:59 exon STOP_GAINED tCa/tGa S/0 37.5% 4 GG CG GC GC +chr1:1527523 [C/T] chr1 1527523 Cc01_g00940:61 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 25.0% 4 CC CT CC CT +chr1:1527516 [A/G] chr1 1527516 Cc01_g00940:68 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 AA AG GA AA +chr1:1527513 [T/C] chr1 1527513 Cc01_g00940:71 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC CC CC +chr1:1527501 [T/C] chr1 1527501 Cc01_g00940:83 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT TT CT TC +chr1:1527490 [C/A] chr1 1527490 Cc01_g00940:94 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 CC CC AC CC +chr1:1527489 [A/G] chr1 1527489 Cc01_g00940:95 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:1527479 [A/T] chr1 1527479 Cc01_g00940:105 exon NON_SYNONYMOUS_CODING agT/agA S/R 37.5% 4 AA AT TT TT +chr1:1527475 [A/G] chr1 1527475 Cc01_g00940:109 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA AG GA AA +chr1:1527337 [T/C] chr1 1527337 Cc01_g00940:124 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC CT TC +chr1:1527336 [G/A] chr1 1527336 Cc01_g00940:125 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 12.5% 4 GG GA GG GG +chr1:1527333 [G/A] chr1 1527333 Cc01_g00940:128 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG +chr1:1527325 [C/T] chr1 1527325 Cc01_g00940:136 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 CC CT CC CC +chr1:1527324 [A/G] chr1 1527324 Cc01_g00940:137 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA +chr1:1527323 [C/T] chr1 1527323 Cc01_g00940:138 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC TC +chr1:1527310 [G/T] chr1 1527310 Cc01_g00940:151 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 GG GG GG TG +chr1:1527283 [G/A] chr1 1527283 Cc01_g00940:178 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA GA GA +chr1:1527277 [T/C] chr1 1527277 Cc01_g00940:184 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 TT TT TC TT +chr1:1527264 [C/A] chr1 1527264 Cc01_g00940:197 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 CC CA CC CC +chr1:1527261 [T/C] chr1 1527261 Cc01_g00940:200 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 TT CC CC CC +chr1:1527259 [G/A] chr1 1527259 Cc01_g00940:202 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 25.0% 4 GG AA AA AA +chr1:1527237 [G/A] chr1 1527237 Cc01_g00940:224 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG +chr1:1527236 [C/T] chr1 1527236 Cc01_g00940:225 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:1531686 [A/G] chr1 1531686 Cc01_g00950:645 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA GG NN GG +chr1:1531682 [A/G] chr1 1531682 Cc01_g00950:649 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 AA GG NN GG +chr1:1531673 [C/T] chr1 1531673 Cc01_g00950:658 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 CC TT CC CT +chr1:1531659 [A/G] chr1 1531659 Cc01_g00950:672 exon SYNONYMOUS_CODING atT/atC I/I 12.5% 4 AA AA AA AG +chr1:1531644 [A/T] chr1 1531644 Cc01_g00950:687 exon SYNONYMOUS_CODING cgT/cgA R/R 50.0% 4 AA TT TT AA +chr1:1531643 [A/T] chr1 1531643 Cc01_g00950:688 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT TA +chr1:1531641 [C/T] chr1 1531641 Cc01_g00950:690 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC +chr1:1531626 [C/G] chr1 1531626 Cc01_g00950:705 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 50.0% 4 CC GG GG CC +chr1:1531625 [A/G] chr1 1531625 Cc01_g00950:706 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 25.0% 4 AA AA GG AA +chr1:1531616 [T/C] chr1 1531616 Cc01_g00950:715 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT CC TT +chr1:1531606 [T/C] chr1 1531606 Cc01_g00950:725 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 33.3% 3 TT NN CC TT +chr1:1531575 [A/G] chr1 1531575 Cc01_g00950:756 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AG AG +chr1:1531524 [G/A] chr1 1531524 Cc01_g00950:807 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG +chr1:1531385 [A/C] chr1 1531385 Cc01_g00950:946 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 AA AA AA AC +chr1:1531373 [T/G] chr1 1531373 Cc01_g00950:958 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT +chr1:1531330 [C/T] chr1 1531330 Cc01_g00950:1001 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CC CT +chr1:1531324 [C/G] chr1 1531324 Cc01_g00950:1007 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG GG GC +chr1:1530921 [T/A] chr1 1530921 Cc01_g00950:1410 exon NON_SYNONYMOUS_CODING agA/agT R/S 33.3% 3 TT AA NN AA +chr1:1530898 [T/A] chr1 1530898 Cc01_g00950:1433 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 50.0% 3 TT AA NN TA +chr1:1530757 [C/T] chr1 1530757 Cc01_g00950:1574 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 CC TT NN NN +chr1:1530731 [T/G] chr1 1530731 Cc01_g00950:1600 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT GG NN NN +chr1:1530707 [G/A] chr1 1530707 Cc01_g00950:1624 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 2 GG AA NN NN +chr1:1530676 [G/C] chr1 1530676 Cc01_g00950:1655 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 3 GG GC NN CC +chr1:1530668 [T/C] chr1 1530668 Cc01_g00950:1663 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CC TT TT +chr1:1530661 [T/G] chr1 1530661 Cc01_g00950:1670 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 TT TG TT TT +chr1:1530629 [T/G] chr1 1530629 Cc01_g00950:1702 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT TT TT GG +chr1:1530627 [T/C] chr1 1530627 Cc01_g00950:1704 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT CT TT TT +chr1:1530607 [C/T] chr1 1530607 Cc01_g00950:1724 exon STOP_GAINED tGg/tAg W/5 16.7% 3 CC TC CC NN +chr1:1530606 [C/A] chr1 1530606 Cc01_g00950:1725 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 16.7% 3 CC AC CC NN +chr1:1530597 [T/G] chr1 1530597 Cc01_g00950:1734 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 16.7% 3 TT GT TT NN +chr1:1530532 [T/C] chr1 1530532 Cc01_g00950:1799 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 33.3% 3 TT CC TT NN +chr1:1530520 [T/G] chr1 1530520 Cc01_g00950:1811 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 16.7% 3 TT TG TT NN +chr1:1530290 [T/C] chr1 1530290 Cc01_g00950:2041 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 TT TT NN CC +chr1:1530289 [A/G] chr1 1530289 Cc01_g00950:2042 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 33.3% 3 AA AA NN GG +chr1:1530287 [C/A] chr1 1530287 Cc01_g00950:2044 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 33.3% 3 CC CC NN AA +chr1:1530286 [C/T] chr1 1530286 Cc01_g00950:2045 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC CC CC TT +chr1:1538660 [T/G] chr1 1538660 Cc01_g00960:57 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TG TT TT +chr1:1538676 [T/C] chr1 1538676 Cc01_g00960:73 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TC TT TT +chr1:1538690 [A/G] chr1 1538690 Cc01_g00960:87 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AG AA AA +chr1:1538747 [G/A] chr1 1538747 Cc01_g00960:144 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG GA GG GG +chr1:1538777 [T/C] chr1 1538777 Cc01_g00960:174 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:1538784 [G/T] chr1 1538784 Cc01_g00960:181 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG +chr1:1538792 [T/G] chr1 1538792 Cc01_g00960:189 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT +chr1:1538814 [G/C] chr1 1538814 Cc01_g00960:211 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 12.5% 4 GG GC GG GG +chr1:1538834 [T/C] chr1 1538834 Cc01_g00960:231 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:1538885 [C/T] chr1 1538885 Cc01_g00960:282 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:1539091 [G/A] chr1 1539091 Cc01_g00960:488 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA GG GG +chr1:1539183 [A/G] chr1 1539183 Cc01_g00960:580 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA +chr1:1539211 [C/G] chr1 1539211 Cc01_g00960:608 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CC CC CG +chr1:1539272 [G/T] chr1 1539272 Cc01_g00960:669 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 GG GT GG GG +chr1:1539343 [G/A] chr1 1539343 Cc01_g00960:740 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1539365 [A/G] chr1 1539365 Cc01_g00960:762 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AG AA AA +chr1:1539374 [T/G] chr1 1539374 Cc01_g00960:771 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT GT TT TT +chr1:1539408 [T/C] chr1 1539408 Cc01_g00960:805 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT CT TT TT +chr1:1539428 [C/T] chr1 1539428 Cc01_g00960:825 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CT CC CC +chr1:1539430 [G/T] chr1 1539430 Cc01_g00960:827 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GT GG GG +chr1:1539431 [G/T] chr1 1539431 Cc01_g00960:828 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 12.5% 4 GG GT GG GG +chr1:1539509 [A/T] chr1 1539509 Cc01_g00960:906 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA +chr1:1539636 [T/G] chr1 1539636 Cc01_g00960:1033 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 TT TG TT TT +chr1:1539709 [C/G] chr1 1539709 Cc01_g00960:1106 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC +chr1:1539758 [C/T] chr1 1539758 Cc01_g00960:1155 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:1539788 [A/G] chr1 1539788 Cc01_g00960:1185 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA GA AA AA +chr1:1539824 [A/G] chr1 1539824 Cc01_g00960:1221 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:1540980 [G/A] chr1 1540980 Cc01_g00960:1273 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG AG GG GG +chr1:1540985 [T/A] chr1 1540985 Cc01_g00960:1278 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 TT TA TT TT +chr1:1541027 [G/A] chr1 1541027 Cc01_g00960:1320 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA GG GG +chr1:1541065 [A/G] chr1 1541065 Cc01_g00960:1358 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AG AA AA +chr1:1542189 [G/A] chr1 1542189 Cc01_g00960:1460 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 GG GA GG GG +chr1:1542199 [C/A] chr1 1542199 Cc01_g00960:1470 exon SYNONYMOUS_CODING ggC/ggA G/G 37.5% 4 CC AA CA AA +chr1:1542239 [G/A] chr1 1542239 Cc01_g00960:1510 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 GG GA GG GG +chr1:1542286 [T/C] chr1 1542286 Cc01_g00960:1557 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:1542364 [A/G] chr1 1542364 Cc01_g00960:1635 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG +chr1:1542404 [T/G] chr1 1542404 Cc01_g00960:1675 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT +chr1:1542434 [A/C] chr1 1542434 Cc01_g00960:1705 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 12.5% 4 AA CA AA AA +chr1:1546352 [C/G] chr1 1546352 Cc01_g00970:32 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 4 CC GG CG CG +chr1:1546365 [A/G] chr1 1546365 Cc01_g00970:45 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA GG AG GG +chr1:1546409 [G/T] chr1 1546409 Cc01_g00970:89 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 50.0% 4 GG TT GT GT +chr1:1546414 [A/C] chr1 1546414 Cc01_g00970:94 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 4 AA CC AC AC +chr1:1546454 [G/C] chr1 1546454 Cc01_g00970:134 exon NON_SYNONYMOUS_CODING cGc/cCc R/P 50.0% 4 GG CC GC GC +chr1:1546477 [C/G] chr1 1546477 Cc01_g00970:157 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC GG CG GG +chr1:1546480 [A/G] chr1 1546480 Cc01_g00970:160 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG AG GG +chr1:1546484 [T/G] chr1 1546484 Cc01_g00970:164 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 50.0% 4 TT GG TG TG +chr1:1546521 [C/G] chr1 1546521 Cc01_g00970:201 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG +chr1:1546531 [A/T] chr1 1546531 Cc01_g00970:211 exon NON_SYNONYMOUS_CODING Acg/Tcg T/S 25.0% 4 AA TT AA AA +chr1:1546532 [C/G] chr1 1546532 Cc01_g00970:212 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 CC CG CC CC +chr1:1546549 [C/G] chr1 1546549 Cc01_g00970:229 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC GG CC CC +chr1:1546652 [C/A] chr1 1546652 Cc01_g00970:257 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 CC AA CA CC +chr1:1546674 [G/A] chr1 1546674 Cc01_g00970:279 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA +chr1:1546728 [A/G] chr1 1546728 Cc01_g00970:333 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG AG GG +chr1:1547036 [C/T] chr1 1547036 Cc01_g00970:641 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 25.0% 4 CC CT CT CC +chr1:1547145 [G/A] chr1 1547145 Cc01_g00970:750 exon SYNONYMOUS_CODING cgG/cgA R/R 37.5% 4 GG AA GA AA +chr1:1547237 [A/G] chr1 1547237 Cc01_g00970:842 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AG GG +chr1:1547280 [A/G] chr1 1547280 Cc01_g00970:885 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG +chr1:1547353 [T/A] chr1 1547353 Cc01_g00970:958 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 37.5% 4 TT AA TA TT +chr1:1547421 [G/A] chr1 1547421 Cc01_g00970:1026 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG +chr1:1547527 [G/A] chr1 1547527 Cc01_g00970:1132 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG +chr1:1547536 [T/A] chr1 1547536 Cc01_g00970:1141 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 TT TT TT AA +chr1:1547613 [T/C] chr1 1547613 Cc01_g00970:1218 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT +chr1:1547682 [G/A] chr1 1547682 Cc01_g00970:1287 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 GG GA GG GG +chr1:1547853 [C/G] chr1 1547853 Cc01_g00970:1458 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 CC CG CC CC +chr1:1547901 [A/G] chr1 1547901 Cc01_g00970:1506 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA GG AG GG +chr1:1547985 [C/T] chr1 1547985 Cc01_g00970:1590 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CT CC CC +chr1:1548006 [G/A] chr1 1548006 Cc01_g00970:1611 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GG GG AA +chr1:1548171 [A/C] chr1 1548171 Cc01_g00970:1776 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 AA AA AA CC +chr1:1548194 [C/A] chr1 1548194 Cc01_g00970:1799 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 37.5% 4 CC AA CA AA +chr1:1548347 [G/A] chr1 1548347 Cc01_g00970:1952 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG +chr1:1548414 [G/A] chr1 1548414 Cc01_g00970:2019 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG +chr1:1548432 [T/C] chr1 1548432 Cc01_g00970:2037 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT +chr1:1548609 [A/G] chr1 1548609 Cc01_g00970:2214 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AA AG +chr1:1548632 [C/T] chr1 1548632 Cc01_g00970:2237 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 37.5% 4 CC TT CT TT +chr1:1548721 [A/C] chr1 1548721 Cc01_g00970:2326 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AC AA AC +chr1:1565335 [T/C] chr1 1565335 Cc01_g00980:2 exon START_LOST aTg/aCg M/T 12.5% 4 TT TC TT TT +chr1:1565363 [T/A] chr1 1565363 Cc01_g00980:30 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 TT TA TT TT +chr1:1566976 [A/G] chr1 1566976 Cc01_g00980:324 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:1567002 [G/A] chr1 1567002 Cc01_g00980:350 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG +chr1:1567012 [C/T] chr1 1567012 Cc01_g00980:360 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:1568715 [T/C] chr1 1568715 Cc01_g00980:465 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TT TC +chr1:1568812 [A/G] chr1 1568812 Cc01_g00980:562 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:1568822 [T/C] chr1 1568822 Cc01_g00980:572 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TC TT TT +chr1:1569214 [G/A] chr1 1569214 Cc01_g00980:702 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 GG GA GG GG +chr1:1570049 [T/G] chr1 1570049 Cc01_g00980:976 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 12.5% 4 TT TG TT TT +chr1:1570069 [G/C] chr1 1570069 Cc01_g00980:996 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 GG GC GG GG +chr1:1570255 [A/G] chr1 1570255 Cc01_g00980:1068 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA +chr1:1570279 [A/T] chr1 1570279 Cc01_g00980:1092 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT +chr1:1570408 [C/T] chr1 1570408 Cc01_g00980:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT +chr1:1578648 [G/A] chr1 1578648 Cc01_g00990:84 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG GG GG AA +chr1:1577422 [G/C] chr1 1577422 Cc01_g00990:216 exon SYNONYMOUS_CODING cgC/cgG R/R 12.5% 4 GG GC GG GG +chr1:1574681 [T/G] chr1 1574681 Cc01_g00990:474 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 TT TT TG TT +chr1:1589010 [G/A] chr1 1589010 Cc01_g01000:168 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GA GG +chr1:1588986 [T/A] chr1 1588986 Cc01_g01000:192 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TA TT TT +chr1:1588914 [T/G] chr1 1588914 Cc01_g01000:264 exon SYNONYMOUS_CODING ctA/ctC L/L 25.0% 4 TT GG TT TT +chr1:1588838 [G/A] chr1 1588838 Cc01_g01000:340 exon STOP_GAINED Cga/Tga R/4 25.0% 4 GG AA GG GG +chr1:1588837 [C/A] chr1 1588837 Cc01_g01000:341 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 CC AA CC CC +chr1:1588277 [T/C] chr1 1588277 Cc01_g01000:901 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT CC TT TT +chr1:1588220 [G/A] chr1 1588220 Cc01_g01000:958 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 GG GG GA GG +chr1:1588137 [G/A] chr1 1588137 Cc01_g01000:1041 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 GG AA GG GG +chr1:1588135 [A/G] chr1 1588135 Cc01_g01000:1043 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG +chr1:1587967 [G/A] chr1 1587967 Cc01_g01000:1211 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 25.0% 4 GG GG GA GA +chr1:1587921 [A/G] chr1 1587921 Cc01_g01000:1257 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AG AG +chr1:1587798 [C/T] chr1 1587798 Cc01_g01000:1380 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 CC TT CC CC +chr1:1587708 [C/T] chr1 1587708 Cc01_g01000:1470 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC +chr1:1587646 [G/C] chr1 1587646 Cc01_g01000:1532 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 25.0% 4 GG GC GC GG +chr1:1587588 [T/A] chr1 1587588 Cc01_g01000:1590 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 TT AA TT TT +chr1:1587577 [C/T] chr1 1587577 Cc01_g01000:1601 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:1587576 [A/T] chr1 1587576 Cc01_g01000:1602 exon NON_SYNONYMOUS_CODING agT/agA S/R 25.0% 4 AA TT AA AA +chr1:1587527 [G/T] chr1 1587527 Cc01_g01000:1651 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 GG TT GG GG +chr1:1587435 [G/T] chr1 1587435 Cc01_g01000:1743 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 GG TT GG GG +chr1:1595916 [A/T] chr1 1595916 Cc01_g01010:153 exon SYNONYMOUS_CODING gtT/gtA V/V 37.5% 4 AA AT AT AT +chr1:1595665 [A/C] chr1 1595665 Cc01_g01010:278 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 AA AC AC AA +chr1:1594252 [G/A] chr1 1594252 Cc01_g01010:651 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 GG GA GA GA +chr1:1594186 [T/C] chr1 1594186 Cc01_g01010:717 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC +chr1:1593925 [G/A] chr1 1593925 Cc01_g01010:858 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG GA GA GA +chr1:1593817 [T/G] chr1 1593817 Cc01_g01010:966 exon SYNONYMOUS_CODING cgA/cgC R/R 37.5% 4 TT TG TG TG +chr1:1593814 [T/C] chr1 1593814 Cc01_g01010:969 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT +chr1:1593634 [C/T] chr1 1593634 Cc01_g01010:1056 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:1593035 [T/A] chr1 1593035 Cc01_g01010:1221 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT +chr1:1593017 [G/A] chr1 1593017 Cc01_g01010:1239 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG AA GA AA +chr1:1592810 [A/G] chr1 1592810 Cc01_g01010:1341 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG +chr1:1591963 [T/C] chr1 1591963 Cc01_g01010:1515 exon SYNONYMOUS_CODING cgA/cgG R/R 37.5% 4 TT TC TC TC +chr1:1591951 [A/G] chr1 1591951 Cc01_g01010:1527 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG +chr1:1591930 [G/A] chr1 1591930 Cc01_g01010:1548 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG GG GA GA +chr1:1591377 [A/G] chr1 1591377 Cc01_g01010:1560 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AG AA +chr1:1590960 [G/A] chr1 1590960 Cc01_g01010:1788 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG GA GA GA +chr1:1590951 [A/G] chr1 1590951 Cc01_g01010:1797 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA +chr1:1605944 [G/T] chr1 1605944 Cc01_g01020:27 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 GG GT GG GG +chr1:1605987 [T/G] chr1 1605987 Cc01_g01020:70 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 TT TT TG TT +chr1:1606067 [C/G] chr1 1606067 Cc01_g01020:150 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG +chr1:1606163 [A/C] chr1 1606163 Cc01_g01020:246 exon SYNONYMOUS_CODING acA/acC T/T 12.5% 4 AA AA AA AC +chr1:1609099 [T/C] chr1 1609099 Cc01_g01020:536 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TC TT TT +chr1:1609547 [G/C] chr1 1609547 Cc01_g01020:822 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 GG GC GG GG +chr1:1609736 [C/A] chr1 1609736 Cc01_g01020:912 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC CA CC CA +chr1:1609752 [G/C] chr1 1609752 Cc01_g01020:928 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 37.5% 4 GG CC GC CC +chr1:1609769 [A/C] chr1 1609769 Cc01_g01020:945 exon SYNONYMOUS_CODING ctA/ctC L/L 12.5% 4 AA AA AC AA +chr1:1610622 [A/G] chr1 1610622 Cc01_g01020:1431 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 AA AG AA AA +chr1:1610842 [A/G] chr1 1610842 Cc01_g01020:1560 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:1612395 [C/A] chr1 1612395 Cc01_g01020:2229 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 CC CA CC CC +chr1:1613838 [C/T] chr1 1613838 Cc01_g01020:2532 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC TT CC TT +chr1:1613901 [C/T] chr1 1613901 Cc01_g01020:2595 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CC CT +chr1:1615545 [T/G] chr1 1615545 Cc01_g01030:18 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT TG TT TT +chr1:1615529 [T/C] chr1 1615529 Cc01_g01030:34 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT +chr1:1615508 [C/T] chr1 1615508 Cc01_g01030:55 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 37.5% 4 CC TT CT TT +chr1:1615506 [C/T] chr1 1615506 Cc01_g01030:57 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1615500 [T/G] chr1 1615500 Cc01_g01030:63 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 TT TT TT GT +chr1:1615496 [T/C] chr1 1615496 Cc01_g01030:67 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT CT +chr1:1615491 [C/T] chr1 1615491 Cc01_g01030:72 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 CC TT CT TT +chr1:1615477 [G/A] chr1 1615477 Cc01_g01030:86 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG AG +chr1:1615472 [T/G] chr1 1615472 Cc01_g01030:91 exon NON_SYNONYMOUS_CODING Atc/Ctc I/L 37.5% 4 TT GG TG GG +chr1:1615458 [C/T] chr1 1615458 Cc01_g01030:105 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC +chr1:1615440 [T/C] chr1 1615440 Cc01_g01030:123 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT CT +chr1:1615335 [C/T] chr1 1615335 Cc01_g01030:132 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT CT TT +chr1:1615256 [A/T] chr1 1615256 Cc01_g01030:211 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA AT +chr1:1620903 [A/T] chr1 1620903 Cc01_g01040:366 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AT AA AA +chr1:1619369 [G/A] chr1 1619369 Cc01_g01040:648 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA GA GA +chr1:1619341 [G/C] chr1 1619341 Cc01_g01040:676 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CC GC CC +chr1:1619334 [C/T] chr1 1619334 Cc01_g01040:683 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CT TT +chr1:1619270 [C/G] chr1 1619270 Cc01_g01040:747 exon SYNONYMOUS_CODING tcG/tcC S/S 37.5% 4 CC GG CG GG +chr1:1619124 [A/G] chr1 1619124 Cc01_g01040:893 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA +chr1:1618988 [A/G] chr1 1618988 Cc01_g01040:1029 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG +chr1:1618984 [C/G] chr1 1618984 Cc01_g01040:1033 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CC CC CG +chr1:1618978 [C/G] chr1 1618978 Cc01_g01040:1039 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 CC CG CG CG +chr1:1618886 [A/G] chr1 1618886 Cc01_g01040:1131 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA AG +chr1:1618879 [T/A] chr1 1618879 Cc01_g01040:1138 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TT TA +chr1:1618858 [T/G] chr1 1618858 Cc01_g01040:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT GG TG GG +chr1:1618504 [G/A] chr1 1618504 Cc01_g01040:1396 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG GA +chr1:1618376 [T/G] chr1 1618376 Cc01_g01040:1524 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 TT TG TT TT +chr1:1618358 [G/C] chr1 1618358 Cc01_g01040:1542 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC GC +chr1:1618326 [C/T] chr1 1618326 Cc01_g01040:1574 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 CC CC CT CC +chr1:1618307 [G/C] chr1 1618307 Cc01_g01040:1593 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 GG GG GG CG +chr1:1618184 [A/G] chr1 1618184 Cc01_g01040:1716 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:1618117 [G/C] chr1 1618117 Cc01_g01040:1783 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CG GG CC +chr1:1618040 [C/G] chr1 1618040 Cc01_g01040:1860 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 CC CC CG CC +chr1:1618037 [G/A] chr1 1618037 Cc01_g01040:1863 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG GA GA GA +chr1:1618016 [T/C] chr1 1618016 Cc01_g01040:1884 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT +chr1:1617998 [G/C] chr1 1617998 Cc01_g01040:1902 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC CG +chr1:1617793 [C/T] chr1 1617793 Cc01_g01040:2107 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 37.5% 4 CC CT CT CT +chr1:1617773 [T/C] chr1 1617773 Cc01_g01040:2127 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC +chr1:1617769 [T/C] chr1 1617769 Cc01_g01040:2131 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT TC +chr1:1617757 [C/T] chr1 1617757 Cc01_g01040:2143 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:1617670 [C/T] chr1 1617670 Cc01_g01040:2230 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 CC CT CC TT +chr1:1617634 [C/T] chr1 1617634 Cc01_g01040:2266 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CC CT +chr1:1617479 [A/G] chr1 1617479 Cc01_g01040:2421 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG AA AA +chr1:1617238 [G/A] chr1 1617238 Cc01_g01040:2662 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG +chr1:1617119 [A/T] chr1 1617119 Cc01_g01040:2725 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA AT AT AA +chr1:1626903 [A/C] chr1 1626903 Cc01_g01050:132 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 AA CC AC CC +chr1:1626922 [C/G] chr1 1626922 Cc01_g01050:151 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 CC CG CG CC +chr1:1626973 [G/T] chr1 1626973 Cc01_g01050:202 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 GG GT GG TT +chr1:1627071 [T/C] chr1 1627071 Cc01_g01050:300 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TT CC +chr1:1627227 [T/C] chr1 1627227 Cc01_g01050:456 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TC TC TT +chr1:1628554 [A/G] chr1 1628554 Cc01_g01050:650 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA AG AG AA +chr1:1628584 [A/G] chr1 1628584 Cc01_g01050:680 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GA AA GG +chr1:1628763 [G/A] chr1 1628763 Cc01_g01050:859 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GG GA +chr1:1628787 [G/C] chr1 1628787 Cc01_g01050:883 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG GC GG CC +chr1:1628828 [A/G] chr1 1628828 Cc01_g01050:924 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA AG AA GG +chr1:1628942 [A/G] chr1 1628942 Cc01_g01050:1038 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 AA GG AG GG +chr1:1630053 [T/C] chr1 1630053 Cc01_g01050:1464 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TC TT +chr1:1633739 [A/G] chr1 1633739 Cc01_g01060:12 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG +chr1:1633649 [T/C] chr1 1633649 Cc01_g01060:102 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC +chr1:1633602 [T/C] chr1 1633602 Cc01_g01060:149 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT CT TT TT +chr1:1633503 [G/A] chr1 1633503 Cc01_g01060:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GA GG GG +chr1:1633430 [A/T] chr1 1633430 Cc01_g01060:321 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 AA AT AA AA +chr1:1633429 [G/T] chr1 1633429 Cc01_g01060:322 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GT GG GG +chr1:1633388 [A/T] chr1 1633388 Cc01_g01060:363 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 AA AA AT AA +chr1:1752682 [C/T] chr1 1752682 Cc01_g01120:21 exon SYNONYMOUS_CODING acG/acA T/T 33.3% 3 CC TT NN TT +chr1:1752654 [A/T] chr1 1752654 Cc01_g01120:49 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT TT AA +chr1:1752632 [G/T] chr1 1752632 Cc01_g01120:71 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 37.5% 4 GG GT TT GG +chr1:1752577 [C/A] chr1 1752577 Cc01_g01120:126 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC CA CA CC +chr1:1752535 [T/C] chr1 1752535 Cc01_g01120:168 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 TT TT CC TT +chr1:1752526 [C/T] chr1 1752526 Cc01_g01120:177 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 CC CC TT CC +chr1:1750532 [T/G] chr1 1750532 Cc01_g01120:970 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 50.0% 2 TT NN NN GG +chr1:1750461 [C/T] chr1 1750461 Cc01_g01120:1041 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 CC TT CT TT +chr1:1750442 [C/T] chr1 1750442 Cc01_g01120:1060 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 37.5% 4 CC TT CT TT +chr1:1760523 [C/A] chr1 1760523 Cc01_g01130:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC +chr1:1760522 [G/C] chr1 1760522 Cc01_g01130:136 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 GG GG GC GG +chr1:1760486 [A/C] chr1 1760486 Cc01_g01130:172 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 AA AA AA AC +chr1:1760383 [C/T] chr1 1760383 Cc01_g01130:275 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC +chr1:1760328 [T/A] chr1 1760328 Cc01_g01130:330 exon SYNONYMOUS_CODING atA/atT I/I 50.0% 4 TT AA TT AA +chr1:1760185 [T/A] chr1 1760185 Cc01_g01130:473 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT TA TA TT +chr1:1760173 [C/A] chr1 1760173 Cc01_g01130:485 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 CC CC CC CA +chr1:1760172 [T/G] chr1 1760172 Cc01_g01130:486 exon NON_SYNONYMOUS_CODING agA/agC R/S 12.5% 4 TT TT TT TG +chr1:1759408 [A/G] chr1 1759408 Cc01_g01130:603 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA +chr1:1759378 [G/A] chr1 1759378 Cc01_g01130:633 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GA GG +chr1:1759372 [A/G] chr1 1759372 Cc01_g01130:639 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA AG AG AA +chr1:1759371 [T/A] chr1 1759371 Cc01_g01130:640 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 TT TA TA TT +chr1:1759364 [T/G] chr1 1759364 Cc01_g01130:647 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 TT TG TT TT +chr1:1759335 [G/A] chr1 1759335 Cc01_g01130:676 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG GA GA GG +chr1:1758971 [A/G] chr1 1758971 Cc01_g01130:1040 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 3 AA GG AG NN +chr1:1758937 [G/A] chr1 1758937 Cc01_g01130:1074 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 3 GG AA GA NN +chr1:1758885 [C/G] chr1 1758885 Cc01_g01130:1126 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 33.3% 3 CC GG CC NN +chr1:1758882 [C/T] chr1 1758882 Cc01_g01130:1129 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 CC TT CT NN +chr1:1758778 [G/A] chr1 1758778 Cc01_g01130:1233 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG GA GG GG +chr1:1758772 [A/G] chr1 1758772 Cc01_g01130:1239 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AG AA AA +chr1:1758762 [T/C] chr1 1758762 Cc01_g01130:1249 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 TT TC TT TT +chr1:1768762 [G/C] chr1 1768762 Cc01_g01140:100 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GC GG GC +chr1:1768873 [T/C] chr1 1768873 Cc01_g01140:211 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TT TC +chr1:1768956 [T/A] chr1 1768956 Cc01_g01140:294 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TT TT TA +chr1:1768961 [C/A] chr1 1768961 Cc01_g01140:299 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CC CA +chr1:1768967 [C/G] chr1 1768967 Cc01_g01140:305 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 4 CC CG CG GG +chr1:1769000 [A/G] chr1 1769000 Cc01_g01140:338 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG +chr1:1769038 [T/C] chr1 1769038 Cc01_g01140:376 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TC TT TT +chr1:1769040 [T/G] chr1 1769040 Cc01_g01140:378 exon SYNONYMOUS_CODING tcT/tcG S/S 12.5% 4 TT TT TT TG +chr1:1769074 [T/C] chr1 1769074 Cc01_g01140:412 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TT TC +chr1:1769115 [T/C] chr1 1769115 Cc01_g01140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TT TT TC +chr1:1769145 [C/T] chr1 1769145 Cc01_g01140:483 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC CT CT TT +chr1:1769183 [C/T] chr1 1769183 Cc01_g01140:521 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC CT CC CT +chr1:1769193 [A/T] chr1 1769193 Cc01_g01140:531 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA +chr1:1769201 [C/T] chr1 1769201 Cc01_g01140:539 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 CC CT CC CT +chr1:1769253 [A/C] chr1 1769253 Cc01_g01140:591 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 AA AA AA AC +chr1:1769277 [T/A] chr1 1769277 Cc01_g01140:615 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 TT TA TT TA +chr1:1769279 [G/A] chr1 1769279 Cc01_g01140:617 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA +chr1:1769288 [A/C] chr1 1769288 Cc01_g01140:626 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AA CA +chr1:1769296 [A/G] chr1 1769296 Cc01_g01140:634 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 AA AG AA AG +chr1:1769367 [T/C] chr1 1769367 Cc01_g01140:705 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TT TC TC +chr1:1769374 [G/A] chr1 1769374 Cc01_g01140:712 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA +chr1:1769389 [C/T] chr1 1769389 Cc01_g01140:727 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT +chr1:1769398 [T/C] chr1 1769398 Cc01_g01140:736 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TT TC +chr1:1769433 [T/G] chr1 1769433 Cc01_g01140:771 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT +chr1:1769441 [C/T] chr1 1769441 Cc01_g01140:779 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC CT CT CT +chr1:1769448 [A/T] chr1 1769448 Cc01_g01140:786 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 37.5% 4 AA AT AT AT +chr1:1769482 [A/T] chr1 1769482 Cc01_g01140:820 exon STOP_GAINED Aga/Tga R/4 12.5% 4 AA AA AA TA +chr1:1769483 [G/T] chr1 1769483 Cc01_g01140:821 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 GG GG GG TG +chr1:1769501 [C/G] chr1 1769501 Cc01_g01140:839 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CG CC CC +chr1:1769639 [A/G] chr1 1769639 Cc01_g01140:977 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AA AA AG +chr1:1769671 [C/A] chr1 1769671 Cc01_g01140:1009 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 12.5% 4 CC CA CC CC +chr1:1769978 [A/G] chr1 1769978 Cc01_g01140:1256 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 4 AA AG AA AG +chr1:1769992 [A/G] chr1 1769992 Cc01_g01140:1270 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG +chr1:1770017 [G/T] chr1 1770017 Cc01_g01140:1295 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 37.5% 4 GG GT GT GT +chr1:1770029 [C/T] chr1 1770029 Cc01_g01140:1307 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 CC CT CT CT +chr1:1770045 [C/T] chr1 1770045 Cc01_g01140:1323 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT +chr1:1770067 [C/T] chr1 1770067 Cc01_g01140:1345 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 CC CC CT CT +chr1:1770389 [C/G] chr1 1770389 Cc01_g01140:1667 exon STOP_GAINED tCa/tGa S/6 12.5% 4 CC CG CC CC +chr1:1770417 [A/C] chr1 1770417 Cc01_g01140:1695 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 AA AC AA AA +chr1:1770420 [C/A] chr1 1770420 Cc01_g01140:1698 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CA CC CC +chr1:1770531 [A/G] chr1 1770531 Cc01_g01140:1809 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AG AA AA +chr1:1770535 [A/G] chr1 1770535 Cc01_g01140:1813 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA +chr1:1770536 [G/A] chr1 1770536 Cc01_g01140:1814 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA +chr1:1770538 [C/T] chr1 1770538 Cc01_g01140:1816 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT +chr1:1770756 [G/A] chr1 1770756 Cc01_g01140:1972 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA GA AA +chr1:1770764 [A/G] chr1 1770764 Cc01_g01140:1980 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG +chr1:1770768 [A/T] chr1 1770768 Cc01_g01140:1984 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AA AT +chr1:1770781 [G/T] chr1 1770781 Cc01_g01140:1997 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GG GG GT +chr1:1770792 [C/G] chr1 1770792 Cc01_g01140:2008 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CC GC GC +chr1:1770794 [T/C] chr1 1770794 Cc01_g01140:2010 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC +chr1:1770795 [G/A] chr1 1770795 Cc01_g01140:2011 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG +chr1:1770797 [A/T] chr1 1770797 Cc01_g01140:2013 exon SYNONYMOUS_CODING gtA/gtT V/V 12.5% 4 AA AT AA AA +chr1:1770804 [G/C] chr1 1770804 Cc01_g01140:2020 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG +chr1:1770806 [A/G] chr1 1770806 Cc01_g01140:2022 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AG AA AA +chr1:1770807 [A/T] chr1 1770807 Cc01_g01140:2023 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AT AA AA +chr1:1771162 [C/T] chr1 1771162 Cc01_g01140:2032 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT TC TT +chr1:1771185 [T/A] chr1 1771185 Cc01_g01140:2055 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 TT AA AT AA +chr1:1771201 [C/A] chr1 1771201 Cc01_g01140:2071 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 37.5% 4 CC AA AC AA +chr1:1775047 [T/C] chr1 1775047 Cc01_g01150:43 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 2 TT TC NN NN +chr1:1774997 [A/G] chr1 1774997 Cc01_g01150:93 exon SYNONYMOUS_CODING gtT/gtC V/V 33.3% 3 AA AG NN AG +chr1:1774994 [A/G] chr1 1774994 Cc01_g01150:96 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA AG GG GA +chr1:1774991 [C/T] chr1 1774991 Cc01_g01150:99 exon SYNONYMOUS_CODING gtG/gtA V/V 25.0% 4 CC TT TT TT +chr1:1774981 [A/G] chr1 1774981 Cc01_g01150:109 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 AA AG AG AG +chr1:1774977 [C/T] chr1 1774977 Cc01_g01150:113 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT +chr1:1774975 [C/T] chr1 1774975 Cc01_g01150:115 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 CC TC TC TC +chr1:1774972 [T/G] chr1 1774972 Cc01_g01150:118 exon NON_SYNONYMOUS_CODING Act/Cct T/P 37.5% 4 TT TG TG TG +chr1:1774959 [A/G] chr1 1774959 Cc01_g01150:131 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 AA GA GA GA +chr1:1774957 [A/C] chr1 1774957 Cc01_g01150:133 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 37.5% 4 AA CC CC AC +chr1:1774955 [C/A] chr1 1774955 Cc01_g01150:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 37.5% 4 CC AA AA CA +chr1:1774925 [A/C] chr1 1774925 Cc01_g01150:165 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 37.5% 4 AA AC AC AC +chr1:1774919 [A/G] chr1 1774919 Cc01_g01150:171 exon SYNONYMOUS_CODING ccT/ccC P/P 37.5% 4 AA AG AG AG +chr1:1774915 [C/G] chr1 1774915 Cc01_g01150:175 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC +chr1:1774911 [C/T] chr1 1774911 Cc01_g01150:179 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT TT CT +chr1:1774901 [C/A] chr1 1774901 Cc01_g01150:189 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 CC AA AA AA +chr1:1774894 [G/A] chr1 1774894 Cc01_g01150:196 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 37.5% 4 GG GA GA GA +chr1:1800628 [A/T] chr1 1800628 Cc01_g01180:18 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 AA AT AA TT +chr1:1800604 [A/G] chr1 1800604 Cc01_g01180:42 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AA GG +chr1:1800591 [A/C] chr1 1800591 Cc01_g01180:55 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 AA CA AA AA +chr1:1800153 [G/A] chr1 1800153 Cc01_g01180:237 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 GG GG GA GG +chr1:1800141 [C/A] chr1 1800141 Cc01_g01180:249 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 CC CA CC CC +chr1:1800037 [A/T] chr1 1800037 Cc01_g01180:353 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 37.5% 4 AA TT AT TT +chr1:1799883 [A/G] chr1 1799883 Cc01_g01180:507 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 AA AG AA AA +chr1:1799858 [C/A] chr1 1799858 Cc01_g01180:532 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 CC AC CC CA +chr1:1799772 [C/T] chr1 1799772 Cc01_g01180:618 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1799746 [C/A] chr1 1799746 Cc01_g01180:644 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 25.0% 4 CC CA CC AC +chr1:1799703 [T/A] chr1 1799703 Cc01_g01180:687 exon SYNONYMOUS_CODING gcA/gcT A/A 37.5% 4 TT AT TA TA +chr1:1799683 [C/T] chr1 1799683 Cc01_g01180:707 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC +chr1:1799560 [G/A] chr1 1799560 Cc01_g01180:830 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GG GA +chr1:1799253 [G/A] chr1 1799253 Cc01_g01180:1137 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GG GA +chr1:1799138 [C/G] chr1 1799138 Cc01_g01180:1252 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 CC CC CC CG +chr1:1799114 [C/T] chr1 1799114 Cc01_g01180:1276 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT +chr1:1799096 [T/C] chr1 1799096 Cc01_g01180:1294 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TC TC TT +chr1:1798930 [C/T] chr1 1798930 Cc01_g01180:1460 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 37.5% 4 CC CT CT CT +chr1:1798825 [T/C] chr1 1798825 Cc01_g01180:1565 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TT TC +chr1:1798812 [A/C] chr1 1798812 Cc01_g01180:1578 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 AA AA AA AC +chr1:1798782 [T/C] chr1 1798782 Cc01_g01180:1608 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC +chr1:1798753 [T/A] chr1 1798753 Cc01_g01180:1637 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA +chr1:1798733 [T/C] chr1 1798733 Cc01_g01180:1657 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC TC TC +chr1:1798724 [G/A] chr1 1798724 Cc01_g01180:1666 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA +chr1:1798690 [C/A] chr1 1798690 Cc01_g01180:1700 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 12.5% 4 CC CC CC CA +chr1:1798665 [T/C] chr1 1798665 Cc01_g01180:1725 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT +chr1:1798471 [T/A] chr1 1798471 Cc01_g01180:1919 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 12.5% 4 TT TT TT TA +chr1:1798453 [A/G] chr1 1798453 Cc01_g01180:1937 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG +chr1:1798341 [G/A] chr1 1798341 Cc01_g01180:2049 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG AA GA AA +chr1:1798269 [T/C] chr1 1798269 Cc01_g01180:2121 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TT TC +chr1:1798206 [A/G] chr1 1798206 Cc01_g01180:2184 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG +chr1:1798185 [A/T] chr1 1798185 Cc01_g01180:2205 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AA AA AT +chr1:1798172 [G/A] chr1 1798172 Cc01_g01180:2218 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:1798019 [A/G] chr1 1798019 Cc01_g01180:2277 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG +chr1:1797997 [A/C] chr1 1797997 Cc01_g01180:2299 exon NON_SYNONYMOUS_CODING Tgc/Ggc C/G 12.5% 4 AA AA AC AA +chr1:1796639 [G/T] chr1 1796639 Cc01_g01180:2517 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 GG GG GG GT +chr1:1796548 [C/T] chr1 1796548 Cc01_g01180:2608 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC CT +chr1:1796523 [G/C] chr1 1796523 Cc01_g01180:2633 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 GG GG GG GC +chr1:1796504 [G/A] chr1 1796504 Cc01_g01180:2652 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:1796501 [C/T] chr1 1796501 Cc01_g01180:2655 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT +chr1:1796477 [A/G] chr1 1796477 Cc01_g01180:2679 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AA AA AG +chr1:1794530 [C/A] chr1 1794530 Cc01_g01180:2830 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 CC CC CC CA +chr1:1793183 [A/G] chr1 1793183 Cc01_g01180:2975 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AA AG +chr1:1793145 [G/T] chr1 1793145 Cc01_g01180:3013 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT +chr1:1793065 [C/T] chr1 1793065 Cc01_g01180:3093 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC CT CC CC +chr1:1793054 [A/G] chr1 1793054 Cc01_g01180:3104 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 AA AG AA AA +chr1:1793045 [G/T] chr1 1793045 Cc01_g01180:3113 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 12.5% 4 GG GT GG GG +chr1:1792939 [G/T] chr1 1792939 Cc01_g01180:3147 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 GG GT GG GG +chr1:1792909 [A/T] chr1 1792909 Cc01_g01180:3177 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA TA AA AA +chr1:1813729 [G/T] chr1 1813729 Cc01_g01190:306 exon SYNONYMOUS_CODING ccC/ccA P/P 16.7% 3 GG GT NN GG +chr1:1813726 [A/T] chr1 1813726 Cc01_g01190:309 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 AA AT NN AA +chr1:1813696 [T/G] chr1 1813696 Cc01_g01190:339 exon SYNONYMOUS_CODING atA/atC I/I 16.7% 3 TT TG NN TT +chr1:1818371 [T/C] chr1 1818371 Cc01_g01200:87 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 4 TT TC CC TC +chr1:1818296 [A/T] chr1 1818296 Cc01_g01200:162 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AA TT AA +chr1:1818188 [A/G] chr1 1818188 Cc01_g01200:270 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA +chr1:1818116 [A/C] chr1 1818116 Cc01_g01200:342 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 AA AC AA AA +chr1:1818035 [A/G] chr1 1818035 Cc01_g01200:423 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA AG AG GG +chr1:1818018 [T/A] chr1 1818018 Cc01_g01200:440 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 50.0% 4 TT TA TA AA +chr1:1818013 [T/G] chr1 1818013 Cc01_g01200:445 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 25.0% 4 TT TT TG TG +chr1:1822497 [A/G] chr1 1822497 Cc01_g01210:153 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA AG AA AG +chr1:1822491 [C/G] chr1 1822491 Cc01_g01210:159 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 CC CC CC CG +chr1:1822434 [C/T] chr1 1822434 Cc01_g01210:216 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CT CC CC +chr1:1822365 [A/G] chr1 1822365 Cc01_g01210:285 exon SYNONYMOUS_CODING ctT/ctC L/L 37.5% 4 AA GG AA AG +chr1:1822344 [G/C] chr1 1822344 Cc01_g01210:306 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC +chr1:1822311 [G/C] chr1 1822311 Cc01_g01210:339 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GG GC GG +chr1:1822251 [G/A] chr1 1822251 Cc01_g01210:399 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA AG GA +chr1:1822215 [G/T] chr1 1822215 Cc01_g01210:435 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 GG GG TG GG +chr1:1822206 [G/A] chr1 1822206 Cc01_g01210:444 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA AG AA +chr1:1871413 [G/T] chr1 1871413 Cc01_g01220:7 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT GT TT +chr1:1871774 [T/C] chr1 1871774 Cc01_g01220:65 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT TT TT TC +chr1:1871782 [G/C] chr1 1871782 Cc01_g01220:73 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GG GC +chr1:1871785 [G/T] chr1 1871785 Cc01_g01220:76 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GG GT +chr1:1871959 [C/T] chr1 1871959 Cc01_g01220:118 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 CC CT CC CC +chr1:1871977 [G/C] chr1 1871977 Cc01_g01220:136 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 25.0% 4 GG GC GC GG +chr1:1871980 [T/G] chr1 1871980 Cc01_g01220:139 exon NON_SYNONYMOUS_CODING Ttt/Gtt F/V 12.5% 4 TT TG TT TT +chr1:1871994 [C/A] chr1 1871994 Cc01_g01220:153 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 12.5% 4 CC AC CC CC +chr1:1872001 [T/C] chr1 1872001 Cc01_g01220:160 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 12.5% 4 TT CT TT TT +chr1:1872003 [C/T] chr1 1872003 Cc01_g01220:162 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC CT CT CT +chr1:1872004 [A/G] chr1 1872004 Cc01_g01220:163 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA AG AG AG +chr1:1872020 [G/A] chr1 1872020 Cc01_g01220:179 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:1872035 [G/A] chr1 1872035 Cc01_g01220:194 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA +chr1:1872037 [A/G] chr1 1872037 Cc01_g01220:196 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG +chr1:1872051 [A/G] chr1 1872051 Cc01_g01220:210 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG GA GG +chr1:1873065 [C/T] chr1 1873065 Cc01_g01220:247 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC CC CT +chr1:1873088 [T/C] chr1 1873088 Cc01_g01220:270 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TT TC +chr1:1874574 [C/T] chr1 1874574 Cc01_g01230:34 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CC CT +chr1:1874587 [T/G] chr1 1874587 Cc01_g01230:47 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 12.5% 4 TT TT TG TT +chr1:1874774 [C/G] chr1 1874774 Cc01_g01230:135 exon STOP_GAINED taC/taG Y/5 12.5% 4 CC CC CG CC +chr1:1874797 [T/A] chr1 1874797 Cc01_g01230:158 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 25.0% 4 TT TT TA TA +chr1:1874808 [G/T] chr1 1874808 Cc01_g01230:169 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT +chr1:1874816 [G/T] chr1 1874816 Cc01_g01230:177 exon NON_SYNONYMOUS_CODING agG/agT R/S 12.5% 4 GG GT GG GG +chr1:1874818 [G/T] chr1 1874818 Cc01_g01230:179 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG GG GT GT +chr1:1879776 [A/C] chr1 1879776 Cc01_g01240:27 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 4 AA AC AC CC +chr1:1879628 [G/C] chr1 1879628 Cc01_g01240:175 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG GC GG GC +chr1:1879623 [T/C] chr1 1879623 Cc01_g01240:180 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:1907384 [G/A] chr1 1907384 Cc01_g01250:29 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA +chr1:1907400 [C/G] chr1 1907400 Cc01_g01250:45 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC GG GG GG +chr1:1907401 [A/G] chr1 1907401 Cc01_g01250:46 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 AA AG AG GA +chr1:1907418 [G/A] chr1 1907418 Cc01_g01250:63 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GA GA AG +chr1:1907454 [A/C] chr1 1907454 Cc01_g01250:99 exon NON_SYNONYMOUS_CODING caA/caC Q/H 37.5% 4 AA AC AC CA +chr1:1907455 [A/G] chr1 1907455 Cc01_g01250:100 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AG AA +chr1:1907457 [C/G] chr1 1907457 Cc01_g01250:102 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG +chr1:1907460 [T/A] chr1 1907460 Cc01_g01250:105 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 25.0% 4 TT TT AT TA +chr1:1907483 [A/C] chr1 1907483 Cc01_g01250:128 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 AA AA AA CA +chr1:1907485 [G/A] chr1 1907485 Cc01_g01250:130 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA +chr1:1907487 [C/T] chr1 1907487 Cc01_g01250:132 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT TC +chr1:1907489 [T/G] chr1 1907489 Cc01_g01250:134 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 12.5% 4 TT TT TT GT +chr1:1907499 [G/A] chr1 1907499 Cc01_g01250:144 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 GG GG AG GA +chr1:1907514 [T/C] chr1 1907514 Cc01_g01250:159 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TC CT +chr1:1907532 [G/C] chr1 1907532 Cc01_g01250:177 exon SYNONYMOUS_CODING ggG/ggC G/G 25.0% 4 GG CC CC CC +chr1:1907552 [A/G] chr1 1907552 Cc01_g01250:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA AG AG GA +chr1:1907554 [G/A] chr1 1907554 Cc01_g01250:199 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AG GA +chr1:1907571 [A/G] chr1 1907571 Cc01_g01250:216 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG GA +chr1:1907577 [G/A] chr1 1907577 Cc01_g01250:222 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 GG GG GA GG +chr1:1907584 [A/G] chr1 1907584 Cc01_g01250:229 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 37.5% 4 AA AG AG GA +chr1:1907613 [C/T] chr1 1907613 Cc01_g01250:258 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC CT CT TC +chr1:1907628 [G/A] chr1 1907628 Cc01_g01250:273 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA AG +chr1:1907636 [C/G] chr1 1907636 Cc01_g01250:281 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 37.5% 4 CC CG CG GC +chr1:1907643 [A/G] chr1 1907643 Cc01_g01250:288 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG GA +chr1:1907649 [G/T] chr1 1907649 Cc01_g01250:294 exon SYNONYMOUS_CODING ctG/ctT L/L 37.5% 4 GG GT GT TG +chr1:1907663 [A/T] chr1 1907663 Cc01_g01250:308 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA TA AA +chr1:1907745 [T/G] chr1 1907745 Cc01_g01250:390 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 4 TT GG GG GG +chr1:1907751 [G/A] chr1 1907751 Cc01_g01250:396 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 GG GA GA GA +chr1:1907865 [G/A] chr1 1907865 Cc01_g01250:438 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA +chr1:1907867 [C/T] chr1 1907867 Cc01_g01250:440 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC CT TT CT +chr1:1907913 [G/A] chr1 1907913 Cc01_g01250:486 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG AG GG GG +chr1:1907925 [C/T] chr1 1907925 Cc01_g01250:498 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT CT CT +chr1:1907951 [T/A] chr1 1907951 Cc01_g01250:524 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 37.5% 4 TT TA TA TA +chr1:1907955 [C/T] chr1 1907955 Cc01_g01250:528 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC CT CT CT +chr1:1907970 [G/A] chr1 1907970 Cc01_g01250:543 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG AG GG +chr1:1907971 [G/C] chr1 1907971 Cc01_g01250:544 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 GG GG CG GG +chr1:1907976 [A/G] chr1 1907976 Cc01_g01250:549 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 AA GA AA GA +chr1:1907998 [G/A] chr1 1907998 Cc01_g01250:571 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG AG GG +chr1:1908013 [C/G] chr1 1908013 Cc01_g01250:586 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CC GC +chr1:1908043 [T/C] chr1 1908043 Cc01_g01250:616 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC TC TC +chr1:1908051 [G/C] chr1 1908051 Cc01_g01250:624 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG CG GG CG +chr1:1908071 [A/T] chr1 1908071 Cc01_g01250:644 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 AA TT TT TT +chr1:1908072 [A/T] chr1 1908072 Cc01_g01250:645 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA AT AT AT +chr1:1908080 [G/C] chr1 1908080 Cc01_g01250:653 exon NON_SYNONYMOUS_CODING gGc/gCc G/A 37.5% 4 GG GC GC GC +chr1:1908088 [A/G] chr1 1908088 Cc01_g01250:661 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG +chr1:1908103 [C/T] chr1 1908103 Cc01_g01250:676 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 CC CT CT CT +chr1:1908119 [G/A] chr1 1908119 Cc01_g01250:692 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG GG GA GA +chr1:1908120 [G/T] chr1 1908120 Cc01_g01250:693 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG GT GT +chr1:1908140 [A/G] chr1 1908140 Cc01_g01250:713 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AA GA +chr1:1908345 [G/C] chr1 1908345 Cc01_g01250:738 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 GG GC GG GC +chr1:1908360 [C/G] chr1 1908360 Cc01_g01250:753 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC CG GC +chr1:1908383 [A/T] chr1 1908383 Cc01_g01250:776 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 37.5% 4 AA TA AT TA +chr1:1908403 [C/G] chr1 1908403 Cc01_g01250:796 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 CC CC GC CC +chr1:1908407 [G/A] chr1 1908407 Cc01_g01250:800 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG +chr1:1908410 [G/A] chr1 1908410 Cc01_g01250:803 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG +chr1:1908447 [T/C] chr1 1908447 Cc01_g01250:840 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CT TC CT +chr1:1908449 [T/C] chr1 1908449 Cc01_g01250:842 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT +chr1:1908471 [C/G] chr1 1908471 Cc01_g01250:864 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GC CG GC +chr1:1908474 [C/T] chr1 1908474 Cc01_g01250:867 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TC CT TC +chr1:1908527 [T/C] chr1 1908527 Cc01_g01250:920 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT CC CC CC +chr1:1908549 [A/G] chr1 1908549 Cc01_g01250:942 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA +chr1:1908765 [G/A] chr1 1908765 Cc01_g01250:954 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1908789 [C/A] chr1 1908789 Cc01_g01250:978 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 CC CA CA CA +chr1:1908791 [A/C] chr1 1908791 Cc01_g01250:980 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 12.5% 4 AA CA AA AA +chr1:1908792 [G/A] chr1 1908792 Cc01_g01250:981 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 GG AA AA AA +chr1:1908828 [C/T] chr1 1908828 Cc01_g01250:1017 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 CC CT CT CT +chr1:1908831 [G/A] chr1 1908831 Cc01_g01250:1020 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 GG GA GA GA +chr1:1908907 [A/G] chr1 1908907 Cc01_g01250:1096 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG +chr1:1908909 [A/G] chr1 1908909 Cc01_g01250:1098 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG AG AG +chr1:1908915 [T/C] chr1 1908915 Cc01_g01250:1104 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT TC TC TC +chr1:1908942 [G/A] chr1 1908942 Cc01_g01250:1131 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA AA AA +chr1:1908962 [G/A] chr1 1908962 Cc01_g01250:1151 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG AG +chr1:1908976 [A/G] chr1 1908976 Cc01_g01250:1165 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA AA GA AA +chr1:1909020 [A/G] chr1 1909020 Cc01_g01250:1209 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AA AG AA +chr1:1909071 [A/C] chr1 1909071 Cc01_g01250:1260 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA AC NN AC +chr1:1909091 [G/A] chr1 1909091 Cc01_g01250:1280 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG +chr1:1909122 [G/A] chr1 1909122 Cc01_g01250:1311 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG AA AA AA +chr1:1909165 [C/A] chr1 1909165 Cc01_g01250:1354 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC +chr1:1909186 [G/A] chr1 1909186 Cc01_g01250:1375 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GA GG +chr1:1909203 [C/T] chr1 1909203 Cc01_g01250:1392 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC TC CC +chr1:1909210 [G/T] chr1 1909210 Cc01_g01250:1399 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GT GG GG +chr1:1909247 [G/C] chr1 1909247 Cc01_g01250:1436 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 25.0% 4 GG CC CC CC +chr1:1909284 [G/A] chr1 1909284 Cc01_g01250:1473 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA GA GA +chr1:1909294 [C/G] chr1 1909294 Cc01_g01250:1483 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC GG GG GG +chr1:1909302 [T/C] chr1 1909302 Cc01_g01250:1491 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT CC CC CC +chr1:1909308 [C/T] chr1 1909308 Cc01_g01250:1497 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT +chr1:1909332 [C/T] chr1 1909332 Cc01_g01250:1521 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC TC TC TC +chr1:1909361 [G/A] chr1 1909361 Cc01_g01250:1550 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 GG GA GA GA +chr1:1909447 [G/A] chr1 1909447 Cc01_g01250:1636 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG GA GA GA +chr1:1909475 [C/T] chr1 1909475 Cc01_g01250:1664 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 25.0% 4 CC TT TT TT +chr1:1909487 [A/G] chr1 1909487 Cc01_g01250:1676 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GA AA GA +chr1:1909530 [A/G] chr1 1909530 Cc01_g01250:1719 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG AG +chr1:1909566 [A/G] chr1 1909566 Cc01_g01250:1755 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA +chr1:1909582 [C/T] chr1 1909582 Cc01_g01250:1771 exon STOP_GAINED Cga/Tga R/1 12.5% 4 CC CC CC CT +chr1:1909609 [G/A] chr1 1909609 Cc01_g01250:1798 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GG GG AG +chr1:1909635 [C/T] chr1 1909635 Cc01_g01250:1824 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT +chr1:1909662 [C/T] chr1 1909662 Cc01_g01250:1851 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC CT TT CT +chr1:1909686 [C/T] chr1 1909686 Cc01_g01250:1875 exon SYNONYMOUS_CODING ccC/ccT P/P 37.5% 4 CC CT CT CT +chr1:1909689 [A/T] chr1 1909689 Cc01_g01250:1878 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA TA AA +chr1:1909703 [A/G] chr1 1909703 Cc01_g01250:1892 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA +chr1:1909742 [G/T] chr1 1909742 Cc01_g01250:1931 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 37.5% 4 GG GT GT TG +chr1:1909746 [T/G] chr1 1909746 Cc01_g01250:1935 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 TT TG TG GT +chr1:1909748 [G/A] chr1 1909748 Cc01_g01250:1937 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 GG AA AA AA +chr1:1909805 [G/A] chr1 1909805 Cc01_g01250:1994 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 37.5% 4 GG GA GA AG +chr1:1909856 [C/T] chr1 1909856 Cc01_g01250:2045 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 25.0% 4 CC TC CC CT +chr1:1909857 [A/T] chr1 1909857 Cc01_g01250:2046 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT +chr1:1909887 [G/A] chr1 1909887 Cc01_g01250:2076 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG +chr1:1909896 [A/G] chr1 1909896 Cc01_g01250:2085 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG +chr1:1909917 [A/G] chr1 1909917 Cc01_g01250:2106 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG +chr1:1909941 [G/A] chr1 1909941 Cc01_g01250:2130 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GA GA +chr1:1909992 [C/G] chr1 1909992 Cc01_g01250:2181 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC +chr1:2012155 [G/A] chr1 2012155 Cc01_g01280:207 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 GG GA NN GG +chr1:2012138 [G/A] chr1 2012138 Cc01_g01280:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG AA AA AA +chr1:2012066 [A/G] chr1 2012066 Cc01_g01280:296 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 33.3% 3 AA GG GG NN +chr1:2011950 [C/G] chr1 2011950 Cc01_g01280:412 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG CC CC +chr1:2011879 [G/A] chr1 2011879 Cc01_g01280:483 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GA NN GG +chr1:2029017 [G/C] chr1 2029017 Cc01_g01300:239 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 37.5% 4 GG CC CC GC +chr1:2028341 [A/G] chr1 2028341 Cc01_g01300:366 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG GG AG +chr1:2028339 [G/A] chr1 2028339 Cc01_g01300:368 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 GG AG GG GG +chr1:2028335 [A/C] chr1 2028335 Cc01_g01300:372 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 AA CC CC CC +chr1:2028322 [C/T] chr1 2028322 Cc01_g01300:385 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC TC CC CC +chr1:2028306 [C/G] chr1 2028306 Cc01_g01300:401 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CG CC +chr1:2028289 [T/C] chr1 2028289 Cc01_g01300:418 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 TT CC NN CC +chr1:2084455 [A/G] chr1 2084455 Cc01_g01330:36 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 AA AG AG GG +chr1:2084476 [G/C] chr1 2084476 Cc01_g01330:57 exon NON_SYNONYMOUS_CODING atG/atC M/I 37.5% 4 GG CG CC CC +chr1:2084479 [C/T] chr1 2084479 Cc01_g01330:60 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC TC CC CC +chr1:2084490 [C/A] chr1 2084490 Cc01_g01330:71 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC AC CC CC +chr1:2084532 [A/G] chr1 2084532 Cc01_g01330:113 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 4 AA AG AG GG +chr1:2084551 [A/G] chr1 2084551 Cc01_g01330:132 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA GA AA AA +chr1:2084565 [C/G] chr1 2084565 Cc01_g01330:146 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 50.0% 4 CC CG CG GG +chr1:2084606 [G/T] chr1 2084606 Cc01_g01330:187 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 4 GG GT GT TT +chr1:2084666 [A/G] chr1 2084666 Cc01_g01330:247 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG AG GG +chr1:2084667 [C/T] chr1 2084667 Cc01_g01330:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 CC TT TT TT +chr1:2084687 [G/A] chr1 2084687 Cc01_g01330:268 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 4 GG GA GA AA +chr1:2084690 [C/G] chr1 2084690 Cc01_g01330:271 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC +chr1:2084692 [A/G] chr1 2084692 Cc01_g01330:273 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA +chr1:2084718 [C/T] chr1 2084718 Cc01_g01330:299 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 33.3% 3 CC TT TT NN +chr1:2084791 [T/A] chr1 2084791 Cc01_g01330:372 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TA TT +chr1:2084820 [A/G] chr1 2084820 Cc01_g01330:401 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AA GA AG +chr1:2084834 [G/A] chr1 2084834 Cc01_g01330:415 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG AG +chr1:2084842 [G/C] chr1 2084842 Cc01_g01330:423 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG GG GC CG +chr1:2084851 [A/G] chr1 2084851 Cc01_g01330:432 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GA AG +chr1:2084863 [C/T] chr1 2084863 Cc01_g01330:444 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC TC CC +chr1:2084924 [A/T] chr1 2084924 Cc01_g01330:505 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA AT AT NN +chr1:2085060 [T/C] chr1 2085060 Cc01_g01330:641 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN +chr1:2085102 [A/C] chr1 2085102 Cc01_g01330:683 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 25.0% 4 AA AA CC AA +chr1:2085109 [T/G] chr1 2085109 Cc01_g01330:690 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 TT TT GG TT +chr1:2085145 [G/A] chr1 2085145 Cc01_g01330:726 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG GG AA GG +chr1:2085162 [C/G] chr1 2085162 Cc01_g01330:743 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC CG GG CC +chr1:2085194 [G/A] chr1 2085194 Cc01_g01330:775 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GG GA +chr1:2085203 [C/A] chr1 2085203 Cc01_g01330:784 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 CC CA CA CA +chr1:2085208 [A/G] chr1 2085208 Cc01_g01330:789 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG +chr1:2085218 [G/C] chr1 2085218 Cc01_g01330:799 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 GG GC GG CC +chr1:2085227 [T/G] chr1 2085227 Cc01_g01330:808 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 37.5% 4 TT TG TT GG +chr1:2085271 [A/G] chr1 2085271 Cc01_g01330:852 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AG AA NN +chr1:2085356 [C/G] chr1 2085356 Cc01_g01330:937 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 16.7% 3 CC CC CG NN +chr1:2085358 [T/A] chr1 2085358 Cc01_g01330:939 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT TT TA NN +chr1:2086315 [G/T] chr1 2086315 Cc01_g01330:1073 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GG GT GT +chr1:2086354 [A/G] chr1 2086354 Cc01_g01330:1112 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GA AA +chr1:2086380 [C/A] chr1 2086380 Cc01_g01330:1138 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 CC CC CA AA +chr1:2086424 [A/G] chr1 2086424 Cc01_g01330:1182 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AA AG GG +chr1:2086438 [C/T] chr1 2086438 Cc01_g01330:1196 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 CC TT TT TT +chr1:2086581 [G/T] chr1 2086581 Cc01_g01330:1261 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG +chr1:2086594 [T/C] chr1 2086594 Cc01_g01330:1274 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT TT TC TC +chr1:2086608 [T/C] chr1 2086608 Cc01_g01330:1288 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 37.5% 4 TT TC TC TC +chr1:2086613 [T/C] chr1 2086613 Cc01_g01330:1293 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT TC TC TC +chr1:2086637 [C/A] chr1 2086637 Cc01_g01330:1317 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 CC CA CC AA +chr1:2086679 [G/A] chr1 2086679 Cc01_g01330:1359 exon SYNONYMOUS_CODING gaG/gaA E/E 12.5% 4 GG GG GG GA +chr1:2086682 [C/T] chr1 2086682 Cc01_g01330:1362 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CC CT CT +chr1:2086716 [G/A] chr1 2086716 Cc01_g01330:1396 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GG AA +chr1:2086756 [G/A] chr1 2086756 Cc01_g01330:1436 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG GA +chr1:2086758 [C/G] chr1 2086758 Cc01_g01330:1438 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC CC CG GC +chr1:2086789 [T/A] chr1 2086789 Cc01_g01330:1469 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 TT AA AA AA +chr1:2086811 [A/G] chr1 2086811 Cc01_g01330:1491 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA +chr1:2086840 [T/A] chr1 2086840 Cc01_g01330:1520 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT AA TT TT +chr1:2093852 [C/T] chr1 2093852 Cc01_g01340:4 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 CC CT NN CC +chr1:2093847 [C/A] chr1 2093847 Cc01_g01340:9 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 4 CC AC AA CA +chr1:2093810 [G/A] chr1 2093810 Cc01_g01340:46 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG AG GG GG +chr1:2093799 [A/G] chr1 2093799 Cc01_g01340:57 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GA GG AA +chr1:2093778 [A/G] chr1 2093778 Cc01_g01340:78 exon SYNONYMOUS_CODING gaT/gaC D/D 16.7% 3 AA AA NN GA +chr1:2093758 [G/A] chr1 2093758 Cc01_g01340:98 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 33.3% 3 GG GA NN GA +chr1:2093731 [C/A] chr1 2093731 Cc01_g01340:125 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 16.7% 3 CC CC NN CA +chr1:2093721 [C/G] chr1 2093721 Cc01_g01340:135 exon SYNONYMOUS_CODING tcG/tcC S/S 50.0% 4 CC CG GG CG +chr1:2093714 [A/C] chr1 2093714 Cc01_g01340:142 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 50.0% 4 AA AC CC AC +chr1:2093686 [A/G] chr1 2093686 Cc01_g01340:170 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 AA AG GG AG +chr1:2093684 [T/C] chr1 2093684 Cc01_g01340:172 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 TT TC CC TC +chr1:2093683 [G/C] chr1 2093683 Cc01_g01340:173 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 12.5% 4 GG GC GG GG +chr1:2093672 [C/A] chr1 2093672 Cc01_g01340:184 exon STOP_GAINED Gag/Tag E/2 37.5% 4 CC CA CA CA +chr1:2093663 [G/A] chr1 2093663 Cc01_g01340:193 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 GG GG GG AG +chr1:2093646 [A/G] chr1 2093646 Cc01_g01340:210 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA AG AG AA +chr1:2093644 [T/C] chr1 2093644 Cc01_g01340:212 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 TT TC TC TC +chr1:2093642 [C/T] chr1 2093642 Cc01_g01340:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TC TC TC +chr1:2093636 [T/G] chr1 2093636 Cc01_g01340:220 exon NON_SYNONYMOUS_CODING Acc/Ccc T/P 25.0% 4 TT TG TG TT +chr1:2093635 [G/T] chr1 2093635 Cc01_g01340:221 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 25.0% 4 GG GT GG GT +chr1:2093634 [G/A] chr1 2093634 Cc01_g01340:222 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GA GG GG +chr1:2093633 [C/T] chr1 2093633 Cc01_g01340:223 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 CC CC CC CT +chr1:2093602 [A/T] chr1 2093602 Cc01_g01340:254 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 33.3% 3 AA AT NN AT +chr1:2093600 [C/G] chr1 2093600 Cc01_g01340:256 exon NON_SYNONYMOUS_CODING Gga/Cga G/R 16.7% 3 CC CG NN CC +chr1:2093588 [T/G] chr1 2093588 Cc01_g01340:268 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 16.7% 3 TT TG NN TT +chr1:2093575 [A/G] chr1 2093575 Cc01_g01340:281 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 50.0% 3 AA GG NN AG +chr1:2093569 [G/A] chr1 2093569 Cc01_g01340:287 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 16.7% 3 GG GG NN GA +chr1:2093565 [G/A] chr1 2093565 Cc01_g01340:291 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GG NN GA +chr1:2093525 [C/G] chr1 2093525 Cc01_g01340:331 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 50.0% 3 CC GG NN CG +chr1:2093515 [T/C] chr1 2093515 Cc01_g01340:341 exon SYNONYMOUS_STOP tAa/tGa 1/1 33.3% 3 TT CC NN TT +chr1:2095269 [G/A] chr1 2095269 Cc01_g01350:16 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG +chr1:2095295 [A/G] chr1 2095295 Cc01_g01350:42 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA +chr1:2095321 [A/T] chr1 2095321 Cc01_g01350:68 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA +chr1:2095431 [C/A] chr1 2095431 Cc01_g01350:178 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CA CC CC +chr1:2095629 [C/T] chr1 2095629 Cc01_g01350:376 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC CC CT CT +chr1:2095745 [G/A] chr1 2095745 Cc01_g01350:492 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA AA GG +chr1:2095959 [C/G] chr1 2095959 Cc01_g01350:706 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CG CC +chr1:2095960 [A/G] chr1 2095960 Cc01_g01350:707 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG GA AA +chr1:2095964 [C/T] chr1 2095964 Cc01_g01350:711 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC TC CC +chr1:2095974 [C/T] chr1 2095974 Cc01_g01350:721 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC +chr1:2095975 [A/C] chr1 2095975 Cc01_g01350:722 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 AA AA CA AA +chr1:2095983 [A/C] chr1 2095983 Cc01_g01350:730 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 12.5% 4 AA AC AA AA +chr1:2096351 [T/A] chr1 2096351 Cc01_g01350:980 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT +chr1:2096710 [C/G] chr1 2096710 Cc01_g01350:1261 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CG CC +chr1:2100328 [A/C] chr1 2100328 Cc01_g01360:24 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 50.0% 3 AA NN AC CC +chr1:2100313 [T/A] chr1 2100313 Cc01_g01360:39 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA +chr1:2100304 [T/C] chr1 2100304 Cc01_g01360:48 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 TT CC CC TC +chr1:2100300 [C/T] chr1 2100300 Cc01_g01360:52 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC TT TT TT +chr1:2100299 [G/A] chr1 2100299 Cc01_g01360:53 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG AA AA GA +chr1:2100295 [A/G] chr1 2100295 Cc01_g01360:57 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA GG GG AG +chr1:2100286 [A/G] chr1 2100286 Cc01_g01360:66 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG GG AA +chr1:2100277 [C/T] chr1 2100277 Cc01_g01360:75 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT TT TT +chr1:2100255 [C/T] chr1 2100255 Cc01_g01360:97 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TT CT TT +chr1:2100252 [A/T] chr1 2100252 Cc01_g01360:100 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 37.5% 4 AA TT AT TT +chr1:2100249 [C/T] chr1 2100249 Cc01_g01360:103 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 CC TT CT TT +chr1:2100244 [A/T] chr1 2100244 Cc01_g01360:108 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA TT AT TT +chr1:2100237 [T/C] chr1 2100237 Cc01_g01360:115 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 37.5% 4 TT CC TC CC +chr1:2100226 [G/A] chr1 2100226 Cc01_g01360:126 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA +chr1:2100223 [A/C] chr1 2100223 Cc01_g01360:129 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 3 AA NN AC CC +chr1:2100218 [C/T] chr1 2100218 Cc01_g01360:134 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 2 CC NN CT NN +chr1:2100189 [T/C] chr1 2100189 Cc01_g01360:163 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 TT CC TT TC +chr1:2100184 [G/A] chr1 2100184 Cc01_g01360:168 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GA GG GA +chr1:2100164 [A/G] chr1 2100164 Cc01_g01360:188 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 3 AA GG NN AG +chr1:2100139 [A/G] chr1 2100139 Cc01_g01360:213 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 2 AA NN NN AG +chr1:2105898 [A/G] chr1 2105898 Cc01_g01370:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA AG AA AG +chr1:2105943 [C/G] chr1 2105943 Cc01_g01370:68 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC +chr1:2105974 [T/G] chr1 2105974 Cc01_g01370:99 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT TG TT TG +chr1:2105998 [T/C] chr1 2105998 Cc01_g01370:123 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT CT TT +chr1:2106006 [G/C] chr1 2106006 Cc01_g01370:131 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 50.0% 4 GG CC GC GC +chr1:2106086 [G/A] chr1 2106086 Cc01_g01370:211 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG +chr1:2106188 [G/C] chr1 2106188 Cc01_g01370:313 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 4 GG GC GG GC +chr1:2106190 [G/A] chr1 2106190 Cc01_g01370:315 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA +chr1:2106216 [C/G] chr1 2106216 Cc01_g01370:341 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC CG CC CG +chr1:2106220 [T/C] chr1 2106220 Cc01_g01370:345 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TC TT TC +chr1:2106236 [T/C] chr1 2106236 Cc01_g01370:361 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT TC TT TC +chr1:2106264 [G/A] chr1 2106264 Cc01_g01370:389 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG +chr1:2106271 [C/A] chr1 2106271 Cc01_g01370:396 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA +chr1:2106279 [G/A] chr1 2106279 Cc01_g01370:404 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 GG GG GA GA +chr1:2106291 [A/C] chr1 2106291 Cc01_g01370:416 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 37.5% 4 AA AC AC AC +chr1:2106302 [A/G] chr1 2106302 Cc01_g01370:427 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG GG AG +chr1:2106324 [T/G] chr1 2106324 Cc01_g01370:449 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 37.5% 4 TT TG TG TG +chr1:2106332 [C/G] chr1 2106332 Cc01_g01370:457 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:2106375 [A/G] chr1 2106375 Cc01_g01370:500 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 37.5% 4 AA AG AG AG +chr1:2106435 [A/T] chr1 2106435 Cc01_g01370:560 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 AA AT AA AT +chr1:2106441 [T/G] chr1 2106441 Cc01_g01370:566 exon NON_SYNONYMOUS_CODING aTg/aGg M/R 25.0% 4 TT TG TT TG +chr1:2106443 [C/G] chr1 2106443 Cc01_g01370:568 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC +chr1:2106602 [A/G] chr1 2106602 Cc01_g01370:633 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG +chr1:2106604 [T/G] chr1 2106604 Cc01_g01370:635 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 TT TG TG TG +chr1:2106695 [G/C] chr1 2106695 Cc01_g01370:726 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG CC GG GG +chr1:2106696 [A/G] chr1 2106696 Cc01_g01370:727 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 AA GG GG AA +chr1:2106708 [G/A] chr1 2106708 Cc01_g01370:739 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG +chr1:2106774 [A/G] chr1 2106774 Cc01_g01370:805 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AA AG +chr1:2106839 [T/C] chr1 2106839 Cc01_g01370:870 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TT TC +chr1:2106857 [T/A] chr1 2106857 Cc01_g01370:888 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 50.0% 4 TT AA TA TA +chr1:2106878 [G/A] chr1 2106878 Cc01_g01370:909 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA GA +chr1:2106908 [A/G] chr1 2106908 Cc01_g01370:939 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA +chr1:2107068 [C/A] chr1 2107068 Cc01_g01370:980 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC +chr1:2107109 [G/C] chr1 2107109 Cc01_g01370:1021 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GC GG +chr1:2107131 [A/C] chr1 2107131 Cc01_g01370:1043 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 25.0% 4 AA CA AA AC +chr1:2107150 [G/A] chr1 2107150 Cc01_g01370:1062 exon STOP_GAINED tgG/tgA W/4 12.5% 4 GG GA GG GG +chr1:2107161 [T/C] chr1 2107161 Cc01_g01370:1073 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT CT TT +chr1:2107171 [C/G] chr1 2107171 Cc01_g01370:1083 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 12.5% 4 CC CC GC CC +chr1:2107215 [G/A] chr1 2107215 Cc01_g01370:1127 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 50.0% 4 GG AA GA GA +chr1:2107325 [A/C] chr1 2107325 Cc01_g01370:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 AA AC AC AC +chr1:2107345 [A/G] chr1 2107345 Cc01_g01370:1179 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG AG +chr1:2107361 [T/A] chr1 2107361 Cc01_g01370:1195 exon NON_SYNONYMOUS_CODING Tct/Act S/T 37.5% 4 TT TA TA TA +chr1:2107390 [A/C] chr1 2107390 Cc01_g01370:1224 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA AC +chr1:2107405 [T/A] chr1 2107405 Cc01_g01370:1239 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA +chr1:2107431 [C/T] chr1 2107431 Cc01_g01370:1265 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 CC CT CT CT +chr1:2107467 [A/T] chr1 2107467 Cc01_g01370:1301 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA TA AA AA +chr1:2107472 [G/A] chr1 2107472 Cc01_g01370:1306 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG AG GG +chr1:2107516 [T/C] chr1 2107516 Cc01_g01370:1350 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TC TC +chr1:2107607 [C/T] chr1 2107607 Cc01_g01370:1441 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT +chr1:2117223 [A/G] chr1 2117223 Cc01_g01380:117 exon SYNONYMOUS_CODING cgT/cgC R/R 33.3% 3 AA GG NN GG +chr1:2117210 [T/G] chr1 2117210 Cc01_g01380:130 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 33.3% 3 TT GG NN GG +chr1:2117175 [C/G] chr1 2117175 Cc01_g01380:165 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 2 CC GG NN NN +chr1:2117171 [C/T] chr1 2117171 Cc01_g01380:169 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 CC TT NN NN +chr1:2116944 [A/G] chr1 2116944 Cc01_g01380:240 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 AA NN NN GG +chr1:2116934 [T/A] chr1 2116934 Cc01_g01380:250 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 TT NN NN AA +chr1:2116932 [C/G] chr1 2116932 Cc01_g01380:252 exon NON_SYNONYMOUS_CODING atG/atC M/I 50.0% 2 CC NN NN GG +chr1:2116917 [C/A] chr1 2116917 Cc01_g01380:267 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 CC NN NN AA +chr1:2116877 [T/A] chr1 2116877 Cc01_g01380:307 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 50.0% 2 TT NN NN AA +chr1:2116873 [T/C] chr1 2116873 Cc01_g01380:311 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 TT NN NN CC +chr1:2116861 [A/G] chr1 2116861 Cc01_g01380:323 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 2 AA NN NN GG +chr1:2169162 [C/G] chr1 2169162 Cc01_g01390:5 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC +chr1:2169167 [C/G] chr1 2169167 Cc01_g01390:10 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 37.5% 4 CC CG CG CG +chr1:2169279 [A/G] chr1 2169279 Cc01_g01390:122 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG +chr1:2169286 [A/T] chr1 2169286 Cc01_g01390:129 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA AA AT AA +chr1:2169346 [T/C] chr1 2169346 Cc01_g01390:189 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TC TC TT +chr1:2169353 [G/A] chr1 2169353 Cc01_g01390:196 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG +chr1:2169630 [T/A] chr1 2169630 Cc01_g01390:473 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT AA TA AA +chr1:2169828 [C/A] chr1 2169828 Cc01_g01390:671 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CA CA CC +chr1:2169829 [G/C] chr1 2169829 Cc01_g01390:672 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GC GG +chr1:2169862 [C/T] chr1 2169862 Cc01_g01390:705 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:2169958 [T/C] chr1 2169958 Cc01_g01390:801 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:2169967 [C/T] chr1 2169967 Cc01_g01390:810 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CC CT CC +chr1:2170037 [G/C] chr1 2170037 Cc01_g01390:880 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG +chr1:2170043 [G/A] chr1 2170043 Cc01_g01390:886 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG +chr1:2170057 [C/T] chr1 2170057 Cc01_g01390:900 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC TC CC +chr1:2170129 [T/C] chr1 2170129 Cc01_g01390:972 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TT TC TT +chr1:2170192 [G/T] chr1 2170192 Cc01_g01390:1035 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GT GG GG +chr1:2170204 [T/C] chr1 2170204 Cc01_g01390:1047 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:2170362 [A/T] chr1 2170362 Cc01_g01390:1080 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 AA AT AT AA +chr1:2170446 [T/C] chr1 2170446 Cc01_g01390:1164 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CC TC CC +chr1:2170635 [T/C] chr1 2170635 Cc01_g01390:1275 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 TT CC TT CC +chr1:2170650 [T/C] chr1 2170650 Cc01_g01390:1290 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT +chr1:2170761 [T/G] chr1 2170761 Cc01_g01390:1401 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 37.5% 4 TT GG TG GG +chr1:2170780 [C/T] chr1 2170780 Cc01_g01390:1420 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CT CC +chr1:2170800 [G/A] chr1 2170800 Cc01_g01390:1440 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG AA GG AA +chr1:2170865 [C/A] chr1 2170865 Cc01_g01390:1505 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CA CC +chr1:2170868 [A/C] chr1 2170868 Cc01_g01390:1508 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 4 AA CC AA CC +chr1:2170873 [A/G] chr1 2170873 Cc01_g01390:1513 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AG AA AA +chr1:2170884 [C/T] chr1 2170884 Cc01_g01390:1524 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC TT CC TT +chr1:2174798 [C/T] chr1 2174798 Cc01_g01400:21 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC CT CT TT +chr1:2174809 [A/G] chr1 2174809 Cc01_g01400:32 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AG AG +chr1:2174843 [G/A] chr1 2174843 Cc01_g01400:66 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG GG GA GA +chr1:2174851 [G/A] chr1 2174851 Cc01_g01400:74 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GG AG GG +chr1:2174873 [C/A] chr1 2174873 Cc01_g01400:96 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA +chr1:2174883 [T/C] chr1 2174883 Cc01_g01400:106 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT TT TC TC +chr1:2174888 [T/C] chr1 2174888 Cc01_g01400:111 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TC TC +chr1:2174899 [T/C] chr1 2174899 Cc01_g01400:122 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 TT TT TT CT +chr1:2174901 [C/T] chr1 2174901 Cc01_g01400:124 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 CC CC CT CT +chr1:2174903 [T/C] chr1 2174903 Cc01_g01400:126 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TT TC TC +chr1:2174906 [T/G] chr1 2174906 Cc01_g01400:129 exon SYNONYMOUS_CODING acT/acG T/T 25.0% 4 TT TT TG TG +chr1:2174908 [C/A] chr1 2174908 Cc01_g01400:131 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 25.0% 4 CC CC CA CA +chr1:2174912 [T/G] chr1 2174912 Cc01_g01400:135 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 12.5% 4 TT TG TT TT +chr1:2174940 [C/A] chr1 2174940 Cc01_g01400:163 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CC CA CA +chr1:2174949 [T/G] chr1 2174949 Cc01_g01400:172 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 25.0% 4 TT TT TG TG +chr1:2174958 [G/A] chr1 2174958 Cc01_g01400:181 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GG GA GA +chr1:2174961 [C/T] chr1 2174961 Cc01_g01400:184 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 37.5% 4 CC CC TT CT +chr1:2174991 [G/A] chr1 2174991 Cc01_g01400:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG +chr1:2174992 [A/G] chr1 2174992 Cc01_g01400:215 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA GA AA GA +chr1:2174997 [C/T] chr1 2174997 Cc01_g01400:220 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC CT CT TT +chr1:2174999 [T/C] chr1 2174999 Cc01_g01400:222 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC TC +chr1:2175021 [G/C] chr1 2175021 Cc01_g01400:244 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 25.0% 4 GG GG GC GC +chr1:2175025 [C/G] chr1 2175025 Cc01_g01400:248 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 25.0% 4 CC CC CG CG +chr1:2175026 [T/C] chr1 2175026 Cc01_g01400:249 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT TC TC +chr1:2175072 [A/C] chr1 2175072 Cc01_g01400:295 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AC AA AA +chr1:2175151 [T/G] chr1 2175151 Cc01_g01400:374 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 12.5% 4 TT TT TT TG +chr1:2175157 [C/A] chr1 2175157 Cc01_g01400:380 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CC AC +chr1:2175167 [C/T] chr1 2175167 Cc01_g01400:390 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:2175183 [A/G] chr1 2175183 Cc01_g01400:406 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA +chr1:2175248 [C/T] chr1 2175248 Cc01_g01400:471 exon SYNONYMOUS_CODING taC/taT Y/Y 33.3% 3 CC TT NN TT +chr1:2175317 [A/C] chr1 2175317 Cc01_g01400:540 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 AA AA AA AC +chr1:2175371 [T/C] chr1 2175371 Cc01_g01400:594 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC +chr1:2175512 [C/T] chr1 2175512 Cc01_g01400:735 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CC CT +chr1:2175561 [G/T] chr1 2175561 Cc01_g01400:784 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT GG GG +chr1:2175562 [C/G] chr1 2175562 Cc01_g01400:785 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG CC CC +chr1:2175613 [G/T] chr1 2175613 Cc01_g01400:836 exon NON_SYNONYMOUS_CODING cGt/cTt R/L 25.0% 4 GG GG GG TT +chr1:2175705 [T/A] chr1 2175705 Cc01_g01400:928 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT TT TA TT +chr1:2175977 [G/A] chr1 2175977 Cc01_g01400:1088 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 GG GG GG GA +chr1:2176009 [G/A] chr1 2176009 Cc01_g01400:1120 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG +chr1:2176010 [A/C] chr1 2176010 Cc01_g01400:1121 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AC AA AA +chr1:2176046 [C/A] chr1 2176046 Cc01_g01400:1157 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 CC CA CC CC +chr1:2176075 [G/C] chr1 2176075 Cc01_g01400:1186 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GC GG +chr1:2176085 [G/A] chr1 2176085 Cc01_g01400:1196 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 GG GG GA GG +chr1:2176089 [A/G] chr1 2176089 Cc01_g01400:1200 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AG AA +chr1:2176098 [C/T] chr1 2176098 Cc01_g01400:1209 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:2176099 [G/A] chr1 2176099 Cc01_g01400:1210 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG AG GG GG +chr1:2176255 [G/A] chr1 2176255 Cc01_g01400:1285 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG +chr1:2176279 [T/A] chr1 2176279 Cc01_g01400:1309 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TT TT TA +chr1:2176311 [C/A] chr1 2176311 Cc01_g01400:1341 exon SYNONYMOUS_CODING atC/atA I/I 12.5% 4 CC CA CC CC +chr1:2176321 [G/A] chr1 2176321 Cc01_g01400:1351 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA +chr1:2176345 [C/G] chr1 2176345 Cc01_g01400:1375 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 12.5% 4 CC CG CC CC +chr1:2176383 [A/G] chr1 2176383 Cc01_g01400:1413 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:2176387 [A/T] chr1 2176387 Cc01_g01400:1417 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AT AA AA +chr1:2177071 [T/G] chr1 2177071 Cc01_g01410:37 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT GG NN TT +chr1:2177072 [G/T] chr1 2177072 Cc01_g01410:38 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 33.3% 3 GG GG NN TT +chr1:2177953 [T/C] chr1 2177953 Cc01_g01410:198 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT NN NN CC +chr1:2185597 [C/A] chr1 2185597 Cc01_g01420:45 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 CC CA CC CA +chr1:2185587 [T/C] chr1 2185587 Cc01_g01420:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TC TT TT +chr1:2185534 [T/C] chr1 2185534 Cc01_g01420:108 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TC TT +chr1:2185452 [G/C] chr1 2185452 Cc01_g01420:190 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 12.5% 4 GG GG GC GG +chr1:2185431 [T/C] chr1 2185431 Cc01_g01420:211 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC +chr1:2185418 [T/C] chr1 2185418 Cc01_g01420:224 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 12.5% 4 TT TT CT TT +chr1:2185408 [C/T] chr1 2185408 Cc01_g01420:234 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT TT CT +chr1:2185315 [A/C] chr1 2185315 Cc01_g01420:327 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 AA AA AA AC +chr1:2185281 [A/G] chr1 2185281 Cc01_g01420:361 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA +chr1:2185274 [G/T] chr1 2185274 Cc01_g01420:368 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 4 GG GG TT GG +chr1:2185232 [C/T] chr1 2185232 Cc01_g01420:410 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CT CC +chr1:2185228 [A/T] chr1 2185228 Cc01_g01420:414 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA TA AA +chr1:2185186 [A/G] chr1 2185186 Cc01_g01420:456 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AG AA AA +chr1:2185185 [T/A] chr1 2185185 Cc01_g01420:457 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 25.0% 4 TT AT TT TA +chr1:2185150 [A/G] chr1 2185150 Cc01_g01420:492 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GA AA AG +chr1:2185136 [T/G] chr1 2185136 Cc01_g01420:506 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 12.5% 4 TT TG TT TT +chr1:2185131 [A/T] chr1 2185131 Cc01_g01420:511 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 4 AA TT AT AT +chr1:2185130 [C/G] chr1 2185130 Cc01_g01420:512 exon NON_SYNONYMOUS_CODING tGg/tCg W/S 50.0% 4 CC GG CG CG +chr1:2185056 [C/T] chr1 2185056 Cc01_g01420:586 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CT CC CC +chr1:2185024 [C/G] chr1 2185024 Cc01_g01420:618 exon SYNONYMOUS_CODING cgG/cgC R/R 12.5% 4 CC CC CG CC +chr1:2184985 [C/T] chr1 2184985 Cc01_g01420:657 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:2184978 [A/G] chr1 2184978 Cc01_g01420:664 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 AA AA AG AA +chr1:2184967 [C/T] chr1 2184967 Cc01_g01420:675 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 CC CC CT CC +chr1:2184923 [T/C] chr1 2184923 Cc01_g01420:719 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT +chr1:2184900 [G/A] chr1 2184900 Cc01_g01420:742 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 GG GG GA GG +chr1:2184858 [C/T] chr1 2184858 Cc01_g01420:784 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC +chr1:2184847 [T/G] chr1 2184847 Cc01_g01420:795 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 12.5% 4 TT TT TG TT +chr1:2184843 [A/G] chr1 2184843 Cc01_g01420:799 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG GG GG +chr1:2184715 [A/G] chr1 2184715 Cc01_g01420:927 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:2184631 [A/G] chr1 2184631 Cc01_g01420:1011 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AG AA AA +chr1:2184436 [C/T] chr1 2184436 Cc01_g01420:1087 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC TT CT TT +chr1:2184420 [C/T] chr1 2184420 Cc01_g01420:1103 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC TC CC +chr1:2184375 [A/C] chr1 2184375 Cc01_g01420:1148 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 25.0% 4 AA CC CC CC +chr1:2184365 [C/T] chr1 2184365 Cc01_g01420:1158 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT +chr1:2184361 [T/C] chr1 2184361 Cc01_g01420:1162 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 4 TT CC CC TT +chr1:2184164 [T/A] chr1 2184164 Cc01_g01420:1280 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 37.5% 4 TT AA AA AT +chr1:2184085 [C/T] chr1 2184085 Cc01_g01420:1359 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 CC CC TT CC +chr1:2184069 [A/G] chr1 2184069 Cc01_g01420:1375 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG GG GG +chr1:2184058 [T/A] chr1 2184058 Cc01_g01420:1386 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA +chr1:2184010 [T/C] chr1 2184010 Cc01_g01420:1434 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TT TC +chr1:2183902 [T/C] chr1 2183902 Cc01_g01420:1542 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC +chr1:2191614 [T/C] chr1 2191614 Cc01_g01430:14 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 TT TC TC TC +chr1:2190583 [G/T] chr1 2190583 Cc01_g01430:511 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG GT GG GT +chr1:2190560 [C/G] chr1 2190560 Cc01_g01430:534 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CC CC GC +chr1:2190508 [A/G] chr1 2190508 Cc01_g01430:586 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA +chr1:2190494 [A/G] chr1 2190494 Cc01_g01430:600 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA +chr1:2189807 [A/T] chr1 2189807 Cc01_g01430:897 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA AT AT AA +chr1:2189651 [T/C] chr1 2189651 Cc01_g01430:1053 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC +chr1:2189636 [A/G] chr1 2189636 Cc01_g01430:1068 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG +chr1:2189634 [A/T] chr1 2189634 Cc01_g01430:1070 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 AA AA TA AA +chr1:2188570 [T/C] chr1 2188570 Cc01_g01430:1166 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT +chr1:2188551 [A/G] chr1 2188551 Cc01_g01430:1185 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA +chr1:2196422 [A/G] chr1 2196422 Cc01_g01440:36 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AG AA AG +chr1:2196341 [T/C] chr1 2196341 Cc01_g01440:117 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC TC TC +chr1:2196333 [G/C] chr1 2196333 Cc01_g01440:125 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG CG GG GG +chr1:2196286 [C/A] chr1 2196286 Cc01_g01440:172 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 37.5% 4 CC AA CC CA +chr1:2196284 [T/G] chr1 2196284 Cc01_g01440:174 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT GT TT TT +chr1:2196257 [A/G] chr1 2196257 Cc01_g01440:201 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:2196212 [A/G] chr1 2196212 Cc01_g01440:246 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA +chr1:2196172 [A/G] chr1 2196172 Cc01_g01440:286 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 AA AA GG AA +chr1:2196160 [A/G] chr1 2196160 Cc01_g01440:298 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 AA GG AA AG +chr1:2196140 [A/G] chr1 2196140 Cc01_g01440:318 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA AA GG AA +chr1:2196134 [G/C] chr1 2196134 Cc01_g01440:324 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GC GG GG +chr1:2196132 [C/T] chr1 2196132 Cc01_g01440:326 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC +chr1:2196068 [T/A] chr1 2196068 Cc01_g01440:390 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 37.5% 4 TT TA TA TA +chr1:2196065 [T/C] chr1 2196065 Cc01_g01440:393 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC +chr1:2195449 [A/G] chr1 2195449 Cc01_g01440:536 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 AA AA AA AG +chr1:2195438 [T/A] chr1 2195438 Cc01_g01440:547 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 37.5% 4 TT TA TA TA +chr1:2195424 [C/A] chr1 2195424 Cc01_g01440:561 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC CA CA CC +chr1:2195362 [G/A] chr1 2195362 Cc01_g01440:623 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 GG AG GG GA +chr1:2195350 [A/G] chr1 2195350 Cc01_g01440:635 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AA AG +chr1:2195327 [T/C] chr1 2195327 Cc01_g01440:658 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CT TT TC +chr1:2195242 [C/G] chr1 2195242 Cc01_g01440:743 exon NON_SYNONYMOUS_CODING gGa/gCa G/A 12.5% 4 CC CG CC CC +chr1:2195189 [A/G] chr1 2195189 Cc01_g01440:796 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA GA AA AA +chr1:2195153 [T/C] chr1 2195153 Cc01_g01440:832 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT TT TC CC +chr1:2195139 [A/G] chr1 2195139 Cc01_g01440:846 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA +chr1:2194136 [C/T] chr1 2194136 Cc01_g01440:878 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC TC CC CC +chr1:2194114 [G/A] chr1 2194114 Cc01_g01440:900 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG AA AA AA +chr1:2194101 [G/T] chr1 2194101 Cc01_g01440:913 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG TG GG GG +chr1:2194096 [T/G] chr1 2194096 Cc01_g01440:918 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 TT TG TT TT +chr1:2194092 [C/T] chr1 2194092 Cc01_g01440:922 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC +chr1:2194052 [T/A] chr1 2194052 Cc01_g01440:962 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TA TT +chr1:2193981 [A/G] chr1 2193981 Cc01_g01440:1033 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 AA AG AA AA +chr1:2193975 [T/C] chr1 2193975 Cc01_g01440:1039 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT +chr1:2193955 [C/A] chr1 2193955 Cc01_g01440:1059 exon SYNONYMOUS_CODING gcG/gcT A/A 37.5% 4 CC AA CC CA +chr1:2209238 [C/T] chr1 2209238 Cc01_g01450:478 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 25.0% 4 CC CC CC TT +chr1:2209206 [G/T] chr1 2209206 Cc01_g01450:510 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG GG TT NN +chr1:2208545 [T/C] chr1 2208545 Cc01_g01450:868 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT +chr1:2208543 [G/T] chr1 2208543 Cc01_g01450:870 exon NON_SYNONYMOUS_CODING agC/agA S/R 12.5% 4 GG GT GG GG +chr1:2208524 [T/A] chr1 2208524 Cc01_g01450:889 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 12.5% 4 TT TA TT TT +chr1:2208480 [C/T] chr1 2208480 Cc01_g01450:933 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC +chr1:2208471 [A/G] chr1 2208471 Cc01_g01450:942 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA GA AA AA +chr1:2208398 [C/T] chr1 2208398 Cc01_g01450:1015 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 33.3% 3 CC TT NN TT +chr1:2208295 [T/G] chr1 2208295 Cc01_g01450:1118 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 TT TG TT TT +chr1:2208265 [G/A] chr1 2208265 Cc01_g01450:1148 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GA GG GG +chr1:2208247 [G/T] chr1 2208247 Cc01_g01450:1166 exon NON_SYNONYMOUS_CODING cCa/cAa P/Q 25.0% 4 GG GT GG GT +chr1:2208199 [T/A] chr1 2208199 Cc01_g01450:1214 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 TT TT TA TT +chr1:2208185 [C/T] chr1 2208185 Cc01_g01450:1228 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC TC CC +chr1:2208178 [T/C] chr1 2208178 Cc01_g01450:1235 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT +chr1:2208133 [G/A] chr1 2208133 Cc01_g01450:1280 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 GG GA GG GG +chr1:2274354 [C/T] chr1 2274354 Cc01_g01460:831 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC TT NN TT +chr1:2274363 [T/C] chr1 2274363 Cc01_g01460:840 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT CC NN CC +chr1:2274385 [G/C] chr1 2274385 Cc01_g01460:862 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 33.3% 3 GG CC NN CC +chr1:2274390 [A/T] chr1 2274390 Cc01_g01460:867 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT +chr1:2274408 [A/C] chr1 2274408 Cc01_g01460:885 exon SYNONYMOUS_CODING atA/atC I/I 50.0% 2 AA NN NN CC +chr1:2274417 [C/T] chr1 2274417 Cc01_g01460:894 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 CC TT NN TT +chr1:2300221 [C/T] chr1 2300221 Cc01_g01470:1228 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 CC NN NN TT +chr1:2300215 [T/C] chr1 2300215 Cc01_g01470:1234 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 2 TT NN NN CC +chr1:2300214 [G/A] chr1 2300214 Cc01_g01470:1235 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 GG NN NN AA +chr1:2343380 [T/C] chr1 2343380 Cc01_g01490:11 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TT TT TC +chr1:2343353 [T/C] chr1 2343353 Cc01_g01490:38 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT CC CC CC +chr1:2343351 [G/C] chr1 2343351 Cc01_g01490:40 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 GG CC CC CC +chr1:2343348 [T/C] chr1 2343348 Cc01_g01490:43 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT CC CC CC +chr1:2343347 [A/G] chr1 2343347 Cc01_g01490:44 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 4 AA GG GG GG +chr1:2343346 [C/T] chr1 2343346 Cc01_g01490:45 exon NON_SYNONYMOUS_CODING atG/atA M/I 37.5% 4 CC CC TT TC +chr1:2343313 [A/G] chr1 2343313 Cc01_g01490:78 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 AA AA GG GA +chr1:2343300 [G/A] chr1 2343300 Cc01_g01490:91 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG AG +chr1:2343296 [C/T] chr1 2343296 Cc01_g01490:95 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 25.0% 4 CC TT TT TT +chr1:2343283 [A/G] chr1 2343283 Cc01_g01490:108 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG AG GG +chr1:2343280 [T/G] chr1 2343280 Cc01_g01490:111 exon SYNONYMOUS_CODING acA/acC T/T 50.0% 4 TT TG TG GG +chr1:2343274 [A/C] chr1 2343274 Cc01_g01490:117 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 AA AA AC CA +chr1:2343261 [C/A] chr1 2343261 Cc01_g01490:130 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 CC CA CC AA +chr1:2343259 [C/G] chr1 2343259 Cc01_g01490:132 exon SYNONYMOUS_CODING gtG/gtC V/V 37.5% 4 CC CG CC GG +chr1:2343244 [G/T] chr1 2343244 Cc01_g01490:147 exon NON_SYNONYMOUS_CODING caC/caA H/Q 25.0% 4 GG GG GG TT +chr1:2343241 [T/G] chr1 2343241 Cc01_g01490:150 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 TT TT TG GG +chr1:2343235 [G/C] chr1 2343235 Cc01_g01490:156 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG GC CC +chr1:2343232 [A/C] chr1 2343232 Cc01_g01490:159 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AA AC CC +chr1:2343229 [A/T] chr1 2343229 Cc01_g01490:162 exon SYNONYMOUS_CODING tcT/tcA S/S 37.5% 4 AA AA AT TT +chr1:2343225 [T/C] chr1 2343225 Cc01_g01490:166 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 TT TT TC CC +chr1:2343092 [T/C] chr1 2343092 Cc01_g01490:299 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT TT CC +chr1:2342875 [G/A] chr1 2342875 Cc01_g01490:516 exon SYNONYMOUS_CODING ttC/ttT F/F 33.3% 3 GG AA NN AA +chr1:2342772 [C/T] chr1 2342772 Cc01_g01490:619 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC +chr1:2342382 [C/T] chr1 2342382 Cc01_g01490:636 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC TT NN CC +chr1:2342352 [A/T] chr1 2342352 Cc01_g01490:666 exon SYNONYMOUS_CODING atT/atA I/I 37.5% 4 AA TT TT AT +chr1:2342154 [T/G] chr1 2342154 Cc01_g01490:774 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 TT TT TG GG +chr1:2342153 [A/G] chr1 2342153 Cc01_g01490:775 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 37.5% 4 AA AA AG GG +chr1:2342152 [C/T] chr1 2342152 Cc01_g01490:776 exon STOP_GAINED tGg/tAg W/9 37.5% 4 CC CC CT TT +chr1:2342133 [G/A] chr1 2342133 Cc01_g01490:795 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 GG GA GA AA +chr1:2342078 [G/A] chr1 2342078 Cc01_g01490:850 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA +chr1:2342048 [C/A] chr1 2342048 Cc01_g01490:880 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 25.0% 4 CC AA AA AA +chr1:2342034 [A/G] chr1 2342034 Cc01_g01490:894 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG GG GG +chr1:2342013 [T/G] chr1 2342013 Cc01_g01490:915 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT GG GG GG +chr1:2342007 [T/A] chr1 2342007 Cc01_g01490:921 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 TT TT TT TA +chr1:2342001 [G/T] chr1 2342001 Cc01_g01490:927 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 GG TT GT TT +chr1:2341971 [A/G] chr1 2341971 Cc01_g01490:957 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA +chr1:2341944 [T/C] chr1 2341944 Cc01_g01490:984 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC +chr1:2341934 [C/T] chr1 2341934 Cc01_g01490:994 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 50.0% 4 CC CT CT TT +chr1:2341930 [A/C] chr1 2341930 Cc01_g01490:998 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 AA AC AA CC +chr1:2341921 [C/T] chr1 2341921 Cc01_g01490:1007 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 CC CT CC TT +chr1:2341915 [G/A] chr1 2341915 Cc01_g01490:1013 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 37.5% 4 GG GA GG AA +chr1:2341914 [T/G] chr1 2341914 Cc01_g01490:1014 exon SYNONYMOUS_CODING acA/acC T/T 37.5% 4 TT TG TT GG +chr1:2341905 [G/A] chr1 2341905 Cc01_g01490:1023 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG GA GA AA +chr1:2341899 [A/G] chr1 2341899 Cc01_g01490:1029 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 AA AG AG GG +chr1:2341885 [G/A] chr1 2341885 Cc01_g01490:1043 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG AA AA AA +chr1:2341855 [C/T] chr1 2341855 Cc01_g01490:1073 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 CC TT TT TT +chr1:2341853 [A/G] chr1 2341853 Cc01_g01490:1075 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG +chr1:2341843 [T/G] chr1 2341843 Cc01_g01490:1085 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 25.0% 4 TT GG GG GG +chr1:2341816 [C/T] chr1 2341816 Cc01_g01490:1112 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT +chr1:2341814 [G/C] chr1 2341814 Cc01_g01490:1114 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 GG CC CC CC +chr1:2341761 [A/G] chr1 2341761 Cc01_g01490:1167 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG +chr1:2341752 [T/G] chr1 2341752 Cc01_g01490:1176 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GG GG GG +chr1:2341742 [G/A] chr1 2341742 Cc01_g01490:1186 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA +chr1:2341734 [T/C] chr1 2341734 Cc01_g01490:1194 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT TC TC CC +chr1:2341733 [G/T] chr1 2341733 Cc01_g01490:1195 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 GG GT GT TT +chr1:2341731 [A/C] chr1 2341731 Cc01_g01490:1197 exon NON_SYNONYMOUS_CODING caT/caG H/Q 50.0% 4 AA AC AC CC +chr1:2341728 [G/A] chr1 2341728 Cc01_g01490:1200 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 GG GA GA AA +chr1:2341719 [C/G] chr1 2341719 Cc01_g01490:1209 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 CC GG GG GG +chr1:2341697 [T/C] chr1 2341697 Cc01_g01490:1231 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TT TC +chr1:2341685 [C/G] chr1 2341685 Cc01_g01490:1243 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC +chr1:2340685 [G/A] chr1 2340685 Cc01_g01490:1261 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA +chr1:2340667 [T/C] chr1 2340667 Cc01_g01490:1279 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC CC CC +chr1:2334881 [A/G] chr1 2334881 Cc01_g01490:1362 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA +chr1:2334835 [T/C] chr1 2334835 Cc01_g01490:1408 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT CC CT CC +chr1:2334831 [G/T] chr1 2334831 Cc01_g01490:1412 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 50.0% 4 GG GT TG TT +chr1:2334799 [A/C] chr1 2334799 Cc01_g01490:1444 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 25.0% 4 AA AC AA AC +chr1:2334780 [A/T] chr1 2334780 Cc01_g01490:1463 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 12.5% 4 AA TA AA AA +chr1:2334662 [A/T] chr1 2334662 Cc01_g01490:1581 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AA AT AA +chr1:2334642 [G/T] chr1 2334642 Cc01_g01490:1601 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 GG TT GT TT +chr1:2334620 [A/C] chr1 2334620 Cc01_g01490:1623 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC +chr1:2334584 [G/A] chr1 2334584 Cc01_g01490:1659 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AA GA AA +chr1:2334185 [G/A] chr1 2334185 Cc01_g01490:1719 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:2334144 [C/G] chr1 2334144 Cc01_g01490:1760 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 50.0% 4 CC GG CC GG +chr1:2334140 [A/C] chr1 2334140 Cc01_g01490:1764 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AC AA AA +chr1:2334026 [T/C] chr1 2334026 Cc01_g01490:1878 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC +chr1:2333864 [T/C] chr1 2333864 Cc01_g01490:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 TT CC TC TC +chr1:2360212 [G/A] chr1 2360212 Cc01_g01510:67 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 33.3% 3 GG AA NN GG +chr1:2360304 [G/T] chr1 2360304 Cc01_g01510:159 exon SYNONYMOUS_CODING ggG/ggT G/G 33.3% 3 GG TT NN GG +chr1:2360308 [C/T] chr1 2360308 Cc01_g01510:163 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 CC TT NN CC +chr1:2360310 [A/G] chr1 2360310 Cc01_g01510:165 exon SYNONYMOUS_CODING ctA/ctG L/L 33.3% 3 AA GG NN AA +chr1:2360316 [A/G] chr1 2360316 Cc01_g01510:171 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA AA NN GG +chr1:2360324 [G/A] chr1 2360324 Cc01_g01510:179 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 50.0% 2 GG AA NN NN +chr1:2360326 [G/A] chr1 2360326 Cc01_g01510:181 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN +chr1:2360328 [C/A] chr1 2360328 Cc01_g01510:183 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 50.0% 2 CC AA NN NN +chr1:2361074 [C/T] chr1 2361074 Cc01_g01510:929 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 16.7% 3 CC CC NN CT +chr1:2361629 [A/G] chr1 2361629 Cc01_g01510:1263 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 2 AA NN NN GG +chr1:2361636 [T/C] chr1 2361636 Cc01_g01510:1270 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT NN NN CC +chr1:2361659 [G/A] chr1 2361659 Cc01_g01510:1293 exon SYNONYMOUS_CODING gaG/gaA E/E 50.0% 2 GG NN NN AA +chr1:2361716 [G/A] chr1 2361716 Cc01_g01510:1350 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN NN AA +chr1:2383654 [G/A] chr1 2383654 Cc01_g01520:42 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG +chr1:2383674 [T/C] chr1 2383674 Cc01_g01520:62 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 25.0% 4 TT CC TT TT +chr1:2383681 [C/T] chr1 2383681 Cc01_g01520:69 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT CC CC +chr1:2383712 [G/A] chr1 2383712 Cc01_g01520:100 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GG GG GA +chr1:2383714 [T/C] chr1 2383714 Cc01_g01520:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:2383758 [T/C] chr1 2383758 Cc01_g01520:146 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 TT CC CC CC +chr1:2383785 [A/G] chr1 2383785 Cc01_g01520:173 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA GG AA AA +chr1:2383795 [C/A] chr1 2383795 Cc01_g01520:183 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 50.0% 4 CC AA CC AA +chr1:2383839 [G/A] chr1 2383839 Cc01_g01520:227 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GG AA GG +chr1:2383851 [A/T] chr1 2383851 Cc01_g01520:239 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AT AA AA +chr1:2383866 [C/T] chr1 2383866 Cc01_g01520:254 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC +chr1:2383874 [T/A] chr1 2383874 Cc01_g01520:262 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TA TT TT +chr1:2383920 [G/T] chr1 2383920 Cc01_g01520:308 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG GG TT GG +chr1:2383927 [T/C] chr1 2383927 Cc01_g01520:315 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT +chr1:2384077 [T/G] chr1 2384077 Cc01_g01520:465 exon NON_SYNONYMOUS_CODING agT/agG S/R 25.0% 4 TT TT TT GG +chr1:2384181 [A/G] chr1 2384181 Cc01_g01520:569 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 AA AA AA AG +chr1:2384200 [C/T] chr1 2384200 Cc01_g01520:588 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC TT CC +chr1:2384756 [T/G] chr1 2384756 Cc01_g01520:1041 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT TG TT TT +chr1:2385308 [T/C] chr1 2385308 Cc01_g01520:1470 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TC TT TT +chr1:2409054 [C/A] chr1 2409054 Cc01_g01530:78 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA CC CC +chr1:2409092 [T/C] chr1 2409092 Cc01_g01530:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC TT TT +chr1:2409231 [A/C] chr1 2409231 Cc01_g01530:255 exon SYNONYMOUS_CODING tcA/tcC S/S 16.7% 3 AA AC NN AA +chr1:2409249 [C/T] chr1 2409249 Cc01_g01530:273 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 3 CC CT NN TT +chr1:2409678 [A/G] chr1 2409678 Cc01_g01530:702 exon SYNONYMOUS_CODING ctA/ctG L/L 16.7% 3 AA NN AA AG +chr1:2409702 [T/C] chr1 2409702 Cc01_g01530:726 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 TT TC CC CC +chr1:2409721 [T/A] chr1 2409721 Cc01_g01530:745 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 TT TT TT TA +chr1:2409726 [C/T] chr1 2409726 Cc01_g01530:750 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT +chr1:2425980 [A/G] chr1 2425980 Cc01_g01540:231 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG AA +chr1:2426360 [G/A] chr1 2426360 Cc01_g01540:397 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG AA GA GG +chr1:2426489 [T/C] chr1 2426489 Cc01_g01540:526 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 12.5% 4 TT TC TT TT +chr1:2427186 [G/A] chr1 2427186 Cc01_g01540:843 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GA GG GG +chr1:2427440 [T/C] chr1 2427440 Cc01_g01540:936 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC TT +chr1:2428201 [A/G] chr1 2428201 Cc01_g01540:1375 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 AA GG AG AA +chr1:2428270 [A/G] chr1 2428270 Cc01_g01540:1444 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA AG AA +chr1:2429289 [T/A] chr1 2429289 Cc01_g01540:1547 exon NON_SYNONYMOUS_CODING aTg/aAg M/K 12.5% 4 TT TA TT TT +chr1:2431687 [G/A] chr1 2431687 Cc01_g01540:1638 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:2432530 [C/T] chr1 2432530 Cc01_g01540:1850 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC +chr1:2432737 [A/G] chr1 2432737 Cc01_g01540:1942 exon NON_SYNONYMOUS_CODING Act/Gct T/A 12.5% 4 AA AA AG AA +chr1:2433099 [T/C] chr1 2433099 Cc01_g01540:2141 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:2434119 [T/A] chr1 2434119 Cc01_g01540:2374 exon NON_SYNONYMOUS_CODING Tct/Act S/T 12.5% 4 TT TA TT TT +chr1:2434512 [A/G] chr1 2434512 Cc01_g01540:2553 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA +chr1:2436532 [A/G] chr1 2436532 Cc01_g01550:172 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AG AA AA +chr1:2436544 [G/A] chr1 2436544 Cc01_g01550:184 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG +chr1:2436558 [G/A] chr1 2436558 Cc01_g01550:198 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG +chr1:2436572 [G/A] chr1 2436572 Cc01_g01550:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG +chr1:2439858 [T/C] chr1 2439858 Cc01_g01550:505 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 TT TC TT TC +chr1:2440047 [T/C] chr1 2440047 Cc01_g01550:597 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:2440153 [C/G] chr1 2440153 Cc01_g01550:703 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CG CC CG +chr1:2440191 [A/G] chr1 2440191 Cc01_g01550:741 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG +chr1:2440206 [A/G] chr1 2440206 Cc01_g01550:756 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AG AA AG +chr1:2444991 [C/G] chr1 2444991 Cc01_g01560:39 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC +chr1:2445037 [C/T] chr1 2445037 Cc01_g01560:85 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CC CT +chr1:2445130 [G/A] chr1 2445130 Cc01_g01560:178 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA +chr1:2445144 [G/C] chr1 2445144 Cc01_g01560:192 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC CC CC +chr1:2445153 [C/T] chr1 2445153 Cc01_g01560:201 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT CC TT +chr1:2445246 [G/A] chr1 2445246 Cc01_g01560:294 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GG AA +chr1:2445335 [G/T] chr1 2445335 Cc01_g01560:383 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 GG TT TT TT +chr1:2445435 [T/C] chr1 2445435 Cc01_g01560:483 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC CC CC +chr1:2445449 [C/G] chr1 2445449 Cc01_g01560:497 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 16.7% 3 CC CG CC NN +chr1:2445473 [A/G] chr1 2445473 Cc01_g01560:521 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 16.7% 3 AA AA AG NN +chr1:2445488 [G/A] chr1 2445488 Cc01_g01560:536 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 33.3% 3 GG GG AA NN +chr1:2445537 [A/T] chr1 2445537 Cc01_g01560:585 exon SYNONYMOUS_CODING atA/atT I/I 16.7% 3 AA AT AA NN +chr1:2445552 [C/G] chr1 2445552 Cc01_g01560:600 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC +chr1:2445610 [G/C] chr1 2445610 Cc01_g01560:658 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GC GG GG +chr1:2445684 [G/A] chr1 2445684 Cc01_g01560:732 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA +chr1:2445697 [C/G] chr1 2445697 Cc01_g01560:745 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC CG CC GG +chr1:2445722 [T/G] chr1 2445722 Cc01_g01560:770 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 37.5% 4 TT TG TT GG +chr1:2445747 [A/T] chr1 2445747 Cc01_g01560:795 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA TA AA AA +chr1:2445750 [T/C] chr1 2445750 Cc01_g01560:798 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TT TT CC +chr1:2445796 [A/T] chr1 2445796 Cc01_g01560:844 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 AA AT AA TT +chr1:2445815 [A/G] chr1 2445815 Cc01_g01560:863 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA AG AA NN +chr1:2445816 [G/A] chr1 2445816 Cc01_g01560:864 exon SYNONYMOUS_CODING gaG/gaA E/E 16.7% 3 GG AG GG NN +chr1:2445827 [G/T] chr1 2445827 Cc01_g01560:875 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 16.7% 3 GG GT GG NN +chr1:2483851 [A/G] chr1 2483851 Cc01_g01570:110 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 AA GG NN NN +chr1:2483849 [A/G] chr1 2483849 Cc01_g01570:112 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 AA GG NN NN +chr1:2483845 [A/G] chr1 2483845 Cc01_g01570:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 2 AA GG NN NN +chr1:2524880 [C/T] chr1 2524880 Cc01_g01600:173 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 CC CT CC CC +chr1:2523795 [C/T] chr1 2523795 Cc01_g01600:1189 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC +chr1:2523742 [G/A] chr1 2523742 Cc01_g01600:1242 exon SYNONYMOUS_CODING ttC/ttT F/F 16.7% 3 GG NN GG GA +chr1:2522662 [T/C] chr1 2522662 Cc01_g01600:2133 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 TT TT CC TT +chr1:2522423 [T/A] chr1 2522423 Cc01_g01600:2279 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 TT TT TT TA +chr1:2522420 [A/G] chr1 2522420 Cc01_g01600:2282 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AG AA AA +chr1:2522274 [T/C] chr1 2522274 Cc01_g01600:2428 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 TT CC TT TC +chr1:2522265 [A/G] chr1 2522265 Cc01_g01600:2437 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 16.7% 3 AA NN AA GA +chr1:2522182 [G/C] chr1 2522182 Cc01_g01600:2439 exon SYNONYMOUS_CODING tcC/tcG S/S 33.3% 3 GG NN CC GG +chr1:2522124 [G/A] chr1 2522124 Cc01_g01600:2497 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA GG GG +chr1:2522105 [T/C] chr1 2522105 Cc01_g01600:2516 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC +chr1:2522103 [C/T] chr1 2522103 Cc01_g01600:2518 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC +chr1:2522070 [G/A] chr1 2522070 Cc01_g01600:2551 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG AA GG GG +chr1:2522006 [C/A] chr1 2522006 Cc01_g01600:2615 exon NON_SYNONYMOUS_CODING cGg/cTg R/L 12.5% 4 CC CC CC CA +chr1:2521969 [T/C] chr1 2521969 Cc01_g01600:2652 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TT TC +chr1:2521892 [T/C] chr1 2521892 Cc01_g01600:2729 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT +chr1:2521826 [G/A] chr1 2521826 Cc01_g01600:2795 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG GG AA GA +chr1:2521810 [G/C] chr1 2521810 Cc01_g01600:2811 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GG GC +chr1:2521773 [A/G] chr1 2521773 Cc01_g01600:2848 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA GG GG GG +chr1:2521725 [G/C] chr1 2521725 Cc01_g01600:2896 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 50.0% 4 GG CC GC GC +chr1:2521724 [T/A] chr1 2521724 Cc01_g01600:2897 exon NON_SYNONYMOUS_CODING cAg/cTg Q/L 12.5% 4 TT TA TT TT +chr1:2521694 [C/A] chr1 2521694 Cc01_g01600:2927 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 CC AC CC CC +chr1:2521672 [T/C] chr1 2521672 Cc01_g01600:2949 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT CT TT +chr1:2521665 [G/A] chr1 2521665 Cc01_g01600:2956 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 37.5% 4 GG GA GA GA +chr1:2521659 [T/C] chr1 2521659 Cc01_g01600:2962 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 TT TC TT TT +chr1:2521567 [C/T] chr1 2521567 Cc01_g01600:3054 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:2521560 [A/T] chr1 2521560 Cc01_g01600:3061 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT +chr1:2521545 [G/A] chr1 2521545 Cc01_g01600:3076 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GA GG GG +chr1:2521544 [C/G] chr1 2521544 Cc01_g01600:3077 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 12.5% 4 CC CC CG CC +chr1:2521538 [G/A] chr1 2521538 Cc01_g01600:3083 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GA GG +chr1:2521522 [G/A] chr1 2521522 Cc01_g01600:3099 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG AG GG +chr1:2521518 [G/A] chr1 2521518 Cc01_g01600:3103 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG AG GG +chr1:2521434 [C/T] chr1 2521434 Cc01_g01600:3187 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 12.5% 4 CC CC CC CT +chr1:2521424 [T/C] chr1 2521424 Cc01_g01600:3197 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC +chr1:2521409 [A/C] chr1 2521409 Cc01_g01600:3212 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 37.5% 4 AA AA CC CA +chr1:2521377 [C/A] chr1 2521377 Cc01_g01600:3244 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 CC CA CC CA +chr1:2521375 [T/C] chr1 2521375 Cc01_g01600:3246 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT TC TT CT +chr1:2521230 [G/A] chr1 2521230 Cc01_g01600:3301 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA AA GG +chr1:2520587 [T/C] chr1 2520587 Cc01_g01600:3322 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 TT CC CC CC +chr1:2520583 [C/T] chr1 2520583 Cc01_g01600:3326 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CT CC CC +chr1:2520561 [A/G] chr1 2520561 Cc01_g01600:3348 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG +chr1:2520556 [G/T] chr1 2520556 Cc01_g01600:3353 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 25.0% 4 GG TT TT TT +chr1:2520547 [A/G] chr1 2520547 Cc01_g01600:3362 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG GG GG +chr1:2520537 [T/C] chr1 2520537 Cc01_g01600:3372 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC TC +chr1:2520525 [C/T] chr1 2520525 Cc01_g01600:3384 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CT CC +chr1:2520511 [A/G] chr1 2520511 Cc01_g01600:3398 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 AA GG GG GG +chr1:2526140 [A/T] chr1 2526140 Cc01_g01610:233 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 AA AA TT AA +chr1:2528701 [G/C] chr1 2528701 Cc01_g01610:265 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 33.3% 3 GG GG NN CC +chr1:2528783 [T/C] chr1 2528783 Cc01_g01610:347 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TT TT TC +chr1:2528803 [T/C] chr1 2528803 Cc01_g01610:367 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TT CC +chr1:2528813 [T/C] chr1 2528813 Cc01_g01610:377 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TC TT +chr1:2528941 [T/G] chr1 2528941 Cc01_g01610:433 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG +chr1:2528952 [C/G] chr1 2528952 Cc01_g01610:444 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC CG CC CG +chr1:2529568 [A/G] chr1 2529568 Cc01_g01610:557 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 2 AA NN NN GG +chr1:2530078 [A/G] chr1 2530078 Cc01_g01610:1067 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA AG AG AG +chr1:2551182 [G/A] chr1 2551182 Cc01_g01620:26 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG AA GG GG +chr1:2551151 [G/T] chr1 2551151 Cc01_g01620:57 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG TT NN GG +chr1:2551113 [C/T] chr1 2551113 Cc01_g01620:95 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CC CT +chr1:2551100 [G/A] chr1 2551100 Cc01_g01620:108 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 GG AA GG GG +chr1:2551069 [T/A] chr1 2551069 Cc01_g01620:139 exon NON_SYNONYMOUS_CODING Agc/Tgc S/C 25.0% 4 TT AA TT TT +chr1:2551068 [C/A] chr1 2551068 Cc01_g01620:140 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 25.0% 4 CC AA CC CC +chr1:2551000 [T/A] chr1 2551000 Cc01_g01620:208 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 12.5% 4 TT TT TT TA +chr1:2550995 [T/C] chr1 2550995 Cc01_g01620:213 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC +chr1:2550979 [G/A] chr1 2550979 Cc01_g01620:229 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA +chr1:2550929 [G/C] chr1 2550929 Cc01_g01620:279 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GG CG +chr1:2550905 [G/A] chr1 2550905 Cc01_g01620:303 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG AA GG GA +chr1:2550878 [T/C] chr1 2550878 Cc01_g01620:330 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TT TT TC +chr1:2550853 [G/A] chr1 2550853 Cc01_g01620:355 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 GG AA NN AA +chr1:2550817 [C/T] chr1 2550817 Cc01_g01620:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT +chr1:2550788 [A/G] chr1 2550788 Cc01_g01620:420 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GG AA AG +chr1:2550718 [C/A] chr1 2550718 Cc01_g01620:490 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 33.3% 3 CC AA NN AA +chr1:2550703 [A/G] chr1 2550703 Cc01_g01620:505 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA AA NN GG +chr1:2550656 [A/C] chr1 2550656 Cc01_g01620:552 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 AA AC AA AA +chr1:2550608 [A/G] chr1 2550608 Cc01_g01620:600 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA GG NN AG +chr1:2550457 [A/C] chr1 2550457 Cc01_g01620:751 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 AA CC AA NN +chr1:2550455 [A/T] chr1 2550455 Cc01_g01620:753 exon STOP_GAINED tgT/tgA C/1 33.3% 3 AA TT AA NN +chr1:2550410 [G/A] chr1 2550410 Cc01_g01620:798 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 GG AA NN AA +chr1:2550352 [A/C] chr1 2550352 Cc01_g01620:856 exon STOP_LOST Taa/Gaa 2/E 33.3% 3 AA CC AA NN +chr1:2565722 [C/G] chr1 2565722 Cc01_g01630:400 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 CC CG CC CC +chr1:2565615 [C/T] chr1 2565615 Cc01_g01630:437 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC TC CC CC +chr1:2558672 [A/G] chr1 2558672 Cc01_g01630:759 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG +chr1:2558633 [T/C] chr1 2558633 Cc01_g01630:798 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC CT +chr1:2558434 [T/C] chr1 2558434 Cc01_g01630:859 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 37.5% 4 TT TC CT CT +chr1:2558347 [C/A] chr1 2558347 Cc01_g01630:946 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 12.5% 4 CC CA CC CC +chr1:2558280 [T/G] chr1 2558280 Cc01_g01630:1013 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TG TT TT +chr1:2558276 [G/A] chr1 2558276 Cc01_g01630:1017 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GA GG GG +chr1:2558203 [G/A] chr1 2558203 Cc01_g01630:1090 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG +chr1:2558132 [G/C] chr1 2558132 Cc01_g01630:1161 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG +chr1:2558129 [G/A] chr1 2558129 Cc01_g01630:1164 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:2558028 [G/A] chr1 2558028 Cc01_g01630:1265 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 12.5% 4 GG GA GG GG +chr1:2557954 [G/C] chr1 2557954 Cc01_g01630:1339 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 12.5% 4 GG GC GG GG +chr1:2557932 [A/T] chr1 2557932 Cc01_g01630:1361 exon NON_SYNONYMOUS_CODING aTa/aAa I/K 12.5% 4 AA AT AA AA +chr1:2557907 [G/A] chr1 2557907 Cc01_g01630:1386 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:2557619 [T/C] chr1 2557619 Cc01_g01630:1575 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TC TT TT +chr1:2557277 [T/C] chr1 2557277 Cc01_g01630:1917 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TC TT TT +chr1:2557173 [A/G] chr1 2557173 Cc01_g01630:2021 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AG AA AA +chr1:2557145 [T/C] chr1 2557145 Cc01_g01630:2049 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TC TT TT +chr1:2557074 [C/A] chr1 2557074 Cc01_g01630:2120 exon NON_SYNONYMOUS_CODING gGa/gTa G/V 12.5% 4 CC CA CC CC +chr1:2557055 [G/A] chr1 2557055 Cc01_g01630:2139 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GA GG GG +chr1:2557019 [T/C] chr1 2557019 Cc01_g01630:2175 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT +chr1:2557016 [A/G] chr1 2557016 Cc01_g01630:2178 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA +chr1:2610598 [G/T] chr1 2610598 Cc01_g01650:233 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GT GG GG +chr1:2611238 [T/C] chr1 2611238 Cc01_g01650:279 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT +chr1:2612873 [T/C] chr1 2612873 Cc01_g01650:375 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT +chr1:2612964 [C/T] chr1 2612964 Cc01_g01650:466 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT +chr1:2613791 [G/C] chr1 2613791 Cc01_g01650:835 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GG GC +chr1:2613877 [G/A] chr1 2613877 Cc01_g01650:921 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA +chr1:2613943 [C/T] chr1 2613943 Cc01_g01650:987 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC +chr1:2615356 [A/T] chr1 2615356 Cc01_g01650:1179 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 AA AA AT AA +chr1:2618568 [T/C] chr1 2618568 Cc01_g01650:1693 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT +chr1:2618665 [C/T] chr1 2618665 Cc01_g01650:1790 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:2618850 [C/T] chr1 2618850 Cc01_g01650:1886 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CC CT +chr1:2618880 [A/G] chr1 2618880 Cc01_g01650:1916 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AG AA +chr1:2619302 [A/G] chr1 2619302 Cc01_g01650:2224 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA +chr1:2619373 [C/T] chr1 2619373 Cc01_g01650:2295 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC +chr1:2622083 [C/T] chr1 2622083 Cc01_g01650:2580 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CT CC CC +chr1:2622084 [A/C] chr1 2622084 Cc01_g01650:2581 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA +chr1:2622099 [C/G] chr1 2622099 Cc01_g01650:2596 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC GC CC CC +chr1:2623353 [A/C] chr1 2623353 Cc01_g01650:2974 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AA AA AC +chr1:2624213 [G/T] chr1 2624213 Cc01_g01650:3039 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 25.0% 4 GG GT GG TG +chr1:2624222 [T/A] chr1 2624222 Cc01_g01650:3048 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA TT AT +chr1:2624249 [T/C] chr1 2624249 Cc01_g01650:3075 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TC TT TT +chr1:2624263 [T/A] chr1 2624263 Cc01_g01650:3089 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT +chr1:2624270 [T/A] chr1 2624270 Cc01_g01650:3096 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 TT TA TT TT +chr1:2624289 [G/T] chr1 2624289 Cc01_g01650:3115 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG TG +chr1:2624433 [C/T] chr1 2624433 Cc01_g01650:3173 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC CT +chr1:2668103 [C/G] chr1 2668103 Cc01_g01670:315 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG GG GG +chr1:2668636 [A/G] chr1 2668636 Cc01_g01670:848 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 25.0% 4 AA AA AA GG +chr1:2668660 [G/A] chr1 2668660 Cc01_g01670:872 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG +chr1:2668692 [T/C] chr1 2668692 Cc01_g01670:904 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN TT +chr1:2668715 [T/G] chr1 2668715 Cc01_g01670:927 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT NN TT GG +chr1:2668739 [T/A] chr1 2668739 Cc01_g01670:951 exon SYNONYMOUS_CODING ccT/ccA P/P 50.0% 2 TT NN AA NN +chr1:2668764 [A/T] chr1 2668764 Cc01_g01670:976 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 AA NN TT NN +chr1:2668782 [C/T] chr1 2668782 Cc01_g01670:994 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC NN TT TT +chr1:2668811 [G/A] chr1 2668811 Cc01_g01670:1023 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA AA +chr1:2669258 [A/C] chr1 2669258 Cc01_g01670:1470 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA NN CC CC +chr1:2669279 [T/A] chr1 2669279 Cc01_g01670:1491 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 2 TT NN AA NN +chr1:2669349 [A/G] chr1 2669349 Cc01_g01670:1519 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN GG AA +chr1:2669357 [T/A] chr1 2669357 Cc01_g01670:1527 exon SYNONYMOUS_CODING cgT/cgA R/R 33.3% 3 TT NN AA AA +chr1:2669424 [A/G] chr1 2669424 Cc01_g01670:1594 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA NN GG GG +chr1:2669466 [G/T] chr1 2669466 Cc01_g01670:1636 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 33.3% 3 GG NN TT GG +chr1:2669497 [A/G] chr1 2669497 Cc01_g01670:1667 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 33.3% 3 AA NN GG AA +chr1:2669523 [T/C] chr1 2669523 Cc01_g01670:1693 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TC TT TT +chr1:2669527 [G/T] chr1 2669527 Cc01_g01670:1697 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG GG TT GG +chr1:2669572 [G/A] chr1 2669572 Cc01_g01670:1742 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG +chr1:2669581 [C/A] chr1 2669581 Cc01_g01670:1751 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CC AA CC +chr1:2669627 [T/C] chr1 2669627 Cc01_g01670:1797 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC CC CC +chr1:2669629 [A/G] chr1 2669629 Cc01_g01670:1799 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 50.0% 4 AA GG GG AA +chr1:2669742 [A/C] chr1 2669742 Cc01_g01670:1912 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 25.0% 4 AA CC CC CC +chr1:2669750 [T/C] chr1 2669750 Cc01_g01670:1920 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT CC TT TT +chr1:2669752 [A/T] chr1 2669752 Cc01_g01670:1922 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 25.0% 4 AA TT AA AA +chr1:2669754 [G/A] chr1 2669754 Cc01_g01670:1924 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA GG AA +chr1:2669766 [G/T] chr1 2669766 Cc01_g01670:1936 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 50.0% 4 GG GG TT TT +chr1:2669787 [A/G] chr1 2669787 Cc01_g01670:1957 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA GG AA AA +chr1:2669788 [T/C] chr1 2669788 Cc01_g01670:1958 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 TT CC CC CC +chr1:2669790 [C/A] chr1 2669790 Cc01_g01670:1960 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 33.3% 3 CC AA NN AA +chr1:2669868 [C/T] chr1 2669868 Cc01_g01670:2038 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 33.3% 3 CC TT NN CC +chr1:2670063 [C/T] chr1 2670063 Cc01_g01670:2233 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 33.3% 3 CC NN CC TT +chr1:2670072 [C/T] chr1 2670072 Cc01_g01670:2242 exon STOP_GAINED Cga/Tga R/8 25.0% 4 CC CC CC TT +chr1:2670078 [G/A] chr1 2670078 Cc01_g01670:2248 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG +chr1:2670084 [T/A] chr1 2670084 Cc01_g01670:2254 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 50.0% 4 TT AA AA TT +chr1:2670086 [A/G] chr1 2670086 Cc01_g01670:2256 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA GG GG NN +chr1:2672520 [A/G] chr1 2672520 Cc01_g01670:2295 exon SYNONYMOUS_CODING agA/agG R/R 33.3% 3 AA AA NN GG +chr1:2672522 [C/G] chr1 2672522 Cc01_g01670:2297 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 33.3% 3 CC CC NN GG +chr1:2672529 [A/T] chr1 2672529 Cc01_g01670:2304 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT +chr1:2672531 [T/C] chr1 2672531 Cc01_g01670:2306 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 33.3% 3 TT TT NN CC +chr1:2672554 [T/A] chr1 2672554 Cc01_g01670:2329 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 33.3% 3 TT TT NN AA +chr1:2672699 [C/T] chr1 2672699 Cc01_g01670:2474 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 25.0% 2 CC CT NN NN +chr1:2672995 [T/C] chr1 2672995 Cc01_g01670:2770 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT CC NN NN +chr1:2672999 [C/T] chr1 2672999 Cc01_g01670:2774 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 2 CC CT NN NN +chr1:2673033 [A/G] chr1 2673033 Cc01_g01670:2808 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG +chr1:2673073 [A/T] chr1 2673073 Cc01_g01670:2848 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 33.3% 3 AA TT TT NN +chr1:2673080 [T/C] chr1 2673080 Cc01_g01670:2855 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 TT CC TT NN +chr1:2673111 [G/T] chr1 2673111 Cc01_g01670:2886 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG TT GG +chr1:2673117 [A/T] chr1 2673117 Cc01_g01670:2892 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 AA AA AA TT +chr1:2673163 [T/G] chr1 2673163 Cc01_g01670:2938 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 25.0% 4 TT TT GG TT +chr1:2673186 [G/C] chr1 2673186 Cc01_g01670:2961 exon NON_SYNONYMOUS_CODING atG/atC M/I 33.3% 3 GG GG NN CC +chr1:2673191 [G/A] chr1 2673191 Cc01_g01670:2966 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 2 GG GA NN NN +chr1:2673238 [C/G] chr1 2673238 Cc01_g01670:3013 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 2 CC CG NN NN +chr1:2673525 [G/A] chr1 2673525 Cc01_g01670:3300 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA +chr1:2673526 [G/T] chr1 2673526 Cc01_g01670:3301 exon STOP_GAINED Gag/Tag E/1 25.0% 4 GG GT GG GT +chr1:2673538 [T/G] chr1 2673538 Cc01_g01670:3313 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GG TG +chr1:2673541 [C/T] chr1 2673541 Cc01_g01670:3316 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 25.0% 4 CC TC CC CT +chr1:2673542 [C/T] chr1 2673542 Cc01_g01670:3317 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 CC TC CC CT +chr1:2673543 [G/T] chr1 2673543 Cc01_g01670:3318 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG TG GG GT +chr1:2674163 [G/A] chr1 2674163 Cc01_g01670:3319 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 GG AG GA GA +chr1:2674174 [G/C] chr1 2674174 Cc01_g01670:3330 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 37.5% 4 GG CG GC GC +chr1:2674189 [A/C] chr1 2674189 Cc01_g01670:3345 exon SYNONYMOUS_CODING ggA/ggC G/G 25.0% 4 AA CA AA AC +chr1:2674276 [C/T] chr1 2674276 Cc01_g01680:15 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC +chr1:2674294 [G/A] chr1 2674294 Cc01_g01680:33 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA AA AA +chr1:2674295 [C/G] chr1 2674295 Cc01_g01680:34 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 25.0% 4 CC GG GG GG +chr1:2674297 [G/T] chr1 2674297 Cc01_g01680:36 exon NON_SYNONYMOUS_CODING caG/caT Q/H 25.0% 4 GG GG GG TT +chr1:2674941 [A/G] chr1 2674941 Cc01_g01680:48 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA +chr1:2674945 [C/T] chr1 2674945 Cc01_g01680:52 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC TC CC +chr1:2674962 [G/A] chr1 2674962 Cc01_g01680:69 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG +chr1:2674964 [G/T] chr1 2674964 Cc01_g01680:71 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 37.5% 4 GG GT GG TT +chr1:2674973 [T/A] chr1 2674973 Cc01_g01680:80 exon STOP_GAINED tTg/tAg L/7 37.5% 4 TT TA AA AA +chr1:2674983 [G/T] chr1 2674983 Cc01_g01680:90 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 GG TT TT TT +chr1:2675001 [T/C] chr1 2675001 Cc01_g01680:108 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 2 TT TC NN NN +chr1:2675015 [T/A] chr1 2675015 Cc01_g01680:122 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 16.7% 3 TT TA NN TT +chr1:2675040 [T/A] chr1 2675040 Cc01_g01680:147 exon SYNONYMOUS_CODING ccT/ccA P/P 33.3% 3 TT AA NN AA +chr1:2675043 [C/T] chr1 2675043 Cc01_g01680:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT +chr1:2675048 [G/A] chr1 2675048 Cc01_g01680:155 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG AG NN GG +chr1:2675053 [A/T] chr1 2675053 Cc01_g01680:160 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 3 AA AT NN TT +chr1:2732265 [A/G] chr1 2732265 Cc01_g01700:720 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 2 AA NN NN AG +chr1:2836390 [A/T] chr1 2836390 Cc01_g01710:126 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA TT NN NN +chr1:2836415 [G/C] chr1 2836415 Cc01_g01710:151 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG GC NN NN +chr1:2836420 [G/C] chr1 2836420 Cc01_g01710:156 exon SYNONYMOUS_CODING gcG/gcC A/A 50.0% 2 GG CC NN NN +chr1:2836423 [C/T] chr1 2836423 Cc01_g01710:159 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 2 CC CT NN NN +chr1:2836441 [C/A] chr1 2836441 Cc01_g01710:177 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 CC AA CC NN +chr1:2836445 [G/A] chr1 2836445 Cc01_g01710:181 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN +chr1:2836460 [G/A] chr1 2836460 Cc01_g01710:196 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:2836484 [A/G] chr1 2836484 Cc01_g01710:220 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 16.7% 3 AA AG AA NN +chr1:2836488 [C/T] chr1 2836488 Cc01_g01710:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 CC CT CC NN +chr1:2836561 [A/G] chr1 2836561 Cc01_g01710:297 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 2 AA GG NN NN +chr1:2837031 [G/A] chr1 2837031 Cc01_g01720:58 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN +chr1:2837037 [A/G] chr1 2837037 Cc01_g01720:64 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA GG NN NN +chr1:2837164 [A/G] chr1 2837164 Cc01_g01720:191 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AA GG +chr1:2837166 [A/G] chr1 2837166 Cc01_g01720:193 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA GG AA AA +chr1:2837171 [A/G] chr1 2837171 Cc01_g01720:198 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG AA AA +chr1:2837187 [G/C] chr1 2837187 Cc01_g01720:214 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 50.0% 4 GG GG CC CC +chr1:2837200 [T/G] chr1 2837200 Cc01_g01720:227 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 37.5% 4 TT TT TG GG +chr1:2837207 [A/G] chr1 2837207 Cc01_g01720:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:2837244 [G/A] chr1 2837244 Cc01_g01720:271 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA +chr1:2837245 [A/G] chr1 2837245 Cc01_g01720:272 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 25.0% 4 AA GG GG GG +chr1:2837246 [T/C] chr1 2837246 Cc01_g01720:273 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TT CC TC +chr1:2837248 [G/A] chr1 2837248 Cc01_g01720:275 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 37.5% 4 GG GG AA GA +chr1:2837259 [T/C] chr1 2837259 Cc01_g01720:286 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 TT CC TT CT +chr1:2837266 [A/G] chr1 2837266 Cc01_g01720:293 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AA GA +chr1:2837271 [C/T] chr1 2837271 Cc01_g01720:298 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 CC CC TT CT +chr1:2837287 [G/T] chr1 2837287 Cc01_g01720:314 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 33.3% 3 GG TT NN GG +chr1:2837295 [T/C] chr1 2837295 Cc01_g01720:322 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN CC +chr1:2837310 [A/C] chr1 2837310 Cc01_g01720:337 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 50.0% 3 AA AC NN CC +chr1:2837316 [G/A] chr1 2837316 Cc01_g01720:343 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 50.0% 3 GG GA NN AA +chr1:2837318 [G/C] chr1 2837318 Cc01_g01720:345 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG GG NN CC +chr1:2837319 [G/C] chr1 2837319 Cc01_g01720:346 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG GG NN CC +chr1:2837348 [A/G] chr1 2837348 Cc01_g01720:375 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA AG NN AG +chr1:2837391 [G/A] chr1 2837391 Cc01_g01720:418 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 3 GG GA NN AA +chr1:2837393 [A/T] chr1 2837393 Cc01_g01720:420 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA TA NN AA +chr1:2837420 [C/T] chr1 2837420 Cc01_g01720:447 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT +chr1:2837423 [T/G] chr1 2837423 Cc01_g01720:450 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 TT GG NN GG +chr1:2837425 [T/G] chr1 2837425 Cc01_g01720:452 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 33.3% 3 TT GG NN GG +chr1:2837433 [A/G] chr1 2837433 Cc01_g01720:460 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 AA GG NN GG +chr1:2837480 [T/C] chr1 2837480 Cc01_g01720:507 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC +chr1:2837519 [G/A] chr1 2837519 Cc01_g01720:546 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG AA NN AA +chr1:2837526 [G/T] chr1 2837526 Cc01_g01720:553 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 33.3% 3 GG TT NN TT +chr1:2837537 [G/A] chr1 2837537 Cc01_g01720:564 exon SYNONYMOUS_CODING aaG/aaA K/K 33.3% 3 GG AA NN AA +chr1:2837615 [T/C] chr1 2837615 Cc01_g01720:642 exon SYNONYMOUS_CODING gcT/gcC A/A 50.0% 2 TT NN CC NN +chr1:2837629 [T/A] chr1 2837629 Cc01_g01720:656 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 50.0% 2 TT NN AA NN +chr1:2837640 [A/G] chr1 2837640 Cc01_g01720:667 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN GG NN +chr1:2901565 [C/A] chr1 2901565 Cc01_g01730:118 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CA CC CC +chr1:2901573 [A/T] chr1 2901573 Cc01_g01730:126 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA AT NN AA +chr1:2901666 [T/C] chr1 2901666 Cc01_g01730:219 exon SYNONYMOUS_CODING ttT/ttC F/F 16.7% 3 TT TC NN TT +chr1:2902604 [C/T] chr1 2902604 Cc01_g01730:618 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT +chr1:2902609 [A/G] chr1 2902609 Cc01_g01730:623 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 3 AA AG NN GG +chr1:2902632 [G/A] chr1 2902632 Cc01_g01730:646 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 33.3% 3 GG AA NN AA +chr1:2902646 [A/C] chr1 2902646 Cc01_g01730:660 exon NON_SYNONYMOUS_CODING caA/caC Q/H 33.3% 3 AA CC NN CC +chr1:2902650 [G/A] chr1 2902650 Cc01_g01730:664 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG AA NN AA +chr1:2902664 [T/C] chr1 2902664 Cc01_g01730:678 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC +chr1:2902673 [T/G] chr1 2902673 Cc01_g01730:687 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG NN GG +chr1:2902849 [T/G] chr1 2902849 Cc01_g01730:863 exon NON_SYNONYMOUS_CODING aTa/aGa I/R 25.0% 2 TT NN NN TG +chr1:2902856 [G/C] chr1 2902856 Cc01_g01730:870 exon SYNONYMOUS_CODING ggG/ggC G/G 50.0% 2 GG NN NN CC +chr1:2902865 [G/A] chr1 2902865 Cc01_g01730:879 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG GG NN AA +chr1:2902892 [A/G] chr1 2902892 Cc01_g01730:906 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 2 AA GG NN NN +chr1:2903083 [G/A] chr1 2903083 Cc01_g01730:1097 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG AA NN AA +chr1:2903094 [G/A] chr1 2903094 Cc01_g01730:1108 exon NON_SYNONYMOUS_CODING Gct/Act A/T 33.3% 3 GG AA NN AA +chr1:2903117 [A/G] chr1 2903117 Cc01_g01730:1131 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA AA GG AA +chr1:2903173 [T/G] chr1 2903173 Cc01_g01730:1187 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 TT GG GG GG +chr1:2903230 [C/G] chr1 2903230 Cc01_g01730:1244 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 16.7% 3 CC NN CC CG +chr1:2903240 [A/G] chr1 2903240 Cc01_g01730:1254 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:2903273 [A/G] chr1 2903273 Cc01_g01730:1287 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA +chr1:2903283 [G/A] chr1 2903283 Cc01_g01730:1297 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG +chr1:2903292 [G/A] chr1 2903292 Cc01_g01730:1306 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG AG GG GG +chr1:2903341 [A/G] chr1 2903341 Cc01_g01730:1355 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA GG NN NN +chr1:2903558 [C/T] chr1 2903558 Cc01_g01730:1572 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN +chr1:2903571 [C/T] chr1 2903571 Cc01_g01730:1585 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC TT NN NN +chr1:2903610 [G/A] chr1 2903610 Cc01_g01730:1624 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG AA NN NN +chr1:2903621 [T/C] chr1 2903621 Cc01_g01730:1635 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 2 TT CC NN NN +chr1:2903627 [T/G] chr1 2903627 Cc01_g01730:1641 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG TT NN +chr1:2903770 [G/A] chr1 2903770 Cc01_g01730:1784 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 2 GG NN AA NN +chr1:2903814 [G/A] chr1 2903814 Cc01_g01730:1828 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG NN AA GG +chr1:2903816 [G/T] chr1 2903816 Cc01_g01730:1830 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 33.3% 3 GG NN GG TT +chr1:2903820 [G/T] chr1 2903820 Cc01_g01730:1834 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 33.3% 3 GG NN TT GG +chr1:2903823 [A/G] chr1 2903823 Cc01_g01730:1837 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN AA GG +chr1:2904055 [G/T] chr1 2904055 Cc01_g01730:1910 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN +chr1:2904064 [A/G] chr1 2904064 Cc01_g01730:1919 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 50.0% 2 AA GG NN NN +chr1:2904368 [T/C] chr1 2904368 Cc01_g01730:2163 exon SYNONYMOUS_CODING acT/acC T/T 50.0% 2 TT NN CC NN +chr1:2904423 [C/T] chr1 2904423 Cc01_g01730:2218 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 3 CC CT TT NN +chr1:2986926 [T/C] chr1 2986926 Cc01_g01750:549 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 2 TT CC NN NN +chr1:2986947 [A/C] chr1 2986947 Cc01_g01750:570 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 2 AA AC NN NN +chr1:2988225 [A/G] chr1 2988225 Cc01_g01750:1848 exon SYNONYMOUS_CODING cgA/cgG R/R 50.0% 2 AA GG NN NN +chr1:2988245 [A/G] chr1 2988245 Cc01_g01750:1868 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 2 AA GG NN NN +chr1:2989009 [G/A] chr1 2989009 Cc01_g01750:2542 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG AA NN NN +chr1:2989157 [G/T] chr1 2989157 Cc01_g01750:2690 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 50.0% 2 GG NN NN TT +chr1:2989172 [A/G] chr1 2989172 Cc01_g01750:2705 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG +chr1:2989569 [T/C] chr1 2989569 Cc01_g01750:3021 exon SYNONYMOUS_CODING taT/taC Y/Y 33.3% 3 TT NN CC CC +chr1:2989571 [T/G] chr1 2989571 Cc01_g01750:3023 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT GG GG GG +chr1:2989664 [A/G] chr1 2989664 Cc01_g01750:3116 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 33.3% 3 AA GG NN GG +chr1:2989678 [G/C] chr1 2989678 Cc01_g01750:3130 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC NN CC +chr1:2989702 [G/A] chr1 2989702 Cc01_g01750:3154 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GA NN GG +chr1:2989705 [A/G] chr1 2989705 Cc01_g01750:3157 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 AA GG GG AA +chr1:2989708 [G/A] chr1 2989708 Cc01_g01750:3160 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA +chr1:2989742 [A/G] chr1 2989742 Cc01_g01750:3194 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA AG AG AG +chr1:2989743 [A/T] chr1 2989743 Cc01_g01750:3195 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA TA TA TA +chr1:2989751 [G/A] chr1 2989751 Cc01_g01750:3203 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 GG GG AG GG +chr1:2989752 [G/T] chr1 2989752 Cc01_g01750:3204 exon SYNONYMOUS_CODING cgG/cgT R/R 12.5% 4 GG GG TG GG +chr1:2989766 [G/A] chr1 2989766 Cc01_g01750:3218 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 4 GG AA GA AG +chr1:2989770 [A/G] chr1 2989770 Cc01_g01750:3222 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AA GA +chr1:2989771 [C/T] chr1 2989771 Cc01_g01750:3223 exon STOP_GAINED Cga/Tga R/5 12.5% 4 CC CC CT CC +chr1:2989797 [C/T] chr1 2989797 Cc01_g01750:3249 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT +chr1:2989804 [T/G] chr1 2989804 Cc01_g01750:3256 exon STOP_LOST Tag/Gag 1/E 50.0% 2 TT GG NN NN +chr1:2996368 [A/C] chr1 2996368 Cc01_g01760:9 exon SYNONYMOUS_CODING cgA/cgC R/R 33.3% 3 AA CC NN CC +chr1:2996399 [G/A] chr1 2996399 Cc01_g01760:40 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG GA NN GA +chr1:2996415 [G/A] chr1 2996415 Cc01_g01760:56 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG GG NN AG +chr1:2996419 [A/G] chr1 2996419 Cc01_g01760:60 exon SYNONYMOUS_CODING caA/caG Q/Q 16.7% 3 AA AA NN AG +chr1:2996421 [A/G] chr1 2996421 Cc01_g01760:62 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA GG NN GG +chr1:2996436 [G/T] chr1 2996436 Cc01_g01760:77 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG GG GG TT +chr1:2997079 [G/A] chr1 2997079 Cc01_g01760:118 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GA GG GA +chr1:2997084 [T/C] chr1 2997084 Cc01_g01760:123 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC TT CC +chr1:2997085 [A/C] chr1 2997085 Cc01_g01760:124 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 25.0% 4 AA AA CC AA +chr1:2997097 [G/C] chr1 2997097 Cc01_g01760:136 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG CG GG CG +chr1:2997102 [A/T] chr1 2997102 Cc01_g01760:141 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA AA AT +chr1:2997106 [A/G] chr1 2997106 Cc01_g01760:145 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA +chr1:2997108 [T/C] chr1 2997108 Cc01_g01760:147 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 TT CC TT CC +chr1:2997111 [T/C] chr1 2997111 Cc01_g01760:150 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC +chr1:2997112 [G/A] chr1 2997112 Cc01_g01760:151 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA +chr1:2997122 [T/A] chr1 2997122 Cc01_g01760:161 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT TA TT AT +chr1:2997125 [C/T] chr1 2997125 Cc01_g01760:164 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CT CC +chr1:2997133 [A/G] chr1 2997133 Cc01_g01760:172 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 AA AG GA AG +chr1:2997137 [G/A] chr1 2997137 Cc01_g01760:176 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:2997152 [T/C] chr1 2997152 Cc01_g01760:191 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT CT TT +chr1:2997154 [G/C] chr1 2997154 Cc01_g01760:193 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 GG CG GG GC +chr1:2997157 [A/G] chr1 2997157 Cc01_g01760:196 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 AA GA AA AG +chr1:2997163 [G/C] chr1 2997163 Cc01_g01760:202 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 GG CC CG GC +chr1:2997173 [C/T] chr1 2997173 Cc01_g01760:212 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC +chr1:2997174 [T/G] chr1 2997174 Cc01_g01760:213 exon SYNONYMOUS_CODING gcT/gcG A/A 12.5% 4 TT TT TG TT +chr1:2997191 [C/T] chr1 2997191 Cc01_g01760:230 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC TC +chr1:2997196 [T/C] chr1 2997196 Cc01_g01760:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC CT CT +chr1:2997204 [A/G] chr1 2997204 Cc01_g01760:243 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG GA AG +chr1:2997206 [G/A] chr1 2997206 Cc01_g01760:245 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA +chr1:2997213 [C/G] chr1 2997213 Cc01_g01760:252 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC GC CG +chr1:2997215 [C/T] chr1 2997215 Cc01_g01760:254 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC CT TC TC +chr1:2997227 [T/G] chr1 2997227 Cc01_g01760:266 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT TT TG GT +chr1:2997231 [C/T] chr1 2997231 Cc01_g01760:270 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 CC CT CC CC +chr1:2997233 [G/C] chr1 2997233 Cc01_g01760:272 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 25.0% 4 GG GG GC CG +chr1:2997243 [T/A] chr1 2997243 Cc01_g01760:282 exon SYNONYMOUS_CODING atT/atA I/I 25.0% 4 TT AA AA AA +chr1:2997247 [C/G] chr1 2997247 Cc01_g01760:286 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CG CC CC +chr1:2997250 [C/T] chr1 2997250 Cc01_g01760:289 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC +chr1:2997252 [T/C] chr1 2997252 Cc01_g01760:291 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC CT +chr1:2997275 [C/A] chr1 2997275 Cc01_g01760:314 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC +chr1:2997294 [G/T] chr1 2997294 Cc01_g01760:333 exon STOP_LOST taG/taT 1/Y 25.0% 4 GG GG GG TT +chr1:3052579 [G/A] chr1 3052579 Cc01_g01770:91 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 50.0% 2 GG NN NN AA +chr1:3052586 [C/T] chr1 3052586 Cc01_g01770:98 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT +chr1:3052603 [G/A] chr1 3052603 Cc01_g01770:115 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 2 GG NN NN AA +chr1:3052725 [G/A] chr1 3052725 Cc01_g01770:237 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GA GA +chr1:3052735 [C/A] chr1 3052735 Cc01_g01770:247 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 CC AA AA AA +chr1:3052737 [C/A] chr1 3052737 Cc01_g01770:249 exon NON_SYNONYMOUS_CODING caC/caA H/Q 12.5% 4 CC CC CC CA +chr1:3052781 [T/C] chr1 3052781 Cc01_g01770:293 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT +chr1:3052796 [G/A] chr1 3052796 Cc01_g01770:308 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 50.0% 2 GG NN AA NN +chr1:3052819 [G/A] chr1 3052819 Cc01_g01770:331 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GG GA NN +chr1:3052820 [C/A] chr1 3052820 Cc01_g01770:332 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 16.7% 3 CC CC CA NN +chr1:3052827 [T/C] chr1 3052827 Cc01_g01770:339 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC TT NN +chr1:3052878 [C/G] chr1 3052878 Cc01_g01770:390 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 33.3% 3 CC GG GG NN +chr1:3053184 [T/A] chr1 3053184 Cc01_g01770:696 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT NN TA TT +chr1:3053253 [T/C] chr1 3053253 Cc01_g01770:765 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC +chr1:3053284 [A/G] chr1 3053284 Cc01_g01770:796 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 4 AA AA GG GG +chr1:3053300 [A/G] chr1 3053300 Cc01_g01770:812 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 4 AA AA GG GG +chr1:3053448 [T/A] chr1 3053448 Cc01_g01770:886 exon NON_SYNONYMOUS_CODING Tct/Act S/T 50.0% 2 TT NN NN AA +chr1:3053505 [C/T] chr1 3053505 Cc01_g01770:943 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 CC TT TT NN +chr1:3053568 [T/C] chr1 3053568 Cc01_g01770:1006 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT +chr1:3053590 [A/C] chr1 3053590 Cc01_g01770:1028 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 50.0% 4 AA AC CA CC +chr1:3053591 [T/C] chr1 3053591 Cc01_g01770:1029 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT CT TT TT +chr1:3053592 [T/G] chr1 3053592 Cc01_g01770:1030 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GT GG +chr1:3053593 [A/G] chr1 3053593 Cc01_g01770:1031 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 4 AA AG GA GG +chr1:3053596 [A/C] chr1 3053596 Cc01_g01770:1034 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AC AA +chr1:3053597 [A/C] chr1 3053597 Cc01_g01770:1035 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 AA AA CA CC +chr1:3053608 [G/A] chr1 3053608 Cc01_g01770:1046 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG +chr1:3053622 [A/C] chr1 3053622 Cc01_g01770:1060 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 16.7% 3 AA NN CA AA +chr1:3053627 [C/T] chr1 3053627 Cc01_g01770:1065 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC NN CC TT +chr1:3053887 [T/C] chr1 3053887 Cc01_g01770:1325 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 2 TT NN NN CC +chr1:3054011 [A/G] chr1 3054011 Cc01_g01770:1449 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AA AG NN +chr1:3054042 [G/A] chr1 3054042 Cc01_g01770:1480 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3054054 [G/T] chr1 3054054 Cc01_g01770:1492 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 GG TT GG GG +chr1:3054055 [T/A] chr1 3054055 Cc01_g01770:1493 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT TT TA AA +chr1:3054103 [C/T] chr1 3054103 Cc01_g01770:1541 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 4 CC CC TT CC +chr1:3054112 [T/G] chr1 3054112 Cc01_g01770:1550 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 33.3% 3 TT NN GG TT +chr1:3054118 [T/C] chr1 3054118 Cc01_g01770:1556 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 33.3% 3 TT NN CC TT +chr1:3054218 [G/T] chr1 3054218 Cc01_g01770:1605 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 GG NN NN TT +chr1:3054264 [C/T] chr1 3054264 Cc01_g01770:1651 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 2 CC TT NN NN +chr1:3054265 [G/A] chr1 3054265 Cc01_g01770:1652 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 50.0% 2 GG AA NN NN +chr1:3054271 [G/T] chr1 3054271 Cc01_g01770:1658 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN +chr1:3054274 [T/A] chr1 3054274 Cc01_g01770:1661 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 50.0% 2 TT AA NN NN +chr1:3054279 [G/A] chr1 3054279 Cc01_g01770:1666 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:3054354 [G/A] chr1 3054354 Cc01_g01770:1741 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GA GG +chr1:3054370 [A/G] chr1 3054370 Cc01_g01770:1757 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA GG AA NN +chr1:3054389 [G/A] chr1 3054389 Cc01_g01770:1776 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG AA GG NN +chr1:3054402 [C/G] chr1 3054402 Cc01_g01770:1789 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 33.3% 3 CC CC GG NN +chr1:3054406 [G/A] chr1 3054406 Cc01_g01770:1793 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 33.3% 3 GG GG AA NN +chr1:3054411 [T/G] chr1 3054411 Cc01_g01770:1798 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT TT GG NN +chr1:3054417 [A/T] chr1 3054417 Cc01_g01770:1804 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 33.3% 3 AA AA TT NN +chr1:3054423 [C/G] chr1 3054423 Cc01_g01770:1810 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 33.3% 3 CC CC NN GG +chr1:3054432 [A/T] chr1 3054432 Cc01_g01770:1819 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA AT NN AA +chr1:3054439 [A/G] chr1 3054439 Cc01_g01770:1826 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 AA AG NN AA +chr1:3054447 [A/T] chr1 3054447 Cc01_g01770:1834 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 33.3% 3 AA AA NN TT +chr1:3054480 [G/A] chr1 3054480 Cc01_g01770:1867 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 33.3% 3 GG AA NN GG +chr1:3054501 [C/T] chr1 3054501 Cc01_g01770:1888 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC TT NN CC +chr1:3054566 [C/G] chr1 3054566 Cc01_g01770:1953 exon SYNONYMOUS_CODING acC/acG T/T 33.3% 3 CC CC NN GG +chr1:3054570 [A/C] chr1 3054570 Cc01_g01770:1957 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 33.3% 3 AA AA NN CC +chr1:3054575 [G/C] chr1 3054575 Cc01_g01770:1962 exon NON_SYNONYMOUS_CODING agG/agC R/S 16.7% 3 GG GC NN GG +chr1:3054596 [A/G] chr1 3054596 Cc01_g01770:1983 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 3 AA AG NN GG +chr1:3054734 [C/G] chr1 3054734 Cc01_g01770:2121 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 CC CG CC CC +chr1:3054743 [A/G] chr1 3054743 Cc01_g01770:2130 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AG AA AA +chr1:3054746 [A/G] chr1 3054746 Cc01_g01770:2133 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA +chr1:3054764 [G/C] chr1 3054764 Cc01_g01770:2151 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 GG GG GG CC +chr1:3054783 [C/A] chr1 3054783 Cc01_g01770:2170 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CC CC AA +chr1:3054800 [A/T] chr1 3054800 Cc01_g01770:2187 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT +chr1:3054820 [A/G] chr1 3054820 Cc01_g01770:2207 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA +chr1:3054956 [A/C] chr1 3054956 Cc01_g01770:2238 exon SYNONYMOUS_CODING cgA/cgC R/R 50.0% 2 AA NN NN CC +chr1:3054966 [T/C] chr1 3054966 Cc01_g01770:2248 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN CC CC +chr1:3054968 [A/G] chr1 3054968 Cc01_g01770:2250 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA NN GG GG +chr1:3054987 [C/G] chr1 3054987 Cc01_g01770:2269 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 25.0% 4 CC CC CC GG +chr1:3055134 [T/C] chr1 3055134 Cc01_g01770:2416 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 TT TT CC TT +chr1:3055136 [C/T] chr1 3055136 Cc01_g01770:2418 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CT CC CC +chr1:3055137 [G/A] chr1 3055137 Cc01_g01770:2419 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3055144 [C/A] chr1 3055144 Cc01_g01770:2426 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 4 CC CC AA CC +chr1:3055154 [C/A] chr1 3055154 Cc01_g01770:2436 exon SYNONYMOUS_CODING cgC/cgA R/R 25.0% 4 CC CA CC CA +chr1:3055178 [A/G] chr1 3055178 Cc01_g01770:2460 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG GG AA +chr1:3055254 [T/G] chr1 3055254 Cc01_g01770:2470 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 25.0% 4 TT GT TG TT +chr1:3055255 [A/T] chr1 3055255 Cc01_g01770:2471 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 AA AT AA AA +chr1:3055257 [T/C] chr1 3055257 Cc01_g01770:2473 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TC TT +chr1:3055258 [T/C] chr1 3055258 Cc01_g01770:2474 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 25.0% 4 TT TC TC TT +chr1:3055259 [T/G] chr1 3055259 Cc01_g01770:2475 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 TT TT TG TT +chr1:3076176 [T/C] chr1 3076176 Cc01_g01770:2481 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT CT CC CC +chr1:3076177 [G/A] chr1 3076177 Cc01_g01770:2482 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG GA GG AA +chr1:3076201 [A/G] chr1 3076201 Cc01_g01770:2506 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA +chr1:3076211 [A/T] chr1 3076211 Cc01_g01770:2516 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA AT AA +chr1:3076217 [C/T] chr1 3076217 Cc01_g01770:2522 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC TC CT CT +chr1:3076219 [G/A] chr1 3076219 Cc01_g01770:2524 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG GA AG GG +chr1:3076221 [C/T] chr1 3076221 Cc01_g01770:2526 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 CC TT CT TT +chr1:3076224 [A/G] chr1 3076224 Cc01_g01770:2529 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG GA AA +chr1:3076239 [G/A] chr1 3076239 Cc01_g01770:2544 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GA GG GA +chr1:3076622 [T/G] chr1 3076622 Cc01_g01770:2572 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 12.5% 4 TT TT GT TT +chr1:3080563 [C/T] chr1 3080563 Cc01_g01780:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 CC TT NN NN +chr1:3080566 [T/A] chr1 3080566 Cc01_g01780:17 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 50.0% 2 TT AA NN NN +chr1:3080588 [T/C] chr1 3080588 Cc01_g01780:39 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT TT CC NN +chr1:3080607 [C/T] chr1 3080607 Cc01_g01780:58 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 37.5% 4 CC CT TT TT +chr1:3080619 [G/A] chr1 3080619 Cc01_g01780:70 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG GA AA AA +chr1:3080771 [T/C] chr1 3080771 Cc01_g01780:138 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TT CC +chr1:3080777 [A/G] chr1 3080777 Cc01_g01780:144 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:3080789 [T/C] chr1 3080789 Cc01_g01780:156 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TC TT TC +chr1:3080803 [T/A] chr1 3080803 Cc01_g01780:170 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 25.0% 4 TT TA TT TA +chr1:3080819 [C/A] chr1 3080819 Cc01_g01780:186 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CC CC AC +chr1:3080919 [C/A] chr1 3080919 Cc01_g01780:200 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA CC CC +chr1:3080921 [C/T] chr1 3080921 Cc01_g01780:202 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 37.5% 4 CC CC TT TC +chr1:3080927 [C/G] chr1 3080927 Cc01_g01780:208 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CC CG CG +chr1:3080944 [G/A] chr1 3080944 Cc01_g01780:225 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG AA AA GA +chr1:3080947 [A/G] chr1 3080947 Cc01_g01780:228 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA AA GG AG +chr1:3080956 [T/A] chr1 3080956 Cc01_g01780:237 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA +chr1:3081805 [A/T] chr1 3081805 Cc01_g01780:415 exon STOP_GAINED Aga/Tga R/9 50.0% 3 AA TT NN AT +chr1:3081884 [T/A] chr1 3081884 Cc01_g01780:494 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TA TA TT +chr1:3081885 [T/A] chr1 3081885 Cc01_g01780:495 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 37.5% 4 TT AT TT AA +chr1:3081886 [T/A] chr1 3081886 Cc01_g01780:496 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 TT TA TA TT +chr1:3081887 [T/A] chr1 3081887 Cc01_g01780:497 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TT TA +chr1:3081888 [T/A] chr1 3081888 Cc01_g01780:498 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 TT TA TT TT +chr1:3100066 [G/C] chr1 3100066 Cc01_g01790:442 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG GC GG CC +chr1:3100063 [C/T] chr1 3100063 Cc01_g01790:445 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC CT CC TT +chr1:3099861 [T/C] chr1 3099861 Cc01_g01790:647 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 TT TC TT NN +chr1:3099819 [A/G] chr1 3099819 Cc01_g01790:689 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 AA AG AA NN +chr1:3099817 [A/G] chr1 3099817 Cc01_g01790:691 exon SYNONYMOUS_CODING Tta/Cta L/L 16.7% 3 AA AG AA NN +chr1:3099361 [C/T] chr1 3099361 Cc01_g01790:921 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT +chr1:3099178 [C/T] chr1 3099178 Cc01_g01790:1104 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC +chr1:3098863 [C/T] chr1 3098863 Cc01_g01790:1419 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 CC NN TT NN +chr1:3098710 [T/G] chr1 3098710 Cc01_g01790:1572 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 33.3% 3 TT NN GG TT +chr1:3098694 [C/T] chr1 3098694 Cc01_g01790:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC TT CC +chr1:3098670 [C/T] chr1 3098670 Cc01_g01790:1612 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 25.0% 4 CC CC CC TT +chr1:3098669 [A/T] chr1 3098669 Cc01_g01790:1613 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 AA AA AA TT +chr1:3098646 [G/A] chr1 3098646 Cc01_g01790:1636 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 33.3% 3 GG NN GG AA +chr1:3098643 [C/T] chr1 3098643 Cc01_g01790:1639 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 CC NN TT CC +chr1:3098575 [T/A] chr1 3098575 Cc01_g01790:1707 exon SYNONYMOUS_CODING gtA/gtT V/V 33.3% 3 TT TT NN AA +chr1:3098545 [C/T] chr1 3098545 Cc01_g01790:1737 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 CC NN NN CT +chr1:3098445 [T/G] chr1 3098445 Cc01_g01790:1837 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 33.3% 3 TT GG TT NN +chr1:3098439 [A/C] chr1 3098439 Cc01_g01790:1843 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA AC AC NN +chr1:3098433 [C/T] chr1 3098433 Cc01_g01790:1849 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 CC CC TC NN +chr1:3098416 [A/G] chr1 3098416 Cc01_g01790:1866 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 AA AA GA NN +chr1:3098249 [T/G] chr1 3098249 Cc01_g01790:1982 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN GG NN +chr1:3098236 [T/G] chr1 3098236 Cc01_g01790:1995 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT TG TG TT +chr1:3098217 [T/C] chr1 3098217 Cc01_g01790:2014 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT TT TT CC +chr1:3098210 [C/A] chr1 3098210 Cc01_g01790:2021 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 CC AC AC CC +chr1:3098185 [G/T] chr1 3098185 Cc01_g01790:2046 exon SYNONYMOUS_CODING ccC/ccA P/P 25.0% 4 GG GG GG TT +chr1:3098182 [C/T] chr1 3098182 Cc01_g01790:2049 exon SYNONYMOUS_CODING caG/caA Q/Q 37.5% 4 CC CC TC TT +chr1:3098175 [C/T] chr1 3098175 Cc01_g01790:2056 exon NON_SYNONYMOUS_CODING Gct/Act A/T 25.0% 4 CC CC TC CT +chr1:3098148 [A/G] chr1 3098148 Cc01_g01790:2083 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 25.0% 4 AA GG GG GG +chr1:3098140 [C/G] chr1 3098140 Cc01_g01790:2091 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 CC CC GC CG +chr1:3098133 [C/A] chr1 3098133 Cc01_g01790:2098 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 37.5% 4 CC AA CA CC +chr1:3098100 [T/C] chr1 3098100 Cc01_g01790:2131 exon NON_SYNONYMOUS_CODING Act/Gct T/A 25.0% 4 TT TT TC TC +chr1:3098097 [C/T] chr1 3098097 Cc01_g01790:2134 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CC TC +chr1:3098083 [C/G] chr1 3098083 Cc01_g01790:2148 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CG CC +chr1:3098073 [G/C] chr1 3098073 Cc01_g01790:2158 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 GG CC CG GG +chr1:3098015 [T/C] chr1 3098015 Cc01_g01790:2216 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC +chr1:3097800 [C/T] chr1 3097800 Cc01_g01790:2431 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 50.0% 2 CC NN NN TT +chr1:3130398 [G/A] chr1 3130398 Cc01_g01800:5 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG GA GA GA +chr1:3130394 [G/A] chr1 3130394 Cc01_g01800:9 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG AG GG +chr1:3130389 [G/A] chr1 3130389 Cc01_g01800:14 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG +chr1:3130367 [A/G] chr1 3130367 Cc01_g01800:36 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA GA AG GA +chr1:3130332 [C/T] chr1 3130332 Cc01_g01800:71 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC CC TC CC +chr1:3130320 [A/G] chr1 3130320 Cc01_g01800:83 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA GA AA AA +chr1:3130313 [C/T] chr1 3130313 Cc01_g01800:90 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC TT TT TT +chr1:3130268 [G/C] chr1 3130268 Cc01_g01800:135 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG CC GC GG +chr1:3130244 [G/A] chr1 3130244 Cc01_g01800:159 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA +chr1:3130238 [G/T] chr1 3130238 Cc01_g01800:165 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 GG TT GT GG +chr1:3130227 [T/C] chr1 3130227 Cc01_g01800:176 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 4 TT CC TC TC +chr1:3130205 [T/C] chr1 3130205 Cc01_g01800:198 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CC TC TT +chr1:3130073 [A/C] chr1 3130073 Cc01_g01800:276 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 AA CC CC NN +chr1:3130016 [G/T] chr1 3130016 Cc01_g01800:333 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 3 GG NN TT GT +chr1:3129989 [G/C] chr1 3129989 Cc01_g01800:360 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GC GG GG +chr1:3129968 [G/C] chr1 3129968 Cc01_g01800:381 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GC GG +chr1:3129955 [C/T] chr1 3129955 Cc01_g01800:394 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 37.5% 4 CC TT TC CC +chr1:3129939 [G/C] chr1 3129939 Cc01_g01800:410 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 GG GG GG GC +chr1:3129936 [G/A] chr1 3129936 Cc01_g01800:413 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GG GG GA +chr1:3129931 [T/G] chr1 3129931 Cc01_g01800:418 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG +chr1:3129930 [C/T] chr1 3129930 Cc01_g01800:419 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC CC TC +chr1:3129911 [A/G] chr1 3129911 Cc01_g01800:438 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AA GA +chr1:3129147 [T/C] chr1 3129147 Cc01_g01800:481 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 TT CC NN NN +chr1:3129110 [C/T] chr1 3129110 Cc01_g01800:518 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC TT NN NN +chr1:3129103 [G/A] chr1 3129103 Cc01_g01800:525 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 2 GG AA NN NN +chr1:3128596 [C/T] chr1 3128596 Cc01_g01800:1032 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC +chr1:3128592 [T/C] chr1 3128592 Cc01_g01800:1036 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 TT NN CC TT +chr1:3128555 [A/G] chr1 3128555 Cc01_g01800:1073 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 16.7% 3 AA NN AG AA +chr1:3128551 [T/C] chr1 3128551 Cc01_g01800:1077 exon SYNONYMOUS_CODING gcA/gcG A/A 16.7% 3 TT NN TC TT +chr1:3128512 [A/C] chr1 3128512 Cc01_g01800:1116 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 AA NN CC CC +chr1:3128013 [A/T] chr1 3128013 Cc01_g01800:1525 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN TT AA +chr1:3127995 [T/A] chr1 3127995 Cc01_g01800:1543 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 33.3% 3 TT NN TT AA +chr1:3127863 [C/T] chr1 3127863 Cc01_g01800:1675 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 CC NN TT CC +chr1:3127784 [G/T] chr1 3127784 Cc01_g01800:1754 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 33.3% 3 GG NN GG TT +chr1:3127444 [C/G] chr1 3127444 Cc01_g01800:2094 exon NON_SYNONYMOUS_CODING caG/caC Q/H 50.0% 2 CC NN NN GG +chr1:3127440 [C/A] chr1 3127440 Cc01_g01800:2098 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 33.3% 3 CC NN CC AA +chr1:3127337 [C/T] chr1 3127337 Cc01_g01800:2201 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 33.3% 3 CC TT CC NN +chr1:3127308 [G/A] chr1 3127308 Cc01_g01800:2230 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 GG GA AA NN +chr1:3127296 [T/C] chr1 3127296 Cc01_g01800:2242 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 33.3% 3 TT CC CC NN +chr1:3127276 [C/T] chr1 3127276 Cc01_g01800:2262 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC CC TT NN +chr1:3127267 [C/T] chr1 3127267 Cc01_g01800:2271 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 CC TT TT NN +chr1:3127260 [A/C] chr1 3127260 Cc01_g01800:2278 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA CC AA NN +chr1:3127254 [T/G] chr1 3127254 Cc01_g01800:2284 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 2 TT NN GG NN +chr1:3127253 [C/T] chr1 3127253 Cc01_g01800:2285 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 CC TT TT NN +chr1:3127252 [C/T] chr1 3127252 Cc01_g01800:2286 exon SYNONYMOUS_CODING agG/agA R/R 33.3% 3 CC TT TT NN +chr1:3127234 [G/A] chr1 3127234 Cc01_g01800:2304 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 2 GG NN GA NN +chr1:3127034 [G/A] chr1 3127034 Cc01_g01800:2411 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 GG AA NN NN +chr1:3127033 [T/A] chr1 3127033 Cc01_g01800:2412 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 TT AA NN NN +chr1:3126983 [A/G] chr1 3126983 Cc01_g01800:2462 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA AA AA GG +chr1:3126979 [A/G] chr1 3126979 Cc01_g01800:2466 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA +chr1:3126953 [A/C] chr1 3126953 Cc01_g01800:2492 exon NON_SYNONYMOUS_CODING cTc/cGc L/R 33.3% 3 AA NN AA CC +chr1:3126937 [G/T] chr1 3126937 Cc01_g01800:2508 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG NN GG TT +chr1:3126913 [C/T] chr1 3126913 Cc01_g01800:2532 exon SYNONYMOUS_CODING tcG/tcA S/S 16.7% 3 CC NN CT CC +chr1:3126816 [G/A] chr1 3126816 Cc01_g01800:2569 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 33.3% 3 GG NN GG AA +chr1:3126795 [C/T] chr1 3126795 Cc01_g01800:2590 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC CC TT +chr1:3126780 [A/T] chr1 3126780 Cc01_g01800:2605 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 25.0% 4 AA AA AA TT +chr1:3126751 [G/A] chr1 3126751 Cc01_g01800:2634 exon SYNONYMOUS_CODING gaC/gaT D/D 33.3% 3 GG AA AA NN +chr1:3126700 [G/T] chr1 3126700 Cc01_g01800:2685 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT +chr1:3126699 [G/A] chr1 3126699 Cc01_g01800:2686 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 GG GA GG GA +chr1:3126690 [C/G] chr1 3126690 Cc01_g01800:2695 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 CC GG CC GG +chr1:3126637 [A/G] chr1 3126637 Cc01_g01800:2748 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG AA GG +chr1:3126626 [C/T] chr1 3126626 Cc01_g01800:2759 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 33.3% 3 CC TT CC NN +chr1:3126612 [G/A] chr1 3126612 Cc01_g01800:2773 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 GG AA GG NN +chr1:3126600 [A/T] chr1 3126600 Cc01_g01800:2785 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 33.3% 3 AA TT AA NN +chr1:3126553 [T/A] chr1 3126553 Cc01_g01800:2832 exon SYNONYMOUS_CODING ccA/ccT P/P 33.3% 3 TT TT AA NN +chr1:3126547 [G/T] chr1 3126547 Cc01_g01800:2838 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG GG TT NN +chr1:3126532 [T/A] chr1 3126532 Cc01_g01800:2853 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 33.3% 3 TT TT AA NN +chr1:3126528 [T/C] chr1 3126528 Cc01_g01800:2857 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT CC TT NN +chr1:3126526 [T/A] chr1 3126526 Cc01_g01800:2859 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 TT TT TT AA +chr1:3126503 [C/T] chr1 3126503 Cc01_g01800:2882 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CC CT CC +chr1:3126400 [T/C] chr1 3126400 Cc01_g01800:2985 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 TT CC TT NN +chr1:3126397 [C/T] chr1 3126397 Cc01_g01800:2988 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TT TT TT +chr1:3126364 [G/T] chr1 3126364 Cc01_g01800:3021 exon SYNONYMOUS_CODING cgC/cgA R/R 50.0% 4 GG TT GG TT +chr1:3126267 [A/G] chr1 3126267 Cc01_g01800:3118 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 33.3% 3 AA GG GG NN +chr1:3126189 [T/C] chr1 3126189 Cc01_g01800:3196 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 TT NN CC NN +chr1:3126120 [T/G] chr1 3126120 Cc01_g01800:3265 exon SYNONYMOUS_CODING Aga/Cga R/R 33.3% 3 TT GG GG NN +chr1:3148320 [G/C] chr1 3148320 Cc01_g01810:19 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 25.0% 4 GG CC CC CC +chr1:3148319 [T/G] chr1 3148319 Cc01_g01810:20 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TT TT TG +chr1:3148309 [A/T] chr1 3148309 Cc01_g01810:30 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT TT TT +chr1:3148308 [A/C] chr1 3148308 Cc01_g01810:31 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 AA CC CC CC +chr1:3148305 [G/A] chr1 3148305 Cc01_g01810:34 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG AA AA AA +chr1:3148268 [G/T] chr1 3148268 Cc01_g01810:71 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 GG GG GT GG +chr1:3148255 [A/T] chr1 3148255 Cc01_g01810:84 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AT AA +chr1:3148238 [A/G] chr1 3148238 Cc01_g01810:101 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 AA GG GA GG +chr1:3148222 [G/C] chr1 3148222 Cc01_g01810:117 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 12.5% 4 GG GG CG GG +chr1:3148212 [A/G] chr1 3148212 Cc01_g01810:127 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 12.5% 4 AA AG AA AA +chr1:3148211 [C/T] chr1 3148211 Cc01_g01810:128 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 37.5% 4 CC TT TC TT +chr1:3148184 [T/C] chr1 3148184 Cc01_g01810:155 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 TT CT TT TT +chr1:3148162 [G/A] chr1 3148162 Cc01_g01810:177 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 GG AG GG GG +chr1:3148147 [C/T] chr1 3148147 Cc01_g01810:192 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT +chr1:3148104 [T/C] chr1 3148104 Cc01_g01810:202 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TC TT +chr1:3148094 [G/T] chr1 3148094 Cc01_g01810:212 exon STOP_GAINED tCa/tAa S/1 12.5% 4 GG GG GG GT +chr1:3148091 [G/T] chr1 3148091 Cc01_g01810:215 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 GG GG GG GT +chr1:3191460 [A/G] chr1 3191460 Cc01_g01820:313 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG AA AA +chr1:3191468 [T/G] chr1 3191468 Cc01_g01820:321 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 TT TG TT TT +chr1:3191469 [G/A] chr1 3191469 Cc01_g01820:322 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG AA AA AA +chr1:3191497 [A/G] chr1 3191497 Cc01_g01820:350 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AA AA AG +chr1:3191499 [G/A] chr1 3191499 Cc01_g01820:352 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG GA +chr1:3191505 [C/G] chr1 3191505 Cc01_g01820:358 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC CC GG +chr1:3191507 [A/G] chr1 3191507 Cc01_g01820:360 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 AA GA AA GG +chr1:3191521 [C/A] chr1 3191521 Cc01_g01820:374 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CA CC +chr1:3191526 [G/T] chr1 3191526 Cc01_g01820:379 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GG GT GG +chr1:3191552 [T/C] chr1 3191552 Cc01_g01820:405 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC +chr1:3191561 [A/G] chr1 3191561 Cc01_g01820:414 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA GA +chr1:3191576 [T/C] chr1 3191576 Cc01_g01820:429 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TC TC +chr1:3191774 [T/C] chr1 3191774 Cc01_g01820:627 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT +chr1:3191801 [A/G] chr1 3191801 Cc01_g01820:654 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG +chr1:3191814 [A/G] chr1 3191814 Cc01_g01820:667 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG +chr1:3191835 [G/A] chr1 3191835 Cc01_g01820:688 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG AG +chr1:3191836 [G/A] chr1 3191836 Cc01_g01820:689 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GA GG +chr1:3191840 [A/G] chr1 3191840 Cc01_g01820:693 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA +chr1:3191846 [A/C] chr1 3191846 Cc01_g01820:699 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 AA AA AC AA +chr1:3191856 [C/A] chr1 3191856 Cc01_g01820:709 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CA CC AC +chr1:3191872 [G/A] chr1 3191872 Cc01_g01820:725 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 GG GA GG AG +chr1:3191876 [A/C] chr1 3191876 Cc01_g01820:729 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA CA +chr1:3191881 [A/G] chr1 3191881 Cc01_g01820:734 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AG AG AA +chr1:3191888 [A/C] chr1 3191888 Cc01_g01820:741 exon NON_SYNONYMOUS_CODING caA/caC Q/H 12.5% 4 AA AA CA AA +chr1:3191897 [G/A] chr1 3191897 Cc01_g01820:750 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GG GA +chr1:3191902 [A/G] chr1 3191902 Cc01_g01820:755 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:3191903 [G/A] chr1 3191903 Cc01_g01820:756 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG GG GA +chr1:3191912 [T/A] chr1 3191912 Cc01_g01820:765 exon SYNONYMOUS_CODING ctT/ctA L/L 50.0% 4 TT TT AA AA +chr1:3192960 [A/G] chr1 3192960 Cc01_g01820:1688 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 2 AA NN GG NN +chr1:3192995 [G/T] chr1 3192995 Cc01_g01820:1723 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 25.0% 2 GG NN GT NN +chr1:3193034 [T/A] chr1 3193034 Cc01_g01820:1762 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 3 TT AA TA NN +chr1:3193036 [G/T] chr1 3193036 Cc01_g01820:1764 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 50.0% 3 GG TT GT NN +chr1:3193095 [A/G] chr1 3193095 Cc01_g01820:1823 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 2 AA NN NN AG +chr1:3193128 [G/A] chr1 3193128 Cc01_g01820:1856 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG AA GG NN +chr1:3193178 [T/C] chr1 3193178 Cc01_g01820:1906 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 TT CC TT NN +chr1:3193205 [G/A] chr1 3193205 Cc01_g01820:1933 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3193208 [C/G] chr1 3193208 Cc01_g01820:1936 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 33.3% 3 CC GG GG NN +chr1:3193232 [G/A] chr1 3193232 Cc01_g01820:1960 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN +chr1:3193249 [T/A] chr1 3193249 Cc01_g01820:1977 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 33.3% 3 TT AA TT NN +chr1:3193250 [A/G] chr1 3193250 Cc01_g01820:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 33.3% 3 AA GG AA NN +chr1:3193251 [G/A] chr1 3193251 Cc01_g01820:1979 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 GG AA GG NN +chr1:3193257 [A/T] chr1 3193257 Cc01_g01820:1985 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 33.3% 3 AA TT AA NN +chr1:3193258 [A/T] chr1 3193258 Cc01_g01820:1986 exon NON_SYNONYMOUS_CODING caA/caT Q/H 33.3% 3 AA TT AA NN +chr1:3193262 [G/A] chr1 3193262 Cc01_g01820:1990 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN +chr1:3193330 [T/C] chr1 3193330 Cc01_g01820:2058 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 TT NN CC NN +chr1:3193551 [A/C] chr1 3193551 Cc01_g01820:2279 exon NON_SYNONYMOUS_CODING tAt/tCt Y/S 50.0% 4 AA CC AA CC +chr1:3193556 [A/G] chr1 3193556 Cc01_g01820:2284 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA AA AA GG +chr1:3193561 [T/C] chr1 3193561 Cc01_g01820:2289 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT TT TT CC +chr1:3193565 [C/A] chr1 3193565 Cc01_g01820:2293 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 CC AA CC CC +chr1:3193580 [A/T] chr1 3193580 Cc01_g01820:2308 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA AA AA TT +chr1:3193581 [C/T] chr1 3193581 Cc01_g01820:2309 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 CC CC CC TT +chr1:3193590 [G/A] chr1 3193590 Cc01_g01820:2318 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 GG AA GG GG +chr1:3193598 [G/A] chr1 3193598 Cc01_g01820:2326 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG AA GG GG +chr1:3193621 [A/G] chr1 3193621 Cc01_g01820:2349 exon SYNONYMOUS_CODING caA/caG Q/Q 33.3% 3 AA NN AA GG +chr1:3193623 [G/A] chr1 3193623 Cc01_g01820:2351 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA +chr1:3193638 [T/C] chr1 3193638 Cc01_g01820:2366 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 33.3% 3 TT NN TT CC +chr1:3193642 [G/T] chr1 3193642 Cc01_g01820:2370 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GT GG +chr1:3193647 [A/T] chr1 3193647 Cc01_g01820:2375 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 37.5% 4 AA TT AT AA +chr1:3193825 [G/T] chr1 3193825 Cc01_g01820:2553 exon SYNONYMOUS_CODING tcG/tcT S/S 16.7% 3 GG GG GT NN +chr1:3193843 [A/G] chr1 3193843 Cc01_g01820:2571 exon SYNONYMOUS_CODING gaA/gaG E/E 33.3% 3 AA GG AA NN +chr1:3193848 [A/G] chr1 3193848 Cc01_g01820:2576 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA AG AG NN +chr1:3193868 [G/A] chr1 3193868 Cc01_g01820:2596 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN +chr1:3193975 [T/C] chr1 3193975 Cc01_g01820:2703 exon SYNONYMOUS_CODING gcT/gcC A/A 33.3% 3 TT NN TT CC +chr1:3194001 [G/A] chr1 3194001 Cc01_g01820:2729 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG NN GG AA +chr1:3197392 [A/G] chr1 3197392 Cc01_g01830:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA +chr1:3197403 [C/T] chr1 3197403 Cc01_g01830:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT TT CC +chr1:3197417 [A/G] chr1 3197417 Cc01_g01830:153 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 AA AG GG AG +chr1:3197423 [A/G] chr1 3197423 Cc01_g01830:159 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AA AG +chr1:3197426 [A/G] chr1 3197426 Cc01_g01830:162 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG AA AG +chr1:3197433 [T/A] chr1 3197433 Cc01_g01830:169 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 50.0% 4 TT TA AA TA +chr1:3197457 [T/C] chr1 3197457 Cc01_g01830:193 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT CT TT CT +chr1:3197458 [C/T] chr1 3197458 Cc01_g01830:194 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC +chr1:3197465 [T/G] chr1 3197465 Cc01_g01830:201 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 TT TT TG TG +chr1:3197474 [C/T] chr1 3197474 Cc01_g01830:210 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT TC CT +chr1:3197478 [T/C] chr1 3197478 Cc01_g01830:214 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 TT TT TC TT +chr1:3197482 [T/C] chr1 3197482 Cc01_g01830:218 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 37.5% 4 TT CT TC CT +chr1:3197490 [G/A] chr1 3197490 Cc01_g01830:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3197494 [T/C] chr1 3197494 Cc01_g01830:230 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 12.5% 4 TT CT TT TT +chr1:3197498 [C/T] chr1 3197498 Cc01_g01830:234 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC TC CC CC +chr1:3197500 [T/C] chr1 3197500 Cc01_g01830:236 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 TT CT TC TT +chr1:3197504 [C/T] chr1 3197504 Cc01_g01830:240 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC +chr1:3197513 [G/T] chr1 3197513 Cc01_g01830:249 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GG GT GG +chr1:3197514 [C/A] chr1 3197514 Cc01_g01830:250 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CA AC CC +chr1:3197516 [T/G] chr1 3197516 Cc01_g01830:252 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT GT TG TT +chr1:3197529 [G/A] chr1 3197529 Cc01_g01830:265 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 4 GG GA GA AA +chr1:3197531 [C/T] chr1 3197531 Cc01_g01830:267 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC CC CT +chr1:3197533 [A/T] chr1 3197533 Cc01_g01830:269 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA AT +chr1:3197544 [T/G] chr1 3197544 Cc01_g01830:280 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 12.5% 4 TT TT TT GT +chr1:3197558 [C/T] chr1 3197558 Cc01_g01830:294 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CT CC +chr1:3293623 [C/T] chr1 3293623 Cc01_g01840:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT +chr1:3293672 [A/C] chr1 3293672 Cc01_g01840:199 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AA AC AA +chr1:3293717 [G/A] chr1 3293717 Cc01_g01840:244 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG +chr1:3294121 [G/C] chr1 3294121 Cc01_g01840:555 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 25.0% 4 GG CC GG GG +chr1:3294122 [A/C] chr1 3294122 Cc01_g01840:556 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AA CC AA +chr1:3294138 [T/A] chr1 3294138 Cc01_g01840:572 exon NON_SYNONYMOUS_CODING cTc/cAc L/H 33.3% 3 TT TT AA NN +chr1:3294175 [A/G] chr1 3294175 Cc01_g01840:609 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA AA NN AG +chr1:3294278 [G/A] chr1 3294278 Cc01_g01840:655 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA NN AA +chr1:3294351 [C/T] chr1 3294351 Cc01_g01840:728 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 25.0% 4 CC CC TT CC +chr1:3294386 [A/G] chr1 3294386 Cc01_g01840:763 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 AA GG NN GG +chr1:3294489 [G/T] chr1 3294489 Cc01_g01840:866 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG TT TT TT +chr1:3294543 [C/T] chr1 3294543 Cc01_g01840:920 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CT CC CC +chr1:3295343 [G/C] chr1 3295343 Cc01_g01840:1501 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC GG NN +chr1:3295400 [G/A] chr1 3295400 Cc01_g01840:1558 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG GA GG AA +chr1:3295407 [C/A] chr1 3295407 Cc01_g01840:1565 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC CC AA CC +chr1:3295410 [T/A] chr1 3295410 Cc01_g01840:1568 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 25.0% 4 TT TT TT AA +chr1:3295411 [T/G] chr1 3295411 Cc01_g01840:1569 exon SYNONYMOUS_CODING gtT/gtG V/V 50.0% 4 TT GG TT GG +chr1:3295423 [G/T] chr1 3295423 Cc01_g01840:1581 exon SYNONYMOUS_CODING ccG/ccT P/P 12.5% 4 GG TG GG GG +chr1:3295466 [G/A] chr1 3295466 Cc01_g01840:1624 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA NN AA +chr1:3295709 [T/C] chr1 3295709 Cc01_g01840:1867 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 50.0% 2 TT NN NN CC +chr1:3295750 [A/G] chr1 3295750 Cc01_g01840:1908 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA NN NN GG +chr1:3295781 [G/A] chr1 3295781 Cc01_g01840:1939 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GG NN GA +chr1:3295793 [T/A] chr1 3295793 Cc01_g01840:1951 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 25.0% 4 TT TT TT AA +chr1:3295794 [G/A] chr1 3295794 Cc01_g01840:1952 exon STOP_GAINED tGg/tAg W/1 50.0% 4 GG AA GG AA +chr1:3295796 [T/G] chr1 3295796 Cc01_g01840:1954 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 TT TT NN GG +chr1:3295811 [C/G] chr1 3295811 Cc01_g01840:1969 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC CG CC GG +chr1:3295832 [G/C] chr1 3295832 Cc01_g01840:1990 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 50.0% 3 GG CC NN GC +chr1:3295834 [T/A] chr1 3295834 Cc01_g01840:1992 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 3 TT AA NN TA +chr1:3295846 [A/G] chr1 3295846 Cc01_g01840:2004 exon SYNONYMOUS_CODING acA/acG T/T 33.3% 3 AA AG NN GA +chr1:3295852 [T/C] chr1 3295852 Cc01_g01840:2010 exon SYNONYMOUS_CODING ccT/ccC P/P 33.3% 3 TT CC NN CC +chr1:3295877 [T/A] chr1 3295877 Cc01_g01840:2035 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 33.3% 3 TT TT AA NN +chr1:3295893 [G/A] chr1 3295893 Cc01_g01840:2051 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 33.3% 3 GG NN AA GG +chr1:3323377 [T/C] chr1 3323377 Cc01_g01850:669 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC +chr1:3323201 [C/T] chr1 3323201 Cc01_g01850:845 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 16.7% 3 CC CT NN CC +chr1:3337218 [C/A] chr1 3337218 Cc01_g01860:15 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 CC CA CC CC +chr1:3337216 [G/A] chr1 3337216 Cc01_g01860:17 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 GG GG GG GA +chr1:3337209 [G/C] chr1 3337209 Cc01_g01860:24 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG +chr1:3337191 [C/T] chr1 3337191 Cc01_g01860:42 exon SYNONYMOUS_CODING ctG/ctA L/L 37.5% 4 CC TT TC CC +chr1:3337176 [G/T] chr1 3337176 Cc01_g01860:57 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 4 GG TT TT GG +chr1:3337167 [C/T] chr1 3337167 Cc01_g01860:66 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 CC TT TC CC +chr1:3337129 [C/T] chr1 3337129 Cc01_g01860:104 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 CC TT TT TT +chr1:3336284 [G/A] chr1 3336284 Cc01_g01860:213 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GG GA GG +chr1:3336266 [G/A] chr1 3336266 Cc01_g01860:231 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 GG GA GA AA +chr1:3336239 [T/C] chr1 3336239 Cc01_g01860:258 exon SYNONYMOUS_CODING gaA/gaG E/E 50.0% 4 TT TC CC TC +chr1:3333450 [A/T] chr1 3333450 Cc01_g01860:400 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 AA AA AT AA +chr1:3333413 [G/C] chr1 3333413 Cc01_g01860:437 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GC GG GG +chr1:3333326 [G/A] chr1 3333326 Cc01_g01860:524 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 12.5% 4 GG GG GG GA +chr1:3333322 [T/C] chr1 3333322 Cc01_g01860:528 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TT TC TT +chr1:3333297 [C/T] chr1 3333297 Cc01_g01860:553 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC TC CC +chr1:3333229 [G/A] chr1 3333229 Cc01_g01860:621 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GG GA +chr1:3333223 [C/T] chr1 3333223 Cc01_g01860:627 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CT CC +chr1:3332599 [C/T] chr1 3332599 Cc01_g01860:669 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 CC CC CT CC +chr1:3332597 [C/G] chr1 3332597 Cc01_g01860:671 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 CC CC GC CC +chr1:3332395 [T/C] chr1 3332395 Cc01_g01860:775 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TC TT +chr1:3332371 [G/C] chr1 3332371 Cc01_g01860:799 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 GG GG CG GG +chr1:3332350 [T/C] chr1 3332350 Cc01_g01860:820 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC TT TT +chr1:3332348 [T/C] chr1 3332348 Cc01_g01860:822 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC CC TC +chr1:3332316 [A/G] chr1 3332316 Cc01_g01860:854 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 AA AG AA AA +chr1:3332250 [A/G] chr1 3332250 Cc01_g01860:920 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 12.5% 4 AA AA AA AG +chr1:3332219 [G/A] chr1 3332219 Cc01_g01860:951 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG +chr1:3332209 [T/C] chr1 3332209 Cc01_g01860:961 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC CC TC +chr1:3338434 [G/T] chr1 3338434 Cc01_g01870:20 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 16.7% 3 GG GG GT NN +chr1:3338449 [A/G] chr1 3338449 Cc01_g01870:35 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 2 AA NN AG NN +chr1:3338455 [C/G] chr1 3338455 Cc01_g01870:41 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 50.0% 2 CC NN GG NN +chr1:3338489 [T/G] chr1 3338489 Cc01_g01870:75 exon SYNONYMOUS_CODING gcT/gcG A/A 16.7% 3 TT TT TG NN +chr1:3338523 [A/G] chr1 3338523 Cc01_g01870:109 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 2 AA NN AG NN +chr1:3338527 [C/G] chr1 3338527 Cc01_g01870:113 exon NON_SYNONYMOUS_CODING cCg/cGg P/R 25.0% 2 CC NN CG NN +chr1:3338584 [C/A] chr1 3338584 Cc01_g01870:170 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 25.0% 4 CC CC AA CC +chr1:3338618 [G/A] chr1 3338618 Cc01_g01870:204 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG GG AA GG +chr1:3338682 [A/G] chr1 3338682 Cc01_g01870:268 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA +chr1:3340569 [G/C] chr1 3340569 Cc01_g01870:341 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GC GG +chr1:3340586 [C/A] chr1 3340586 Cc01_g01870:358 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CA CA CC +chr1:3340636 [A/T] chr1 3340636 Cc01_g01870:408 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AT AT AA +chr1:3341154 [G/A] chr1 3341154 Cc01_g01870:609 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA GG GG +chr1:3341373 [A/G] chr1 3341373 Cc01_g01870:828 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AG AG AA +chr1:3341763 [C/A] chr1 3341763 Cc01_g01870:1039 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC CA CA CC +chr1:3341885 [T/G] chr1 3341885 Cc01_g01870:1161 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT GG TT +chr1:3341925 [G/T] chr1 3341925 Cc01_g01870:1201 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 25.0% 4 GG GG TT GG +chr1:3341957 [C/T] chr1 3341957 Cc01_g01870:1233 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CT CC +chr1:3342026 [A/G] chr1 3342026 Cc01_g01870:1302 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AA GG AA +chr1:3342047 [T/C] chr1 3342047 Cc01_g01870:1323 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT +chr1:3342053 [G/A] chr1 3342053 Cc01_g01870:1329 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG GG AA GG +chr1:3342122 [T/G] chr1 3342122 Cc01_g01870:1398 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TG TG TT +chr1:3342260 [C/G] chr1 3342260 Cc01_g01870:1441 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:3342603 [G/A] chr1 3342603 Cc01_g01870:1728 exon SYNONYMOUS_CODING aaG/aaA K/K 16.7% 3 GG GG GA NN +chr1:3342762 [T/C] chr1 3342762 Cc01_g01870:1887 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 TT TC TC TT +chr1:3342780 [C/T] chr1 3342780 Cc01_g01870:1905 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC TC CC +chr1:3342870 [C/T] chr1 3342870 Cc01_g01870:1995 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CT CT CC +chr1:3342879 [T/C] chr1 3342879 Cc01_g01870:2004 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TC TT +chr1:3342996 [C/T] chr1 3342996 Cc01_g01870:2121 exon SYNONYMOUS_CODING gtC/gtT V/V 33.3% 3 CC CT CT NN +chr1:3342999 [A/T] chr1 3342999 Cc01_g01870:2124 exon SYNONYMOUS_CODING gcA/gcT A/A 33.3% 3 AA AT AT NN +chr1:3343053 [T/A] chr1 3343053 Cc01_g01870:2178 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 TT TT TA NN +chr1:3343056 [T/C] chr1 3343056 Cc01_g01870:2181 exon SYNONYMOUS_CODING gcT/gcC A/A 16.7% 3 TT TT TC NN +chr1:3343080 [C/T] chr1 3343080 Cc01_g01870:2205 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 CC NN CT CC +chr1:3343146 [T/C] chr1 3343146 Cc01_g01870:2271 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TC TT +chr1:3343149 [C/T] chr1 3343149 Cc01_g01870:2274 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC NN CT CC +chr1:3343251 [C/T] chr1 3343251 Cc01_g01870:2376 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC +chr1:3343348 [G/A] chr1 3343348 Cc01_g01870:2473 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GG AA GG +chr1:3343425 [A/T] chr1 3343425 Cc01_g01870:2550 exon SYNONYMOUS_CODING acA/acT T/T 16.7% 3 AA NN AT AA +chr1:3343449 [A/G] chr1 3343449 Cc01_g01870:2574 exon SYNONYMOUS_CODING tcA/tcG S/S 16.7% 3 AA NN AG AA +chr1:3343557 [G/A] chr1 3343557 Cc01_g01870:2682 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 2 GG NN GA NN +chr1:3343584 [G/C] chr1 3343584 Cc01_g01870:2709 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 12.5% 4 GG GG GC GG +chr1:3343605 [T/C] chr1 3343605 Cc01_g01870:2730 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3343713 [G/A] chr1 3343713 Cc01_g01870:2838 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GA GG +chr1:3343793 [A/G] chr1 3343793 Cc01_g01870:2918 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA NN GG AA +chr1:3343946 [T/A] chr1 3343946 Cc01_g01870:3071 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TA TT +chr1:3343980 [T/A] chr1 3343980 Cc01_g01870:3105 exon SYNONYMOUS_CODING ctT/ctA L/L 12.5% 4 TT TT TA TT +chr1:3344061 [T/C] chr1 3344061 Cc01_g01870:3186 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT +chr1:3344094 [C/G] chr1 3344094 Cc01_g01870:3219 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC +chr1:3344225 [A/C] chr1 3344225 Cc01_g01870:3350 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 25.0% 4 AA AC AC AA +chr1:3344291 [A/G] chr1 3344291 Cc01_g01870:3416 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AG AA +chr1:3344304 [A/G] chr1 3344304 Cc01_g01870:3429 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AG AG AA +chr1:3344335 [A/T] chr1 3344335 Cc01_g01870:3460 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AA AT AA +chr1:3344340 [A/G] chr1 3344340 Cc01_g01870:3465 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AG AA +chr1:3344367 [G/A] chr1 3344367 Cc01_g01870:3492 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GA GG +chr1:3344610 [A/G] chr1 3344610 Cc01_g01870:3646 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AG AA +chr1:3344615 [C/T] chr1 3344615 Cc01_g01870:3651 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CT CT CC +chr1:3344705 [T/C] chr1 3344705 Cc01_g01870:3741 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC CC TT +chr1:3344765 [C/T] chr1 3344765 Cc01_g01870:3801 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC CT CT CC +chr1:3344998 [C/G] chr1 3344998 Cc01_g01870:3928 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC GG CC +chr1:3345023 [C/G] chr1 3345023 Cc01_g01870:3953 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC +chr1:3345239 [G/A] chr1 3345239 Cc01_g01870:4077 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 GG GA AA GG +chr1:3345251 [G/A] chr1 3345251 Cc01_g01870:4089 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG +chr1:3345257 [A/G] chr1 3345257 Cc01_g01870:4095 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AG AA +chr1:3345539 [A/G] chr1 3345539 Cc01_g01870:4290 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA GG AA +chr1:3346036 [G/A] chr1 3346036 Cc01_g01870:4488 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG +chr1:3346713 [T/C] chr1 3346713 Cc01_g01870:4716 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TC TC TT +chr1:3346848 [C/T] chr1 3346848 Cc01_g01870:4851 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CT CT CC +chr1:3346851 [T/G] chr1 3346851 Cc01_g01870:4854 exon SYNONYMOUS_CODING cgT/cgG R/R 12.5% 4 TT TT TG TT +chr1:3346917 [G/A] chr1 3346917 Cc01_g01870:4920 exon SYNONYMOUS_CODING gaG/gaA E/E 33.3% 3 GG GA GA NN +chr1:3346920 [T/G] chr1 3346920 Cc01_g01870:4923 exon SYNONYMOUS_CODING ctT/ctG L/L 16.7% 3 TT TT GT NN +chr1:3347106 [T/C] chr1 3347106 Cc01_g01870:5109 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TC TC TT +chr1:3347181 [C/A] chr1 3347181 Cc01_g01870:5184 exon SYNONYMOUS_CODING acC/acA T/T 25.0% 4 CC CA CA CC +chr1:3347198 [T/C] chr1 3347198 Cc01_g01870:5201 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT +chr1:3347363 [C/T] chr1 3347363 Cc01_g01870:5280 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CT CT CC +chr1:3347553 [A/G] chr1 3347553 Cc01_g01870:5361 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AA AG AA +chr1:3347739 [C/T] chr1 3347739 Cc01_g01870:5547 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CT CC +chr1:3347754 [A/G] chr1 3347754 Cc01_g01870:5562 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AG AA +chr1:3347884 [T/C] chr1 3347884 Cc01_g01870:5616 exon SYNONYMOUS_CODING cgT/cgC R/R 12.5% 4 TT TT TC TT +chr1:3347890 [A/C] chr1 3347890 Cc01_g01870:5622 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 AA AA AC AA +chr1:3348120 [T/A] chr1 3348120 Cc01_g01870:5852 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 25.0% 4 TT AA AA AA +chr1:3348121 [C/A] chr1 3348121 Cc01_g01870:5853 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA AA AA +chr1:3348167 [A/G] chr1 3348167 Cc01_g01870:5899 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AA AG AA +chr1:3348225 [A/G] chr1 3348225 Cc01_g01870:5957 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA +chr1:3348593 [G/A] chr1 3348593 Cc01_g01870:6109 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GG GA +chr1:3348598 [C/T] chr1 3348598 Cc01_g01870:6114 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC +chr1:3348607 [G/A] chr1 3348607 Cc01_g01870:6123 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GA GG +chr1:3348689 [G/T] chr1 3348689 Cc01_g01870:6205 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG +chr1:3348691 [T/C] chr1 3348691 Cc01_g01870:6207 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT +chr1:3348799 [C/T] chr1 3348799 Cc01_g01870:6219 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC CT CT CC +chr1:3348886 [T/C] chr1 3348886 Cc01_g01870:6306 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3348950 [T/C] chr1 3348950 Cc01_g01870:6370 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TT TC TT +chr1:3349098 [C/A] chr1 3349098 Cc01_g01870:6441 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CC CA CC +chr1:3349159 [A/T] chr1 3349159 Cc01_g01870:6502 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AT AA +chr1:3349258 [T/C] chr1 3349258 Cc01_g01870:6601 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT +chr1:3349275 [T/C] chr1 3349275 Cc01_g01870:6618 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TT TC TT +chr1:3349309 [A/G] chr1 3349309 Cc01_g01870:6652 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 AA AA AA GG +chr1:3349550 [A/G] chr1 3349550 Cc01_g01870:6731 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG +chr1:3349635 [A/G] chr1 3349635 Cc01_g01870:6816 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG GG AA +chr1:3349684 [A/C] chr1 3349684 Cc01_g01870:6865 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 AA AC AC AA +chr1:3349692 [T/C] chr1 3349692 Cc01_g01870:6873 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT +chr1:3349701 [G/A] chr1 3349701 Cc01_g01870:6882 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 GG GG GA GA +chr1:3349725 [T/C] chr1 3349725 Cc01_g01870:6906 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT +chr1:3349872 [T/A] chr1 3349872 Cc01_g01870:6942 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT TA TA TT +chr1:3349938 [A/G] chr1 3349938 Cc01_g01870:7008 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AA AG AA +chr1:3349953 [T/G] chr1 3349953 Cc01_g01870:7023 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TT TG TT +chr1:3349955 [A/G] chr1 3349955 Cc01_g01870:7025 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AG AA +chr1:3349959 [C/G] chr1 3349959 Cc01_g01870:7029 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 CC GG GG GG +chr1:3349968 [T/C] chr1 3349968 Cc01_g01870:7038 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC TT TT +chr1:3350026 [A/G] chr1 3350026 Cc01_g01870:7096 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 AA AG GG AA +chr1:3350040 [C/T] chr1 3350040 Cc01_g01870:7110 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CT CC CC +chr1:3362501 [A/T] chr1 3362501 Cc01_g01900:15 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 AA NN TT TT +chr1:3362493 [G/C] chr1 3362493 Cc01_g01900:23 exon STOP_GAINED tCa/tGa S8* 25.0% 4 GG CC CC CC +chr1:3362488 [C/T] chr1 3362488 Cc01_g01900:28 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC TT TT TT +chr1:3362464 [C/G] chr1 3362464 Cc01_g01900:52 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 25.0% 4 CC GG GG GG +chr1:3362461 [C/G] chr1 3362461 Cc01_g01900:55 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG GG GG +chr1:3362423 [T/G] chr1 3362423 Cc01_g01900:93 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 50.0% 4 TT TT GG GG +chr1:3383330 [A/T] chr1 3383330 Cc01_g01910:149 exon NON_SYNONYMOUS_CODING aTc/aAc I/N 50.0% 2 AA TT NN NN +chr1:3383254 [C/T] chr1 3383254 Cc01_g01910:225 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT +chr1:3383250 [A/C] chr1 3383250 Cc01_g01910:229 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 50.0% 2 AA NN NN CC +chr1:3383240 [T/G] chr1 3383240 Cc01_g01910:239 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN NN GG +chr1:3543339 [T/C] chr1 3543339 Cc01_g01950:133 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 37.5% 4 TT CC TT TC +chr1:3543344 [T/C] chr1 3543344 Cc01_g01950:138 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TC TT TT +chr1:3543798 [C/T] chr1 3543798 Cc01_g01950:592 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CT CC CC +chr1:3544052 [T/C] chr1 3544052 Cc01_g01950:846 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TC TT TT +chr1:3563539 [T/A] chr1 3563539 Cc01_g01960:208 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 TT AA TT NN +chr1:3563667 [G/A] chr1 3563667 Cc01_g01960:336 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 GG GG NN GA +chr1:3563754 [G/C] chr1 3563754 Cc01_g01960:423 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GG GC +chr1:3563771 [A/G] chr1 3563771 Cc01_g01960:440 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 AA GG AG AG +chr1:3563793 [T/C] chr1 3563793 Cc01_g01960:462 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT +chr1:3574473 [G/C] chr1 3574473 Cc01_g01970:51 exon SYNONYMOUS_CODING gcC/gcG A/A 33.3% 3 GG NN CC GG +chr1:3574458 [A/G] chr1 3574458 Cc01_g01970:66 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 AA NN AA GG +chr1:3574326 [A/T] chr1 3574326 Cc01_g01970:198 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 33.3% 3 AA NN TT TT +chr1:3574296 [A/G] chr1 3574296 Cc01_g01970:228 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AA GG +chr1:3574115 [T/C] chr1 3574115 Cc01_g01970:409 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT NN CC CC +chr1:3574063 [G/A] chr1 3574063 Cc01_g01970:461 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG GG AA GG +chr1:3574027 [A/T] chr1 3574027 Cc01_g01970:497 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT +chr1:3573800 [C/T] chr1 3573800 Cc01_g01970:724 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC TT TT TT +chr1:3573759 [A/G] chr1 3573759 Cc01_g01970:765 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 AA NN AA GG +chr1:3573736 [C/T] chr1 3573736 Cc01_g01970:788 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 50.0% 4 CC TT CC TT +chr1:3573699 [G/C] chr1 3573699 Cc01_g01970:825 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG GG CC GG +chr1:3573693 [A/G] chr1 3573693 Cc01_g01970:831 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA GG AA GG +chr1:3573559 [A/T] chr1 3573559 Cc01_g01970:965 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT +chr1:3573509 [A/T] chr1 3573509 Cc01_g01970:1015 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN AA TT +chr1:3573370 [C/T] chr1 3573370 Cc01_g01970:1053 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 CC NN CC TT +chr1:3573336 [C/A] chr1 3573336 Cc01_g01970:1087 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 CC AA CC AA +chr1:3573271 [C/G] chr1 3573271 Cc01_g01970:1152 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 CC NN GG CC +chr1:3573239 [G/C] chr1 3573239 Cc01_g01970:1184 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 GG NN CC CC +chr1:3573098 [G/T] chr1 3573098 Cc01_g01970:1251 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT +chr1:3573097 [T/G] chr1 3573097 Cc01_g01970:1252 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 50.0% 4 TT GG TT GG +chr1:3572965 [G/A] chr1 3572965 Cc01_g01970:1384 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 33.3% 3 GG NN AA AA +chr1:3572931 [A/G] chr1 3572931 Cc01_g01970:1418 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 AA NN GG GG +chr1:3572899 [T/C] chr1 3572899 Cc01_g01970:1450 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT CC CC CC +chr1:3572885 [C/G] chr1 3572885 Cc01_g01970:1464 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC GG GG GG +chr1:3572859 [C/T] chr1 3572859 Cc01_g01970:1490 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT +chr1:3572854 [G/T] chr1 3572854 Cc01_g01970:1495 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG TT TT TT +chr1:3572835 [T/A] chr1 3572835 Cc01_g01970:1514 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT AA TT +chr1:3649364 [A/T] chr1 3649364 Cc01_g01980:156 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AA AA AT +chr1:3649391 [C/T] chr1 3649391 Cc01_g01980:183 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC CT +chr1:3649422 [C/G] chr1 3649422 Cc01_g01980:214 exon NON_SYNONYMOUS_CODING Cgc/Ggc R/G 25.0% 4 CC GG CC CC +chr1:3649490 [G/A] chr1 3649490 Cc01_g01980:282 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG +chr1:3649502 [T/C] chr1 3649502 Cc01_g01980:294 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC CC +chr1:3649727 [T/C] chr1 3649727 Cc01_g01980:519 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT +chr1:3649746 [G/T] chr1 3649746 Cc01_g01980:538 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT TT TT +chr1:3661555 [G/C] chr1 3661555 Cc01_g01990:23 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 33.3% 3 GG CC GG NN +chr1:3661523 [T/C] chr1 3661523 Cc01_g01990:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 TT CC CC NN +chr1:3661511 [C/G] chr1 3661511 Cc01_g01990:67 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 33.3% 3 CC GG NN CC +chr1:3661507 [A/C] chr1 3661507 Cc01_g01990:71 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 33.3% 3 AA CC NN AA +chr1:3661453 [T/C] chr1 3661453 Cc01_g01990:125 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT +chr1:3661403 [A/T] chr1 3661403 Cc01_g01990:175 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 AA TT AA NN +chr1:3661345 [G/T] chr1 3661345 Cc01_g01990:233 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 GG GG NN TT +chr1:3661344 [A/G] chr1 3661344 Cc01_g01990:234 exon SYNONYMOUS_CODING tcT/tcC S/S 16.7% 3 AA AG NN AA +chr1:3660894 [T/C] chr1 3660894 Cc01_g01990:273 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 TT CC NN TT +chr1:3660770 [C/T] chr1 3660770 Cc01_g01990:319 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 33.3% 3 CC NN TT CC +chr1:3660756 [A/C] chr1 3660756 Cc01_g01990:333 exon NON_SYNONYMOUS_CODING caT/caG H/Q 25.0% 4 AA CC AA AA +chr1:3660584 [T/C] chr1 3660584 Cc01_g01990:379 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TT TT CC +chr1:3660566 [G/A] chr1 3660566 Cc01_g01990:397 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA AA GG +chr1:3660548 [C/T] chr1 3660548 Cc01_g01990:415 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC CT TT CC +chr1:3660530 [C/T] chr1 3660530 Cc01_g01990:433 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 CC TT TT TT +chr1:3660529 [C/A] chr1 3660529 Cc01_g01990:434 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 50.0% 4 CC AA AA CC +chr1:3660523 [C/T] chr1 3660523 Cc01_g01990:440 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 50.0% 4 CC TT TT CC +chr1:3660509 [T/C] chr1 3660509 Cc01_g01990:454 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 TT CC TT TT +chr1:3660489 [T/G] chr1 3660489 Cc01_g01990:474 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 4 TT GG GG TT +chr1:3660392 [T/G] chr1 3660392 Cc01_g01990:571 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT GG GG GG +chr1:3660382 [T/A] chr1 3660382 Cc01_g01990:581 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 TT AA TT TT +chr1:3660368 [T/C] chr1 3660368 Cc01_g01990:595 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 TT CC CC CC +chr1:3663378 [T/A] chr1 3663378 Cc01_g02000:123 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT +chr1:3663363 [C/T] chr1 3663363 Cc01_g02000:138 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC +chr1:3663324 [G/A] chr1 3663324 Cc01_g02000:177 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG AG GG GG +chr1:3663323 [C/T] chr1 3663323 Cc01_g02000:178 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC CT CC +chr1:3663308 [A/T] chr1 3663308 Cc01_g02000:193 exon STOP_LOST Tag/Aag 6/K 37.5% 4 AA TT AT AA +chr1:3704574 [A/T] chr1 3704574 Cc01_g02010:179 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 AA TT TT TT +chr1:3704558 [T/A] chr1 3704558 Cc01_g02010:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT +chr1:3704537 [A/G] chr1 3704537 Cc01_g02010:216 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AG AA +chr1:3704524 [A/T] chr1 3704524 Cc01_g02010:229 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT +chr1:3704520 [G/C] chr1 3704520 Cc01_g02010:233 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG +chr1:3704494 [C/T] chr1 3704494 Cc01_g02010:259 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 25.0% 4 CC TT TT TT +chr1:3702641 [A/T] chr1 3702641 Cc01_g02010:350 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 AA AT AA AA +chr1:3702616 [T/A] chr1 3702616 Cc01_g02010:375 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TA TT TT +chr1:3702601 [T/C] chr1 3702601 Cc01_g02010:390 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC +chr1:3702599 [T/A] chr1 3702599 Cc01_g02010:392 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 TT TT TT AT +chr1:3702582 [C/T] chr1 3702582 Cc01_g02010:409 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC +chr1:3702367 [T/C] chr1 3702367 Cc01_g02010:534 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT TT CC +chr1:3702346 [A/T] chr1 3702346 Cc01_g02010:555 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 AA AA AT AA +chr1:3702331 [G/A] chr1 3702331 Cc01_g02010:570 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA AA GG +chr1:3702283 [G/A] chr1 3702283 Cc01_g02010:618 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG AA AA AA +chr1:3702270 [A/G] chr1 3702270 Cc01_g02010:631 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA AG AA AA +chr1:3702235 [A/G] chr1 3702235 Cc01_g02010:666 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA GA AA AA +chr1:3702233 [T/C] chr1 3702233 Cc01_g02010:668 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT TC CC TT +chr1:3702222 [T/G] chr1 3702222 Cc01_g02010:679 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG +chr1:3702218 [T/C] chr1 3702218 Cc01_g02010:683 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TT CT +chr1:3701396 [C/T] chr1 3701396 Cc01_g02010:708 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT +chr1:3701386 [A/G] chr1 3701386 Cc01_g02010:718 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA AA AA GG +chr1:3701243 [T/C] chr1 3701243 Cc01_g02010:861 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT +chr1:3701240 [G/A] chr1 3701240 Cc01_g02010:864 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GG AA +chr1:3701237 [C/T] chr1 3701237 Cc01_g02010:867 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC +chr1:3700510 [C/T] chr1 3700510 Cc01_g02010:931 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 16.7% 3 CC CC CT NN +chr1:3699429 [C/T] chr1 3699429 Cc01_g02010:1020 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC CC CC TT +chr1:3699397 [G/C] chr1 3699397 Cc01_g02010:1052 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 16.7% 3 GG GG GC NN +chr1:3699002 [C/A] chr1 3699002 Cc01_g02010:1192 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 CC CA CC AA +chr1:3698979 [A/G] chr1 3698979 Cc01_g02010:1215 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG +chr1:3698964 [T/C] chr1 3698964 Cc01_g02010:1230 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 TT TT TC TT +chr1:3698934 [C/T] chr1 3698934 Cc01_g02010:1260 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC CT CT TT +chr1:3698922 [C/T] chr1 3698922 Cc01_g02010:1272 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC CC CC TT +chr1:3698901 [C/T] chr1 3698901 Cc01_g02010:1293 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC CC CT TT +chr1:3698886 [A/G] chr1 3698886 Cc01_g02010:1308 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 AA AA AG AA +chr1:3698880 [T/C] chr1 3698880 Cc01_g02010:1314 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT +chr1:3698871 [T/A] chr1 3698871 Cc01_g02010:1323 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 TT TT TT AA +chr1:3698841 [T/A] chr1 3698841 Cc01_g02010:1353 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 TT AA AA AA +chr1:3698450 [C/T] chr1 3698450 Cc01_g02010:1477 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CT CC +chr1:3698412 [G/A] chr1 3698412 Cc01_g02010:1515 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GG GG AA +chr1:3698398 [T/A] chr1 3698398 Cc01_g02010:1529 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 12.5% 4 TT TA TT TT +chr1:3698247 [A/G] chr1 3698247 Cc01_g02010:1680 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 AA AA AA GG +chr1:3697989 [T/C] chr1 3697989 Cc01_g02010:1692 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT +chr1:3696904 [A/T] chr1 3696904 Cc01_g02010:1866 exon NON_SYNONYMOUS_CODING caT/caA H/Q 50.0% 2 AA NN TT NN +chr1:3696445 [A/G] chr1 3696445 Cc01_g02010:1945 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 AA AA AA GG +chr1:3696441 [C/T] chr1 3696441 Cc01_g02010:1949 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT +chr1:3696389 [C/T] chr1 3696389 Cc01_g02010:2001 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 CC CC CT TT +chr1:3696380 [C/T] chr1 3696380 Cc01_g02010:2010 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT +chr1:3696362 [T/C] chr1 3696362 Cc01_g02010:2028 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TT TT CC +chr1:3696314 [T/G] chr1 3696314 Cc01_g02010:2076 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 TT TT TT GG +chr1:3696312 [C/G] chr1 3696312 Cc01_g02010:2078 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG CG CC +chr1:3695395 [A/G] chr1 3695395 Cc01_g02010:2114 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG +chr1:3695358 [T/C] chr1 3695358 Cc01_g02010:2151 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT CT +chr1:3695350 [T/C] chr1 3695350 Cc01_g02010:2159 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 TT CC CC TT +chr1:3695299 [G/A] chr1 3695299 Cc01_g02010:2210 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG GG GG AA +chr1:3725796 [T/C] chr1 3725796 Cc01_g02020:642 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 TT NN TT TC +chr1:3725964 [A/G] chr1 3725964 Cc01_g02020:810 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA NN GG GG +chr1:3727454 [C/T] chr1 3727454 Cc01_g02020:1724 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT +chr1:3727458 [A/T] chr1 3727458 Cc01_g02020:1728 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 2 AA NN NN TT +chr1:3727501 [G/A] chr1 3727501 Cc01_g02020:1771 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AA AA GA +chr1:3727517 [T/C] chr1 3727517 Cc01_g02020:1787 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TT TC +chr1:3727787 [T/A] chr1 3727787 Cc01_g02020:2057 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN AA TT +chr1:3727789 [A/G] chr1 3727789 Cc01_g02020:2059 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 AA NN NN GG +chr1:3727802 [T/G] chr1 3727802 Cc01_g02020:2072 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 50.0% 2 TT NN NN GG +chr1:3727809 [C/T] chr1 3727809 Cc01_g02020:2079 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 2 CC NN NN TT +chr1:3727827 [T/C] chr1 3727827 Cc01_g02020:2097 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT NN NN CC +chr1:3727876 [T/G] chr1 3727876 Cc01_g02020:2146 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG +chr1:3727959 [G/A] chr1 3727959 Cc01_g02020:2229 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 2 GG NN NN GA +chr1:3727969 [T/C] chr1 3727969 Cc01_g02020:2239 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 33.3% 3 TT TT NN CC +chr1:3728011 [C/T] chr1 3728011 Cc01_g02020:2281 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 2 CC NN NN CT +chr1:3728022 [C/T] chr1 3728022 Cc01_g02020:2292 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 2 CC NN NN CT +chr1:3728064 [G/A] chr1 3728064 Cc01_g02020:2334 exon SYNONYMOUS_CODING gcG/gcA A/A 50.0% 2 GG NN NN AA +chr1:3728080 [T/A] chr1 3728080 Cc01_g02020:2350 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 50.0% 2 TT NN NN AA +chr1:3740570 [G/A] chr1 3740570 Cc01_g02030:19 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA AA NN +chr1:3740594 [G/A] chr1 3740594 Cc01_g02030:43 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA GG NN +chr1:3740608 [G/T] chr1 3740608 Cc01_g02030:57 exon SYNONYMOUS_CODING tcG/tcT S/S 50.0% 2 GG TT NN NN +chr1:3740686 [G/A] chr1 3740686 Cc01_g02030:135 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA GG GG +chr1:3740718 [C/T] chr1 3740718 Cc01_g02030:167 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC +chr1:3740764 [C/T] chr1 3740764 Cc01_g02030:213 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC NN TT CC +chr1:3740817 [C/A] chr1 3740817 Cc01_g02030:266 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC NN AA CC +chr1:3750735 [C/T] chr1 3750735 Cc01_g02040:6 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CT CC CT +chr1:3750711 [C/G] chr1 3750711 Cc01_g02040:30 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CG CC CC +chr1:3750587 [C/T] chr1 3750587 Cc01_g02040:154 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 CC CC CC CT +chr1:3750577 [C/T] chr1 3750577 Cc01_g02040:164 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CT CC CC +chr1:3750569 [T/C] chr1 3750569 Cc01_g02040:172 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TT TC +chr1:3750546 [T/A] chr1 3750546 Cc01_g02040:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT +chr1:3750522 [A/G] chr1 3750522 Cc01_g02040:219 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 4 AA AA GG GG +chr1:3750505 [G/C] chr1 3750505 Cc01_g02040:236 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG +chr1:3748656 [T/C] chr1 3748656 Cc01_g02040:302 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC +chr1:3748610 [C/T] chr1 3748610 Cc01_g02040:348 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CC CC CT +chr1:3748546 [C/T] chr1 3748546 Cc01_g02040:412 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC +chr1:3748306 [A/G] chr1 3748306 Cc01_g02040:562 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AA AA AG +chr1:3748282 [C/T] chr1 3748282 Cc01_g02040:586 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT TT TT +chr1:3748213 [T/C] chr1 3748213 Cc01_g02040:655 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT TT TT CC +chr1:3748170 [A/C] chr1 3748170 Cc01_g02040:698 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 12.5% 4 AA AA AA AC +chr1:3747303 [G/A] chr1 3747303 Cc01_g02040:777 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG +chr1:3747255 [G/A] chr1 3747255 Cc01_g02040:825 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG AA AA AA +chr1:3747226 [T/G] chr1 3747226 Cc01_g02040:854 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG +chr1:3745743 [G/A] chr1 3745743 Cc01_g02040:1024 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 4 GG GG AA AA +chr1:3745742 [C/T] chr1 3745742 Cc01_g02040:1025 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC TT CC CC +chr1:3745322 [A/T] chr1 3745322 Cc01_g02040:1191 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT +chr1:3745225 [G/T] chr1 3745225 Cc01_g02040:1288 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT +chr1:3745223 [G/A] chr1 3745223 Cc01_g02040:1290 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG AG +chr1:3745208 [T/C] chr1 3745208 Cc01_g02040:1305 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC TT CC +chr1:3745196 [T/C] chr1 3745196 Cc01_g02040:1317 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 TT TT TC CT +chr1:3745187 [T/A] chr1 3745187 Cc01_g02040:1326 exon SYNONYMOUS_CODING ctA/ctT L/L 12.5% 4 TT TT TT TA +chr1:3745165 [G/A] chr1 3745165 Cc01_g02040:1348 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG AG +chr1:3745164 [C/T] chr1 3745164 Cc01_g02040:1349 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 CC CC CT CC +chr1:3744647 [G/C] chr1 3744647 Cc01_g02040:1598 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC +chr1:3744596 [C/T] chr1 3744596 Cc01_g02040:1649 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CC CT +chr1:3744575 [T/C] chr1 3744575 Cc01_g02040:1670 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT +chr1:3744299 [T/A] chr1 3744299 Cc01_g02040:1698 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TA TT +chr1:3742967 [T/C] chr1 3742967 Cc01_g02040:1935 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TC TT +chr1:3742922 [G/A] chr1 3742922 Cc01_g02040:1980 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG AA GG GA +chr1:3742793 [C/T] chr1 3742793 Cc01_g02040:2109 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC +chr1:3741865 [T/G] chr1 3741865 Cc01_g02040:2131 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TG TT TT +chr1:3741857 [A/G] chr1 3741857 Cc01_g02040:2139 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 AA AA AA AG +chr1:3741842 [T/C] chr1 3741842 Cc01_g02040:2154 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC +chr1:3741793 [C/T] chr1 3741793 Cc01_g02040:2203 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT +chr1:3759622 [T/A] chr1 3759622 Cc01_g02050:54 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT TT TA TA +chr1:3762484 [A/G] chr1 3762484 Cc01_g02050:82 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 AA AA AA AG +chr1:3762723 [A/G] chr1 3762723 Cc01_g02050:202 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AA AG +chr1:3762755 [A/G] chr1 3762755 Cc01_g02050:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG GG GG +chr1:3762781 [A/C] chr1 3762781 Cc01_g02050:260 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA +chr1:3762848 [G/A] chr1 3762848 Cc01_g02050:327 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA +chr1:3763034 [A/G] chr1 3763034 Cc01_g02050:411 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA +chr1:3763038 [C/A] chr1 3763038 Cc01_g02050:415 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC AA CC CC +chr1:3763049 [G/A] chr1 3763049 Cc01_g02050:426 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG AA GG GG +chr1:3763055 [A/T] chr1 3763055 Cc01_g02050:432 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT +chr1:3763064 [A/G] chr1 3763064 Cc01_g02050:441 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA GG AA AA +chr1:3763079 [G/A] chr1 3763079 Cc01_g02050:456 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GG AA GA +chr1:3766634 [T/G] chr1 3766634 Cc01_g02060:471 exon SYNONYMOUS_CODING ccT/ccG P/P 33.3% 3 TT GG NN TT +chr1:3766695 [T/C] chr1 3766695 Cc01_g02060:532 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN TT CC +chr1:3920385 [G/T] chr1 3920385 Cc01_g02110:211 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 GG NN TT NN +chr1:3920402 [T/C] chr1 3920402 Cc01_g02110:228 exon SYNONYMOUS_CODING tcT/tcC S/S 50.0% 2 TT NN CC NN +chr1:3923592 [A/T] chr1 3923592 Cc01_g02120:176 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AA AA AT +chr1:3923713 [C/T] chr1 3923713 Cc01_g02120:207 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC +chr1:3923759 [C/T] chr1 3923759 Cc01_g02120:253 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC +chr1:3923905 [C/T] chr1 3923905 Cc01_g02120:399 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT CT CT +chr1:3923938 [T/A] chr1 3923938 Cc01_g02120:432 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 TT TA TT TT +chr1:3923947 [C/T] chr1 3923947 Cc01_g02120:441 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC TT CT CT +chr1:3924037 [G/A] chr1 3924037 Cc01_g02120:531 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG +chr1:3924086 [C/T] chr1 3924086 Cc01_g02120:580 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CT CC CC +chr1:3924307 [T/C] chr1 3924307 Cc01_g02120:801 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT +chr1:3924337 [G/A] chr1 3924337 Cc01_g02120:831 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA AA AA +chr1:3924341 [C/G] chr1 3924341 Cc01_g02120:835 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC +chr1:3924368 [C/A] chr1 3924368 Cc01_g02120:862 exon NON_SYNONYMOUS_CODING Cct/Act P/T 12.5% 4 CC AC CC CC +chr1:3924378 [A/G] chr1 3924378 Cc01_g02120:872 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA +chr1:3924397 [G/A] chr1 3924397 Cc01_g02120:891 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG +chr1:3924554 [A/C] chr1 3924554 Cc01_g02120:1048 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA +chr1:3924566 [T/C] chr1 3924566 Cc01_g02120:1060 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TT TT TC +chr1:3924571 [C/A] chr1 3924571 Cc01_g02120:1065 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC +chr1:3924632 [G/T] chr1 3924632 Cc01_g02120:1126 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG TG GG GG +chr1:3924644 [G/A] chr1 3924644 Cc01_g02120:1138 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG +chr1:3924648 [A/C] chr1 3924648 Cc01_g02120:1142 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA +chr1:3924703 [A/G] chr1 3924703 Cc01_g02120:1197 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA +chr1:3924857 [G/C] chr1 3924857 Cc01_g02120:1351 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GC GG GG +chr1:3924860 [G/A] chr1 3924860 Cc01_g02120:1354 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG +chr1:3924877 [A/C] chr1 3924877 Cc01_g02120:1371 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 AA CA AA AA +chr1:3925027 [T/C] chr1 3925027 Cc01_g02120:1521 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT +chr1:3925086 [C/T] chr1 3925086 Cc01_g02120:1580 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 CC TC CC CC +chr1:3925308 [G/A] chr1 3925308 Cc01_g02120:1650 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GA GA GA +chr1:3925317 [T/C] chr1 3925317 Cc01_g02120:1659 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TC TC TC +chr1:3925320 [G/T] chr1 3925320 Cc01_g02120:1662 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 37.5% 4 GG GT GT GT +chr1:3925346 [A/G] chr1 3925346 Cc01_g02120:1688 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AG AA AG +chr1:3930848 [G/T] chr1 3930848 Cc01_g02130:14 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 GG GT GG GG +chr1:3930877 [G/T] chr1 3930877 Cc01_g02130:43 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 12.5% 4 GG GG GG GT +chr1:3930883 [G/T] chr1 3930883 Cc01_g02130:49 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 50.0% 4 GG TT GT GT +chr1:3930897 [T/A] chr1 3930897 Cc01_g02130:63 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT +chr1:3931056 [C/T] chr1 3931056 Cc01_g02130:222 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CT CT CC +chr1:3931087 [C/A] chr1 3931087 Cc01_g02130:253 exon SYNONYMOUS_CODING Cga/Aga R/R 37.5% 4 CC AA CA CC +chr1:3931218 [A/G] chr1 3931218 Cc01_g02130:267 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GA AA AG +chr1:3931281 [T/C] chr1 3931281 Cc01_g02130:330 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 4 TT CC TC CT +chr1:3931307 [C/T] chr1 3931307 Cc01_g02130:356 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 50.0% 4 CC TT CT TC +chr1:3932233 [C/T] chr1 3932233 Cc01_g02130:381 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CT CT CT +chr1:3932286 [G/A] chr1 3932286 Cc01_g02130:434 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 37.5% 4 GG GA GA GA +chr1:3932490 [A/G] chr1 3932490 Cc01_g02130:492 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AA GA +chr1:3933113 [G/T] chr1 3933113 Cc01_g02130:592 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GT GG GG +chr1:3933131 [G/A] chr1 3933131 Cc01_g02130:610 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GG GA GA +chr1:3933913 [C/T] chr1 3933913 Cc01_g02130:645 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 CC TT CT CT +chr1:3933970 [T/C] chr1 3933970 Cc01_g02130:702 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT TC TC TT +chr1:3933994 [C/T] chr1 3933994 Cc01_g02130:726 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT +chr1:3934095 [A/G] chr1 3934095 Cc01_g02130:733 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 AA AG AG AA +chr1:3934103 [C/T] chr1 3934103 Cc01_g02130:741 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC +chr1:3934155 [G/A] chr1 3934155 Cc01_g02130:793 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AG GG GA +chr1:3935070 [A/G] chr1 3935070 Cc01_g02130:858 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AG AG AA +chr1:3935127 [A/G] chr1 3935127 Cc01_g02130:915 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA GG AG GG +chr1:3935145 [A/T] chr1 3935145 Cc01_g02130:933 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 AA AT AT AA +chr1:3935149 [G/C] chr1 3935149 Cc01_g02130:937 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 12.5% 4 GG GG GG GC +chr1:3935722 [A/C] chr1 3935722 Cc01_g02130:949 exon SYNONYMOUS_CODING Aga/Cga R/R 25.0% 4 AA AC AC AA +chr1:3935742 [A/G] chr1 3935742 Cc01_g02130:969 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA +chr1:3935757 [G/A] chr1 3935757 Cc01_g02130:984 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG AG +chr1:3935791 [T/G] chr1 3935791 Cc01_g02130:1018 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 37.5% 4 TT GG TG GG +chr1:3935805 [T/G] chr1 3935805 Cc01_g02130:1032 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT TT TT TG +chr1:3935956 [A/C] chr1 3935956 Cc01_g02130:1061 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AA AA AC +chr1:3935975 [G/A] chr1 3935975 Cc01_g02130:1080 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG GA +chr1:3936792 [A/G] chr1 3936792 Cc01_g02130:1125 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA AG +chr1:3936831 [A/G] chr1 3936831 Cc01_g02130:1164 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 4 AA AG AG GG +chr1:3936971 [G/C] chr1 3936971 Cc01_g02130:1222 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 37.5% 4 GG CC GC CC +chr1:3942733 [G/A] chr1 3942733 Cc01_g02140:62 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 GG AA GG GG +chr1:3942723 [T/A] chr1 3942723 Cc01_g02140:72 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA TT TT +chr1:3940926 [G/A] chr1 3940926 Cc01_g02140:213 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG +chr1:3940777 [C/A] chr1 3940777 Cc01_g02140:362 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC +chr1:3940686 [A/G] chr1 3940686 Cc01_g02140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA +chr1:3940475 [A/G] chr1 3940475 Cc01_g02140:664 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA AA AA AG +chr1:3940287 [C/T] chr1 3940287 Cc01_g02140:852 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT CC CC +chr1:3940278 [G/A] chr1 3940278 Cc01_g02140:861 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG +chr1:3940190 [T/C] chr1 3940190 Cc01_g02140:949 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT +chr1:3940062 [G/A] chr1 3940062 Cc01_g02140:1077 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG AA GA AA +chr1:3939962 [C/A] chr1 3939962 Cc01_g02140:1177 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 12.5% 4 CC CA CC CC +chr1:3939959 [G/T] chr1 3939959 Cc01_g02140:1180 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 GG TT GG GG +chr1:3939916 [C/T] chr1 3939916 Cc01_g02140:1223 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC +chr1:3938977 [G/C] chr1 3938977 Cc01_g02140:1335 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GC GG GG +chr1:3938798 [T/G] chr1 3938798 Cc01_g02140:1369 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 37.5% 4 TT GG TG TT +chr1:3938797 [C/G] chr1 3938797 Cc01_g02140:1370 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC CC CG +chr1:3938792 [G/A] chr1 3938792 Cc01_g02140:1375 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 GG GG GG AG +chr1:3938784 [C/T] chr1 3938784 Cc01_g02140:1383 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TC CT CC +chr1:3938738 [C/T] chr1 3938738 Cc01_g02140:1429 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC +chr1:3938734 [T/C] chr1 3938734 Cc01_g02140:1433 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 TT TT TC CT +chr1:3938731 [A/G] chr1 3938731 Cc01_g02140:1436 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA +chr1:3938674 [C/T] chr1 3938674 Cc01_g02140:1493 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC +chr1:3950327 [A/C] chr1 3950327 Cc01_g02150:300 exon NON_SYNONYMOUS_CODING caT/caG H/Q 37.5% 4 AA CC AC AA +chr1:3949508 [G/T] chr1 3949508 Cc01_g02150:438 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 GG GT GG GG +chr1:3949500 [T/C] chr1 3949500 Cc01_g02150:446 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 TT TT TC TT +chr1:3949478 [G/A] chr1 3949478 Cc01_g02150:468 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 GG GG GA GG +chr1:3949470 [C/T] chr1 3949470 Cc01_g02150:476 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 CC TT CC CC +chr1:3949465 [C/G] chr1 3949465 Cc01_g02150:481 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 37.5% 4 CC GG CG CC +chr1:3949086 [C/T] chr1 3949086 Cc01_g02150:541 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC CT CC +chr1:3967535 [C/T] chr1 3967535 Cc01_g02160:57 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CT CC CC +chr1:3967530 [A/T] chr1 3967530 Cc01_g02160:62 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA AA AT +chr1:3967524 [G/A] chr1 3967524 Cc01_g02160:68 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 37.5% 4 GG AG GA AG +chr1:3967512 [A/G] chr1 3967512 Cc01_g02160:80 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AG AA +chr1:3967435 [A/G] chr1 3967435 Cc01_g02160:157 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 AA AG AA AG +chr1:3967421 [G/A] chr1 3967421 Cc01_g02160:171 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG AG GG GG +chr1:3967412 [A/C] chr1 3967412 Cc01_g02160:180 exon STOP_GAINED taT/taG Y/0 37.5% 4 AA AC AC AC +chr1:3967382 [A/G] chr1 3967382 Cc01_g02160:210 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA GA GA AA +chr1:3967354 [G/T] chr1 3967354 Cc01_g02160:238 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG GG GG GT +chr1:3967352 [T/C] chr1 3967352 Cc01_g02160:240 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT CC CT CC +chr1:3967310 [G/C] chr1 3967310 Cc01_g02160:282 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG GC GC GC +chr1:3967300 [C/T] chr1 3967300 Cc01_g02160:292 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC TC +chr1:3967295 [G/A] chr1 3967295 Cc01_g02160:297 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG +chr1:3966909 [T/A] chr1 3966909 Cc01_g02160:683 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 TT TA TT TT +chr1:3966784 [G/A] chr1 3966784 Cc01_g02160:808 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 16.7% 3 GG NN GA GG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/result.txt Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,21 @@ +Chromosome Position SNPs +chr1 200000 355 +chr1 400000 228 +chr1 600000 63 +chr1 800000 191 +chr1 1000000 88 +chr1 1200000 90 +chr1 1400000 190 +chr1 1600000 267 +chr1 1800000 226 +chr1 2000000 163 +chr1 2200000 357 +chr1 2400000 132 +chr1 2600000 158 +chr1 2800000 104 +chr1 3000000 146 +chr1 3200000 331 +chr1 3400000 181 +chr1 3600000 36 +chr1 3800000 167 +chr1 4000000 110
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNP_density/test-data/result_bysample.txt Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,21 @@ +Chromosome BA58 BA59 BD54 +chr1 220 197 225 +chr1 130 119 133 +chr1 43 43 40 +chr1 139 167 141 +chr1 62 72 78 +chr1 35 76 38 +chr1 98 123 82 +chr1 133 205 135 +chr1 94 141 151 +chr1 112 116 117 +chr1 228 238 204 +chr1 86 95 96 +chr1 60 106 82 +chr1 60 74 64 +chr1 106 112 115 +chr1 199 220 228 +chr1 151 94 64 +chr1 18 32 27 +chr1 87 90 100 +chr1 54 75 47
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCF2Hapmap/VCF2FastaAndHapmap.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,525 @@ + +#!/usr/bin/perl + +use strict; +use Getopt::Long; + +my $usage = qq~Usage:$0 <args> [<opts>] + +where <args> are: + + -v, --vcf <VCF input> + -o, --out <Output basename> + +<opts> are: + + -r, --reference <Reference fasta file> + -g, --gff <GFF input file to create alignments of genes> +~; +$usage .= "\n"; + +my ($input,$out,$reference,$gff); + + + +GetOptions( + "vcf=s" => \$input, + "out=s" => \$out, + "reference=s" => \$reference, + "gff=s" => \$gff +); + + +die $usage + if ( !$input || !$out); + +if ($gff && !$reference) +{ + die "You must provide a Fasta reference file when providing GFF annotation\n"; +} + + +my %ref_sequences; +if ($reference) +{ + my $id; + my $sequence = ""; + open(my $R,$reference) or die "cannot open file: $reference"; + while(<$R>) + { + my $line =$_; + $line =~s/\n//g; + $line =~s/\r//g; + if ($line =~ />([^\s]+)/){ + $ref_sequences{$id} = $sequence; + $id=$1;$sequence=""; + } + else + { + $sequence .= $line; + } + } + close($R); + $ref_sequences{$id} = $sequence; +} + + +my %chr_of_gene; +my %ann; +if ($gff) +{ + open(my $G,$gff) or die "cannot open file: $gff"; + while(<$G>) + { + my $line =$_; + $line =~s/\n//g; + $line =~s/\r//g; + my @i = split(/\t/,$line); + my $chr = $i[0]; + my $feature = $i[2]; + my $strand = $i[6]; + my $start = $i[3]; + my $stop = $i[4]; + my $inf = $i[8]; + if ($feature eq 'gene') + { + if ($inf =~/Name=([\w\-\.]+)[;\s]*/){$inf = $1;} + $ann{$inf}{"start"}=$start; + $ann{$inf}{"stop"}=$stop; + $ann{$inf}{"strand"}=$strand; + $chr_of_gene{$inf} = $chr; + } + } + close($G); +} + + + +my %IUPAC = +( + '[A/G]'=> "R", + '[G/A]'=> "R", + '[C/T]'=> "Y", + '[T/C]'=> "Y", + '[T/G]'=> "K", + '[G/T]'=> "K", + '[C/G]'=> "S", + '[G/C]'=> "S", + '[A/T]'=> "W", + '[T/A]'=> "W", + '[A/C]'=> "M", + '[C/A]'=> "M", + '[C/A/T]'=> "H", + '[A/T/C]'=> "H", + '[A/C/T]'=> "H", + '[C/T/A]'=> "H", + '[T/C/A]'=> "H", + '[T/A/C]'=> "H", + '[C/A/G]'=> "V", + '[A/G/C]'=> "V", + '[A/C/G]'=> "V", + '[C/G/A]'=> "V", + '[G/C/A]'=> "V", + '[G/A/C]'=> "V", + '[C/T/G]'=> "B", + '[T/G/C]'=> "B", + '[T/C/G]'=> "B", + '[C/G/T]'=> "B", + '[G/C/T]'=> "B", + '[G/T/C]'=> "B", + '[T/A/G]'=> "D", + '[A/G/T]'=> "D", + '[A/T/G]'=> "D", + '[T/G/A]'=> "D", + '[G/T/A]'=> "D", + '[G/A/T]'=> "D", +); + +my %snps_of_gene; +my %snps_of_gene2; +my %indiv_order; +my $indiv_list; +my %genotyping_infos; +my $num_line = 0; +my $genename_rank_in_snpeff = 4; + +my $find_annotations = `grep -c 'EFF=' $input`; + +open(my $HAPMAP,">$out.hapmap"); +print $HAPMAP "rs# alleles chrom pos gene feature effect codon_change amino_acid_change MAF missing_data"; +open(my $VCF,$input); +while(<$VCF>) +{ + my $line = $_; + chomp($line); + my @infos = split(/\t/,$line); + + if (/^##INFO=\<ID=EFF/ && /Amino_Acid_length \| Gene_Name \| Transcript_BioType \| Gene_Coding/) + { + $genename_rank_in_snpeff = 8; + } + + if (scalar @infos > 9) + { + if (/#CHROM/) + { + for (my $j=9;$j<=$#infos;$j++) + { + my $individu = $infos[$j]; + $indiv_list .= " $individu"; + $indiv_order{$j} = $individu; + } + print $HAPMAP "$indiv_list\n"; + } + elsif (!/^#/) + { + $num_line++; + + my $chromosome = $infos[0]; + my $chromosome_position = $infos[1]; + my $ref_allele = $infos[3]; + my $alt_allele = $infos[4]; + + if ($ref_allele =~/\w\w+/) + { + $ref_allele = "A"; + $alt_allele = "T"; + } + elsif ($alt_allele =~/\w\w+/) + { + $ref_allele = "T"; + $alt_allele = "A"; + } + + my $info = $infos[7]; + my $is_in_exon = "#"; + my $is_synonyme = "#"; + my $gene; + if ($find_annotations > 1) + { + $gene = "intergenic"; + } + else + { + $gene = $chromosome; + } + my $modif_codon = "#"; + my $modif_aa = "#"; + my $geneposition; + if ($info =~/EFF=(.*)/) + { + my @annotations = split(",",$1); + foreach my $annotation(@annotations) + { + my ($syn, $additional) = split(/\(/,$annotation); + + if ($syn =~/STREAM/){next;} + + $is_in_exon = "exon"; + if ($syn =~/UTR/) + { + $is_in_exon = $syn; + } + else + { + $is_synonyme = $syn; + } + my @infos_additional = split(/\|/,$additional); + $gene = $infos_additional[$genename_rank_in_snpeff]; + $modif_codon = $infos_additional[2]; + $modif_aa = $infos_additional[3]; + + if ($syn =~/INTERGENIC/) + { + $is_synonyme = "#"; + $gene = "intergenic"; + $is_in_exon = "#"; + } + elsif ($syn =~/SYNONYM/) + { + $is_in_exon = "exon"; + } + elsif ($syn =~/INTRON/ or $syn =~/SPLICE_SITE_DONOR/) + { + $is_in_exon = "intron"; + $is_synonyme = "#"; + } + + + if ($modif_aa =~/(\w)(\d+)$/) + { + $modif_aa = "$1/$1"; + } + elsif ($modif_aa =~/(\w)(\d+)(\w)/) + { + $modif_aa = "$1/$3"; + } + if ($infos_additional[8] =~/Exon/) + { + $is_in_exon = "exon"; + } + + if (!$modif_aa){$modif_aa="#";} + if (!$modif_codon){$modif_codon="#";} + } + } + $gene =~s/\.\d//g; + if ($ann{$gene}{"start"}) + { + my $strand = $ann{$gene}{"strand"}; + if ($strand eq '-') + { + $geneposition = $ann{$gene}{"stop"} - $chromosome_position; + } + else + { + $geneposition = $chromosome_position - $ann{$gene}{"start"}; + } + } + #if ($info =~/GenePos=(\d+);/) + #{ + # $geneposition = $1; + #} + my $ratio_missing_data; + my $snp_frequency; + my $genotyping = ""; + + if (2 > 1) + { + + $genotyping_infos{"ref"} = "$ref_allele$ref_allele"; + + my %alleles_found; + my $nb_readable_ind = 0; + for (my $i = 9;$i <= $#infos;$i++) + { + my $dnasample = $indiv_order{$i}; + my @infos_alleles = split(":",$infos[$i]); + my $genotype = $infos_alleles[0]; + $genotype =~s/0/$ref_allele/g; + + if ($alt_allele =~/,/) + { + my @alt_alleles = split(",",$alt_allele); + my $num_all = 1; + foreach my $alt_al(@alt_alleles) + { + $genotype =~s/$num_all/$alt_al/g; + $num_all++; + } + } + else + { + $genotype =~s/1/$alt_allele/g; + } + if ($genotype eq '.'){$genotype = "./.";} + $genotype =~s/\./N/g; + if ($genotype !~/N\/N/) + { + $nb_readable_ind++; + } + my @alleles; + if ($genotype =~/\//) + { + @alleles = split(/\//,$genotype); + } + else + { + @alleles = split(/\|/,$genotype); + } + $genotyping .= join("",@alleles) . " "; + $genotyping_infos{$dnasample} = join("",@alleles); + + foreach my $al(@alleles) + { + if ($al ne 'N'){$alleles_found{$al}++;} + } + } + chop($genotyping); + + $snp_frequency = 0; + + my $max = 0; + my $min = 10000000; + my $total = 0; + foreach my $al(keys(%alleles_found)) + { + my $nb = $alleles_found{$al}; + $total+= $nb; + if ($nb > $max) + { + $max = $nb; + } + if ($nb < $min) + { + $min = $nb; + } + } + if ($total > 0) + { + $snp_frequency = sprintf("%.1f",($min/$total)*100); + } + + $ratio_missing_data = 100 - ($nb_readable_ind / ($#infos - 8)) * 100; + $ratio_missing_data = sprintf("%.1f",$ratio_missing_data); + + foreach my $dna(keys(%genotyping_infos)) + { + $snps_of_gene{$gene}{$geneposition}{$dna} = $genotyping_infos{$dna}; + } + } + my $snp_type = "[$ref_allele/$alt_allele]"; + $snps_of_gene2{$chromosome}{$chromosome_position} = $snp_type; + #print $HAPMAP "$chromosome:$chromosome_position\t$snp_type\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$nb_readable_ind\t$genotyping\n"; + print $HAPMAP "$chromosome:$chromosome_position\t$ref_allele/$alt_allele\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$ratio_missing_data%\t$genotyping\n"; + } + } +} +close($VCF); +close($HAPMAP); + + +if (!$reference){exit;} + +################################################################# +# generate flanking sequences for Illumina VeraCode technology +################################################################# +open(my $FLANKING,">$out.flanking.txt"); +foreach my $seq(keys(%ref_sequences)) +{ + if ($snps_of_gene2{$seq}) + { + my $refhash = $snps_of_gene2{$seq}; + my %hashreal = %$refhash; + + # create consensus + my $refseq = $ref_sequences{$seq}; + my $consensus = ""; + my $previous = 0; + foreach my $pos(sort {$a<=>$b} keys(%hashreal)) + { + my $length = $pos - $previous - 1; + $consensus .= substr($refseq,$previous,$length); + my $iupac_code = $IUPAC{$snps_of_gene2{$seq}{$pos}}; + $consensus .= $iupac_code; + $previous = $pos; + } + my $length = length($refseq) - $previous; + $consensus .= substr($refseq,$previous,$length); + + foreach my $pos(sort {$a<=>$b} keys(%hashreal)) + { + my $snp_name = "$seq-$pos"; + my $flanking_length = 60; + my $length = $flanking_length; + my $start = $pos - $flanking_length - 1; + if ($pos <= $flanking_length) + { + $length = $pos - 1; + $start = 0; + } + my $sequence = substr($consensus,$start,$length); + + $sequence .= $snps_of_gene2{$seq}{$pos}; + $sequence .= substr($consensus,$pos,$flanking_length); + print $FLANKING "$snp_name,$sequence,0,0,0,Project_name,0,diploid,Other,Forward\n"; + } + } + } + + close($FLANKING); + + if (!$gff){exit;} + + my @individuals_list = split(/\t/,$indiv_list); + if ((scalar @individuals_list * scalar keys(%snps_of_gene)) > 800000) + { + print "Sorry, too many sequences to manage ...\n"; + exit; + } + + open(my $ALIGN_EGGLIB,">$out.gene_alignment.fas"); + my %alignments_ind; + foreach my $seq(keys(%snps_of_gene)) + { + if ($snps_of_gene{$seq}) + { + my $refhash = $snps_of_gene{$seq}; + my %hashreal = %$refhash; + + # get flanking sequences + my %flanking5; + my $start = $ann{$seq}{"start"}; + my $stop = $ann{$seq}{"stop"}; + my $strand = $ann{$seq}{"strand"}; + my $genelength = $stop - $start+1; + my $chr = $chr_of_gene{$seq}; + my $refseq = substr($ref_sequences{$chr},$start-1,$genelength); + if ($strand eq '-') + { + $refseq =~ tr /atcgATCG/tagcTAGC/; $refseq = reverse($refseq); + } + #print "$seq $chr $start $stop $refseq \n"; + my $previous = 0; + foreach my $pos(sort {$a<=>$b} keys(%hashreal)) + { + my $length = $pos - $previous - 1; + $flanking5{$pos} = substr($refseq,$previous,$length); + $previous = $pos; + } + my $length = length($refseq) - $previous; + my $flanking3 = substr($refseq,$previous,$length); + foreach my $ind(@individuals_list) + { + my $nb_missing_data_for_this_individual = 0; + if ($ind) + { + my $alignment_for_ind = ""; + my $seq_without_underscore = $seq; + $seq_without_underscore =~s/_//g; + $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_1\n"; + foreach my $pos(sort {$a<=>$b} keys(%hashreal)) + { + $alignment_for_ind .= $flanking5{$pos}; + my $geno = $snps_of_gene{$seq}{$pos}{$ind}; + $geno =~s/N/?/g; + if ($geno =~/\?/){$nb_missing_data_for_this_individual++;} + my @alleles = split("",$geno); + $alignment_for_ind .= $alleles[0]; + if ($alleles[0] eq $alleles[1]) + { + $alignments_ind{$ind} .= $alleles[1]; + } + else + { + my $snp_type = "[" . $alleles[0] . "/" . $alleles[1] . "]"; + $alignments_ind{$ind} .= $IUPAC{$snp_type}; + } + } + $alignment_for_ind .= $flanking3; + $alignment_for_ind .= "\n"; + + + $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_2\n"; + foreach my $pos(sort {$a<=>$b} keys(%hashreal)) + { + $alignment_for_ind .= $flanking5{$pos}; + my $geno = $snps_of_gene{$seq}{$pos}{$ind}; + $geno =~s/N/?/g; + my @alleles = split("",$geno); + $alignment_for_ind .= $alleles[1]; + } + $alignment_for_ind .= $flanking3; + $alignment_for_ind .= "\n"; + if (keys(%hashreal) != $nb_missing_data_for_this_individual) + { + print $ALIGN_EGGLIB $alignment_for_ind; + } + } + } + } +} +close($ALIGN_EGGLIB); + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCF2Hapmap/vcf2FastaAndHapmap.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,45 @@ +#!/bin/bash + +tool_path=$(dirname $0) + + + +filein=$1 +fileout_label=$2 +fileout=$3 +option=$4 + +option_text='' + + +if [ "$option" != "none" ] +then fileout_seq=$5 + fileout_fa1=$6 + filefasta=$7 + if [ "$option" == "fasta_gff" ] + then filegff=$8 + fi +fi + +if [ "$option" == "fasta" ] +then option_text="--reference $filefasta" +fi + +if [ "$option" == "fasta_gff" ] +then option_text="--reference $filefasta --gff $filegff" +fi + + +perl $tool_path/VCF2FastaAndHapmap.pl --vcf $filein --out $fileout_label $option_text + + +cp $fileout_label.hapmap $fileout ; rm $fileout_label.hapmap + +if [ "$option" == "fasta_gff" ] +then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; cp $fileout_label.gene_alignment.fas $fileout_fa1 ; rm $fileout_label.gene_alignment.fas ; +fi + +if [ "$option" == "fasta" ] +then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; +fi +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCF2Hapmap/vcf2FastaAndHapmap.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,251 @@ +<tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Convert VCF to Hapmap </description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="bash"> + vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt + #if str( $optional.file_opt ) != "none": + $fileout_seq $fileout_fa1 $filefasta + #if str( $optional.file_opt ) == "fasta_gff": + $filegff + #end if + #end if + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> + <param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/> + <conditional name="optional" > + <param name="file_opt" type="select" label="Optional files" > + <option value="none" selected="true">No</option> + <option value="fasta">Fasta</option> + <option value="fasta_gff">Fasta and GFF</option> + </param> + <when value="none" /> + <when value="fasta"> + <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" /> + </when> + <when value="fasta_gff"> + <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" /> + <param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" /> + </when> + </conditional> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout" format="txt" label="${fileout_label}.hapmap" /> + <data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt"> + <filter>(optional['file_opt'] != 'none')</filter> + </data> + <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas"> + <filter>(optional['file_opt'] == 'fasta_gff')</filter> + </data> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <test> + <param name="filein" value="sample.vcf" /> + <param name="otpional.file_opt" value="none" /> + <output name="fileout" file="result1.hapmap" /> + </test> + <test> + <param name="filein" value="sample.vcf" /> + <param name="otpional.file_opt" value="fasta" /> + <param name="filefasta" value="reference.fa" /> + <output name="fileout" file="result2.hapmap" /> + <output name="fileout_seq" file="result2.flanking.txt" /> + <output name="fileout_fa1" file="result2.gene_alignment.fas" /> + </test> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr + +--------------------------------------------------- + +======================= +VCF to Hapmap +======================= + +----------- +Description +----------- + + | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided. + | Furthermore it also creates fasta alignment of genes if GFF annotation is provided + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ========================== ======= +Name output file(s) format +=============== ========================== ======= +VCFtools Filter VCF file VCF +=============== ========================== ======= + + +**Downstream tool** + +=============== ========================== =========== +Name input file(s) format +=============== ========================== =========== +SNP density Hapmap file tabular +=============== ========================== =========== + + +---------- +Input file +---------- + +VCF file + VCF file with all SNPs + +---------- +Parameters +---------- + +Output file basename + Prefix for the output VCF file + +Optional files + To add additional files fasta file and GFF file. + +------------ +Output files +------------ + +Hapmap file + Hapmap converted file + +Additional files + If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +VCF file +--------- + +:: + + #fileformat=VCFv4.1 + #FILTER=<ID=LowQual,Description="Low quality"> + #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> + [...] + CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 + chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 + +Fasta file +---------- + + +:: + + >chr1 + CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT + +Parameters +========== + +Output name -> input + +Optional files -> Fasta + + +Output files +============ + +input.hapmap +------------ + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1 + chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT + chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC + +input.flanking.txt +------------------ + +:: + + chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward + chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward + +input.gene_alignment.fas +------------------------ + +:: + + >chr1_CATB1_1 + TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT + + + </help> + + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + }</citation> + + </citations> + +</tool>
--- a/VCFToolFilter/VCFToolsFilter.pl Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,214 +0,0 @@ - -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $usage = qq~Usage:$0 <args> [<opts>] - -where <args> are: - - -i, --input <VCF input> - -o, --out <Output basename> - - <opts> are: - - -s, --samples <Samples to be analyzed. Comma separated list> - -c, --chromosomes <Chromosomes to be analyzed. Comma separated list> - -e, --export <Output format (VCF/freq/plink. Default: VCF> - -f, --frequency <Minimum MAF. Default: 0.001> - -m, --max_freq <Maximum MAF. Default: 0.5> - -a, --allow_missing <Allowed missing data proportion per site. Must be comprised between 0 and 1. Default: 0> - -n, --nb_alleles <Accepted number of alleles (min,max). Default: 2,4> - -t, --type <Type of polymorphisms to keep (ALL/SNP/INDEL). Default: ALL> - -b, --bounds <Lower bound and upper bound for a range of sites to be processed (start,end). Default: 1, 100000000> -~; -$usage .= "\n"; - -my ($input,$out); - - -#my $indel_size_max = 500; -#my $indel_size_min = 1; -my $frequency_max = 0.5; -my $frequency_min = 0.001; -my $pos_max = 100000000000; -my $pos_min = 0; -my $filter_snp_type = "all"; - -my $missing_data = 0; -my $export = "VCF"; -my $type = "ALL"; -my $nb_alleles; -my $bounds; -my $samples; -my $chromosomes; - -GetOptions( - "input=s" => \$input, - "out=s" => \$out, - "samples=s" => \$samples, - "chromosomes=s" => \$chromosomes, - "frequency=s" => \$frequency_min, - "max_freq=s" => \$frequency_max, - "allow_missing=s"=> \$missing_data, - "export=s" => \$export, - "type=s" => \$type, - "nb_alleles=s" => \$nb_alleles, - "bounds=s" => \$bounds, -); - - -die $usage - if ( !$input || !$out); - -if ($samples && $samples =~/^([\w\,]+)\s*$/){ - $samples = $1; -} -elsif ($samples){ - die "Error: Samples must be a comma separated list of string\n"; -} -if ($chromosomes && $chromosomes =~/^([\w\,]+)\s*$/){ - $chromosomes = $1; -} -elsif($chromosomes){ - die "Error: Chromosomes must be a comma separated list of string\n"; -} -if ($bounds && $bounds =~/^([\d\,]+)\s*$/){ - $bounds = $1; -} -elsif($bounds){ - die "Error: Bounds must be a comma separated list of integers\n"; -} - -if ($frequency_min && $frequency_min =~/^([\d\.]+)\s*$/){ - $frequency_min = $1; -} -elsif ($frequency_min){ - die "Error: frequency must be an integer\n"; -} -if ($frequency_max && $frequency_max =~/^([\d\.]+)\s*$/){ - $frequency_max = $1; -} -elsif($frequency_max){ - die "Error: frequency must be an integer\n"; -} -if ($missing_data && $missing_data =~/^([\d\.]+)\s*$/){ - $missing_data = $1; -} -elsif ($missing_data){ - die "Error: Missing data must be an integer\n"; -} -if ($nb_alleles && $nb_alleles =~/^([\d\.\,]+)\s*$/){ - $nb_alleles = $1; -} -elsif($nb_alleles){ - die "Error: Nb alleles must be two integers\n"; -} -if ($export && $export =~/^([\w]+)\s*$/){ - $export = $1; -} -elsif($export){ - die "Error: Export must be a string\n"; -} -if ($type && $type =~/^([\w]+)\s*$/){ - $type = $1; -} -elsif($type){ - die "Error: Type must be a string\n"; -} - - -my @dnasamples; -if ($samples) -{ - @dnasamples = split(",",$samples); -} -my @nalleles; -if ($nb_alleles) -{ - @nalleles = split(",",$nb_alleles); -} -my @boundaries; -if ($bounds) -{ - @boundaries = split(",",$bounds); -} -my @chromosomes_list; -if ($chromosomes) -{ - @chromosomes_list = split(",",$chromosomes); -} - - -my $experiment = "chromosomes"; -my $table = ""; -my %genes; -my @snp_ids; -my @snp_ids_and_positions; -my @snp_ids_and_positions_all; -my $gene; -my $snp_num = 0; -my %ref_sequences; -my %snps_of_gene; - - - - -my $indiv_cmd = ""; -if (@dnasamples) -{ - $indiv_cmd = "--indv " . join(" --indv ",@dnasamples); -} - -my $chrom_cmd = ""; -if (@chromosomes_list) -{ - $chrom_cmd = "--chr " . join(" --chr ",@chromosomes_list); -} - -my $export_cmd = "--recode"; -if ($export eq "freq") -{ - $export_cmd = "--freq"; -} -if ($export eq "plink") -{ - $export_cmd = "--plink"; -} - - - -my $nb_alleles_cmd = "--min-alleles 1 --max-alleles 4"; -if (@nalleles) -{ - $nb_alleles_cmd = "--min-alleles $nalleles[0] --max-alleles $nalleles[1]"; -} -my $bounds_cmd = "--from-bp 1 --to-bp 100000000"; -if (@boundaries) -{ - $bounds_cmd = "--from-bp $boundaries[0] --to-bp $boundaries[1]"; -} - - -my $type_cmd = ""; -if ($type eq "INDEL") -{ - $type_cmd = "--keep-only-indels"; -} -if ($type eq "SNP") -{ - $type_cmd = "--remove-indels"; -} - - -system("vcftools --vcf $input --out $out --keep-INFO-all --remove-filtered-all $type_cmd $export_cmd $chrom_cmd $indiv_cmd $nb_alleles_cmd --maf $frequency_min --max-maf $frequency_max --max-missing $missing_data >>vcftools.log 2>&1"); - - - - - - -
--- a/VCFToolFilter/test-data/result.log Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --chr chr1 - --recode-INFO-all - --maf 0.001 - --max-alleles 4 - --max-maf 0.5 - --min-alleles 2 - --max-missing 1 - --out filtered - --recode - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting VCF file... -After filtering, kept 3616 out of a possible 4955 Sites -Run Time = 0.00 seconds
--- a/VCFToolFilter/test-data/result.vcf Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3661 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER=<ID=LowQual,Description="Low quality"> -##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> -##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> -##contig=<ID=chr1,length=38193400> -##contig=<ID=chr10,length=27624748> -##contig=<ID=chr11,length=33540656> -##contig=<ID=chr2,length=54522928> -##contig=<ID=chr3,length=32030951> -##contig=<ID=chr4,length=28191985> -##contig=<ID=chr5,length=29137935> -##contig=<ID=chr6,length=37293965> -##contig=<ID=chr7,length=29833120> -##contig=<ID=chr8,length=31585744> -##contig=<ID=chr9,length=22352177> -##contig=<ID=chr0,length=205603396> -##reference=file:///data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta -##SnpEffVersion="2.0.5d (build 2012-01-19), by Pablo Cingolani" -##SnpEffCmd="SnpEff eff coffea /apps/www/sniplay.cirad.fr/data/Coffee/Argemo_genomic.nonannotated.vcf.2 -i VCF -o VCF -c snpEff.config " -##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' "> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 -chr1 2264 . C T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=5;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=0.358;QD=13.75;ReadPosRankSum=-1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:2,3:5:53:97,0,53 -chr1 2353 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.5027;MLEAC=1;MLEAF=0.500;MQ=31.07;MQ0=3;MQRankSum=0.261;QD=1.18;ReadPosRankSum=-1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:19,7:26:59:59,0,409 -chr1 2482 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.294;DP=19;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=26.95;MQ0=7;MQRankSum=0.370;QD=10.94;ReadPosRankSum=-1.109;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:5,14:19:83:236,0,83 -chr1 2558 . A T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=45;Dels=0.00;FS=4.170;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=28.40;MQ0=13;MQRankSum=0.121;QD=17.55;ReadPosRankSum=-0.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,32:45:99:818,0,101 -chr1 2925 . A T 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.619;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=5.7776;MLEAC=1;MLEAF=0.500;MQ=38.24;MQ0=1;MQRankSum=0.372;QD=17.59;ReadPosRankSum=-1.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:380,0,275 -chr1 2941 . A G 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.63;MQ0=1;MQRankSum=1.524;QD=14.78;ReadPosRankSum=0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:7,8:15:99:250,0,227 -chr1 4945 . G A 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=29;Dels=0.00;FS=3.123;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.25;MQ0=1;MQRankSum=3.132;QD=11.10;ReadPosRankSum=3.363;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,15:29:43:350,0,43 -chr1 4947 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.742;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.38;MQ0=1;MQRankSum=3.401;QD=11.64;ReadPosRankSum=3.360;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:16,15:31:40:389,0,40 -chr1 4961 . C T 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.427;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.65;MQ0=1;MQRankSum=-3.749;QD=0.99;ReadPosRankSum=-0.165;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,25:43:71:71,0,437 -chr1 4967 . T C 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.980;DP=41;Dels=0.00;FS=1.219;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=26.25;MQ0=1;MQRankSum=4.072;QD=10.09;ReadPosRankSum=-0.897;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,16:41:70:442,0,70 -chr1 4981 . A C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=6.8693;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=3.500;QD=6.80;ReadPosRankSum=-1.759;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,11:36:88:273,0,88 -chr1 4987 . T G 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.583;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=13.8254;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=-2.450;QD=1.66;ReadPosRankSum=1.983;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,15:36:88:88,0,296 -chr1 5110 . A G 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.328;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.75;MQ0=3;MQRankSum=-0.421;QD=4.51;ReadPosRankSum=-1.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:123,0,278 -chr1 5170 . A G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.23;MQ0=2;MQRankSum=0.212;QD=3.65;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,7:15:83:83,0,127 -chr1 5171 . T G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=26.11;MQ0=1;MQRankSum=0.212;QD=3.91;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,6:14:83:83,0,122 -chr1 5284 . A C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.9827;MLEAC=1;MLEAF=0.500;MQ=34.72;MQ0=1;MQRankSum=-0.784;QD=3.49;ReadPosRankSum=-1.445;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:105,0,410 -chr1 5324 . C T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=3;MQRankSum=1.491;QD=10.44;ReadPosRankSum=-0.818;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:10,10:20:99:237,0,166 -chr1 5361 . A G 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=24.40;MQ0=2;MQRankSum=1.412;QD=11.41;ReadPosRankSum=0.688;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,14:24:44:302,0,44 -chr1 5889 . T G 147.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=21.23;MQ0=4;MQRankSum=-0.248;QD=8.17;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:4,14:18:11:175,0,11 -chr1 5938 . C G 64.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.520;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.73;MQ0=10;MQRankSum=1.034;QD=3.08;ReadPosRankSum=0.597;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,6:21:69:93,0,69 -chr1 5974 . A G 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.818;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=18.51;MQ0=8;MQRankSum=0.296;QD=1.88;ReadPosRankSum=1.580;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:14,4:18:62:62,0,114 -chr1 6350 . T G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=16.20;MQ0=21;MQRankSum=1.670;QD=2.93;ReadPosRankSum=-0.085;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:163,0,206 -chr1 6426 . T C 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=25.78;MQ0=2;MQRankSum=-1.099;QD=5.25;ReadPosRankSum=0.859;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:301,0,677 -chr1 6486 . A G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=16;MQRankSum=-0.330;QD=8.00;ReadPosRankSum=0.268;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:39,25:64:99:540,0,604 -chr1 6532 . C T 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=53;Dels=0.00;FS=4.619;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=17.32;MQ0=28;MQRankSum=0.087;QD=2.22;ReadPosRankSum=-0.379;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:146,0,419 -chr1 6577 . G A 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.35;MQ0=17;MQRankSum=-1.883;QD=6.11;ReadPosRankSum=0.269;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,25:33:28:230,0,28 -chr1 6607 . T C 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=-1.702;QD=2.28;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:117,0,385 -chr1 6609 . G T 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=0.904;QD=2.30;ReadPosRankSum=-0.204;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:32,7:39:99:118,0,377 -chr1 6675 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=52;Dels=0.00;FS=8.076;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.45;MQ0=15;MQRankSum=-1.788;QD=1.13;ReadPosRankSum=-0.973;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,16:52:87:87,0,729 -chr1 6691 . G T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=49;Dels=0.00;FS=8.321;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=17;MQRankSum=-0.467;QD=0.71;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,13:49:63:63,0,703 -chr1 6725 . G A 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=26;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=22.03;MQ0=9;MQRankSum=-0.927;QD=7.45;ReadPosRankSum=-0.146;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,13:26:99:222,0,183 -chr1 6942 . G C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.400;DP=21;Dels=0.00;FS=13.222;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.08;MQ0=7;MQRankSum=0.267;QD=2.66;ReadPosRankSum=-1.067;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,7:21:84:84,0,137 -chr1 7384 . T G 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.91;MQ0=30;MQRankSum=0.259;QD=1.40;ReadPosRankSum=0.583;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,16:42:87:87,0,93 -chr1 8682 . T G 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.57;MQ0=23;MQRankSum=-1.898;QD=7.02;ReadPosRankSum=0.429;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:8,30:38:99:295,0,141 -chr1 8785 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.453;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.27;MQ0=40;MQRankSum=-2.450;QD=1.48;ReadPosRankSum=1.668;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:102,0,173 -chr1 8936 . C T 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;DP=47;Dels=0.00;FS=11.458;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.37;MQ0=14;MQRankSum=2.448;QD=5.61;ReadPosRankSum=1.430;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,12:47:99:292,0,700 -chr1 8946 . A G 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.028;DP=39;Dels=0.00;FS=15.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=13;MQRankSum=1.417;QD=5.94;ReadPosRankSum=0.472;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:260,0,533 -chr1 9013 . A T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=33;Dels=0.00;FS=3.522;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.84;MQ0=24;MQRankSum=0.729;QD=2.05;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,9:33:96:96,0,100 -chr1 9080 . C T 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.47;MQ0=24;MQRankSum=-1.866;QD=1.82;ReadPosRankSum=0.633;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,13:34:90:90,0,190 -chr1 10540 . G C 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.965;DP=45;Dels=0.00;FS=17.175;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.78;MQ0=1;MQRankSum=-1.779;QD=6.82;ReadPosRankSum=2.279;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:335,0,1095 -chr1 10565 . T C 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.695;DP=49;Dels=0.00;FS=38.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.02;MQ0=2;MQRankSum=0.662;QD=20.57;ReadPosRankSum=-2.211;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,31:49:99:1036,0,420 -chr1 10997 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=59;Dels=0.00;FS=1.096;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=27.99;MQ0=9;MQRankSum=0.204;QD=10.11;ReadPosRankSum=-0.961;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:625,0,593 -chr1 11025 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.654;QD=4.94;ReadPosRankSum=1.721;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:310,0,779 -chr1 11026 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.814;QD=4.84;ReadPosRankSum=1.694;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:304,0,778 -chr1 11199 . G A 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.053;DP=54;Dels=0.00;FS=15.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.97;MQ0=5;MQRankSum=-2.335;QD=4.79;ReadPosRankSum=2.164;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:287,0,1004 -chr1 11255 . A G 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=45;Dels=0.00;FS=8.137;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=44.39;MQ0=0;MQRankSum=-1.761;QD=1.79;ReadPosRankSum=-2.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,10:45:99:109,0,1164 -chr1 11591 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.305;DP=31;Dels=0.00;FS=8.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.119;QD=4.96;ReadPosRankSum=-1.665;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:182,0,762 -chr1 11750 . A T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.197;DP=39;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.68;MQ0=1;MQRankSum=-4.052;QD=2.58;ReadPosRankSum=-2.335;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:129,0,976 -chr1 11773 . T C 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=49;Dels=0.00;FS=8.883;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.29;MQ0=1;MQRankSum=-5.316;QD=5.40;ReadPosRankSum=-0.400;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:293,0,1185 -chr1 11891 . A T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.82;MQ0=0;MQRankSum=-3.709;QD=8.61;ReadPosRankSum=-0.055;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:433,0,1013 -chr1 11902 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.656;DP=42;Dels=0.00;FS=1.270;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.98;MQ0=0;MQRankSum=-3.019;QD=7.21;ReadPosRankSum=-0.525;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:331,0,973 -chr1 11906 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.095;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.51;MQ0=0;MQRankSum=-2.883;QD=7.41;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:332,0,920 -chr1 11911 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=38;Dels=0.00;FS=3.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.65;MQ0=0;MQRankSum=-2.124;QD=4.81;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:211,0,908 -chr1 11921 . A T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.641;DP=38;Dels=0.00;FS=5.870;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-1.608;QD=3.52;ReadPosRankSum=0.348;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,10:38:99:162,0,926 -chr1 11929 . A G 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.970;DP=36;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.95;MQ0=0;MQRankSum=-1.465;QD=3.13;ReadPosRankSum=-0.171;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,8:36:99:141,0,932 -chr1 11994 . G A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.393;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=38.03;MQ0=3;MQRankSum=-1.960;QD=1.98;ReadPosRankSum=0.635;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:127,0,1191 -chr1 12008 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=38.65;MQ0=3;MQRankSum=-3.004;QD=4.01;ReadPosRankSum=0.628;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:265,0,1308 -chr1 12023 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=68;Dels=0.00;FS=3.645;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=41.63;MQ0=3;MQRankSum=-1.795;QD=7.56;ReadPosRankSum=-1.088;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:43,25:68:99:542,0,1441 -chr1 12050 . G C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=68;Dels=0.00;FS=5.033;HaplotypeScore=2.9268;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=3;MQRankSum=-1.538;QD=11.88;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:836,0,1326 -chr1 12090 . A G 888.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=57;Dels=0.00;FS=2.245;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=0;MQRankSum=-4.892;QD=15.59;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:917,0,995 -chr1 12162 . A T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.98;MQ0=2;MQRankSum=-4.602;QD=6.88;ReadPosRankSum=-0.119;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:21,13:34:99:262,0,708 -chr1 12186 . G C 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=38;Dels=0.00;FS=3.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=2;MQRankSum=-3.949;QD=6.10;ReadPosRankSum=-1.854;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:25,13:38:99:260,0,884 -chr1 12195 . C G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.111;DP=39;Dels=0.00;FS=1.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=2;MQRankSum=-3.882;QD=4.64;ReadPosRankSum=-1.898;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:209,0,927 -chr1 12249 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.999;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.19;MQ0=0;MQRankSum=-5.596;QD=11.75;ReadPosRankSum=2.865;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:686,0,1109 -chr1 12250 . C A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.017;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=-5.563;QD=11.66;ReadPosRankSum=2.848;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:33,23:56:99:681,0,1094 -chr1 12252 . T C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.084;DP=55;Dels=0.00;FS=2.426;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.486;QD=12.00;ReadPosRankSum=2.722;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:688,0,1075 -chr1 12271 . A G 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.19;ReadPosRankSum=0.908;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,18:47:99:507,0,1022 -chr1 12273 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.00;ReadPosRankSum=0.711;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:498,0,1029 -chr1 12283 . T G 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=45;Dels=0.00;FS=6.601;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.612;QD=8.97;ReadPosRankSum=-0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,16:45:99:432,0,953 -chr1 12293 . G C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.726;DP=43;Dels=0.00;FS=13.073;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=-4.370;QD=9.81;ReadPosRankSum=-2.000;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:28,15:43:99:450,0,932 -chr1 12461 . A T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=31;Dels=0.00;FS=6.929;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.06;MQ0=0;MQRankSum=-3.047;QD=3.44;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:135,0,662 -chr1 12610 . A C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=16;Dels=0.00;FS=2.796;HaplotypeScore=10.5708;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=1.371;QD=2.99;ReadPosRankSum=-2.526;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:13,3:16:76:76,0,324 -chr1 12964 . G C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=38;Dels=0.00;FS=15.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-3.703;QD=1.41;ReadPosRankSum=1.421;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,6:38:82:82,0,1161 -chr1 12993 . G T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=43;Dels=0.00;FS=25.224;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.523;QD=5.20;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:252,0,1151 -chr1 12994 . A T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=43;Dels=0.00;FS=21.598;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.528;QD=4.25;ReadPosRankSum=-1.193;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:211,0,1187 -chr1 13041 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=33;Dels=0.00;FS=12.234;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-3.337;QD=2.66;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,6:33:99:116,0,945 -chr1 13045 . G A 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=32;Dels=0.00;FS=12.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=0;MQRankSum=-3.307;QD=2.77;ReadPosRankSum=2.148;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,6:32:99:117,0,908 -chr1 13136 . C T 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=41;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.46;MQ0=0;MQRankSum=-1.074;QD=4.43;ReadPosRankSum=3.016;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,11:41:99:210,0,1033 -chr1 13137 . C T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=42;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.95;MQ0=0;MQRankSum=0.715;QD=24.21;ReadPosRankSum=-3.118;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:11,31:42:99:1045,0,215 -chr1 13273 . A T 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=30;Dels=0.00;FS=2.876;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.55;MQ0=3;MQRankSum=-3.741;QD=9.36;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:309,0,598 -chr1 13280 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.606;DP=28;Dels=0.00;FS=2.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.14;MQ0=2;MQRankSum=-3.610;QD=8.85;ReadPosRankSum=-1.080;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:276,0,564 -chr1 13292 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=29;Dels=0.00;FS=5.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.02;MQ0=2;MQRankSum=-3.138;QD=10.03;ReadPosRankSum=-0.276;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:319,0,601 -chr1 13308 . T G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=29;Dels=0.00;FS=2.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=-3.380;QD=9.68;ReadPosRankSum=3.332;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,644 -chr1 13344 . T C 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=19;Dels=0.00;FS=23.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=1;MQRankSum=-0.592;QD=1.94;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,3:19:65:65,0,546 -chr1 13347 . A T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.846;DP=21;Dels=0.00;FS=37.433;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=1;MQRankSum=1.196;QD=5.47;ReadPosRankSum=-2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:143,0,499 -chr1 13363 . G A 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=17;Dels=0.00;FS=33.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.13;MQ0=0;MQRankSum=0.818;QD=13.87;ReadPosRankSum=0.337;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:264,0,308 -chr1 13378 . C G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=13;Dels=0.00;FS=19.956;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=0.529;QD=15.29;ReadPosRankSum=1.461;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,7:13:99:227,0,159 -chr1 13390 . T C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=13;Dels=0.00;FS=21.553;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.47;MQ0=0;MQRankSum=-0.212;QD=17.52;ReadPosRankSum=2.927;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,8:13:99:256,0,126 -chr1 13403 . G A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-1.580;QD=21.18;ReadPosRankSum=2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,7:10:88:240,0,88 -chr1 13404 . T A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=0.895;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,217 -chr1 13405 . A G 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,244 -chr1 13407 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=19.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.48;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:83:83,0,214 -chr1 13424 . C A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;DP=7;Dels=0.00;FS=15.441;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=54.99;MQ0=0;MQRankSum=-1.754;QD=13.25;ReadPosRankSum=-0.550;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,4:7:90:121,0,90 -chr1 13484 . T A 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=11;Dels=0.00;FS=6.264;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=0;MQRankSum=-2.228;QD=9.07;ReadPosRankSum=-1.398;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,4:11:99:128,0,245 -chr1 13514 . C T 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.67;ReadPosRankSum=1.312;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:128,0,321 -chr1 13526 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.91;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:131,0,293 -chr1 13529 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.700;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,261 -chr1 13533 . A C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,316 -chr1 13543 . G T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=13;Dels=0.00;FS=16.782;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=0.377;QD=13.06;ReadPosRankSum=-2.777;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,6:13:99:198,0,209 -chr1 13601 . C T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.355;DP=33;Dels=0.00;FS=6.893;HaplotypeScore=2.5316;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-0.954;QD=18.30;ReadPosRankSum=1.732;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:12,20:33:99:632,0,392 -chr1 13654 . T G 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;DP=32;Dels=0.00;FS=2.000;HaplotypeScore=17.2143;MLEAC=1;MLEAF=0.500;MQ=44.78;MQ0=0;MQRankSum=-3.367;QD=6.71;ReadPosRankSum=0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:243,0,696 -chr1 13805 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=1.000;QD=13.95;ReadPosRankSum=1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:712,0,955 -chr1 13962 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=56;Dels=0.00;FS=1.048;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.041;QD=15.07;ReadPosRankSum=0.567;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:872,0,1029 -chr1 14025 . A G 1167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=4.5620;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.490;QD=19.14;ReadPosRankSum=0.702;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,36:61:99:1196,0,669 -chr1 14039 . C T 781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.305;DP=61;Dels=0.00;FS=1.002;HaplotypeScore=2.6609;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.839;QD=12.82;ReadPosRankSum=-1.116;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:810,0,1140 -chr1 14053 . A G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.152;DP=61;Dels=0.00;FS=3.495;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.107;QD=16.44;ReadPosRankSum=1.469;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1031,0,874 -chr1 14525 . C T 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=57;Dels=0.00;FS=7.529;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.041;QD=20.52;ReadPosRankSum=0.447;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1198,0,732 -chr1 14531 . A G 1030.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=54;Dels=0.00;FS=7.625;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.153;QD=19.09;ReadPosRankSum=0.045;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,31:54:99:1059,0,726 -chr1 14540 . C T 1109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.716;DP=56;Dels=0.00;FS=9.774;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.899;QD=19.82;ReadPosRankSum=-0.716;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1138,0,754 -chr1 14569 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.646;QD=16.28;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:956,0,955 -chr1 14614 . T G 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.395;QD=17.88;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:958,0,770 -chr1 14674 . G T 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.419;QD=17.11;ReadPosRankSum=1.228;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:952,0,875 -chr1 14957 . C T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=43;Dels=0.00;FS=2.756;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=1;MQRankSum=-0.253;QD=16.99;ReadPosRankSum=-0.758;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:759,0,646 -chr1 15110 . T A 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=65;Dels=0.00;FS=0.970;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.569;QD=12.66;ReadPosRankSum=0.261;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:39,26:65:99:851,0,1349 -chr1 15135 . A G 1010.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.364;QD=16.04;ReadPosRankSum=-1.767;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1039,0,1093 -chr1 15597 . C A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=47;Dels=0.00;FS=6.639;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.617;QD=9.89;ReadPosRankSum=-0.797;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:493,0,1065 -chr1 15875 . A C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=42;Dels=0.00;FS=1.222;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=1;MQRankSum=-0.066;QD=12.90;ReadPosRankSum=1.064;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:570,0,798 -chr1 15977 . A T 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.672;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=53.37;MQ0=3;MQRankSum=-3.958;QD=12.64;ReadPosRankSum=-1.385;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:736,0,832 -chr1 16017 . T G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=72;Dels=0.00;FS=1.018;HaplotypeScore=11.7597;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=3;MQRankSum=-3.104;QD=11.80;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,28:72:99:878,0,1143 -chr1 16621 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=65;Dels=0.00;FS=3.448;HaplotypeScore=2.7337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.323;QD=18.41;ReadPosRankSum=-1.247;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1225,0,946 -chr1 16671 . C T 1029.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=52;Dels=0.00;FS=2.477;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.746;QD=19.80;ReadPosRankSum=0.075;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1058,0,684 -chr1 16700 . C G 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=1.092;QD=18.80;ReadPosRankSum=-0.912;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:893,0,570 -chr1 16782 . C T 1114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9279;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.342;QD=17.69;ReadPosRankSum=-0.791;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1143,0,988 -chr1 16871 . T C 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=59;Dels=0.00;FS=5.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.494;QD=14.76;ReadPosRankSum=-0.373;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:899,0,1075 -chr1 16912 . T A 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.631;DP=51;Dels=0.00;FS=7.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.556;QD=15.86;ReadPosRankSum=-1.724;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:837,0,878 -chr1 16926 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.660;DP=48;Dels=0.00;FS=6.044;HaplotypeScore=2.7745;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=0.042;QD=14.35;ReadPosRankSum=-0.249;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:717,0,884 -chr1 17027 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=65;Dels=0.00;FS=4.856;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.944;QD=14.46;ReadPosRankSum=-0.495;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:968,0,1247 -chr1 17241 . C G 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.811;QD=17.86;ReadPosRankSum=-0.258;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S190C|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_17170_17247),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:975,0,797 -chr1 17324 . T G 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.562;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.432;QD=18.63;ReadPosRankSum=0.875;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,675 -chr1 17672 . A G 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.381;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.326;QD=14.24;ReadPosRankSum=1.143;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:555,0,636 -chr1 17713 . A T 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.481;DP=51;Dels=0.00;FS=2.418;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=15.64;ReadPosRankSum=-0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:826,0,870 -chr1 17738 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=56;Dels=0.00;FS=2.356;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=12.19;ReadPosRankSum=0.820;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:711,0,1047 -chr1 17873 . G C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.910;QD=21.06;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:997,0,530 -chr1 17905 . A G 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=57;Dels=0.00;FS=2.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.659;QD=19.52;ReadPosRankSum=0.773;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1141,0,733 -chr1 18041 . A G 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=57;Dels=0.00;FS=2.316;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.610;QD=18.47;ReadPosRankSum=-0.569;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I221V|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18036_18114) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1081,0,804 -chr1 18164 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.433;QD=11.99;ReadPosRankSum=-0.972;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:568,0,952 -chr1 18454 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=45;Dels=0.00;FS=1.130;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=0.329;QD=16.22;ReadPosRankSum=0.102;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T314M|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:22,23:45:99:758,0,703 -chr1 18478 . T C 502.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=1.364;QD=13.59;ReadPosRankSum=1.242;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L322P|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:21,16:37:99:531,0,711 -chr1 18624 . T A 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=47;Dels=0.00;FS=4.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.140;QD=13.06;ReadPosRankSum=1.194;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:642,0,913 -chr1 19081 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.091;QD=22.92;ReadPosRankSum=-0.051;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A390|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:16,35:51:99:1197,0,486 -chr1 19138 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.496;DP=58;Dels=0.00;FS=5.223;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.717;QD=14.88;ReadPosRankSum=-0.655;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y409|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:31,27:58:99:891,0,1083 -chr1 19465 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=16.00;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:924,0,944 -chr1 19863 . T G 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.194;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.2772;MLEAC=1;MLEAF=0.500;MQ=60.50;MQ0=0;MQRankSum=-0.350;QD=8.83;ReadPosRankSum=-0.868;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,14:43:99:408,0,1042 -chr1 20158 . T C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.686;QD=16.39;ReadPosRankSum=-0.668;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:897,0,842 -chr1 20454 . T C 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-1.324;QD=15.62;ReadPosRankSum=0.255;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:700,0,709 -chr1 20566 . G T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=35;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-1.275;QD=14.34;ReadPosRankSum=-2.633;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:530,0,669 -chr1 20614 . T C 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.266;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.223;QD=15.59;ReadPosRankSum=1.394;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:761,0,807 -chr1 20629 . A G 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.400;DP=45;Dels=0.00;FS=1.143;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=15.64;ReadPosRankSum=2.446;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:732,0,822 -chr1 20630 . A C 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.984;QD=16.60;ReadPosRankSum=1.956;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:742,0,712 -chr1 20726 . T G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.220;DP=40;Dels=0.00;FS=1.408;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.190;QD=10.77;ReadPosRankSum=0.512;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:459,0,906 -chr1 20954 . G T 1159.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.566;QD=14.14;ReadPosRankSum=1.500;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1188,0,1568 -chr1 21221 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.356;QD=18.35;ReadPosRankSum=0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L545|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_20985_21233) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1056,0,780 -chr1 21683 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=0.586;QD=14.07;ReadPosRankSum=-0.823;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:802,0,1087 -chr1 21687 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.157;DP=55;Dels=0.00;FS=1.070;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.182;QD=20.14;ReadPosRankSum=-0.026;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1136,0,682 -chr1 21744 . A G 953.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.008;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.188;QD=16.73;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:57:99:982,0,944 -chr1 21947 . T G 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.907;QD=12.46;ReadPosRankSum=-0.326;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:701,0,1131 -chr1 22299 . T C 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=48;Dels=0.00;FS=6.116;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.826;QD=19.77;ReadPosRankSum=0.324;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A649|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:20,28:48:99:977,0,660 -chr1 22327 . T G 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=45;Dels=0.00;FS=4.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.767;QD=21.53;ReadPosRankSum=-0.059;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S659A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:17,28:45:99:997,0,550 -chr1 23334 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=39;Dels=0.00;FS=2.875;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.928;QD=12.87;ReadPosRankSum=-0.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A994|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:23,16:39:99:530,0,737 -chr1 23394 . A T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=52;Dels=0.00;FS=2.388;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.410;QD=16.90;ReadPosRankSum=0.531;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,27:52:99:907,0,841 -chr1 23447 . T A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=47;Dels=0.00;FS=1.119;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.054;QD=16.36;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:797,0,690 -chr1 23455 . T G 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768;DP=47;Dels=0.00;FS=2.552;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.646;QD=18.46;ReadPosRankSum=-0.821;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:896,0,614 -chr1 23725 . G A 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=42;Dels=0.00;FS=6.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.428;QD=16.80;ReadPosRankSum=1.384;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:734,0,720 -chr1 23982 . C T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=55;Dels=0.00;FS=2.640;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-1.005;QD=19.45;ReadPosRankSum=0.885;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,33:55:99:1098,0,682 -chr1 24069 . T A 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.713;DP=48;Dels=0.00;FS=8.862;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=1;MQRankSum=0.330;QD=15.50;ReadPosRankSum=0.713;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:772,0,789 -chr1 24151 . A G 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.694;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.785;QD=17.06;ReadPosRankSum=1.854;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1021|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24104_24302) GT:AD:DP:GQ:PL 0/1:21,25:46:99:813,0,677 -chr1 24389 . C A 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=48;Dels=0.00;FS=6.267;HaplotypeScore=27.9952;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=1;MQRankSum=0.567;QD=17.52;ReadPosRankSum=-0.546;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:869,0,711 -chr1 24436 . T C 934.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.691;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=-1.964;QD=18.33;ReadPosRankSum=-0.577;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1080|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24411_24543) GT:AD:DP:GQ:PL 0/1:23,28:51:99:963,0,687 -chr1 24548 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=46;Dels=0.00;FS=6.474;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.411;QD=21.39;ReadPosRankSum=1.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:1012,0,541 -chr1 24661 . C G 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-1.176;QD=13.44;ReadPosRankSum=1.960;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:687,0,875 -chr1 24708 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=43;Dels=0.00;FS=1.164;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-1.588;QD=11.79;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:535,0,872 -chr1 24751 . C T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=50;Dels=0.00;FS=8.018;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.278;QD=12.94;ReadPosRankSum=-1.022;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:675,0,1009 -chr1 24820 . T A 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.600;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.461;QD=18.66;ReadPosRankSum=1.129;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1148,0,824 -chr1 24862 . T C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.409;DP=51;Dels=0.00;FS=13.641;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.789;QD=13.52;ReadPosRankSum=-0.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:718,0,995 -chr1 24930 . T C 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;DP=52;Dels=0.00;FS=27.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.560;QD=15.23;ReadPosRankSum=0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:820,0,960 -chr1 25113 . T A 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=40;Dels=0.00;FS=16.130;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.639;QD=18.64;ReadPosRankSum=1.998;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:774,0,623 -chr1 25137 . G A 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=0.665;QD=17.66;ReadPosRankSum=-0.317;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:664,0,574 -chr1 25267 . A G 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.616;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.877;QD=18.93;ReadPosRankSum=-2.014;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:861,0,649 -chr1 25375 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.084;QD=16.13;ReadPosRankSum=0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:980,0,985 -chr1 25379 . A G 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.716;QD=17.74;ReadPosRankSum=0.093;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1004,0,818 -chr1 25601 . A G 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.979;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=16.39;ReadPosRankSum=1.281;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:995,0,972 -chr1 25678 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=47;Dels=0.00;FS=2.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.653;QD=11.34;ReadPosRankSum=0.875;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1175|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:30,17:47:99:561,0,1005 -chr1 25747 . G A 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.324;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.246;QD=9.48;ReadPosRankSum=1.361;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1198|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:29,14:43:99:436,0,1051 -chr1 25763 . G C 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.339;DP=44;Dels=0.00;FS=9.359;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.817;QD=10.97;ReadPosRankSum=-1.570;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V1204L|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:27,16:44:99:511,0,956 -chr1 26087 . A G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=54;Dels=0.00;FS=1.059;HaplotypeScore=2.6207;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.099;QD=17.55;ReadPosRankSum=1.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:976,0,871 -chr1 26119 . G T 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=55;Dels=0.00;FS=2.268;HaplotypeScore=2.9962;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.557;QD=16.52;ReadPosRankSum=-1.540;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:937,0,919 -chr1 26334 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.965;DP=50;Dels=0.00;FS=1.280;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-0.080;QD=6.24;ReadPosRankSum=3.146;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:340,0,1268 -chr1 26702 . A T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.942;DP=54;Dels=0.00;FS=10.090;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.192;QD=12.53;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:705,0,1095 -chr1 26910 . T G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.210;DP=49;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.332;QD=17.36;ReadPosRankSum=-0.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S1297A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:23,26:49:99:879,0,760 -chr1 27095 . A T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;DP=41;Dels=0.00;FS=4.926;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.784;QD=21.90;ReadPosRankSum=-0.151;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P1358|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:14,27:41:99:926,0,391 -chr1 27394 . A G 928.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=53;Dels=0.00;FS=5.960;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.100;QD=17.52;ReadPosRankSum=-0.809;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1458S|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:21,32:53:99:957,0,694 -chr1 27940 . G T 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.545;QD=15.06;ReadPosRankSum=-0.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:781,0,874 -chr1 28249 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=41;Dels=0.00;FS=1.216;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.088;QD=19.41;ReadPosRankSum=0.696;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:824,0,613 -chr1 28269 . C T 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.609;QD=18.99;ReadPosRankSum=-1.031;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:845,0,552 -chr1 28430 . T C 718.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.035;QD=14.09;ReadPosRankSum=-0.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:747,0,985 -chr1 28468 . T C 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=55;Dels=0.00;FS=3.953;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=1;MQRankSum=0.650;QD=15.50;ReadPosRankSum=0.419;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:881,0,955 -chr1 28990 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.224;DP=58;Dels=0.00;FS=16.948;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.031;QD=17.39;ReadPosRankSum=0.202;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:1037,0,1003 -chr1 29042 . A C 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=57;Dels=0.00;FS=5.341;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.937;QD=18.98;ReadPosRankSum=1.049;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1110,0,905 -chr1 29090 . G T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.457;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.506;QD=23.46;ReadPosRankSum=-0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,36:52:99:1248,0,498 -chr1 29155 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.513;QD=18.08;ReadPosRankSum=-0.050;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:914,0,699 -chr1 29212 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=59;Dels=0.00;FS=2.209;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.359;QD=15.64;ReadPosRankSum=-2.011;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:951,0,1091 -chr1 29443 . T C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.937;DP=47;Dels=0.00;FS=7.013;HaplotypeScore=2.8089;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.184;QD=8.40;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:423,0,970 -chr1 29543 . G C 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=52;Dels=0.00;FS=2.441;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=2;MQRankSum=-0.700;QD=11.09;ReadPosRankSum=0.260;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:605,0,1005 -chr1 29549 . T A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=50;Dels=0.00;FS=4.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=2;MQRankSum=0.096;QD=11.00;ReadPosRankSum=0.607;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:578,0,972 -chr1 29794 . C G 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.493;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.447;QD=14.07;ReadPosRankSum=-0.865;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:746,0,926 -chr1 30062 . C G 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.890;DP=56;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.330;QD=18.85;ReadPosRankSum=0.725;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1084,0,794 -chr1 30505 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.057;DP=59;Dels=0.00;FS=3.878;HaplotypeScore=2.5980;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.388;QD=14.98;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1668|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:32,27:59:99:912,0,1076 -chr1 30578 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=59;Dels=0.00;FS=5.208;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.220;QD=16.66;ReadPosRankSum=0.523;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S1693G|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1011,0,918 -chr1 30610 . G A 853.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.888;DP=63;Dels=0.00;FS=2.122;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.012;QD=13.55;ReadPosRankSum=0.709;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1703|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:33,30:63:99:882,0,1106 -chr1 30810 . T G 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=52;Dels=0.00;FS=1.095;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.743;QD=12.21;ReadPosRankSum=-0.141;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:663,0,1056 -chr1 30850 . G A 1094.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;DP=56;Dels=0.00;FS=1.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.864;QD=19.55;ReadPosRankSum=1.099;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1123,0,720 -chr1 30887 . A C 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.841;QD=16.93;ReadPosRankSum=0.720;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1027,0,969 -chr1 30927 . C G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.191;DP=49;Dels=0.00;FS=8.536;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.040;QD=18.49;ReadPosRankSum=1.296;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:934,0,707 -chr1 31004 . G T 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.387;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.766;QD=15.64;ReadPosRankSum=1.054;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:951,0,1000 -chr1 31025 . A C 964.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=59;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.371;QD=16.35;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:993,0,950 -chr1 31036 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.950;QD=16.34;ReadPosRankSum=-0.770;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:829,0,810 -chr1 31213 . A G 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=51;Dels=0.00;FS=3.933;HaplotypeScore=24.9899;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.293;QD=17.62;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:927,0,826 -chr1 31497 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.007;DP=35;Dels=0.00;FS=4.982;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.347;QD=16.14;ReadPosRankSum=-0.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:593,0,535 -chr1 31710 . G T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.314;DP=41;Dels=0.00;FS=6.637;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=13.19;ReadPosRankSum=0.876;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:569,0,741 -chr1 31714 . A G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.219;DP=40;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.163;QD=15.17;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:635,0,705 -chr1 31754 . A T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=45;Dels=0.00;FS=1.145;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.058;QD=14.73;ReadPosRankSum=0.102;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:691,0,823 -chr1 31917 . G A 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=60;Dels=0.00;FS=3.613;HaplotypeScore=1.9981;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.430;QD=20.53;ReadPosRankSum=0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1260,0,770 -chr1 31921 . G A 1051.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.128;DP=55;Dels=0.00;FS=1.022;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.561;QD=19.12;ReadPosRankSum=0.691;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1080,0,742 -chr1 32111 . A G 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=49;Dels=0.00;FS=2.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.156;QD=18.44;ReadPosRankSum=0.211;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:932,0,729 -chr1 32214 . G A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.166;DP=48;Dels=0.00;FS=6.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=1;MQRankSum=-0.118;QD=14.31;ReadPosRankSum=1.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:715,0,905 -chr1 32230 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.182;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=2;MQRankSum=-0.176;QD=15.49;ReadPosRankSum=-1.233;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:710,0,732 -chr1 32312 . A T 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306;DP=57;Dels=0.00;FS=7.278;HaplotypeScore=0.9159;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.485;QD=16.08;ReadPosRankSum=-0.978;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:945,0,894 -chr1 32410 . A G 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.180;DP=58;Dels=0.00;FS=7.306;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.539;QD=13.43;ReadPosRankSum=-1.008;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:807,0,1109 -chr1 32760 . G T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.396;QD=15.74;ReadPosRankSum=0.648;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:894,0,892 -chr1 32761 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.076;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=1.577;QD=15.01;ReadPosRankSum=1.274;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,925 -chr1 32762 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.506;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.151;QD=14.77;ReadPosRankSum=1.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:811,0,950 -chr1 32810 . T A 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.129;DP=44;Dels=0.00;FS=1.278;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.481;QD=15.63;ReadPosRankSum=0.246;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:716,0,594 -chr1 32950 . A G 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=2.4536;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.302;QD=20.89;ReadPosRankSum=-0.427;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1779|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:1010,0,566 -chr1 33016 . T G 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.707;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=-0.787;QD=2.54;ReadPosRankSum=-1.826;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P1801|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,11:48:99:150,0,1307 -chr1 33031 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=10.1485;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=3;MQRankSum=0.261;QD=2.75;ReadPosRankSum=0.239;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1806|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,13:56:99:182,0,1518 -chr1 33037 . T C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.294;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=22.7136;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=1.518;QD=11.25;ReadPosRankSum=0.008;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1808|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,22:59:99:692,0,1127 -chr1 33046 . T A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.993;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=13.5584;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=-1.164;QD=4.86;ReadPosRankSum=0.237;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1811|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,17:59:99:315,0,1459 -chr1 33129 . A T 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.555;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=2.016;QD=6.77;ReadPosRankSum=-0.990;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K1839I|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,18:65:99:468,0,1588 -chr1 33136 . T A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=61;Dels=0.00;FS=16.845;HaplotypeScore=2.3893;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=2.025;QD=6.85;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1841|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,16:61:99:446,0,1486 -chr1 33139 . G T 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=57;Dels=0.00;FS=11.731;HaplotypeScore=5.2554;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=1.441;QD=6.50;ReadPosRankSum=-1.169;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1842|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:57:99:399,0,1431 -chr1 33146 . A C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.634;DP=65;Dels=0.00;FS=13.675;HaplotypeScore=4.3887;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.261;QD=6.46;ReadPosRankSum=-1.112;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R1845|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:448,0,1646 -chr1 33199 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.004;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.694;QD=8.54;ReadPosRankSum=0.743;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1862|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,21:72:99:643,0,1752 -chr1 33262 . G A 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=78;Dels=0.00;FS=3.343;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-1.196;QD=7.68;ReadPosRankSum=-0.514;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1883|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,24:78:99:627,0,1895 -chr1 33289 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=77;Dels=0.00;FS=6.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.605;QD=8.93;ReadPosRankSum=2.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1892|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:716,0,1845 -chr1 33320 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.494;QD=8.34;ReadPosRankSum=0.778;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,24:75:99:654,0,1810 -chr1 33322 . A G 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.707;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.160;QD=7.88;ReadPosRankSum=0.267;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,23:74:99:611,0,1773 -chr1 33328 . C T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.608;QD=8.90;ReadPosRankSum=-0.662;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1905|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,26:76:99:705,0,1756 -chr1 33511 . T C 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.801;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=28.0954;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.180;QD=7.78;ReadPosRankSum=-0.255;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:63,27:90:99:728,0,2042 -chr1 33518 . T A 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.325;DP=89;Dels=0.00;FS=0.876;HaplotypeScore=29.8838;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.272;QD=8.12;ReadPosRankSum=-1.798;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:751,0,2141 -chr1 33534 . A T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=82;Dels=0.00;FS=1.081;HaplotypeScore=4.6992;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.708;QD=3.67;ReadPosRankSum=0.006;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,16:82:99:329,0,2363 -chr1 33542 . A G 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=84;Dels=0.00;FS=2.421;HaplotypeScore=3.3981;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.159;QD=3.43;ReadPosRankSum=-0.427;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,16:84:99:316,0,2385 -chr1 33544 . T C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.216;DP=85;Dels=0.00;FS=5.901;HaplotypeScore=2.3989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-2.519;QD=2.62;ReadPosRankSum=0.156;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:70,15:85:99:251,0,2424 -chr1 33549 . T C 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.895;DP=85;Dels=0.00;FS=5.608;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.928;QD=3.20;ReadPosRankSum=-0.983;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:300,0,2403 -chr1 33583 . A G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.183;QD=6.04;ReadPosRankSum=-0.048;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,25:100:99:632,0,2624 -chr1 33591 . T G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.576;QD=6.44;ReadPosRankSum=0.766;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,27:102:99:685,0,2559 -chr1 33634 . G T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=92;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.309;QD=10.87;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,33:92:99:1028,0,2053 -chr1 33635 . T A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=93;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.261;QD=10.54;ReadPosRankSum=0.285;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:60,33:93:99:1008,0,2023 -chr1 33648 . T C 1214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.582;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.076;QD=12.40;ReadPosRankSum=-1.008;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,40:98:99:1243,0,1959 -chr1 33649 . T C 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.519;DP=97;Dels=0.00;FS=0.836;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-0.096;QD=8.31;ReadPosRankSum=3.319;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:67,29:97:99:834,0,2354 -chr1 33669 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.973;DP=93;Dels=0.00;FS=2.768;HaplotypeScore=17.9952;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.606;QD=12.58;ReadPosRankSum=0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1198,0,1907 -chr1 33692 . G A 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.680;DP=95;Dels=0.00;FS=8.628;HaplotypeScore=1.7719;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.994;QD=11.82;ReadPosRankSum=1.470;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,38:95:99:1151,0,1994 -chr1 33756 . T A 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.209;DP=101;Dels=0.00;FS=21.595;HaplotypeScore=25.9789;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.917;QD=10.34;ReadPosRankSum=-0.467;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:1073,0,2323 -chr1 33765 . T C 2096.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.987;DP=97;Dels=0.00;FS=2.797;HaplotypeScore=26.9788;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.109;QD=21.62;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,62:97:99:2125,0,1120 -chr1 33800 . T C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=84;Dels=0.00;FS=1.935;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-2.651;QD=8.32;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,25:84:99:727,0,2083 -chr1 33805 . A G 2115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;DP=85;Dels=0.00;FS=0.901;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=4.074;QD=24.89;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,60:85:99:2144,0,700 -chr1 33816 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=74;Dels=0.00;FS=2.126;HaplotypeScore=26.8598;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-5.767;QD=8.16;ReadPosRankSum=0.084;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:632,0,1874 -chr1 33817 . C T 1791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.176;DP=75;Dels=0.00;FS=2.086;HaplotypeScore=25.9931;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-1.936;QD=23.89;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,51:75:99:1820,0,743 -chr1 33825 . C G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.639;DP=73;Dels=0.00;FS=2.189;HaplotypeScore=66.4539;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.355;QD=8.34;ReadPosRankSum=-0.152;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:637,0,1756 -chr1 33827 . A G 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.248;DP=73;Dels=0.00;FS=3.559;HaplotypeScore=65.4541;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.574;QD=8.26;ReadPosRankSum=-0.262;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:631,0,1850 -chr1 33850 . G A 967.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=85;Dels=0.00;FS=5.848;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-4.789;QD=11.39;ReadPosRankSum=-1.730;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:996,0,1874 -chr1 33851 . C T 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=85;Dels=0.00;FS=5.930;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-5.199;QD=11.44;ReadPosRankSum=-1.593;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:1001,0,1842 -chr1 33860 . A T 1131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=94;Dels=0.00;FS=0.798;HaplotypeScore=46.8065;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=2.315;QD=12.04;ReadPosRankSum=-0.705;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,38:94:99:1160,0,1948 -chr1 33863 . A G 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.497;DP=93;Dels=0.00;FS=0.897;HaplotypeScore=49.5927;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=2.899;QD=7.59;ReadPosRankSum=-0.568;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,25:93:99:734,0,2127 -chr1 33867 . T C 877.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=88;Dels=0.00;FS=5.938;HaplotypeScore=51.2136;MLEAC=1;MLEAF=0.500;MQ=58.15;MQ0=0;MQRankSum=-2.770;QD=9.97;ReadPosRankSum=1.358;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,29:88:99:906,0,2073 -chr1 33870 . A T 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.369;DP=86;Dels=0.00;FS=6.242;HaplotypeScore=47.2312;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.848;QD=9.56;ReadPosRankSum=2.170;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:850,0,1959 -chr1 33871 . G C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=86;Dels=0.00;FS=7.832;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.203;QD=10.01;ReadPosRankSum=2.382;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:889,0,1966 -chr1 33872 . A T 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=86;Dels=0.00;FS=5.975;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.211;QD=10.02;ReadPosRankSum=2.503;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,29:86:99:890,0,1958 -chr1 33881 . T C 2424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.386;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=26.4025;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-0.490;QD=25.80;ReadPosRankSum=1.236;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,70:94:99:2453,0,686 -chr1 33890 . C T 1338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.822;DP=97;Dels=0.00;FS=16.850;HaplotypeScore=21.9948;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-2.421;QD=13.80;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,41:97:99:1367,0,1887 -chr1 33916 . A T 1213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.196;DP=82;Dels=0.00;FS=19.829;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.075;QD=14.80;ReadPosRankSum=1.230;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1242,0,1531 -chr1 33959 . A T 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.821;DP=80;Dels=0.00;FS=8.032;HaplotypeScore=19.9908;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.205;QD=10.91;ReadPosRankSum=-0.277;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,28:80:99:901,0,1837 -chr1 33967 . G T 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=83;Dels=0.00;FS=3.410;HaplotypeScore=22.8560;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.531;QD=6.85;ReadPosRankSum=0.160;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:597,0,2149 -chr1 33970 . T C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.516;DP=83;Dels=0.00;FS=4.648;HaplotypeScore=21.8565;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.792;QD=9.15;ReadPosRankSum=-1.739;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,26:83:99:788,0,1880 -chr1 33978 . T C 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.032;QD=8.11;ReadPosRankSum=-1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,23:81:99:685,0,2028 -chr1 33982 . G T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.029;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-3.048;QD=7.57;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,21:77:99:611,0,1932 -chr1 34048 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=83;Dels=0.00;FS=3.608;HaplotypeScore=36.7760;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=1;MQRankSum=2.374;QD=5.44;ReadPosRankSum=1.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:480,0,2239 -chr1 34056 . A T 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.173;DP=83;Dels=0.00;FS=11.444;HaplotypeScore=20.9499;MLEAC=1;MLEAF=0.500;MQ=55.66;MQ0=1;MQRankSum=-5.405;QD=13.89;ReadPosRankSum=-2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,36:83:99:1181,0,1566 -chr1 34066 . T C 1342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;DP=87;Dels=0.00;FS=8.990;HaplotypeScore=6.9949;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=2;MQRankSum=-5.146;QD=15.43;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1371,0,1526 -chr1 34080 . G A 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=97;Dels=0.00;FS=6.820;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-2.713;QD=2.35;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,13:97:99:256,0,2928 -chr1 34096 . C A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.605;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=1;MQRankSum=0.463;QD=5.36;ReadPosRankSum=3.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,22:104:99:586,0,2872 -chr1 34098 . A G 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-3.070;QD=8.59;ReadPosRankSum=3.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,31:103:99:913,0,2440 -chr1 34115 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=117;Dels=0.00;FS=2.007;HaplotypeScore=38.4977;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=0.701;QD=4.35;ReadPosRankSum=0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,22:117:99:537,0,3369 -chr1 34126 . A G 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=133;Dels=0.00;FS=3.779;HaplotypeScore=3.5158;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=1;MQRankSum=4.108;QD=6.87;ReadPosRankSum=-0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,34:133:99:942,0,3399 -chr1 34143 . T C 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.256;DP=120;Dels=0.00;FS=6.188;HaplotypeScore=2.5772;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=1.550;QD=10.02;ReadPosRankSum=-0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,40:120:99:1231,0,2753 -chr1 34161 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.244;DP=113;Dels=0.00;FS=0.978;HaplotypeScore=2.7868;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=1;MQRankSum=-0.596;QD=3.30;ReadPosRankSum=1.772;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,18:113:99:401,0,3276 -chr1 34191 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=45;Dels=0.00;FS=9.532;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=0.990;QD=18.35;ReadPosRankSum=1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:854,0,672 -chr1 34210 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.402;DP=49;Dels=0.00;FS=6.502;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.291;QD=18.63;ReadPosRankSum=0.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:941,0,668 -chr1 34256 . A T 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=36;Dels=0.00;FS=2.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.317;QD=15.52;ReadPosRankSum=1.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:587,0,649 -chr1 34258 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.991;QD=16.78;ReadPosRankSum=1.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:582,0,541 -chr1 34267 . C T 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=43;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.832;QD=12.16;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:551,0,893 -chr1 34273 . T C 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;DP=50;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.867;QD=19.76;ReadPosRankSum=0.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1016,0,658 -chr1 34278 . G C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.618;DP=51;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.998;QD=12.47;ReadPosRankSum=-1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:664,0,1003 -chr1 34304 . G A 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=62;Dels=0.00;FS=23.390;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.136;QD=19.01;ReadPosRankSum=0.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1207,0,837 -chr1 34343 . C T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=52;Dels=0.00;FS=19.687;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.695;QD=19.98;ReadPosRankSum=-1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1067,0,693 -chr1 34345 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;DP=53;Dels=0.00;FS=19.902;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.803;QD=12.77;ReadPosRankSum=1.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:705,0,1098 -chr1 34354 . G A 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=50;Dels=0.00;FS=11.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-1.241;QD=19.06;ReadPosRankSum=-1.182;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:981,0,660 -chr1 34385 . T G 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.698;DP=63;Dels=0.00;FS=57.702;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-5.740;QD=12.35;ReadPosRankSum=-2.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:806,0,989 -chr1 34399 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=48;Dels=0.00;FS=35.938;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.904;QD=7.72;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:48:99:399,0,977 -chr1 34401 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=47;Dels=0.00;FS=33.249;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.64;MQ0=0;MQRankSum=-4.904;QD=7.87;ReadPosRankSum=3.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:47:99:398,0,951 -chr1 34402 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=48;Dels=0.00;FS=36.487;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.958;QD=7.66;ReadPosRankSum=2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,17:48:99:396,0,1008 -chr1 34406 . A C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=49;Dels=0.00;FS=17.048;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-4.478;QD=1.51;ReadPosRankSum=2.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:102,0,1316 -chr1 34420 . C A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.268;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.57;ReadPosRankSum=4.621;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:279,0,1055 -chr1 34423 . G C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.758;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.55;ReadPosRankSum=4.989;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:278,0,1050 -chr1 34434 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=29;Dels=0.00;FS=1.455;HaplotypeScore=1.6637;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.196;QD=12.99;ReadPosRankSum=0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:405,0,509 -chr1 34498 . G A 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.733;DP=43;Dels=0.00;FS=5.601;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.273;QD=5.44;ReadPosRankSum=-0.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:262,0,1179 -chr1 34587 . A G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=1.339;QD=18.49;ReadPosRankSum=-1.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:583,0,433 -chr1 34750 . C T 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=43;Dels=0.00;FS=6.795;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=0.628;QD=19.09;ReadPosRankSum=-1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:849,0,524 -chr1 34784 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.92;MQ0=4;MQRankSum=-2.318;QD=1.69;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,6:46:99:106,0,1235 -chr1 34787 . C T 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.62;MQ0=4;MQRankSum=-2.195;QD=1.88;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,6:45:99:113,0,1162 -chr1 34789 . C G 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=49;Dels=0.00;FS=1.637;HaplotypeScore=3.7163;MLEAC=1;MLEAF=0.500;MQ=47.34;MQ0=4;MQRankSum=-2.928;QD=2.06;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:129,0,1309 -chr1 34798 . A G 471.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.7158;MLEAC=1;MLEAF=0.500;MQ=43.82;MQ0=4;MQRankSum=-3.693;QD=7.86;ReadPosRankSum=-1.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:500,0,1302 -chr1 34809 . A C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=57;Dels=0.00;FS=2.399;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-4.370;QD=11.56;ReadPosRankSum=-0.063;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:687,0,973 -chr1 34810 . A T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.662;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-3.916;QD=8.31;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:502,0,1179 -chr1 34837 . G A 96.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.873;DP=54;Dels=0.00;FS=3.624;HaplotypeScore=73.4163;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=4;MQRankSum=-0.811;QD=1.79;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:125,0,1456 -chr1 34841 . G A 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.447;DP=52;Dels=0.00;FS=1.656;HaplotypeScore=90.4049;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=4;MQRankSum=-0.555;QD=2.05;ReadPosRankSum=2.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,10:52:99:135,0,1269 -chr1 34864 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=48;Dels=0.00;FS=9.092;HaplotypeScore=49.3566;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-4.082;QD=7.35;ReadPosRankSum=3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,14:48:99:381,0,1135 -chr1 34865 . A G 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=48;Dels=0.00;FS=19.848;HaplotypeScore=56.3327;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-2.525;QD=1.75;ReadPosRankSum=3.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,7:48:99:112,0,1393 -chr1 34879 . G C 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=71;Dels=0.04;FS=44.625;HaplotypeScore=41.5658;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=4;MQRankSum=-6.053;QD=8.41;ReadPosRankSum=-2.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,27:68:99:625,0,1412 -chr1 34886 . A T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=74;Dels=0.00;FS=13.029;HaplotypeScore=24.3736;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=4;MQRankSum=-3.738;QD=0.75;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:84:84,0,2145 -chr1 34898 . G A 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.605;DP=77;Dels=0.00;FS=42.789;HaplotypeScore=2.7797;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=4;MQRankSum=-5.924;QD=7.45;ReadPosRankSum=0.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,27:77:99:602,0,1708 -chr1 34999 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=46;Dels=0.00;FS=5.844;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=-2.426;QD=3.97;ReadPosRankSum=-3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,9:46:99:211,0,1278 -chr1 35001 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.443;DP=47;Dels=0.00;FS=8.113;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=-2.404;QD=4.29;ReadPosRankSum=-3.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,10:47:99:230,0,1358 -chr1 35021 . C A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.012;DP=128;Dels=0.00;FS=17.106;HaplotypeScore=9.9826;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=18;MQRankSum=-0.515;QD=0.24;ReadPosRankSum=2.376;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:118,10:128:59:59,0,3327 -chr1 35026 . C T 1359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.350;DP=127;Dels=0.00;FS=27.172;HaplotypeScore=10.7166;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=18;MQRankSum=-7.635;QD=10.71;ReadPosRankSum=-3.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,50:127:99:1388,0,1991 -chr1 35045 . T C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=133;Dels=0.00;FS=0.000;HaplotypeScore=40.6483;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=16;MQRankSum=3.328;QD=1.80;ReadPosRankSum=-0.988;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,16:133:99:267,0,3398 -chr1 35046 . A G 1154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.005;DP=127;Dels=0.00;FS=27.280;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=47.31;MQ0=14;MQRankSum=-8.458;QD=9.09;ReadPosRankSum=4.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,44:127:99:1183,0,2391 -chr1 35047 . T C 1481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.640;DP=126;Dels=0.00;FS=10.732;HaplotypeScore=40.9141;MLEAC=1;MLEAF=0.500;MQ=47.97;MQ0=14;MQRankSum=-8.951;QD=11.76;ReadPosRankSum=7.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,51:126:99:1510,0,2115 -chr1 35052 . A T 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=120;Dels=0.00;FS=2.223;HaplotypeScore=77.1059;MLEAC=1;MLEAF=0.500;MQ=49.27;MQ0=9;MQRankSum=2.565;QD=2.49;ReadPosRankSum=-2.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,16:120:99:327,0,3293 -chr1 35058 . C T 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.351;DP=119;Dels=0.00;FS=4.666;HaplotypeScore=52.1779;MLEAC=1;MLEAF=0.500;MQ=50.70;MQ0=5;MQRankSum=-5.373;QD=3.75;ReadPosRankSum=2.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,23:119:99:475,0,3197 -chr1 35060 . G A 79.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.055;DP=117;Dels=0.00;FS=17.881;HaplotypeScore=51.1782;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=4;MQRankSum=-5.477;QD=0.68;ReadPosRankSum=3.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:103,14:117:99:108,0,3463 -chr1 35062 . G A 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.950;DP=113;Dels=0.00;FS=18.470;HaplotypeScore=57.1737;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-8.371;QD=7.89;ReadPosRankSum=5.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,36:113:99:920,0,2624 -chr1 35075 . G C 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.602;DP=107;Dels=0.00;FS=5.257;HaplotypeScore=32.3401;MLEAC=1;MLEAF=0.500;MQ=53.81;MQ0=0;MQRankSum=-8.219;QD=7.81;ReadPosRankSum=1.447;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,33:107:99:864,0,2509 -chr1 35077 . C G 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=33.3400;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=-5.857;QD=2.21;ReadPosRankSum=0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,14:107:99:265,0,2739 -chr1 35087 . C T 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=97;Dels=0.00;FS=2.025;HaplotypeScore=16.1548;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=0;MQRankSum=-7.328;QD=5.34;ReadPosRankSum=-2.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:546,0,2468 -chr1 35095 . C T 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=88;Dels=0.00;FS=1.246;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=0;MQRankSum=-5.345;QD=0.66;ReadPosRankSum=-2.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,11:88:86:86,0,2675 -chr1 35172 . A C 1478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.986;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=29.8173;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=2;MQRankSum=2.017;QD=14.64;ReadPosRankSum=1.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1507,0,1792 -chr1 35248 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.610;DP=59;Dels=0.00;FS=5.425;HaplotypeScore=11.8817;MLEAC=1;MLEAF=0.500;MQ=36.39;MQ0=4;MQRankSum=1.904;QD=4.39;ReadPosRankSum=-1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:287,0,1045 -chr1 35251 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=57;Dels=0.00;FS=6.294;HaplotypeScore=10.9876;MLEAC=1;MLEAF=0.500;MQ=36.08;MQ0=4;MQRankSum=-1.563;QD=8.49;ReadPosRankSum=2.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:512,0,755 -chr1 35260 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=49;Dels=0.00;FS=2.866;HaplotypeScore=5.9548;MLEAC=1;MLEAF=0.500;MQ=32.62;MQ0=4;MQRankSum=-1.252;QD=6.97;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:370,0,613 -chr1 35288 . G T 267.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=6.9868;MLEAC=1;MLEAF=0.500;MQ=37.11;MQ0=2;MQRankSum=-1.073;QD=4.96;ReadPosRankSum=2.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:296,0,926 -chr1 35396 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.266;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.6626;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=3.180;QD=22.13;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,29:43:99:980,0,405 -chr1 35406 . T G 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.6632;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=0;MQRankSum=-2.541;QD=9.24;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:398,0,951 -chr1 35445 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.615;DP=32;Dels=0.00;FS=3.211;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=2.394;QD=21.12;ReadPosRankSum=-0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:704,0,324 -chr1 35483 . T A 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.021;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-1.247;QD=7.15;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:250,0,750 -chr1 35491 . G T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.408;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=1;MLEAF=0.500;MQ=48.70;MQ0=0;MQRankSum=1.222;QD=19.59;ReadPosRankSum=1.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:753,0,428 -chr1 35499 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=21.8612;MLEAC=1;MLEAF=0.500;MQ=48.22;MQ0=1;MQRankSum=-1.459;QD=11.77;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:499,0,781 -chr1 35576 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.516;DP=32;Dels=0.00;FS=3.734;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.149;QD=7.84;ReadPosRankSum=-4.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:279,0,688 -chr1 35588 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=38;Dels=0.00;FS=5.225;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.261;QD=9.02;ReadPosRankSum=-2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,819 -chr1 35691 . T C 1735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.139;DP=81;Dels=0.00;FS=0.889;HaplotypeScore=1.7319;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.513;QD=21.43;ReadPosRankSum=0.601;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,51:81:99:1764,0,836 -chr1 35739 . G A 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=74;Dels=0.00;FS=17.134;HaplotypeScore=1.6483;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-0.689;QD=4.63;ReadPosRankSum=-2.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,16:74:99:371,0,2031 -chr1 35804 . T C 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.427;DP=109;Dels=0.00;FS=5.672;HaplotypeScore=3.9987;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=1;MQRankSum=-6.467;QD=6.13;ReadPosRankSum=0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,28:109:99:696,0,2821 -chr1 35807 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.906;DP=108;Dels=0.00;FS=7.240;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=2;MQRankSum=-6.417;QD=6.27;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,28:108:99:705,0,2709 -chr1 35857 . C A 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=53.9074;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.442;QD=2.19;ReadPosRankSum=-1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,10:68:99:177,0,1820 -chr1 35860 . A C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.173;DP=74;Dels=0.00;FS=3.561;HaplotypeScore=73.8862;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=0;MQRankSum=0.722;QD=6.77;ReadPosRankSum=3.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,20:74:99:529,0,1811 -chr1 35870 . A T 2448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.943;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=27.0091;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=1;MQRankSum=2.228;QD=26.05;ReadPosRankSum=-0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,72:94:99:2477,0,566 -chr1 35900 . T C 3238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355;DP=119;Dels=0.00;FS=8.381;HaplotypeScore=194.4919;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=3;MQRankSum=-1.040;QD=27.22;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,96:119:99:3267,0,489 -chr1 35951 . T A 1015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=2;MQRankSum=-0.149;QD=8.00;ReadPosRankSum=0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,37:127:99:1044,0,2832 -chr1 35979 . G A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.196;DP=96;Dels=0.00;FS=17.564;HaplotypeScore=12.6997;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=2;MQRankSum=-1.392;QD=0.89;ReadPosRankSum=3.011;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,10:96:99:114,0,2869 -chr1 36045 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=132;Dels=0.00;FS=0.896;HaplotypeScore=43.4929;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.565;QD=3.33;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:110,22:132:99:468,0,3861 -chr1 36103 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=141;Dels=0.00;FS=41.173;HaplotypeScore=7.9970;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.254;QD=0.83;ReadPosRankSum=2.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:126,15:141:99:145,0,4391 -chr1 36153 . G C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=89;Dels=0.00;FS=7.730;HaplotypeScore=3.8273;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.014;QD=6.33;ReadPosRankSum=1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,21:89:99:592,0,2434 -chr1 36180 . T A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=100;Dels=0.00;FS=0.858;HaplotypeScore=3.7118;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.137;QD=7.78;ReadPosRankSum=0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,29:100:99:806,0,2559 -chr1 36205 . C T 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.427;DP=124;Dels=0.00;FS=0.755;HaplotypeScore=17.7034;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.466;QD=7.79;ReadPosRankSum=-0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,35:124:99:994,0,3181 -chr1 36213 . T C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.280;DP=132;Dels=0.00;FS=2.347;HaplotypeScore=19.5352;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.237;QD=1.48;ReadPosRankSum=0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,15:132:99:223,0,4265 -chr1 36259 . T C 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.248;DP=134;Dels=0.00;FS=3.770;HaplotypeScore=89.4890;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.222;QD=6.63;ReadPosRankSum=-1.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,33:134:99:916,0,3559 -chr1 36261 . A G 780.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.776;DP=132;Dels=0.00;FS=2.746;HaplotypeScore=86.5740;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.433;QD=5.91;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,32:132:99:809,0,3579 -chr1 36273 . T C 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.181;DP=118;Dels=0.00;FS=1.774;HaplotypeScore=117.6849;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.361;QD=5.75;ReadPosRankSum=-0.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,28:118:99:707,0,3229 -chr1 36286 . A T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=98;Dels=0.00;FS=0.915;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=2.210;QD=5.89;ReadPosRankSum=0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:605,0,2724 -chr1 36287 . A T 2373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.322;DP=96;Dels=0.00;FS=1.851;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=0.853;QD=24.73;ReadPosRankSum=1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,68:96:99:2402,0,835 -chr1 36289 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.239;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=83.8835;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=1;MQRankSum=2.678;QD=5.48;ReadPosRankSum=1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,22:99:99:571,0,2798 -chr1 36290 . A T 2719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=84.8831;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=1;MQRankSum=-1.327;QD=27.20;ReadPosRankSum=-0.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,76:100:99:2748,0,648 -chr1 36320 . T A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=92;Dels=0.00;FS=0.939;HaplotypeScore=45.5348;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-3.017;QD=6.49;ReadPosRankSum=0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,23:92:99:625,0,2459 -chr1 36333 . G A 2428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.737;DP=96;Dels=0.00;FS=12.492;HaplotypeScore=24.9952;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=1;MQRankSum=-3.960;QD=25.30;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,71:96:99:2457,0,747 -chr1 36341 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=100;Dels=0.00;FS=14.157;HaplotypeScore=25.7839;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=1;MQRankSum=-3.263;QD=8.96;ReadPosRankSum=0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,30:100:99:924,0,2374 -chr1 36361 . G A 2302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=91;Dels=0.00;FS=2.218;HaplotypeScore=4.6978;MLEAC=1;MLEAF=0.500;MQ=55.09;MQ0=1;MQRankSum=-4.586;QD=25.31;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,69:91:99:2331,0,612 -chr1 36377 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=102;Dels=0.00;FS=10.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-5.406;QD=9.55;ReadPosRankSum=-0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,34:102:99:1002,0,2367 -chr1 36383 . T C 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.211;DP=103;Dels=0.00;FS=9.011;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-6.104;QD=9.69;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,36:103:99:1026,0,2320 -chr1 36393 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.454;DP=108;Dels=0.00;FS=2.766;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-6.108;QD=8.56;ReadPosRankSum=-0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,38:108:99:953,0,2423 -chr1 36408 . C T 2376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=104;Dels=0.00;FS=4.359;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=0;MQRankSum=-0.816;QD=22.85;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,77:104:99:2405,0,763 -chr1 36427 . A T 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.872;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=3.8148;MLEAC=1;MLEAF=0.500;MQ=51.50;MQ0=0;MQRankSum=-6.246;QD=6.56;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,28:94:99:645,0,2385 -chr1 36447 . A T 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.515;DP=107;Dels=0.00;FS=0.770;HaplotypeScore=3.5157;MLEAC=1;MLEAF=0.500;MQ=51.35;MQ0=0;MQRankSum=-6.584;QD=7.45;ReadPosRankSum=-0.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,35:107:99:825,0,2544 -chr1 36455 . A C 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=26.1134;MLEAC=1;MLEAF=0.500;MQ=51.36;MQ0=0;MQRankSum=-6.423;QD=7.65;ReadPosRankSum=-1.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:832,0,2482 -chr1 36464 . A C 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.836;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=48.2350;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-2.154;QD=5.85;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:602,0,2428 -chr1 36466 . C T 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.251;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=27.3765;MLEAC=1;MLEAF=0.500;MQ=51.39;MQ0=0;MQRankSum=-7.882;QD=17.75;ReadPosRankSum=-0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,59:96:99:1732,0,1115 -chr1 36483 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-3.339;QD=5.65;ReadPosRankSum=0.429;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,21:91:99:542,0,2305 -chr1 36503 . T C 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.33;MQ0=0;MQRankSum=-0.635;QD=0.59;ReadPosRankSum=3.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,9:86:79:79,0,2347 -chr1 36504 . T C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.112;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.130;QD=5.11;ReadPosRankSum=5.608;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,19:88:99:478,0,2018 -chr1 36505 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=79.0748;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.029;QD=4.27;ReadPosRankSum=5.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,17:88:99:404,0,2137 -chr1 36518 . A G 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.366;DP=101;Dels=0.00;FS=5.616;HaplotypeScore=12.9006;MLEAC=1;MLEAF=0.500;MQ=47.84;MQ0=0;MQRankSum=-1.467;QD=8.87;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:924,0,1480 -chr1 36532 . C G 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=115;Dels=0.00;FS=1.129;HaplotypeScore=33.9847;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=0;MQRankSum=2.072;QD=2.35;ReadPosRankSum=-1.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,15:115:99:298,0,2777 -chr1 36538 . C T 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=114;Dels=0.00;FS=3.778;HaplotypeScore=31.9878;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-8.542;QD=10.94;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,62:114:99:1275,0,1800 -chr1 36561 . C T 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=91;Dels=0.00;FS=7.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-6.542;QD=10.96;ReadPosRankSum=0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,33:91:99:1026,0,2069 -chr1 36566 . G A 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=95;Dels=0.00;FS=7.431;HaplotypeScore=17.9938;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-6.234;QD=10.17;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,33:95:99:994,0,2189 -chr1 36574 . G A 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=93;Dels=0.00;FS=3.666;HaplotypeScore=36.9659;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=-1.444;QD=4.45;ReadPosRankSum=1.036;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,18:93:99:442,0,2629 -chr1 36578 . G A 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=3.342;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-5.365;QD=8.58;ReadPosRankSum=0.452;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,25:83:99:740,0,2021 -chr1 36582 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.643;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.757;QD=7.39;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,17:63:99:494,0,1649 -chr1 36587 . G A 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.268;DP=64;Dels=0.00;FS=1.061;HaplotypeScore=19.9719;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-4.946;QD=8.75;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,20:64:99:588,0,1587 -chr1 36616 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-5.166;QD=11.34;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,15:38:99:459,0,805 -chr1 36621 . T C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.251;DP=36;Dels=0.00;FS=1.421;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=56.02;MQ0=0;MQRankSum=-4.460;QD=12.77;ReadPosRankSum=-1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,751 -chr1 36626 . C T 362.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=67;Dels=0.00;FS=6.207;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=53.11;MQ0=0;MQRankSum=-2.986;QD=5.41;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,15:67:99:391,0,1838 -chr1 36644 . A G 2044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.378;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=14.7297;MLEAC=1;MLEAF=0.500;MQ=53.58;MQ0=0;MQRankSum=-4.784;QD=26.56;ReadPosRankSum=-3.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,59:77:99:2073,0,508 -chr1 36651 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.907;DP=75;Dels=0.00;FS=2.457;HaplotypeScore=29.6893;MLEAC=1;MLEAF=0.500;MQ=53.83;MQ0=0;MQRankSum=-2.272;QD=4.60;ReadPosRankSum=-2.563;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:373,0,2131 -chr1 36656 . T C 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.462;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=16.6941;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-3.172;QD=3.11;ReadPosRankSum=2.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:277,0,2375 -chr1 36662 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=33.6895;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-1.103;QD=5.30;ReadPosRankSum=-1.807;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,17:80:99:452,0,2194 -chr1 36667 . A G 1572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.127;DP=88;Dels=0.00;FS=6.014;HaplotypeScore=19.7292;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=-3.331;QD=17.87;ReadPosRankSum=3.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,48:88:99:1601,0,1351 -chr1 36673 . G T 1522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190;DP=87;Dels=0.00;FS=6.027;HaplotypeScore=50.6295;MLEAC=1;MLEAF=0.500;MQ=55.85;MQ0=0;MQRankSum=-3.286;QD=17.50;ReadPosRankSum=4.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,46:87:99:1551,0,1404 -chr1 36680 . G T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.401;DP=83;Dels=0.00;FS=1.073;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=0.921;QD=6.54;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:571,0,2139 -chr1 36681 . C A 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.220;DP=83;Dels=0.00;FS=2.291;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.95;MQ0=0;MQRankSum=0.648;QD=6.82;ReadPosRankSum=0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,21:83:99:594,0,2067 -chr1 36692 . C T 2055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.272;DP=84;Dels=0.00;FS=1.085;HaplotypeScore=21.9809;MLEAC=1;MLEAF=0.500;MQ=56.56;MQ0=0;MQRankSum=-2.422;QD=24.47;ReadPosRankSum=2.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,63:83:99:2084,0,534 -chr1 36698 . C A 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=83;Dels=0.00;FS=8.813;HaplotypeScore=18.7747;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=0;MQRankSum=0.221;QD=9.43;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,26:83:99:811,0,1969 -chr1 36713 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;DP=86;Dels=0.00;FS=1.174;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-5.106;QD=3.24;ReadPosRankSum=1.351;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:307,0,2592 -chr1 36714 . G A 1263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=86;Dels=0.00;FS=13.988;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-2.103;QD=14.69;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,39:86:99:1292,0,1579 -chr1 36726 . G A 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=93;Dels=0.00;FS=12.102;HaplotypeScore=22.7149;MLEAC=1;MLEAF=0.500;MQ=57.37;MQ0=0;MQRankSum=2.213;QD=7.48;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,26:93:99:724,0,2287 -chr1 36731 . A G 2521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.037;DP=95;Dels=0.00;FS=2.183;HaplotypeScore=22.5037;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-1.447;QD=26.54;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,76:95:99:2550,0,452 -chr1 36745 . C G 1591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.959;DP=97;Dels=0.00;FS=21.761;HaplotypeScore=2.1877;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=0;MQRankSum=-3.929;QD=16.41;ReadPosRankSum=1.490;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,49:97:99:1620,0,1518 -chr1 36764 . T C 1128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.112;DP=75;Dels=0.00;FS=17.360;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-2.794;QD=15.05;ReadPosRankSum=4.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,34:75:99:1157,0,1382 -chr1 36765 . T G 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.179;DP=75;Dels=0.00;FS=14.729;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-2.439;QD=14.36;ReadPosRankSum=4.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,33:75:99:1105,0,1430 -chr1 36767 . T C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.723;DP=76;Dels=0.00;FS=14.305;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.429;QD=15.77;ReadPosRankSum=3.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,36:76:99:1227,0,1335 -chr1 36796 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.162;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.8300;MLEAC=1;MLEAF=0.500;MQ=55.32;MQ0=0;MQRankSum=-6.512;QD=3.92;ReadPosRankSum=0.721;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:420,0,2683 -chr1 36817 . A G 1277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149;DP=101;Dels=0.00;FS=1.617;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-2.941;QD=12.65;ReadPosRankSum=0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,45:101:99:1306,0,1931 -chr1 36850 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=113;Dels=0.00;FS=1.797;HaplotypeScore=42.9345;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=2.503;QD=6.50;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,28:113:99:763,0,2839 -chr1 36857 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=112;Dels=0.00;FS=6.385;HaplotypeScore=44.9514;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=-0.969;QD=4.13;ReadPosRankSum=-0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,21:112:99:491,0,3074 -chr1 36860 . T A 1910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.351;DP=112;Dels=0.00;FS=10.516;HaplotypeScore=64.8364;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=0.143;QD=17.06;ReadPosRankSum=-0.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,60:112:99:1939,0,1715 -chr1 36867 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=115;Dels=0.00;FS=2.674;HaplotypeScore=43.9466;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.637;QD=7.66;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:115:99:909,0,2706 -chr1 36869 . A G 1776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;DP=112;Dels=0.00;FS=8.872;HaplotypeScore=21.9682;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=1;MQRankSum=0.192;QD=15.86;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,55:112:99:1805,0,1829 -chr1 36921 . G A 1095.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.776;DP=105;Dels=0.00;FS=1.642;HaplotypeScore=58.3901;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=0.967;QD=10.44;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,37:105:99:1124,0,2298 -chr1 36924 . T C 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=104;Dels=0.01;FS=11.095;HaplotypeScore=64.0672;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=1;MQRankSum=-0.152;QD=6.57;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,27:103:99:711,0,2625 -chr1 36928 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.431;DP=101;Dels=0.01;FS=13.977;HaplotypeScore=62.9043;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=1;MQRankSum=-0.447;QD=6.57;ReadPosRankSum=0.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,26:100:99:692,0,2509 -chr1 36933 . A G 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.768;DP=98;Dels=0.00;FS=1.634;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=3.401;QD=17.77;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,53:98:99:1770,0,1349 -chr1 36937 . C T 1282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=96;Dels=0.00;FS=1.678;HaplotypeScore=21.5624;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-2.005;QD=13.36;ReadPosRankSum=-0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,42:96:99:1311,0,1753 -chr1 36980 . G C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=87;Dels=0.00;FS=5.532;HaplotypeScore=19.2784;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=1;MQRankSum=-2.668;QD=4.49;ReadPosRankSum=1.236;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,17:87:99:419,0,2324 -chr1 36990 . C T 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=88;Dels=0.00;FS=11.050;HaplotypeScore=16.5790;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=-2.013;QD=12.11;ReadPosRankSum=-0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:50,38:88:99:1094,0,1532 -chr1 37033 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=97;Dels=0.00;FS=29.507;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.66;MQ0=1;MQRankSum=1.751;QD=5.93;ReadPosRankSum=-1.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:74,23:97:99:603,0,2295 -chr1 37035 . G A 1683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=95;Dels=0.00;FS=32.836;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.62;MQ0=1;MQRankSum=-1.237;QD=17.72;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:39,56:95:99:1712,0,1110 -chr1 37086 . T C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=83;Dels=0.00;FS=8.748;HaplotypeScore=15.4050;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=1;MQRankSum=0.495;QD=6.67;ReadPosRankSum=-0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:60,23:83:99:582,0,1632 -chr1 37098 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.373;DP=78;Dels=0.00;FS=22.975;HaplotypeScore=17.1337;MLEAC=1;MLEAF=0.500;MQ=38.80;MQ0=1;MQRankSum=2.695;QD=3.33;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,15:78:99:288,0,1577 -chr1 37110 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=70;Dels=0.00;FS=20.054;HaplotypeScore=6.6058;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=1;MQRankSum=2.417;QD=3.65;ReadPosRankSum=-0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:57,13:70:99:284,0,1351 -chr1 37144 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.027;DP=75;Dels=0.01;FS=19.781;HaplotypeScore=21.1656;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=0.880;QD=7.64;ReadPosRankSum=0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:49,25:74:99:601,0,1238 -chr1 37145 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=74;Dels=0.00;FS=1.342;HaplotypeScore=17.3626;MLEAC=1;MLEAF=0.500;MQ=33.28;MQ0=5;MQRankSum=-1.467;QD=1.58;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,11:74:99:145,0,1687 -chr1 37167 . A G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.120;DP=75;Dels=0.00;FS=11.212;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=30.73;MQ0=5;MQRankSum=-0.123;QD=11.62;ReadPosRankSum=0.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:37,38:75:99:900,0,875 -chr1 37195 . A C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.498;DP=63;Dels=0.00;FS=34.326;HaplotypeScore=4.2993;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=6;MQRankSum=0.788;QD=4.57;ReadPosRankSum=1.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T7|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,16:63:99:316,0,1127 -chr1 37208 . A C 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=59;Dels=0.00;FS=17.669;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=6;MQRankSum=0.988;QD=3.18;ReadPosRankSum=-1.371;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R12|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,12:59:99:216,0,1075 -chr1 37263 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=28.54;MQ0=4;MQRankSum=-0.748;QD=15.24;ReadPosRankSum=-0.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R30L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:10,26:36:99:577,0,117 -chr1 37277 . G A 105.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=37;Dels=0.00;FS=1.773;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=34.79;MQ0=3;MQRankSum=-0.596;QD=2.86;ReadPosRankSum=0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D35N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:27,10:37:99:134,0,662 -chr1 37288 . G T 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7802;MLEAC=1;MLEAF=0.500;MQ=39.98;MQ0=2;MQRankSum=-1.717;QD=2.72;ReadPosRankSum=0.610;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E38D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:36,11:47:99:156,0,970 -chr1 37305 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.346;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=23.7316;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-3.229;QD=1.45;ReadPosRankSum=2.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V44A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:58,11:69:99:128,0,1781 -chr1 37314 . T C 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.448;DP=80;Dels=0.00;FS=1.179;HaplotypeScore=13.7857;MLEAC=1;MLEAF=0.500;MQ=48.12;MQ0=1;MQRankSum=1.805;QD=2.56;ReadPosRankSum=-1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I47T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:67,13:80:99:233,0,1973 -chr1 37336 . T C 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=2.6540;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=2.094;QD=8.05;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D54|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:68,31:99:99:825,0,2213 -chr1 37361 . C A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.201;DP=104;Dels=0.00;FS=2.268;HaplotypeScore=5.3893;MLEAC=1;MLEAF=0.500;MQ=47.39;MQ0=6;MQRankSum=-1.098;QD=2.63;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P63T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:85,19:104:99:302,0,2484 -chr1 37414 . C A 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=53;Dels=0.00;FS=5.282;HaplotypeScore=6.9624;MLEAC=1;MLEAF=0.500;MQ=36.19;MQ0=7;MQRankSum=0.103;QD=3.94;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P80|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:40,13:53:99:237,0,933 -chr1 37420 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.384;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=5.8162;MLEAC=1;MLEAF=0.500;MQ=30.80;MQ0=7;MQRankSum=-0.141;QD=2.92;ReadPosRankSum=-0.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A82|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:30,10:40:99:145,0,591 -chr1 37528 . A T 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.145;DP=99;Dels=0.00;FS=1.426;HaplotypeScore=2.0463;MLEAC=1;MLEAF=0.500;MQ=31.63;MQ0=3;MQRankSum=-2.642;QD=0.76;ReadPosRankSum=1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E118D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:80,19:99:99:103,0,1690 -chr1 37553 . C T 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.618;DP=101;Dels=0.00;FS=0.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=32.94;MQ0=5;MQRankSum=-4.815;QD=2.51;ReadPosRankSum=1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L127|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:66,35:101:99:282,0,1683 -chr1 37607 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=74;Dels=0.00;FS=8.462;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=38.66;MQ0=5;MQRankSum=0.654;QD=9.08;ReadPosRankSum=1.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Gta|L145V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:43,31:74:99:700,0,1242 -chr1 37632 . T A 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.285;DP=70;Dels=0.00;FS=1.067;HaplotypeScore=165.3085;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=2;MQRankSum=-0.738;QD=5.55;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:417,0,1466 -chr1 37654 . T C 334.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.313;DP=79;Dels=0.00;FS=1.038;HaplotypeScore=60.4783;MLEAC=1;MLEAF=0.500;MQ=40.53;MQ0=0;MQRankSum=-1.554;QD=4.24;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,19:79:99:363,0,1794 -chr1 37815 . A C 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;DP=107;Dels=0.00;FS=2.466;HaplotypeScore=2.4531;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=2.701;QD=2.40;ReadPosRankSum=1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,15:107:99:285,0,3245 -chr1 37819 . A G 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=106;Dels=0.00;FS=2.428;HaplotypeScore=49.4245;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=2;MQRankSum=3.086;QD=2.82;ReadPosRankSum=0.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:327,0,3127 -chr1 37827 . T C 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.964;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=281.8552;MLEAC=1;MLEAF=0.500;MQ=52.18;MQ0=2;MQRankSum=-1.196;QD=9.12;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:986,0,2427 -chr1 37829 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.186;DP=103;Dels=0.00;FS=1.099;HaplotypeScore=280.8554;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=2;MQRankSum=-5.390;QD=2.67;ReadPosRankSum=-1.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,16:103:99:303,0,3052 -chr1 37845 . C G 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=105;Dels=0.00;FS=1.721;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=2;MQRankSum=-0.287;QD=12.40;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,43:105:99:1330,0,2039 -chr1 37852 . A T 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=114;Dels=0.00;FS=7.406;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=2;MQRankSum=1.342;QD=6.74;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,29:114:99:797,0,2971 -chr1 37891 . A G 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=105;Dels=0.00;FS=3.911;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=1;MQRankSum=1.160;QD=3.39;ReadPosRankSum=-1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,17:105:99:384,0,3122 -chr1 37931 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.853;DP=94;Dels=0.00;FS=6.552;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=3.443;QD=5.77;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,22:94:99:571,0,2560 -chr1 37969 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=52;Dels=0.00;FS=4.310;HaplotypeScore=2.3113;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-4.200;QD=11.26;ReadPosRankSum=1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:614,0,1176 -chr1 38000 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=50;Dels=0.00;FS=9.868;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=-4.276;QD=8.80;ReadPosRankSum=-0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:468,0,1240 -chr1 38009 . A C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=62;Dels=0.00;FS=21.281;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.304;QD=13.03;ReadPosRankSum=-3.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:836,0,1230 -chr1 38043 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=22.795;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.05;MQ0=0;MQRankSum=1.867;QD=15.45;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1048,0,1191 -chr1 38145 . C A 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.426;DP=22;Dels=0.00;FS=4.506;HaplotypeScore=20.3295;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=1.195;QD=18.67;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,13:22:99:439,0,169 -chr1 38190 . A C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=20;Dels=0.00;FS=37.992;HaplotypeScore=15.6751;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-3.279;QD=16.94;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:8,12:20:99:367,0,253 -chr1 38232 . G A 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.397;DP=26;Dels=0.00;FS=45.405;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-4.243;QD=19.84;ReadPosRankSum=-2.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:544,0,277 -chr1 38305 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.174;DP=54;Dels=0.00;FS=1.164;HaplotypeScore=26.0834;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-0.232;QD=7.13;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:413,0,1363 -chr1 38320 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.621;DP=61;Dels=0.00;FS=5.712;HaplotypeScore=186.2137;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=2.727;QD=8.73;ReadPosRankSum=0.530;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:561,0,1414 -chr1 38332 . G C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.367;DP=64;Dels=0.00;FS=1.052;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=3.453;QD=7.42;ReadPosRankSum=-2.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,19:64:99:503,0,1580 -chr1 38333 . G A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.193;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=-3.324;QD=11.43;ReadPosRankSum=2.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:771,0,1350 -chr1 38335 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.608;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=19.8719;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-3.117;QD=12.89;ReadPosRankSum=1.435;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,27:66:99:879,0,1194 -chr1 38350 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=2.904;QD=7.78;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,26:91:99:736,0,2251 -chr1 38352 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.858;DP=91;Dels=0.00;FS=0.951;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=3.445;QD=5.45;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:91:99:524,0,2399 -chr1 38354 . A G 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=92;Dels=0.00;FS=1.151;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=0.796;QD=1.80;ReadPosRankSum=-3.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,13:92:99:194,0,2761 -chr1 38380 . G C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=103;Dels=0.00;FS=1.016;HaplotypeScore=5.5532;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=0.452;QD=3.40;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,18:103:99:378,0,2986 -chr1 38386 . A G 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.945;DP=101;Dels=0.00;FS=2.163;HaplotypeScore=5.8191;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=1.265;QD=4.05;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,18:101:99:437,0,2897 -chr1 38406 . A G 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.994;DP=110;Dels=0.00;FS=0.886;HaplotypeScore=38.9762;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.927;QD=5.29;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,24:110:99:610,0,2961 -chr1 38410 . G C 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=107;Dels=0.00;FS=5.387;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=1.092;QD=8.61;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,32:107:99:949,0,2628 -chr1 38412 . A G 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=107;Dels=0.00;FS=1.876;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.410;QD=5.99;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,26:107:99:669,0,2864 -chr1 38514 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=93;Dels=0.00;FS=5.348;HaplotypeScore=43.8521;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-1.505;QD=3.79;ReadPosRankSum=1.100;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I168V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:73,19:93:99:381,0,2418 -chr1 38519 . A C 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.706;DP=83;Dels=0.00;FS=18.028;HaplotypeScore=44.8742;MLEAC=1;MLEAF=0.500;MQ=49.02;MQ0=0;MQRankSum=-2.301;QD=15.17;ReadPosRankSum=1.618;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A169|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:40,43:83:99:1287,0,1261 -chr1 38524 . G T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=87;Dels=0.00;FS=8.398;HaplotypeScore=47.8556;MLEAC=1;MLEAF=0.500;MQ=48.63;MQ0=0;MQRankSum=0.082;QD=6.37;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G171V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:64,23:87:99:582,0,2000 -chr1 38580 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.789;DP=83;Dels=0.00;FS=10.079;HaplotypeScore=4.2557;MLEAC=1;MLEAF=0.500;MQ=42.00;MQ0=0;MQRankSum=1.229;QD=9.35;ReadPosRankSum=-1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A190T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:49,33:83:99:804,0,1512 -chr1 38614 . G T 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=88;Dels=0.00;FS=8.617;HaplotypeScore=41.5773;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=-1.852;QD=7.99;ReadPosRankSum=-1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R201L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:62,26:88:99:731,0,1964 -chr1 38616 . C T 1299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.710;DP=88;Dels=0.00;FS=3.034;HaplotypeScore=74.9440;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=2.195;QD=14.77;ReadPosRankSum=0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L202|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:45,43:88:99:1328,0,1423 -chr1 38621 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=92;Dels=0.00;FS=8.548;HaplotypeScore=74.6108;MLEAC=1;MLEAF=0.500;MQ=45.88;MQ0=0;MQRankSum=-2.005;QD=6.60;ReadPosRankSum=-1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N203|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:68,24:92:99:635,0,2194 -chr1 38624 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=92;Dels=0.00;FS=18.358;HaplotypeScore=71.5984;MLEAC=1;MLEAF=0.500;MQ=45.57;MQ0=0;MQRankSum=-0.682;QD=4.52;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A204|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:70,22:92:99:444,0,2305 -chr1 38633 . G A 1358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.729;DP=93;Dels=0.00;FS=4.284;HaplotypeScore=20.6300;MLEAC=1;MLEAF=0.500;MQ=46.35;MQ0=0;MQRankSum=1.841;QD=14.61;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P207|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,51:93:99:1387,0,1217 -chr1 38643 . A G 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.552;DP=96;Dels=0.00;FS=1.832;HaplotypeScore=4.1979;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=1.806;QD=17.82;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T211A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,54:96:99:1739,0,1020 -chr1 38657 . C T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.378;DP=85;Dels=0.00;FS=2.540;HaplotypeScore=14.1583;MLEAC=1;MLEAF=0.500;MQ=45.85;MQ0=1;MQRankSum=1.974;QD=26.04;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H215|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,70:85:99:2242,0,177 -chr1 38659 . A C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.241;DP=83;Dels=0.00;FS=9.582;HaplotypeScore=13.1589;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=1.020;QD=5.08;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E216A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:63,20:83:99:450,0,1930 -chr1 38723 . C T 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=4.5678;MLEAC=1;MLEAF=0.500;MQ=34.19;MQ0=2;MQRankSum=1.958;QD=16.83;ReadPosRankSum=-0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S237|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,22:30:76:533,0,76 -chr1 38732 . C T 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;DP=25;Dels=0.00;FS=2.077;HaplotypeScore=8.5290;MLEAC=1;MLEAF=0.500;MQ=28.41;MQ0=2;MQRankSum=1.921;QD=7.63;ReadPosRankSum=-1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F240|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,9:25:99:219,0,204 -chr1 38739 . A G 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.986;DP=21;Dels=0.00;FS=14.564;HaplotypeScore=7.2577;MLEAC=1;MLEAF=0.500;MQ=26.73;MQ0=2;MQRankSum=1.056;QD=11.42;ReadPosRankSum=-1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T243A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:7,14:21:61:268,0,61 -chr1 38754 . C T 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;DP=27;Dels=0.00;FS=23.314;HaplotypeScore=3.4383;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=1;MQRankSum=1.291;QD=6.03;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L248|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:17,10:27:99:191,0,164 -chr1 38813 . G A 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=45;Dels=0.00;FS=10.745;HaplotypeScore=6.7165;MLEAC=1;MLEAF=0.500;MQ=23.36;MQ0=6;MQRankSum=0.418;QD=3.44;ReadPosRankSum=-0.933;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T267|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,14:45:99:183,0,334 -chr1 38818 . G A 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.899;DP=44;Dels=0.00;FS=36.491;HaplotypeScore=10.4483;MLEAC=1;MLEAF=0.500;MQ=23.61;MQ0=6;MQRankSum=2.543;QD=5.45;ReadPosRankSum=-1.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C269Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,12:44:99:268,0,339 -chr1 38827 . G T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.662;DP=48;Dels=0.00;FS=16.528;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.16;MQ0=7;MQRankSum=0.544;QD=3.04;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R272L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,14:48:99:174,0,437 -chr1 38828 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.199;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.63;MQ0=7;MQRankSum=1.593;QD=10.36;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R272|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,33:49:99:536,0,103 -chr1 38834 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.131;DP=50;Dels=0.00;FS=1.394;HaplotypeScore=10.1537;MLEAC=1;MLEAF=0.500;MQ=24.71;MQ0=8;MQRankSum=0.472;QD=5.02;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R274|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,18:50:99:279,0,381 -chr1 38874 . G A 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.215;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=9.5155;MLEAC=1;MLEAF=0.500;MQ=24.48;MQ0=8;MQRankSum=-0.446;QD=6.30;ReadPosRankSum=0.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V288M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:22,21:43:99:299,0,317 -chr1 38881 . G A 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=41;Dels=0.00;FS=18.266;HaplotypeScore=21.0278;MLEAC=1;MLEAF=0.500;MQ=26.69;MQ0=6;MQRankSum=0.334;QD=1.80;ReadPosRankSum=-1.159;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C290Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,11:41:99:102,0,593 -chr1 38886 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=42;Dels=0.00;FS=1.336;HaplotypeScore=14.7997;MLEAC=1;MLEAF=0.500;MQ=27.24;MQ0=6;MQRankSum=0.652;QD=4.83;ReadPosRankSum=2.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V292I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:31,11:42:99:231,0,490 -chr1 38927 . G A 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.113;DP=30;Dels=0.00;FS=1.455;HaplotypeScore=5.5545;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=1;MQRankSum=-0.895;QD=9.99;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G305|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,15:30:99:328,0,330 -chr1 38933 . C T 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.620;DP=28;Dels=0.00;FS=4.494;HaplotypeScore=6.2885;MLEAC=1;MLEAF=0.500;MQ=33.72;MQ0=0;MQRankSum=-1.020;QD=1.35;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y307|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:23,5:28:66:66,0,561 -chr1 38949 . T C 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.480;DP=23;Dels=0.00;FS=6.415;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=34.90;MQ0=0;MQRankSum=1.291;QD=14.51;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,14:23:99:362,0,165 -chr1 38998 . G A 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=22;Dels=0.00;FS=3.358;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=30.79;MQ0=1;MQRankSum=2.426;QD=14.94;ReadPosRankSum=2.499;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G329E|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,13:22:30:357,0,30 -chr1 39012 . C T 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.081;DP=31;Dels=0.00;FS=6.864;HaplotypeScore=3.8698;MLEAC=1;MLEAF=0.500;MQ=29.64;MQ0=2;MQRankSum=0.242;QD=0.99;ReadPosRankSum=1.534;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L334|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:25,6:31:59:59,0,466 -chr1 39047 . T C 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.226;DP=43;Dels=0.00;FS=8.463;HaplotypeScore=12.3919;MLEAC=1;MLEAF=0.500;MQ=26.75;MQ0=5;MQRankSum=0.113;QD=2.27;ReadPosRankSum=-0.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D345|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:36,7:43:99:126,0,608 -chr1 39056 . A T 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.448;DP=51;Dels=0.00;FS=13.801;HaplotypeScore=11.9705;MLEAC=1;MLEAF=0.500;MQ=26.54;MQ0=6;MQRankSum=1.911;QD=6.82;ReadPosRankSum=-0.405;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K348N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,19:51:99:376,0,461 -chr1 39113 . C T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.057;DP=67;Dels=0.00;FS=2.370;HaplotypeScore=12.4314;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=9;MQRankSum=-3.266;QD=8.16;ReadPosRankSum=1.680;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T367|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,41:67:99:575,0,677 -chr1 39116 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.93;MQ0=9;MQRankSum=3.100;QD=8.41;ReadPosRankSum=-0.858;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y368|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,24:67:99:592,0,634 -chr1 39117 . G C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.149;DP=67;Dels=0.00;FS=1.309;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.61;MQ0=9;MQRankSum=1.678;QD=16.32;ReadPosRankSum=-0.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V369L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,49:67:99:1122,0,102 -chr1 39150 . G A 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.147;DP=74;Dels=0.00;FS=5.772;HaplotypeScore=13.8080;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=6;MQRankSum=2.238;QD=5.12;ReadPosRankSum=1.855;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E380K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:57,17:74:99:407,0,823 -chr1 39172 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;DP=58;Dels=0.00;FS=4.464;HaplotypeScore=6.4651;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=1;MQRankSum=2.790;QD=5.15;ReadPosRankSum=0.121;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R387K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:44,14:58:99:327,0,622 -chr1 39178 . A C 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.108;DP=53;Dels=0.00;FS=7.365;HaplotypeScore=8.0329;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=0;MQRankSum=2.138;QD=3.96;ReadPosRankSum=0.384;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E389A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,11:53:99:238,0,621 -chr1 39276 . G T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.189;DP=48;Dels=0.00;FS=2.414;HaplotypeScore=5.3949;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=9;MQRankSum=0.777;QD=1.14;ReadPosRankSum=-0.609;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V422F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,5:48:83:83,0,754 -chr1 39306 . G A 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.9525;MLEAC=1;MLEAF=0.500;MQ=26.06;MQ0=10;MQRankSum=0.296;QD=2.81;ReadPosRankSum=1.235;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D432N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:41,8:49:99:166,0,570 -chr1 39324 . C T 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=8.4793;MLEAC=1;MLEAF=0.500;MQ=22.99;MQ0=11;MQRankSum=0.420;QD=3.08;ReadPosRankSum=-0.128;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L438|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,12:46:99:170,0,488 -chr1 39353 . C T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=9;MQRankSum=-0.726;QD=3.15;ReadPosRankSum=-0.286;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H447|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,13:39:99:151,0,416 -chr1 39356 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=24.07;MQ0=9;MQRankSum=-0.636;QD=1.55;ReadPosRankSum=0.194;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S448|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:27,9:36:84:84,0,463 -chr1 39366 . C G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.6622;MLEAC=1;MLEAF=0.500;MQ=24.65;MQ0=7;MQRankSum=1.387;QD=13.05;ReadPosRankSum=0.000;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R452G|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,25:33:68:459,0,68 -chr1 39447 . T C 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.212;DP=26;Dels=0.00;FS=9.558;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=4;MQRankSum=2.899;QD=4.53;ReadPosRankSum=-0.862;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,5:26:99:146,0,489 -chr1 39510 . G A 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=20;Dels=0.00;FS=2.963;HaplotypeScore=7.6395;MLEAC=1;MLEAF=0.500;MQ=30.59;MQ0=3;MQRankSum=2.583;QD=6.49;ReadPosRankSum=-0.053;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:158,0,271 -chr1 39526 . A G 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=28.66;MQ0=3;MQRankSum=-1.408;QD=6.20;ReadPosRankSum=1.749;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,8:14:99:115,0,155 -chr1 39584 . T C 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.136;DP=38;Dels=0.03;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.96;MQ0=1;MQRankSum=0.330;QD=14.99;ReadPosRankSum=0.330;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:74:598,0,74 -chr1 39587 . T C 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=40;Dels=0.03;FS=7.160;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.64;MQ0=1;MQRankSum=-0.714;QD=1.07;ReadPosRankSum=-0.165;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,7:39:71:71,0,649 -chr1 39596 . A T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=52;Dels=0.00;FS=9.385;HaplotypeScore=3.4616;MLEAC=1;MLEAF=0.500;MQ=33.54;MQ0=1;MQRankSum=-1.360;QD=0.76;ReadPosRankSum=0.065;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,8:52:68:68,0,1009 -chr1 39631 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=77;Dels=0.00;FS=1.669;HaplotypeScore=7.9697;MLEAC=1;MLEAF=0.500;MQ=33.50;MQ0=1;MQRankSum=-0.513;QD=0.63;ReadPosRankSum=1.240;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:77:77:77,0,1546 -chr1 39643 . C A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.541;QD=1.37;ReadPosRankSum=-1.004;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:116,0,1373 -chr1 39644 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.657;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.599;QD=1.54;ReadPosRankSum=-0.966;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:127,0,1357 -chr1 39648 . G C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=58.2273;MLEAC=1;MLEAF=0.500;MQ=35.15;MQ0=0;MQRankSum=3.645;QD=21.79;ReadPosRankSum=-1.153;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,48:62:58:1379,0,58 -chr1 39656 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=58;Dels=0.00;FS=17.787;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-3.172;QD=6.93;ReadPosRankSum=1.492;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:430,0,880 -chr1 39657 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=57;Dels=0.00;FS=10.567;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.40;MQ0=0;MQRankSum=-2.652;QD=3.77;ReadPosRankSum=1.846;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:243,0,1124 -chr1 39659 . C T 63.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=56;Dels=0.00;FS=3.377;HaplotypeScore=37.1251;MLEAC=1;MLEAF=0.500;MQ=36.35;MQ0=0;MQRankSum=0.246;QD=1.14;ReadPosRankSum=0.199;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,8:56:92:92,0,1236 -chr1 39670 . C T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=44;Dels=0.00;FS=2.860;HaplotypeScore=65.0263;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=1.698;QD=6.43;ReadPosRankSum=0.000;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:311,0,662 -chr1 39671 . C A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=69.6870;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=-2.765;QD=0.86;ReadPosRankSum=-0.217;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,11:44:66:66,0,915 -chr1 39673 . C A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.953;DP=42;Dels=0.00;FS=4.360;HaplotypeScore=59.5432;MLEAC=1;MLEAF=0.500;MQ=33.27;MQ0=0;MQRankSum=1.563;QD=9.57;ReadPosRankSum=0.902;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:430,0,510 -chr1 39676 . G A 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=41;Dels=0.00;FS=5.757;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=-0.931;QD=13.90;ReadPosRankSum=-0.215;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,29:41:99:598,0,311 -chr1 39678 . G A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=41;Dels=0.00;FS=6.236;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=1.091;QD=2.77;ReadPosRankSum=1.923;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,7:41:99:142,0,757 -chr1 39681 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=40;Dels=0.00;FS=1.360;HaplotypeScore=29.6132;MLEAC=1;MLEAF=0.500;MQ=33.13;MQ0=0;MQRankSum=1.431;QD=6.37;ReadPosRankSum=-0.635;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:283,0,590 -chr1 39751 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.930;QD=14.14;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:212,0,40 -chr1 39756 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.761;QD=14.60;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:218,0,40 -chr1 39777 . T A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=21.2570;MLEAC=1;MLEAF=0.500;MQ=36.27;MQ0=0;MQRankSum=1.668;QD=22.67;ReadPosRankSum=-0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,21:25:29:595,0,29 -chr1 39820 . T G 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=75;Dels=0.00;FS=0.967;HaplotypeScore=5.9128;MLEAC=1;MLEAF=0.500;MQ=40.90;MQ0=0;MQRankSum=2.599;QD=10.33;ReadPosRankSum=1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:803,0,1331 -chr1 39826 . A C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.234;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=2.9758;MLEAC=1;MLEAF=0.500;MQ=40.59;MQ0=0;MQRankSum=2.470;QD=10.80;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:892,0,1425 -chr1 39890 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.405;DP=34;Dels=0.00;FS=6.017;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.76;MQ0=0;MQRankSum=-2.459;QD=5.43;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:213,0,772 -chr1 39891 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=43;Dels=0.00;FS=1.596;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.93;MQ0=1;MQRankSum=-2.575;QD=3.44;ReadPosRankSum=2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:176,0,1067 -chr1 39914 . A T 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=23.4102;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=4;MQRankSum=0.588;QD=15.15;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:710,0,508 -chr1 39961 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=47;Dels=0.00;FS=1.512;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=42.42;MQ0=3;MQRankSum=1.537;QD=14.12;ReadPosRankSum=-0.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:692,0,570 -chr1 40003 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.65;MQ0=0;MQRankSum=-3.665;QD=10.36;ReadPosRankSum=-2.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:453,0,706 -chr1 40005 . G A 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=42;Dels=0.00;FS=12.410;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=0.221;QD=5.64;ReadPosRankSum=-2.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:265,0,940 -chr1 40007 . T A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=42;Dels=0.00;FS=4.327;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=3.748;QD=16.04;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:702,0,465 -chr1 40020 . C T 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=42;Dels=0.00;FS=15.124;HaplotypeScore=19.7971;MLEAC=1;MLEAF=0.500;MQ=41.55;MQ0=0;MQRankSum=1.991;QD=3.33;ReadPosRankSum=-2.632;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:99:168,0,1045 -chr1 40029 . T C 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=38;Dels=0.00;FS=1.939;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=1.977;QD=25.73;ReadPosRankSum=0.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:5,32:38:68:1006,0,68 -chr1 40032 . T C 1048.85 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=0;MQRankSum=4.052;QD=28.35;ReadPosRankSum=-2.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:17:1077,0,17 -chr1 40053 . C G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=5.5950;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=0;MQRankSum=1.442;QD=5.73;ReadPosRankSum=-0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,11:46:99:292,0,1057 -chr1 40084 . T A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=0.136;QD=13.27;ReadPosRankSum=-0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:665,0,943 -chr1 40096 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=0.374;QD=13.50;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:676,0,875 -chr1 40115 . G A 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.138;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=21.9178;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.379;QD=19.83;ReadPosRankSum=-1.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:980,0,633 -chr1 40187 . T C 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=65;Dels=0.00;FS=14.460;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-3.656;QD=0.92;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,9:65:88:88,0,1926 -chr1 40200 . A G 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=16.7520;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.152;QD=1.71;ReadPosRankSum=-1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:153,0,2048 -chr1 40205 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=74;Dels=0.00;FS=1.321;HaplotypeScore=20.7504;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.008;QD=0.46;ReadPosRankSum=2.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:62:62,0,1934 -chr1 40212 . G A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=73;Dels=0.00;FS=1.331;HaplotypeScore=32.7378;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-0.609;QD=2.30;ReadPosRankSum=1.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,11:73:99:196,0,1961 -chr1 40216 . C T 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=77;Dels=0.00;FS=3.483;HaplotypeScore=23.9149;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=2.932;QD=7.82;ReadPosRankSum=-1.909;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:630,0,1637 -chr1 40235 . A G 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.661;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=35.5558;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-0.751;QD=9.86;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,29:80:99:817,0,1701 -chr1 40238 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.173;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=31.6873;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-3.462;QD=5.38;ReadPosRankSum=-2.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:475,0,2185 -chr1 40257 . G A 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=89;Dels=0.00;FS=1.765;HaplotypeScore=39.6559;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-4.194;QD=14.62;ReadPosRankSum=-0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,40:89:99:1329,0,1466 -chr1 40262 . T C 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;DP=90;Dels=0.00;FS=12.546;HaplotypeScore=41.5222;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.449;QD=14.11;ReadPosRankSum=-0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,40:90:99:1298,0,1623 -chr1 40276 . G A 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;DP=99;Dels=0.00;FS=2.892;HaplotypeScore=39.6083;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=4.526;QD=8.99;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,30:99:99:918,0,2233 -chr1 40299 . T C 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=94;Dels=0.00;FS=4.739;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.77;MQ0=0;MQRankSum=1.944;QD=0.97;ReadPosRankSum=1.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,10:94:99:119,0,2786 -chr1 40300 . A G 1244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=96;Dels=0.00;FS=2.677;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.317;QD=12.97;ReadPosRankSum=1.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,43:96:99:1273,0,1762 -chr1 40316 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=100;Dels=0.00;FS=6.354;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.47;MQ0=0;MQRankSum=-6.856;QD=4.66;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:494,0,2754 -chr1 40317 . G A 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;DP=98;Dels=0.00;FS=6.790;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=0.824;QD=4.58;ReadPosRankSum=-0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:477,0,2577 -chr1 40326 . T C 1103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=102;Dels=0.00;FS=8.509;HaplotypeScore=104.4492;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=5.492;QD=10.82;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,37:102:99:1132,0,2119 -chr1 40331 . C T 611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=42.7177;MLEAC=1;MLEAF=0.500;MQ=54.62;MQ0=0;MQRankSum=3.620;QD=6.58;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:640,0,2316 -chr1 40336 . C T 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;DP=89;Dels=0.00;FS=7.137;HaplotypeScore=40.7185;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=4.995;QD=12.21;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,34:89:99:1115,0,1717 -chr1 40340 . T C 1638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=87;Dels=0.00;FS=8.927;HaplotypeScore=60.7684;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.839;QD=18.84;ReadPosRankSum=-0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,52:87:99:1667,0,1091 -chr1 40350 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.570;DP=100;Dels=0.00;FS=2.227;HaplotypeScore=42.2843;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=0;MQRankSum=-3.916;QD=2.79;ReadPosRankSum=-0.327;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:307,0,2907 -chr1 40357 . A G 1180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=101;Dels=0.00;FS=8.331;HaplotypeScore=60.4654;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-3.892;QD=11.69;ReadPosRankSum=-1.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,40:100:99:1209,0,1863 -chr1 40367 . G A 1455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.630;DP=100;Dels=0.00;FS=2.623;HaplotypeScore=40.4721;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=3.679;QD=14.56;ReadPosRankSum=-0.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,45:100:99:1484,0,1789 -chr1 40385 . A T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.211;DP=99;Dels=0.00;FS=2.269;HaplotypeScore=13.6606;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=0;MQRankSum=-2.742;QD=3.11;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,17:99:99:336,0,2801 -chr1 40390 . C A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=102;Dels=0.00;FS=10.470;HaplotypeScore=47.4671;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=0;MQRankSum=-0.627;QD=2.08;ReadPosRankSum=-1.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,14:102:99:240,0,3128 -chr1 40397 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=99;Dels=0.00;FS=2.447;HaplotypeScore=91.1211;MLEAC=1;MLEAF=0.500;MQ=57.63;MQ0=0;MQRankSum=-2.184;QD=2.04;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:230,0,3009 -chr1 40398 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=98;Dels=0.00;FS=0.959;HaplotypeScore=91.9098;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-0.904;QD=4.41;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:460,0,2711 -chr1 40401 . C A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.162;DP=96;Dels=0.00;FS=2.289;HaplotypeScore=54.1136;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-1.696;QD=3.29;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,16:96:99:344,0,2884 -chr1 40405 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.881;DP=97;Dels=0.00;FS=4.295;HaplotypeScore=68.8441;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=1.976;QD=7.68;ReadPosRankSum=-0.753;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,27:97:99:773,0,2466 -chr1 40415 . A G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.202;DP=95;Dels=0.00;FS=4.129;HaplotypeScore=16.3079;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.121;QD=2.67;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:282,0,2906 -chr1 40423 . G A 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=14.9944;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-0.719;QD=7.61;ReadPosRankSum=-0.969;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,27:94:99:744,0,2306 -chr1 40444 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=25.1958;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=1.888;QD=4.66;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,18:91:99:452,0,2590 -chr1 40450 . C T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=86;Dels=0.00;FS=10.543;HaplotypeScore=36.1917;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=-0.407;QD=1.33;ReadPosRankSum=0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,10:86:99:143,0,2614 -chr1 40451 . C T 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.552;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=37.1784;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=2.698;QD=1.68;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,12:86:99:173,0,2633 -chr1 40455 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=89;Dels=0.00;FS=5.908;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=0.165;QD=8.65;ReadPosRankSum=0.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:798,0,2174 -chr1 40458 . G A 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.752;DP=90;Dels=0.00;FS=1.024;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=1.062;QD=3.88;ReadPosRankSum=0.175;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,17:90:99:377,0,2596 -chr1 40480 . C A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=106;Dels=0.00;FS=4.744;HaplotypeScore=40.7109;MLEAC=1;MLEAF=0.500;MQ=53.17;MQ0=0;MQRankSum=-0.111;QD=4.04;ReadPosRankSum=0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,21:106:99:456,0,3043 -chr1 40490 . T C 2948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=107;Dels=0.00;FS=9.034;HaplotypeScore=71.4806;MLEAC=1;MLEAF=0.500;MQ=52.29;MQ0=0;MQRankSum=1.008;QD=27.56;ReadPosRankSum=2.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,85:107:99:2977,0,405 -chr1 40495 . C G 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.391;DP=114;Dels=0.00;FS=1.985;HaplotypeScore=71.4457;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-0.918;QD=5.58;ReadPosRankSum=1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,23:114:99:664,0,2502 -chr1 40497 . G C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=69.4473;MLEAC=1;MLEAF=0.500;MQ=51.94;MQ0=0;MQRankSum=-0.543;QD=2.38;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,17:112:99:295,0,3323 -chr1 40511 . A G 3183.76 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=39.7486;MLEAC=1;MLEAF=0.500;MQ=52.34;MQ0=0;MQRankSum=0.371;QD=27.45;ReadPosRankSum=0.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,92:116:99:3212,0,569 -chr1 40524 . G A 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.064;DP=123;Dels=0.00;FS=2.035;HaplotypeScore=26.4109;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=0;MQRankSum=-2.672;QD=2.92;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,21:123:99:387,0,3524 -chr1 40526 . G A 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=123;Dels=0.00;FS=2.894;HaplotypeScore=26.2780;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-0.204;QD=5.13;ReadPosRankSum=1.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:123:99:659,0,3056 -chr1 40559 . T A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.703;DP=122;Dels=0.00;FS=1.745;HaplotypeScore=75.4361;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=3.818;QD=5.47;ReadPosRankSum=1.838;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:122:99:695,0,3342 -chr1 40562 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=119;Dels=0.00;FS=6.618;HaplotypeScore=120.3506;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-3.315;QD=3.02;ReadPosRankSum=-1.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,20:119:99:388,0,3464 -chr1 40565 . G A 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=115;Dels=0.00;FS=3.367;HaplotypeScore=128.0268;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-0.666;QD=3.55;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,19:115:99:437,0,3355 -chr1 40570 . T A 2544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=116.1873;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.456;QD=20.86;ReadPosRankSum=-3.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,76:122:99:2573,0,1468 -chr1 40572 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050;DP=126;Dels=0.00;FS=16.724;HaplotypeScore=113.1887;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-3.211;QD=2.10;ReadPosRankSum=-0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,19:126:99:293,0,3847 -chr1 40574 . G A 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.747;DP=128;Dels=0.00;FS=3.770;HaplotypeScore=81.5684;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=1.064;QD=1.61;ReadPosRankSum=1.108;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,16:128:99:234,0,3817 -chr1 40587 . A G 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=153;Dels=0.00;FS=0.744;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=2.151;QD=5.55;ReadPosRankSum=0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,34:153:99:877,0,4088 -chr1 40598 . A T 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.298;DP=145;Dels=0.00;FS=0.898;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=1;MQRankSum=-3.872;QD=2.10;ReadPosRankSum=2.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:124,21:145:99:333,0,4371 -chr1 40601 . T C 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.858;DP=141;Dels=0.00;FS=0.951;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=55.65;MQ0=1;MQRankSum=-4.326;QD=2.24;ReadPosRankSum=3.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:122,19:141:99:344,0,4357 -chr1 40604 . A G 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=140;Dels=0.00;FS=0.952;HaplotypeScore=3.7881;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=-4.123;QD=2.30;ReadPosRankSum=3.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:121,19:140:99:350,0,4326 -chr1 40607 . A T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=138;Dels=0.00;FS=2.058;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=1;MQRankSum=-3.796;QD=2.44;ReadPosRankSum=2.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,19:138:99:365,0,4122 -chr1 40613 . T C 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=138;Dels=0.00;FS=0.884;HaplotypeScore=34.9737;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=1;MQRankSum=-4.247;QD=2.75;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:408,0,4053 -chr1 40618 . A G 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=140;Dels=0.00;FS=8.579;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.14;MQ0=1;MQRankSum=1.916;QD=0.23;ReadPosRankSum=3.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:128,12:140:60:60,0,4583 -chr1 40619 . T G 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.123;DP=141;Dels=0.00;FS=6.410;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.05;MQ0=1;MQRankSum=-2.776;QD=2.23;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:120,20:141:99:342,0,4240 -chr1 40629 . A T 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.928;DP=134;Dels=0.00;FS=0.868;HaplotypeScore=126.7357;MLEAC=1;MLEAF=0.500;MQ=53.57;MQ0=1;MQRankSum=-4.720;QD=3.33;ReadPosRankSum=-1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,22:134:99:474,0,3749 -chr1 40630 . C T 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.225;DP=133;Dels=0.00;FS=2.109;HaplotypeScore=106.7571;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=1;MQRankSum=-3.232;QD=2.08;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:113,19:133:99:305,0,3912 -chr1 40631 . C T 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.935;DP=134;Dels=0.00;FS=0.896;HaplotypeScore=109.5452;MLEAC=1;MLEAF=0.500;MQ=53.51;MQ0=1;MQRankSum=-4.705;QD=3.01;ReadPosRankSum=-1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,21:134:99:432,0,3926 -chr1 40635 . C A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.206;DP=136;Dels=0.00;FS=10.739;HaplotypeScore=148.7017;MLEAC=1;MLEAF=0.500;MQ=53.34;MQ0=1;MQRankSum=5.098;QD=5.45;ReadPosRankSum=-0.010;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,29:136:99:770,0,3047 -chr1 40637 . G T 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.363;DP=138;Dels=0.00;FS=1.925;HaplotypeScore=146.7025;MLEAC=1;MLEAF=0.500;MQ=53.22;MQ0=1;MQRankSum=-4.406;QD=3.06;ReadPosRankSum=-1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:450,0,4023 -chr1 40643 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=137;Dels=0.00;FS=0.905;HaplotypeScore=80.3353;MLEAC=1;MLEAF=0.500;MQ=53.30;MQ0=1;MQRankSum=-4.704;QD=2.56;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,20:137:99:379,0,4082 -chr1 40644 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=136;Dels=0.00;FS=0.917;HaplotypeScore=81.3352;MLEAC=1;MLEAF=0.500;MQ=53.25;MQ0=1;MQRankSum=-4.475;QD=2.54;ReadPosRankSum=-0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,20:136:99:373,0,4107 -chr1 40647 . G A 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=143;Dels=0.00;FS=7.049;HaplotypeScore=90.1298;MLEAC=1;MLEAF=0.500;MQ=52.42;MQ0=1;MQRankSum=6.086;QD=4.35;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:115,28:143:99:650,0,3953 -chr1 40656 . C A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=136;Dels=0.00;FS=2.901;HaplotypeScore=65.3188;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=1;MQRankSum=3.870;QD=4.26;ReadPosRankSum=2.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:109,27:136:99:607,0,3691 -chr1 40663 . C T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;DP=131;Dels=0.00;FS=1.470;HaplotypeScore=51.1808;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=2;MQRankSum=0.022;QD=9.31;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,44:131:99:1248,0,2916 -chr1 40665 . G A 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.989;DP=129;Dels=0.00;FS=4.193;HaplotypeScore=50.1809;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=2;MQRankSum=3.905;QD=4.50;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:101,28:129:99:609,0,3457 -chr1 40679 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=116;Dels=0.00;FS=3.025;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=-6.403;QD=4.21;ReadPosRankSum=0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:517,0,3113 -chr1 40680 . C A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=116;Dels=0.00;FS=5.789;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=3.479;QD=5.26;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,27:116:99:638,0,3045 -chr1 40695 . G A 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=109;Dels=0.00;FS=4.432;HaplotypeScore=15.8769;MLEAC=1;MLEAF=0.500;MQ=48.67;MQ0=1;MQRankSum=4.736;QD=1.38;ReadPosRankSum=0.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,12:109:99:179,0,3292 -chr1 40702 . G A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.179;DP=118;Dels=0.00;FS=1.878;HaplotypeScore=12.9449;MLEAC=1;MLEAF=0.500;MQ=49.34;MQ0=1;MQRankSum=3.135;QD=5.11;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,24:118:99:631,0,3094 -chr1 40724 . C T 2276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.371;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=76.4647;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=1;MQRankSum=-4.544;QD=18.51;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,73:123:99:2305,0,1587 -chr1 40726 . A G 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=121;Dels=0.00;FS=0.855;HaplotypeScore=78.4642;MLEAC=1;MLEAF=0.500;MQ=50.50;MQ0=1;MQRankSum=3.987;QD=5.24;ReadPosRankSum=-0.827;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,25:121:99:662,0,3213 -chr1 40730 . T C 2668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.318;DP=119;Dels=0.00;FS=0.742;HaplotypeScore=131.5265;MLEAC=1;MLEAF=0.500;MQ=50.60;MQ0=1;MQRankSum=-1.336;QD=22.43;ReadPosRankSum=1.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,83:119:99:2697,0,1090 -chr1 40731 . T C 163.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=129.2953;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-0.479;QD=1.38;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,14:119:99:192,0,3588 -chr1 40742 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=108;Dels=0.00;FS=0.859;HaplotypeScore=18.6626;MLEAC=1;MLEAF=0.500;MQ=51.05;MQ0=1;MQRankSum=-5.117;QD=4.95;ReadPosRankSum=-1.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,26:108:99:563,0,2912 -chr1 40757 . C T 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=119;Dels=0.00;FS=2.628;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=-5.477;QD=9.18;ReadPosRankSum=-1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:119:99:1121,0,2615 -chr1 40769 . C T 3289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=123;Dels=0.00;FS=0.861;HaplotypeScore=41.4575;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=1;MQRankSum=-4.495;QD=26.75;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,99:123:99:3318,0,576 -chr1 40773 . G A 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=126;Dels=0.00;FS=2.716;HaplotypeScore=43.4570;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=-2.084;QD=6.91;ReadPosRankSum=2.684;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,32:126:99:899,0,2993 -chr1 40788 . A C 1705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=118;Dels=0.00;FS=2.394;HaplotypeScore=117.6775;MLEAC=1;MLEAF=0.500;MQ=49.33;MQ0=1;MQRankSum=-6.557;QD=14.46;ReadPosRankSum=2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,62:118:99:1734,0,1876 -chr1 40789 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=123;Dels=0.00;FS=11.420;HaplotypeScore=119.6765;MLEAC=1;MLEAF=0.500;MQ=49.20;MQ0=1;MQRankSum=3.191;QD=5.27;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,25:123:99:677,0,3103 -chr1 40791 . A G 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.823;DP=121;Dels=0.00;FS=1.004;HaplotypeScore=70.2853;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=1;MQRankSum=-4.589;QD=2.12;ReadPosRankSum=1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,24:121:99:285,0,3412 -chr1 40795 . A T 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=72.2808;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=1;MQRankSum=-2.514;QD=1.04;ReadPosRankSum=2.201;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:108,17:125:99:158,0,3699 -chr1 40803 . C T 2015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.782;DP=118;Dels=0.00;FS=2.491;HaplotypeScore=47.3955;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=1;MQRankSum=-6.205;QD=17.08;ReadPosRankSum=-0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,71:118:99:2044,0,1478 -chr1 40809 . C T 2959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.887;DP=111;Dels=0.00;FS=0.920;HaplotypeScore=68.1753;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=1;MQRankSum=0.903;QD=26.66;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,91:111:99:2988,0,335 -chr1 40816 . G A 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.969;DP=113;Dels=0.00;FS=9.418;HaplotypeScore=31.1266;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=1;MQRankSum=-1.806;QD=4.02;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,20:113:99:483,0,2777 -chr1 40830 . G C 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=19.6261;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=1;MQRankSum=-2.358;QD=0.59;ReadPosRankSum=1.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,15:120:99:99,0,3552 -chr1 40833 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.298;DP=124;Dels=0.00;FS=3.723;HaplotypeScore=34.4038;MLEAC=1;MLEAF=0.500;MQ=46.84;MQ0=1;MQRankSum=-1.292;QD=2.15;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,20:124:99:295,0,3416 -chr1 40839 . T C 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.184;DP=119;Dels=0.00;FS=8.132;HaplotypeScore=32.8812;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=1;MQRankSum=-0.467;QD=1.86;ReadPosRankSum=0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,17:119:99:249,0,3382 -chr1 40851 . C G 787.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.730;DP=129;Dels=0.00;FS=22.816;HaplotypeScore=16.7771;MLEAC=1;MLEAF=0.500;MQ=48.66;MQ0=1;MQRankSum=2.703;QD=6.11;ReadPosRankSum=-0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,30:129:99:816,0,3155 -chr1 40863 . T C 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.921;DP=118;Dels=0.00;FS=4.700;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.335;QD=12.98;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,57:118:99:1560,0,2100 -chr1 40865 . A G 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.140;DP=120;Dels=0.00;FS=2.661;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=50.52;MQ0=0;MQRankSum=-2.918;QD=7.64;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,36:120:99:945,0,2823 -chr1 40881 . T C 1883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.649;DP=113;Dels=0.00;FS=6.057;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=52.96;MQ0=0;MQRankSum=-3.511;QD=16.67;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,61:113:99:1912,0,1701 -chr1 40884 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.416;DP=112;Dels=0.00;FS=4.487;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=0.616;QD=0.92;ReadPosRankSum=1.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,12:112:99:131,0,3505 -chr1 40908 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=-4.713;QD=3.49;ReadPosRankSum=-0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:444,0,3404 -chr1 40939 . C T 1562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=122;Dels=0.00;FS=5.633;HaplotypeScore=53.6940;MLEAC=1;MLEAF=0.500;MQ=53.55;MQ0=0;MQRankSum=-6.420;QD=12.81;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,53:122:99:1591,0,2373 -chr1 40942 . G C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=117;Dels=0.00;FS=3.010;HaplotypeScore=52.6941;MLEAC=1;MLEAF=0.500;MQ=53.19;MQ0=0;MQRankSum=2.832;QD=5.14;ReadPosRankSum=2.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,24:117:99:630,0,3142 -chr1 40949 . A T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.841;DP=116;Dels=0.00;FS=1.882;HaplotypeScore=91.2099;MLEAC=1;MLEAF=0.500;MQ=51.71;MQ0=1;MQRankSum=2.660;QD=5.38;ReadPosRankSum=3.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:652,0,3037 -chr1 40953 . G T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=114;Dels=0.00;FS=4.536;HaplotypeScore=90.5131;MLEAC=1;MLEAF=0.500;MQ=51.22;MQ0=1;MQRankSum=-6.362;QD=4.05;ReadPosRankSum=-0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,25:114:99:490,0,2704 -chr1 40963 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.072;DP=115;Dels=0.00;FS=2.488;HaplotypeScore=45.8271;MLEAC=1;MLEAF=0.500;MQ=50.61;MQ0=1;MQRankSum=-6.812;QD=9.88;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,45:115:99:1164,0,2427 -chr1 40965 . A C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=111;Dels=0.00;FS=1.995;HaplotypeScore=24.4867;MLEAC=1;MLEAF=0.500;MQ=50.29;MQ0=1;MQRankSum=-5.421;QD=2.79;ReadPosRankSum=1.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,22:111:99:338,0,3112 -chr1 40977 . A G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.248;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=7.5174;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=1;MQRankSum=3.438;QD=5.38;ReadPosRankSum=0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,25:106:99:598,0,2425 -chr1 40988 . C T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=97;Dels=0.00;FS=7.020;HaplotypeScore=26.1924;MLEAC=1;MLEAF=0.500;MQ=46.91;MQ0=1;MQRankSum=1.225;QD=3.47;ReadPosRankSum=-0.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,18:97:99:365,0,2417 -chr1 40989 . T C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.909;DP=94;Dels=0.00;FS=7.233;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=1;MQRankSum=1.405;QD=3.77;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,18:94:99:383,0,2284 -chr1 40990 . C T 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=1;MQRankSum=-4.177;QD=1.04;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,15:92:99:124,0,2472 -chr1 41013 . C T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.016;DP=84;Dels=0.00;FS=15.260;HaplotypeScore=153.8354;MLEAC=1;MLEAF=0.500;MQ=39.77;MQ0=1;MQRankSum=0.325;QD=5.07;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:454,0,1750 -chr1 41015 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=85;Dels=0.00;FS=1.324;HaplotypeScore=57.0601;MLEAC=1;MLEAF=0.500;MQ=39.97;MQ0=1;MQRankSum=-2.501;QD=0.41;ReadPosRankSum=0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:85:63:63,0,2037 -chr1 41026 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.073;DP=97;Dels=0.00;FS=3.387;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=40.65;MQ0=1;MQRankSum=1.677;QD=0.36;ReadPosRankSum=-2.910;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,9:97:63:63,0,2499 -chr1 41043 . C T 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.8776;MLEAC=1;MLEAF=0.500;MQ=42.40;MQ0=1;MQRankSum=0.065;QD=1.44;ReadPosRankSum=0.698;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,12:92:99:161,0,2256 -chr1 41046 . G A 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.146;DP=89;Dels=0.00;FS=6.728;HaplotypeScore=67.8534;MLEAC=1;MLEAF=0.500;MQ=42.77;MQ0=1;MQRankSum=-2.122;QD=0.77;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:97:97,0,2293 -chr1 41054 . G A 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.137;DP=87;Dels=0.00;FS=2.873;HaplotypeScore=97.5277;MLEAC=1;MLEAF=0.500;MQ=43.55;MQ0=0;MQRankSum=-1.875;QD=1.18;ReadPosRankSum=1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,13:87:99:131,0,2231 -chr1 41056 . G T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.880;DP=86;Dels=0.00;FS=12.658;HaplotypeScore=70.2196;MLEAC=1;MLEAF=0.500;MQ=43.45;MQ0=0;MQRankSum=0.504;QD=8.25;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,31:86:99:738,0,1637 -chr1 41059 . A T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=85;Dels=0.00;FS=1.923;HaplotypeScore=62.5392;MLEAC=1;MLEAF=0.500;MQ=43.72;MQ0=0;MQRankSum=-1.385;QD=7.07;ReadPosRankSum=2.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,28:85:99:629,0,1583 -chr1 41064 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=88;Dels=0.00;FS=1.164;HaplotypeScore=86.8690;MLEAC=1;MLEAF=0.500;MQ=44.00;MQ0=0;MQRankSum=-1.609;QD=1.93;ReadPosRankSum=1.221;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,15:88:99:198,0,2343 -chr1 41084 . T C 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=106;Dels=0.00;FS=1.092;HaplotypeScore=17.4304;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=-1.180;QD=1.68;ReadPosRankSum=-2.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,14:106:99:206,0,3074 -chr1 41100 . C A 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.112;DP=116;Dels=0.00;FS=0.765;HaplotypeScore=58.6282;MLEAC=1;MLEAF=0.500;MQ=48.59;MQ0=0;MQRankSum=0.652;QD=7.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,34:116:99:915,0,2691 -chr1 41103 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.020;DP=114;Dels=0.00;FS=7.549;HaplotypeScore=60.6270;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=0.692;QD=5.02;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,25:114:99:601,0,2970 -chr1 41108 . G A 2256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=104;Dels=0.00;FS=1.668;HaplotypeScore=55.9666;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-3.973;QD=21.70;ReadPosRankSum=0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,68:104:99:2285,0,1135 -chr1 41121 . C T 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=106;Dels=0.00;FS=8.022;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=0;MQRankSum=-4.307;QD=11.10;ReadPosRankSum=1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,39:106:99:1205,0,2309 -chr1 41142 . C A 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.819;DP=93;Dels=0.00;FS=4.344;HaplotypeScore=109.3818;MLEAC=1;MLEAF=0.500;MQ=50.67;MQ0=0;MQRankSum=-3.272;QD=1.78;ReadPosRankSum=-0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,12:93:99:194,0,2886 -chr1 41167 . T A 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.059;DP=80;Dels=0.00;FS=2.024;HaplotypeScore=81.4181;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-5.890;QD=8.08;ReadPosRankSum=2.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,24:80:99:675,0,1872 -chr1 41168 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=85;Dels=0.00;FS=1.308;HaplotypeScore=70.7865;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-3.430;QD=1.28;ReadPosRankSum=1.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,10:85:99:137,0,2676 -chr1 41170 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.253;DP=86;Dels=0.00;FS=2.556;HaplotypeScore=38.2377;MLEAC=1;MLEAF=0.500;MQ=51.83;MQ0=0;MQRankSum=-4.581;QD=2.28;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,13:86:99:224,0,2606 -chr1 41179 . T C 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.172;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=18.4473;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-4.595;QD=7.31;ReadPosRankSum=-2.191;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,23:85:99:650,0,2189 -chr1 41195 . C G 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=99;Dels=0.00;FS=3.526;HaplotypeScore=25.2904;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=3.710;QD=4.40;ReadPosRankSum=1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,19:99:99:464,0,2786 -chr1 41199 . C T 552.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=96;Dels=0.00;FS=4.808;HaplotypeScore=40.2922;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=2.060;QD=5.76;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,22:96:99:581,0,2606 -chr1 41208 . T C 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.073;DP=95;Dels=0.00;FS=3.709;HaplotypeScore=57.4526;MLEAC=1;MLEAF=0.500;MQ=52.97;MQ0=0;MQRankSum=3.607;QD=4.12;ReadPosRankSum=2.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,17:95:99:420,0,2797 -chr1 41212 . A C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=95;Dels=0.00;FS=0.946;HaplotypeScore=22.4583;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-3.985;QD=5.00;ReadPosRankSum=-1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,20:95:99:503,0,2582 -chr1 41218 . T A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=96;Dels=0.00;FS=2.139;HaplotypeScore=56.9737;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=4.681;QD=4.80;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,19:96:99:489,0,2728 -chr1 41224 . C T 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=92;Dels=0.00;FS=8.582;HaplotypeScore=46.8527;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=-6.262;QD=11.77;ReadPosRankSum=0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,36:92:99:1111,0,1880 -chr1 41227 . A C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=95;Dels=0.00;FS=1.160;HaplotypeScore=73.8186;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.984;QD=2.05;ReadPosRankSum=1.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:223,0,2919 -chr1 41234 . A T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.452;DP=100;Dels=0.00;FS=2.117;HaplotypeScore=65.6546;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=2.503;QD=4.66;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,20:100:99:494,0,2851 -chr1 41244 . C G 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.262;DP=106;Dels=0.00;FS=4.109;HaplotypeScore=48.8041;MLEAC=1;MLEAF=0.500;MQ=54.46;MQ0=0;MQRankSum=-2.340;QD=1.59;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,13:106:99:197,0,3333 -chr1 41248 . T C 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=109;Dels=0.00;FS=1.115;HaplotypeScore=41.7628;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-3.636;QD=1.78;ReadPosRankSum=0.974;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,14:109:99:222,0,3400 -chr1 41253 . T A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.602;DP=119;Dels=0.00;FS=6.215;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=1;MQRankSum=0.176;QD=4.21;ReadPosRankSum=1.441;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:529,0,3111 -chr1 41254 . A T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.018;DP=120;Dels=0.00;FS=15.351;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=1;MQRankSum=-4.673;QD=0.63;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,13:120:99:104,0,3713 -chr1 41267 . T A 1376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=124;Dels=0.00;FS=10.609;HaplotypeScore=25.9401;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-7.080;QD=11.10;ReadPosRankSum=0.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,47:124:99:1405,0,2587 -chr1 41268 . T C 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=124;Dels=0.00;FS=4.257;HaplotypeScore=82.8206;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-0.901;QD=0.91;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,13:124:99:141,0,3898 -chr1 41278 . G A 2734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.082;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=36.6252;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=1;MQRankSum=1.173;QD=22.98;ReadPosRankSum=0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,80:119:99:2763,0,670 -chr1 41290 . C T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=114;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=51.25;MQ0=1;MQRankSum=-4.504;QD=5.81;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,27:114:99:691,0,2884 -chr1 41305 . C T 1582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.376;DP=107;Dels=0.00;FS=1.558;HaplotypeScore=63.7217;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=1;MQRankSum=-7.979;QD=14.79;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,55:107:99:1611,0,1766 -chr1 41308 . T C 1593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=-8.201;QD=14.90;ReadPosRankSum=0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,56:107:99:1622,0,1675 -chr1 41310 . C G 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.320;DP=105;Dels=0.00;FS=0.974;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=1;MQRankSum=-2.583;QD=3.70;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,21:105:99:417,0,2941 -chr1 41313 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.319;DP=103;Dels=0.00;FS=0.870;HaplotypeScore=103.1863;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=4.857;QD=7.01;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,26:103:99:750,0,2499 -chr1 41322 . G A 1422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=107;Dels=0.00;FS=1.576;HaplotypeScore=70.4344;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=1;MQRankSum=1.616;QD=13.30;ReadPosRankSum=0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,49:107:99:1451,0,1855 -chr1 41331 . C T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=103;Dels=0.00;FS=4.657;HaplotypeScore=99.4972;MLEAC=1;MLEAF=0.500;MQ=48.40;MQ0=1;MQRankSum=4.235;QD=5.51;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,22:103:99:596,0,2616 -chr1 41334 . A C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;DP=101;Dels=0.00;FS=2.142;HaplotypeScore=117.9442;MLEAC=1;MLEAF=0.500;MQ=48.38;MQ0=1;MQRankSum=-2.696;QD=3.51;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,19:101:99:383,0,2677 -chr1 41335 . C A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.870;DP=98;Dels=0.00;FS=0.996;HaplotypeScore=118.9429;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=1;MQRankSum=-3.055;QD=4.25;ReadPosRankSum=-0.712;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:98:99:445,0,2383 -chr1 41337 . G A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=99;Dels=0.00;FS=3.218;HaplotypeScore=122.9204;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=1;MQRankSum=2.970;QD=6.55;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,24:99:99:677,0,2337 -chr1 41343 . G A 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=74.5936;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=1;MQRankSum=-3.683;QD=5.19;ReadPosRankSum=1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:537,0,2493 -chr1 41365 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=86;Dels=0.00;FS=2.433;HaplotypeScore=14.9634;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=0;MQRankSum=1.753;QD=3.47;ReadPosRankSum=1.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,15:86:99:327,0,2341 -chr1 41375 . T C 2374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=87;Dels=0.00;FS=1.026;HaplotypeScore=33.9683;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.561;QD=27.30;ReadPosRankSum=-1.912;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,71:87:99:2403,0,364 -chr1 41376 . T G 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.803;DP=87;Dels=0.00;FS=4.036;HaplotypeScore=34.9615;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=0;MQRankSum=-0.455;QD=3.19;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:306,0,2524 -chr1 41377 . T C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.157;DP=88;Dels=0.00;FS=0.884;HaplotypeScore=39.7608;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-0.490;QD=7.20;ReadPosRankSum=3.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,25:88:99:662,0,2148 -chr1 41395 . A G 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.677;DP=84;Dels=0.00;FS=1.101;HaplotypeScore=112.5646;MLEAC=1;MLEAF=0.500;MQ=48.92;MQ0=0;MQRankSum=2.499;QD=3.81;ReadPosRankSum=0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:348,0,2361 -chr1 41396 . A T 1616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.249;DP=79;Dels=0.00;FS=3.137;HaplotypeScore=87.3597;MLEAC=1;MLEAF=0.500;MQ=48.75;MQ0=0;MQRankSum=-0.300;QD=20.47;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,50:79:99:1645,0,823 -chr1 41398 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.022;DP=81;Dels=0.00;FS=3.484;HaplotypeScore=80.5740;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-1.669;QD=8.63;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,24:81:99:727,0,1467 -chr1 41404 . T C 2294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=97;Dels=0.00;FS=0.832;HaplotypeScore=104.9252;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=4.062;QD=23.66;ReadPosRankSum=2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,68:97:99:2323,0,710 -chr1 41409 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.386;DP=105;Dels=0.00;FS=11.861;HaplotypeScore=51.0534;MLEAC=1;MLEAF=0.500;MQ=48.48;MQ0=0;MQRankSum=-4.669;QD=0.65;ReadPosRankSum=-2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,13:105:96:96,0,3129 -chr1 41415 . G A 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=107;Dels=0.00;FS=11.635;HaplotypeScore=15.7947;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=1.795;QD=3.14;ReadPosRankSum=-0.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,18:107:99:364,0,2936 -chr1 41433 . A G 1679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=111;Dels=0.00;FS=3.563;HaplotypeScore=105.5605;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-5.707;QD=15.13;ReadPosRankSum=1.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,57:111:99:1708,0,1780 -chr1 41435 . A G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=109;Dels=0.00;FS=17.321;HaplotypeScore=102.6178;MLEAC=1;MLEAF=0.500;MQ=49.30;MQ0=0;MQRankSum=-4.352;QD=0.94;ReadPosRankSum=2.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,13:109:99:131,0,3341 -chr1 41438 . T G 3087.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.252;DP=111;Dels=0.00;FS=11.712;HaplotypeScore=118.7379;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=0.604;QD=27.82;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,93:111:99:3116,0,375 -chr1 41441 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=115;Dels=0.00;FS=6.121;HaplotypeScore=118.1844;MLEAC=1;MLEAF=0.500;MQ=49.65;MQ0=0;MQRankSum=5.083;QD=5.02;ReadPosRankSum=-0.127;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,24:115:99:605,0,2982 -chr1 41447 . C T 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=113;Dels=0.00;FS=2.061;HaplotypeScore=55.8367;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-4.171;QD=3.53;ReadPosRankSum=-0.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,22:113:99:427,0,3162 -chr1 41451 . T C 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.403;DP=114;Dels=0.00;FS=25.914;HaplotypeScore=63.6216;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=0;MQRankSum=-4.658;QD=1.12;ReadPosRankSum=3.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,14:114:99:156,0,3508 -chr1 41458 . T G 2070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.880;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=14.9365;MLEAC=1;MLEAF=0.500;MQ=50.88;MQ0=0;MQRankSum=-8.252;QD=17.55;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,67:118:99:2099,0,1630 -chr1 41472 . G A 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=118;Dels=0.00;FS=4.281;HaplotypeScore=23.8857;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=4.715;QD=5.35;ReadPosRankSum=1.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,25:118:99:660,0,3092 -chr1 41477 . C T 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=116;Dels=0.00;FS=24.979;HaplotypeScore=26.4514;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-4.819;QD=2.26;ReadPosRankSum=-1.044;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,17:116:99:290,0,3370 -chr1 41490 . C T 1347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=120;Dels=0.00;FS=7.377;HaplotypeScore=103.2713;MLEAC=1;MLEAF=0.500;MQ=51.74;MQ0=0;MQRankSum=-4.581;QD=11.23;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,43:120:99:1376,0,2560 -chr1 41492 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.358;DP=122;Dels=0.00;FS=4.136;HaplotypeScore=109.9755;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-5.075;QD=4.19;ReadPosRankSum=0.670;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,27:122:99:540,0,3167 -chr1 41495 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=120;Dels=0.00;FS=6.076;HaplotypeScore=130.0290;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-4.101;QD=10.63;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:120:99:1304,0,2562 -chr1 41499 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=121;Dels=0.00;FS=8.830;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=4.822;QD=5.84;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,27:121:99:735,0,3300 -chr1 41500 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=123;Dels=0.00;FS=4.152;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.46;MQ0=0;MQRankSum=-4.922;QD=4.27;ReadPosRankSum=2.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,26:123:99:554,0,3500 -chr1 41503 . T C 2252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=119;Dels=0.00;FS=4.440;HaplotypeScore=73.1398;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-7.475;QD=18.93;ReadPosRankSum=0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,69:119:99:2281,0,1652 -chr1 41543 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=1.422;QD=1.67;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,12:94:99:185,0,2657 -chr1 41544 . C A 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=94;Dels=0.00;FS=5.349;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=0.591;QD=4.56;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:94:99:457,0,2138 -chr1 41562 . G A 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=90;Dels=0.00;FS=3.007;HaplotypeScore=34.8266;MLEAC=1;MLEAF=0.500;MQ=42.64;MQ0=0;MQRankSum=-0.632;QD=6.88;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,28:90:99:647,0,1945 -chr1 41564 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=55.5562;MLEAC=1;MLEAF=0.500;MQ=41.85;MQ0=0;MQRankSum=1.630;QD=1.23;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:99:130,0,2184 -chr1 41569 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.046;DP=76;Dels=0.00;FS=3.973;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.71;MQ0=0;MQRankSum=1.851;QD=5.79;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,18:76:99:468,0,1633 -chr1 41572 . T C 2032.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;DP=75;Dels=0.00;FS=1.682;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.70;MQ0=0;MQRankSum=-0.869;QD=27.11;ReadPosRankSum=-0.537;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,69:75:15:2061,0,15 -chr1 41574 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.327;DP=76;Dels=0.00;FS=3.699;HaplotypeScore=53.4650;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=0;MQRankSum=0.032;QD=9.00;ReadPosRankSum=3.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,25:76:99:712,0,1145 -chr1 41576 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=83;Dels=0.00;FS=1.310;HaplotypeScore=45.4818;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=-1.812;QD=0.39;ReadPosRankSum=-0.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:61:61,0,2187 -chr1 41587 . C T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=59.1819;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=0;MQRankSum=2.270;QD=10.01;ReadPosRankSum=1.892;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:969,0,1542 -chr1 41588 . T A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.902;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=56.1832;MLEAC=1;MLEAF=0.500;MQ=38.88;MQ0=0;MQRankSum=-1.330;QD=3.74;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,21:92:99:372,0,2076 -chr1 41597 . T A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=93;Dels=0.00;FS=1.013;HaplotypeScore=58.9239;MLEAC=1;MLEAF=0.500;MQ=39.40;MQ0=0;MQRankSum=-1.253;QD=3.26;ReadPosRankSum=-0.777;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,19:93:99:331,0,2049 -chr1 41612 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=94;Dels=0.00;FS=3.843;HaplotypeScore=30.0447;MLEAC=1;MLEAF=0.500;MQ=39.90;MQ0=0;MQRankSum=-1.714;QD=1.66;ReadPosRankSum=-0.857;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,15:94:99:184,0,2308 -chr1 41633 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=97;Dels=0.00;FS=0.962;HaplotypeScore=42.7026;MLEAC=1;MLEAF=0.500;MQ=41.75;MQ0=0;MQRankSum=-1.768;QD=4.76;ReadPosRankSum=1.633;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,23:97:99:490,0,2247 -chr1 41638 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.578;DP=99;Dels=0.00;FS=11.653;HaplotypeScore=45.8263;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=1.485;QD=4.36;ReadPosRankSum=-0.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,21:99:99:460,0,2342 -chr1 41642 . C T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=102;Dels=0.00;FS=4.287;HaplotypeScore=43.8379;MLEAC=1;MLEAF=0.500;MQ=42.97;MQ0=0;MQRankSum=-1.538;QD=0.99;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,12:102:99:129,0,2667 -chr1 41645 . G A 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=106;Dels=0.00;FS=2.304;HaplotypeScore=28.8553;MLEAC=1;MLEAF=0.500;MQ=42.92;MQ0=0;MQRankSum=-1.566;QD=1.82;ReadPosRankSum=-1.328;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:221,0,2816 -chr1 41657 . T C 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.271;DP=113;Dels=0.00;FS=4.518;HaplotypeScore=64.9583;MLEAC=1;MLEAF=0.500;MQ=44.13;MQ0=0;MQRankSum=-2.414;QD=4.06;ReadPosRankSum=1.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,23:113:99:487,0,2786 -chr1 41663 . A T 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.503;DP=114;Dels=0.00;FS=3.858;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=-1.442;QD=1.36;ReadPosRankSum=1.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,15:114:99:183,0,3367 -chr1 41665 . T A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=113;Dels=0.00;FS=3.826;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.28;MQ0=0;MQRankSum=-1.612;QD=1.48;ReadPosRankSum=1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,15:113:99:196,0,3343 -chr1 41669 . A G 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.192;DP=119;Dels=0.00;FS=4.933;HaplotypeScore=68.0952;MLEAC=1;MLEAF=0.500;MQ=45.13;MQ0=0;MQRankSum=-1.839;QD=2.10;ReadPosRankSum=0.185;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,19:119:99:278,0,3198 -chr1 41678 . T C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.051;DP=115;Dels=0.00;FS=6.885;HaplotypeScore=79.4081;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=0;MQRankSum=-3.479;QD=3.11;ReadPosRankSum=3.870;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,20:115:99:386,0,3047 -chr1 41679 . G A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.748;DP=111;Dels=0.00;FS=3.602;HaplotypeScore=78.4123;MLEAC=1;MLEAF=0.500;MQ=46.33;MQ0=0;MQRankSum=-3.517;QD=2.09;ReadPosRankSum=-0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,17:111:99:260,0,3158 -chr1 41680 . A C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=108;Dels=0.00;FS=1.071;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-3.109;QD=1.71;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,15:108:99:213,0,3172 -chr1 41687 . G C 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.837;DP=112;Dels=0.00;FS=2.333;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=0;MQRankSum=-2.828;QD=1.31;ReadPosRankSum=-0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,15:112:99:175,0,3221 -chr1 41717 . G C 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.104;DP=101;Dels=0.00;FS=10.379;HaplotypeScore=39.1666;MLEAC=1;MLEAF=0.500;MQ=42.12;MQ0=0;MQRankSum=-0.222;QD=1.90;ReadPosRankSum=2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,15:101:99:220,0,2653 -chr1 41723 . C T 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.845;DP=104;Dels=0.00;FS=7.631;HaplotypeScore=57.0647;MLEAC=1;MLEAF=0.500;MQ=41.47;MQ0=0;MQRankSum=0.585;QD=7.04;ReadPosRankSum=0.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,30:104:99:760,0,2081 -chr1 41727 . T C 1110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=103;Dels=0.00;FS=25.678;HaplotypeScore=89.0081;MLEAC=1;MLEAF=0.500;MQ=41.42;MQ0=0;MQRankSum=-2.718;QD=10.78;ReadPosRankSum=-0.518;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,43:103:99:1139,0,1804 -chr1 41733 . C T 126.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=101;Dels=0.00;FS=8.661;HaplotypeScore=68.3374;MLEAC=1;MLEAF=0.500;MQ=40.86;MQ0=0;MQRankSum=0.319;QD=1.26;ReadPosRankSum=0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,13:101:99:155,0,2688 -chr1 41760 . C T 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=84;Dels=0.00;FS=4.638;HaplotypeScore=16.6682;MLEAC=1;MLEAF=0.500;MQ=38.94;MQ0=0;MQRankSum=2.250;QD=7.74;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,26:84:99:678,0,1606 -chr1 41790 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.449;DP=72;Dels=0.00;FS=0.904;HaplotypeScore=22.5923;MLEAC=1;MLEAF=0.500;MQ=41.27;MQ0=0;MQRankSum=1.292;QD=12.39;ReadPosRankSum=1.235;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,34:72:99:920,0,1016 -chr1 41797 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=56;Dels=0.00;FS=17.110;HaplotypeScore=26.2547;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=0.349;QD=4.44;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:277,0,1304 -chr1 41816 . T C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.517;DP=70;Dels=0.00;FS=19.980;HaplotypeScore=12.2986;MLEAC=1;MLEAF=0.500;MQ=44.44;MQ0=0;MQRankSum=1.485;QD=5.95;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:445,0,1433 -chr1 41832 . A G 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.295;DP=72;Dels=0.00;FS=47.755;HaplotypeScore=25.8822;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=-5.914;QD=4.62;ReadPosRankSum=0.334;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,25:72:99:361,0,1584 -chr1 41839 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104;DP=75;Dels=0.00;FS=46.700;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=1;MQRankSum=-6.222;QD=5.20;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:418,0,1578 -chr1 41841 . A G 1684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=73;Dels=0.00;FS=17.617;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.38;MQ0=1;MQRankSum=3.993;QD=23.08;ReadPosRankSum=2.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,57:73:99:1713,0,219 -chr1 41855 . A G 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=75;Dels=0.00;FS=34.596;HaplotypeScore=5.5757;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=4;MQRankSum=-4.879;QD=2.30;ReadPosRankSum=2.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,17:75:99:201,0,1834 -chr1 41867 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=76;Dels=0.00;FS=7.041;HaplotypeScore=8.7104;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=4;MQRankSum=4.354;QD=8.84;ReadPosRankSum=-1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,24:76:99:700,0,1282 -chr1 41875 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.568;DP=73;Dels=0.00;FS=5.210;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.03;MQ0=4;MQRankSum=3.339;QD=10.49;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,25:73:99:794,0,1121 -chr1 41891 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=76.6927;MLEAC=1;MLEAF=0.500;MQ=45.05;MQ0=4;MQRankSum=1.412;QD=10.65;ReadPosRankSum=0.443;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,24:69:99:763,0,786 -chr1 41931 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=48.90;MQ0=3;MQRankSum=0.304;QD=11.97;ReadPosRankSum=1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:806,0,1148 -chr1 41946 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.696;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=51.55;MQ0=0;MQRankSum=-0.278;QD=14.11;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:776,0,935 -chr1 41954 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.11;MQ0=0;MQRankSum=-0.942;QD=15.68;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:812,0,822 -chr1 41991 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=56;Dels=0.00;FS=7.656;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=1.035;QD=12.37;ReadPosRankSum=0.654;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:721,0,1091 -chr1 42007 . G A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.444;DP=51;Dels=0.00;FS=10.314;HaplotypeScore=2.4441;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=1.161;QD=13.51;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:717,0,897 -chr1 42038 . G T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.265;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=5.5713;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=2.868;QD=10.28;ReadPosRankSum=0.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:532,0,906 -chr1 42046 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=52;Dels=0.00;FS=2.418;HaplotypeScore=4.5717;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=1;MQRankSum=-3.243;QD=17.82;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:955,0,706 -chr1 42061 . C T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.775;DP=49;Dels=0.00;FS=5.764;HaplotypeScore=4.9754;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=1;MQRankSum=3.673;QD=14.79;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:753,0,792 -chr1 42071 . C T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.982;DP=45;Dels=0.00;FS=4.388;HaplotypeScore=4.7774;MLEAC=1;MLEAF=0.500;MQ=49.26;MQ0=1;MQRankSum=-4.302;QD=15.22;ReadPosRankSum=-0.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:713,0,676 -chr1 42083 . G T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.128;DP=49;Dels=0.00;FS=4.144;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=1;MQRankSum=-4.087;QD=13.97;ReadPosRankSum=1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:713,0,858 -chr1 42196 . C T 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=73;Dels=0.00;FS=15.517;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=35.03;MQ0=7;MQRankSum=3.313;QD=10.94;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,28:73:99:827,0,820 -chr1 42204 . C T 644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.569;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.649;QD=10.40;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:673,0,666 -chr1 42208 . C T 643.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=19.1747;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.599;QD=10.38;ReadPosRankSum=2.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:672,0,666 -chr1 42212 . T A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=60;Dels=0.00;FS=12.104;HaplotypeScore=19.4395;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=6;MQRankSum=3.512;QD=10.15;ReadPosRankSum=2.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:637,0,656 -chr1 42221 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=65;Dels=0.00;FS=5.554;HaplotypeScore=8.9344;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=6;MQRankSum=-1.189;QD=9.63;ReadPosRankSum=0.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,30:65:99:654,0,793 -chr1 42234 . A G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=52;Dels=0.00;FS=7.954;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=36.56;MQ0=1;MQRankSum=-1.940;QD=11.46;ReadPosRankSum=0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:624,0,788 -chr1 42260 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;DP=42;Dels=0.00;FS=4.638;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=36.16;MQ0=0;MQRankSum=-1.412;QD=8.95;ReadPosRankSum=0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:404,0,716 -chr1 42263 . G A 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=37;Dels=0.00;FS=4.803;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=0.904;QD=14.56;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:567,0,421 -chr1 42280 . G A 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=36.50;MQ0=2;MQRankSum=0.805;QD=9.84;ReadPosRankSum=2.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:412,0,542 -chr1 42294 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.243;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=36.41;MQ0=2;MQRankSum=-0.883;QD=11.65;ReadPosRankSum=-0.558;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:436,0,494 -chr1 42316 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=38.47;MQ0=2;MQRankSum=-1.556;QD=10.46;ReadPosRankSum=-0.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:457,0,721 -chr1 42344 . C T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7128;MLEAC=1;MLEAF=0.500;MQ=39.55;MQ0=2;MQRankSum=1.059;QD=16.22;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:823,0,592 -chr1 42373 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.78;MQ0=0;MQRankSum=-1.866;QD=13.38;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:657,0,768 -chr1 42400 . A C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=4.7967;MLEAC=1;MLEAF=0.500;MQ=44.88;MQ0=0;MQRankSum=-2.723;QD=12.16;ReadPosRankSum=1.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:612,0,919 -chr1 42416 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.7990;MLEAC=1;MLEAF=0.500;MQ=44.11;MQ0=0;MQRankSum=2.735;QD=16.06;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:735,0,601 -chr1 42478 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.823;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.32;MQ0=1;MQRankSum=-2.431;QD=5.99;ReadPosRankSum=1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,10:21:99:154,0,359 -chr1 42486 . A G 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.373;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.44;MQ0=2;MQRankSum=-2.500;QD=6.25;ReadPosRankSum=0.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:172,0,350 -chr1 42535 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.226;QD=12.17;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,18:33:99:430,0,463 -chr1 42539 . G A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.544;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.381;QD=13.42;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,19:33:99:471,0,422 -chr1 42553 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=39.64;MQ0=2;MQRankSum=0.155;QD=15.72;ReadPosRankSum=-1.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:594,0,398 -chr1 42617 . A T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=1;MQRankSum=0.049;QD=7.30;ReadPosRankSum=-1.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:240,0,633 -chr1 42618 . A G 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.87;MQ0=1;MQRankSum=-0.029;QD=7.03;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:211,0,532 -chr1 42650 . A G 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=22;Dels=0.00;FS=1.719;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=37.75;MQ0=1;MQRankSum=-2.354;QD=6.58;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,9:22:99:173,0,443 -chr1 42680 . G T 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.405;DP=23;Dels=0.00;FS=1.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.36;MQ0=1;MQRankSum=-0.922;QD=17.95;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,17:23:99:441,0,171 -chr1 42698 . A G 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.880;DP=34;Dels=0.00;FS=3.589;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=48.79;MQ0=1;MQRankSum=-0.707;QD=22.93;ReadPosRankSum=1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,25:34:99:808,0,202 -chr1 42700 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.444;DP=35;Dels=0.00;FS=3.712;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=0.156;QD=5.31;ReadPosRankSum=-1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,9:35:99:214,0,848 -chr1 42723 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.200;DP=39;Dels=0.00;FS=3.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=1.358;QD=5.20;ReadPosRankSum=-2.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:231,0,953 -chr1 42747 . C T 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=-1.468;QD=21.23;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:835,0,401 -chr1 42749 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.407;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=2.557;QD=9.02;ReadPosRankSum=-1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,833 -chr1 42840 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.801;DP=40;Dels=0.00;FS=1.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=1;MQRankSum=0.745;QD=14.59;ReadPosRankSum=1.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:612,0,601 -chr1 42845 . A G 575.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=39;Dels=0.00;FS=1.210;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=0.482;QD=14.76;ReadPosRankSum=1.710;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:604,0,571 -chr1 42848 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.965;DP=41;Dels=0.00;FS=1.189;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=1;MQRankSum=0.720;QD=14.29;ReadPosRankSum=1.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:614,0,573 -chr1 42865 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=50;Dels=0.00;FS=4.589;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.645;QD=6.80;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,14:50:99:368,0,1156 -chr1 42867 . G A 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=50;Dels=0.00;FS=2.949;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.500;QD=5.86;ReadPosRankSum=1.965;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,13:50:99:321,0,1202 -chr1 42872 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=49;Dels=0.00;FS=2.969;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=1;MQRankSum=0.821;QD=23.85;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,36:49:99:1197,0,340 -chr1 42886 . C T 1072.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.810;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=2;MQRankSum=1.039;QD=21.46;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1101,0,484 -chr1 42890 . G T 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.510;DP=56;Dels=0.00;FS=1.156;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=2;MQRankSum=-0.672;QD=7.39;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,18:56:99:442,0,1293 -chr1 42926 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.287;DP=58;Dels=0.00;FS=7.798;HaplotypeScore=2.7439;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=-0.975;QD=20.50;ReadPosRankSum=0.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1217,0,729 -chr1 42980 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.991;QD=18.08;ReadPosRankSum=1.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:878,0,734 -chr1 43009 . G A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=2.090;QD=14.47;ReadPosRankSum=0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:578,0,652 -chr1 43030 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=40;Dels=0.00;FS=1.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-2.465;QD=14.89;ReadPosRankSum=-0.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:624,0,708 -chr1 43039 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.020;DP=38;Dels=0.00;FS=2.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.44;MQ0=0;MQRankSum=-1.493;QD=12.99;ReadPosRankSum=0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:522,0,755 -chr1 43040 . G A 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=40;Dels=0.00;FS=4.756;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.155;QD=13.87;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:583,0,758 -chr1 43061 . T A 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.626;DP=49;Dels=0.00;FS=4.322;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=0;MQRankSum=1.606;QD=17.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:893,0,625 -chr1 43067 . C T 855.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=4.058;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-0.462;QD=16.78;ReadPosRankSum=2.101;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:884,0,760 -chr1 43068 . G T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=2.286;QD=16.58;ReadPosRankSum=2.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:907,0,821 -chr1 43150 . T A 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=54;Dels=0.00;FS=2.461;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=1.401;QD=18.50;ReadPosRankSum=-1.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1027,0,700 -chr1 43153 . G A 1106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=58;Dels=0.00;FS=3.788;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=1.366;QD=19.08;ReadPosRankSum=-1.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1135,0,730 -chr1 43187 . G A 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.656;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-0.333;QD=14.13;ReadPosRankSum=0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:749,0,974 -chr1 43197 . G A 1062.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=58;Dels=0.00;FS=1.101;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=0.868;QD=18.32;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1091,0,879 -chr1 43231 . C A 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.226;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=0;MQRankSum=-0.040;QD=12.06;ReadPosRankSum=0.473;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,22:58:99:728,0,1277 -chr1 43246 . T C 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=72;Dels=0.00;FS=7.335;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=53.67;MQ0=0;MQRankSum=-3.808;QD=0.61;ReadPosRankSum=-2.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,8:72:72:72,0,2204 -chr1 43265 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=75;Dels=0.00;FS=7.472;HaplotypeScore=3.7546;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-3.233;QD=0.44;ReadPosRankSum=-2.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,7:75:61:61,0,2183 -chr1 43276 . G A 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.432;DP=69;Dels=0.00;FS=3.775;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-3.715;QD=1.13;ReadPosRankSum=1.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,9:69:99:106,0,2099 -chr1 43278 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.807;DP=70;Dels=0.00;FS=18.468;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-6.081;QD=5.05;ReadPosRankSum=2.009;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:382,0,1868 -chr1 43282 . A G 2155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.741;DP=72;Dels=0.00;FS=5.810;HaplotypeScore=18.7776;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=3.314;QD=29.94;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,62:72:99:2184,0,134 -chr1 43285 . G A 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.628;DP=73;Dels=0.00;FS=5.951;HaplotypeScore=50.5662;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-3.088;QD=1.42;ReadPosRankSum=2.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:132,0,2235 -chr1 43291 . C G 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=74;Dels=0.00;FS=19.101;HaplotypeScore=33.7389;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-3.986;QD=2.73;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:230,0,2102 -chr1 43293 . A T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.021;DP=71;Dels=0.00;FS=10.885;HaplotypeScore=23.8257;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=1;MQRankSum=-3.987;QD=2.73;ReadPosRankSum=2.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:222,0,1937 -chr1 43328 . C G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.840;DP=70;Dels=0.00;FS=18.175;HaplotypeScore=28.9637;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=1;MQRankSum=-1.433;QD=4.03;ReadPosRankSum=-2.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,16:70:99:310,0,1933 -chr1 43332 . G C 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;DP=68;Dels=0.00;FS=31.387;HaplotypeScore=27.9641;MLEAC=1;MLEAF=0.500;MQ=48.56;MQ0=2;MQRankSum=3.076;QD=5.57;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:407,0,1696 -chr1 43333 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.715;DP=63;Dels=0.00;FS=24.273;HaplotypeScore=25.9652;MLEAC=1;MLEAF=0.500;MQ=48.61;MQ0=2;MQRankSum=-3.220;QD=4.08;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:285,0,1646 -chr1 43371 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=73;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.66;MQ0=2;MQRankSum=2.809;QD=6.64;ReadPosRankSum=-0.324;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,18:73:99:513,0,1764 -chr1 43372 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=74;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.31;MQ0=3;MQRankSum=2.584;QD=6.60;ReadPosRankSum=-0.403;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,18:74:99:517,0,1762 -chr1 43392 . C T 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.597;DP=82;Dels=0.00;FS=11.173;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=2;MQRankSum=3.354;QD=9.66;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,27:82:99:820,0,1545 -chr1 43419 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.314;DP=85;Dels=0.00;FS=4.704;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.922;QD=0.80;ReadPosRankSum=-1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,15:85:96:96,0,2450 -chr1 43420 . T C 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=85;Dels=0.00;FS=8.730;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.994;QD=1.48;ReadPosRankSum=-1.438;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:154,0,2361 -chr1 43424 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=86;Dels=0.00;FS=5.028;HaplotypeScore=83.0946;MLEAC=1;MLEAF=0.500;MQ=52.08;MQ0=2;MQRankSum=2.883;QD=9.25;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,27:86:99:824,0,1702 -chr1 43442 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=81;Dels=0.00;FS=4.587;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=51.64;MQ0=1;MQRankSum=-5.183;QD=2.57;ReadPosRankSum=1.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,18:81:99:236,0,2162 -chr1 43464 . T C 1004.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=83;Dels=0.00;FS=6.657;HaplotypeScore=7.8783;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-7.377;QD=12.11;ReadPosRankSum=-0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,40:83:99:1033,0,1434 -chr1 43478 . C T 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=78;Dels=0.00;FS=2.728;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=1;MQRankSum=-1.601;QD=4.14;ReadPosRankSum=-1.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,15:78:99:351,0,2012 -chr1 43500 . C G 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=75;Dels=0.00;FS=9.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=1;MQRankSum=3.454;QD=2.78;ReadPosRankSum=-0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,12:75:99:237,0,2108 -chr1 43510 . A G 135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=78;Dels=0.00;FS=13.593;HaplotypeScore=39.7676;MLEAC=1;MLEAF=0.500;MQ=48.31;MQ0=1;MQRankSum=3.326;QD=1.74;ReadPosRankSum=-1.053;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:78:99:164,0,2251 -chr1 43512 . T C 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=79;Dels=0.00;FS=5.766;HaplotypeScore=29.7717;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=1;MQRankSum=-2.674;QD=5.09;ReadPosRankSum=-1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:430,0,1984 -chr1 43517 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=74;Dels=0.00;FS=7.633;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=47.06;MQ0=1;MQRankSum=-2.543;QD=0.98;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:101,0,2153 -chr1 43520 . C A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=74;Dels=0.00;FS=3.451;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.123;QD=0.54;ReadPosRankSum=0.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:68:68,0,2205 -chr1 43523 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=77;Dels=0.00;FS=9.238;HaplotypeScore=43.3257;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=1;MQRankSum=2.335;QD=0.44;ReadPosRankSum=-0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,7:77:62:62,0,2240 -chr1 43525 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=75;Dels=0.00;FS=2.429;HaplotypeScore=41.3363;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=1;MQRankSum=2.219;QD=4.41;ReadPosRankSum=0.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:359,0,1931 -chr1 43532 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=73;Dels=0.00;FS=11.099;HaplotypeScore=23.1272;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=2;MQRankSum=1.051;QD=8.75;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:667,0,1489 -chr1 43535 . C G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=71;Dels=0.00;FS=13.340;HaplotypeScore=30.0213;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=2;MQRankSum=1.228;QD=8.70;ReadPosRankSum=-0.541;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,24:71:99:646,0,1479 -chr1 43544 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=67;Dels=0.00;FS=8.590;HaplotypeScore=21.3628;MLEAC=1;MLEAF=0.500;MQ=43.73;MQ0=2;MQRankSum=-0.099;QD=12.70;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,30:67:99:879,0,1032 -chr1 43556 . A T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=50;Dels=0.00;FS=20.048;HaplotypeScore=10.4239;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=1;MQRankSum=1.405;QD=6.36;ReadPosRankSum=-0.232;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,981 -chr1 43562 . A C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.681;DP=50;Dels=0.00;FS=14.927;HaplotypeScore=31.3082;MLEAC=1;MLEAF=0.500;MQ=40.43;MQ0=1;MQRankSum=1.421;QD=7.74;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:415,0,1027 -chr1 43569 . T C 1156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.578;DP=43;Dels=0.00;FS=13.268;HaplotypeScore=30.7711;MLEAC=1;MLEAF=0.500;MQ=39.33;MQ0=1;MQRankSum=-1.864;QD=26.90;ReadPosRankSum=1.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,39:43:35:1185,0,35 -chr1 43572 . A G 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=45;Dels=0.00;FS=3.225;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=2;MQRankSum=-0.039;QD=6.37;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:315,0,750 -chr1 43594 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.410;DP=44;Dels=0.00;FS=5.674;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.55;MQ0=2;MQRankSum=0.307;QD=3.77;ReadPosRankSum=0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,10:44:99:194,0,793 -chr1 43610 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=33;Dels=0.00;FS=6.419;HaplotypeScore=4.5214;MLEAC=1;MLEAF=0.500;MQ=33.96;MQ0=2;MQRankSum=-0.609;QD=3.30;ReadPosRankSum=-0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:137,0,510 -chr1 43639 . C T 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=28;Dels=0.00;FS=3.565;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-1.029;QD=4.46;ReadPosRankSum=0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:153,0,405 -chr1 43643 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=13.8923;MLEAC=1;MLEAF=0.500;MQ=36.79;MQ0=1;MQRankSum=0.952;QD=1.16;ReadPosRankSum=-1.543;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,5:29:62:62,0,530 -chr1 43651 . G A 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=33;Dels=0.00;FS=1.393;HaplotypeScore=3.9569;MLEAC=1;MLEAF=0.500;MQ=39.46;MQ0=1;MQRankSum=1.499;QD=7.78;ReadPosRankSum=1.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:285,0,426 -chr1 43662 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.298;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=0;MQRankSum=0.474;QD=3.35;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,6:37:99:152,0,768 -chr1 43664 . A G 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=36;Dels=0.00;FS=5.877;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=45.71;MQ0=0;MQRankSum=-2.505;QD=4.72;ReadPosRankSum=-0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,11:36:99:198,0,750 -chr1 43668 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=39;Dels=0.00;FS=8.049;HaplotypeScore=10.2065;MLEAC=1;MLEAF=0.500;MQ=45.43;MQ0=0;MQRankSum=-2.825;QD=7.71;ReadPosRankSum=-0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:329,0,752 -chr1 43678 . T A 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=52;Dels=0.00;FS=11.972;HaplotypeScore=19.6024;MLEAC=1;MLEAF=0.500;MQ=44.28;MQ0=0;MQRankSum=-1.814;QD=3.86;ReadPosRankSum=1.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,12:52:99:229,0,1169 -chr1 43688 . C T 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=30.3912;MLEAC=1;MLEAF=0.500;MQ=43.92;MQ0=0;MQRankSum=4.253;QD=8.54;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,17:55:99:498,0,1002 -chr1 43698 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;DP=67;Dels=0.00;FS=8.840;HaplotypeScore=47.7369;MLEAC=1;MLEAF=0.500;MQ=45.08;MQ0=0;MQRankSum=-4.239;QD=8.07;ReadPosRankSum=-0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,26:67:99:569,0,1255 -chr1 43705 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=69;Dels=0.00;FS=3.045;HaplotypeScore=32.6622;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=-0.571;QD=2.33;ReadPosRankSum=0.145;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,10:69:99:189,0,1720 -chr1 43713 . A C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.553;DP=77;Dels=0.00;FS=11.201;HaplotypeScore=42.6440;MLEAC=1;MLEAF=0.500;MQ=45.67;MQ0=0;MQRankSum=-5.163;QD=8.23;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,32:77:99:662,0,1440 -chr1 43719 . A T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=81;Dels=0.00;FS=4.781;HaplotypeScore=21.7031;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=-0.691;QD=1.52;ReadPosRankSum=-0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,10:81:99:151,0,2102 -chr1 43742 . A T 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.288;DP=82;Dels=0.00;FS=35.671;HaplotypeScore=38.7529;MLEAC=1;MLEAF=0.500;MQ=46.28;MQ0=0;MQRankSum=1.619;QD=4.07;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,15:82:99:362,0,1988 -chr1 43754 . G A 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.834;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.306;QD=4.89;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:424,0,1874 -chr1 43755 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.189;QD=4.47;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:390,0,1864 -chr1 43771 . C T 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=17.4268;MLEAC=1;MLEAF=0.500;MQ=48.68;MQ0=0;MQRankSum=-0.578;QD=0.63;ReadPosRankSum=-0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,9:84:81:81,0,2479 -chr1 43781 . A C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=27.2915;MLEAC=1;MLEAF=0.500;MQ=50.47;MQ0=0;MQRankSum=-1.448;QD=1.76;ReadPosRankSum=-0.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:99:185,0,2613 -chr1 43786 . G A 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=84;Dels=0.00;FS=1.288;HaplotypeScore=17.3780;MLEAC=1;MLEAF=0.500;MQ=51.33;MQ0=0;MQRankSum=-1.617;QD=1.74;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:174,0,2552 -chr1 43806 . T C 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=35.5387;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-6.251;QD=15.98;ReadPosRankSum=0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,41:82:99:1339,0,1390 -chr1 43810 . C T 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=79;Dels=0.00;FS=10.312;HaplotypeScore=35.5390;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=0;MQRankSum=-2.175;QD=1.48;ReadPosRankSum=1.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:79:99:145,0,2427 -chr1 43816 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=76;Dels=0.00;FS=1.622;HaplotypeScore=86.3319;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-2.822;QD=2.44;ReadPosRankSum=1.394;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,11:76:99:214,0,1931 -chr1 43821 . G A 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.751;DP=80;Dels=0.00;FS=3.003;HaplotypeScore=41.4503;MLEAC=1;MLEAF=0.500;MQ=52.13;MQ0=2;MQRankSum=-3.694;QD=4.70;ReadPosRankSum=0.476;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,16:80:99:404,0,2083 -chr1 43823 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=47.4468;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=3.459;QD=8.60;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,24:81:99:725,0,1844 -chr1 43834 . A C 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.959;DP=87;Dels=0.00;FS=5.047;HaplotypeScore=27.3319;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=2;MQRankSum=-6.863;QD=11.49;ReadPosRankSum=1.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1028,0,1538 -chr1 43840 . C T 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.139;DP=85;Dels=0.00;FS=1.532;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=2;MQRankSum=-0.945;QD=1.09;ReadPosRankSum=-1.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,11:85:99:121,0,2480 -chr1 43841 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=88;Dels=0.00;FS=8.668;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=2;MQRankSum=-6.447;QD=6.87;ReadPosRankSum=1.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:633,0,2003 -chr1 43864 . G A 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.505;DP=94;Dels=0.00;FS=1.845;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.56;MQ0=3;MQRankSum=3.253;QD=11.17;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:1078,0,1669 -chr1 43866 . G C 1601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.813;DP=89;Dels=0.00;FS=2.991;HaplotypeScore=55.7192;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=3;MQRankSum=6.796;QD=18.00;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,49:89:99:1630,0,963 -chr1 43877 . T G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.373;DP=82;Dels=0.00;FS=4.511;HaplotypeScore=22.6567;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=3;MQRankSum=-6.816;QD=8.86;ReadPosRankSum=-0.734;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,34:82:99:755,0,1613 -chr1 43880 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=81;Dels=0.00;FS=3.784;HaplotypeScore=34.1328;MLEAC=1;MLEAF=0.500;MQ=47.59;MQ0=3;MQRankSum=4.821;QD=5.75;ReadPosRankSum=0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,19:81:99:494,0,1845 -chr1 43895 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.900;DP=84;Dels=0.00;FS=3.557;HaplotypeScore=5.7833;MLEAC=1;MLEAF=0.500;MQ=47.29;MQ0=3;MQRankSum=3.874;QD=6.95;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:612,0,1874 -chr1 43919 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.966;DP=90;Dels=0.00;FS=10.596;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=48.00;MQ0=3;MQRankSum=-3.047;QD=1.38;ReadPosRankSum=2.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:90:99:152,0,2472 -chr1 43921 . C T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;DP=89;Dels=0.00;FS=11.456;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=3;MQRankSum=-0.291;QD=12.58;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,38:89:99:1148,0,1412 -chr1 43929 . G C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.254;DP=96;Dels=0.00;FS=0.861;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.78;MQ0=4;MQRankSum=4.123;QD=8.49;ReadPosRankSum=0.847;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,31:96:99:843,0,1928 -chr1 43954 . G A 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=98;Dels=0.00;FS=3.403;HaplotypeScore=31.4020;MLEAC=1;MLEAF=0.500;MQ=48.81;MQ0=3;MQRankSum=-1.940;QD=5.12;ReadPosRankSum=-1.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:530,0,2436 -chr1 43958 . T C 1162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=98;Dels=0.00;FS=0.772;HaplotypeScore=41.3969;MLEAC=1;MLEAF=0.500;MQ=49.49;MQ0=3;MQRankSum=-3.408;QD=11.86;ReadPosRankSum=0.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,42:98:99:1191,0,1753 -chr1 43966 . G T 228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.214;DP=107;Dels=0.00;FS=4.094;HaplotypeScore=60.8308;MLEAC=1;MLEAF=0.500;MQ=49.53;MQ0=3;MQRankSum=-0.729;QD=2.14;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,14:107:99:257,0,2992 -chr1 43969 . G A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=107;Dels=0.00;FS=1.978;HaplotypeScore=35.1970;MLEAC=1;MLEAF=0.500;MQ=49.50;MQ0=3;MQRankSum=-2.173;QD=5.55;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,27:107:99:622,0,2650 -chr1 43976 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.740;DP=112;Dels=0.00;FS=3.944;HaplotypeScore=55.4395;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=4;MQRankSum=-1.018;QD=2.50;ReadPosRankSum=-0.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,15:112:99:308,0,3072 -chr1 43984 . G A 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=118;Dels=0.00;FS=2.892;HaplotypeScore=75.9412;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=4;MQRankSum=0.547;QD=6.90;ReadPosRankSum=-0.638;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,29:118:99:842,0,2830 -chr1 43988 . A C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=116;Dels=0.00;FS=5.433;HaplotypeScore=43.4214;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=4;MQRankSum=4.795;QD=7.25;ReadPosRankSum=-1.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:116:99:869,0,2451 -chr1 44002 . A G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=116;Dels=0.00;FS=0.958;HaplotypeScore=39.4904;MLEAC=1;MLEAF=0.500;MQ=51.56;MQ0=3;MQRankSum=-2.313;QD=3.79;ReadPosRankSum=1.726;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,20:116:99:468,0,2935 -chr1 44007 . T A 1436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.367;DP=111;Dels=0.00;FS=6.411;HaplotypeScore=43.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=3;MQRankSum=-6.177;QD=12.94;ReadPosRankSum=0.970;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,51:111:99:1465,0,1937 -chr1 44026 . T C 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.135;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=6.8459;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=-3.383;QD=0.29;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,12:110:60:60,0,3255 -chr1 44060 . T C 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=84;Dels=0.00;FS=2.470;HaplotypeScore=22.4896;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=4.395;QD=5.53;ReadPosRankSum=0.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,20:84:99:493,0,2021 -chr1 44069 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.048;DP=73;Dels=0.00;FS=3.136;HaplotypeScore=49.4176;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-5.204;QD=3.39;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,13:73:99:276,0,1726 -chr1 44072 . T A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=71;Dels=0.00;FS=1.293;HaplotypeScore=23.4451;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.737;QD=3.56;ReadPosRankSum=-1.197;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:281,0,1830 -chr1 44082 . C T 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=69;Dels=0.00;FS=10.437;HaplotypeScore=20.4044;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.783;QD=3.49;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,13:69:99:269,0,1813 -chr1 44096 . C T 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=19.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=0;MQRankSum=4.352;QD=10.13;ReadPosRankSum=1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,20:60:99:636,0,1132 -chr1 44102 . A C 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.658;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.00;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:122,0,1452 -chr1 44103 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.14;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:129,0,1433 -chr1 44111 . T A 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=55;Dels=0.00;FS=2.927;HaplotypeScore=2.1550;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.824;QD=3.38;ReadPosRankSum=-0.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,13:55:99:214,0,1474 -chr1 44117 . C T 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=61;Dels=0.00;FS=5.158;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-3.964;QD=2.88;ReadPosRankSum=0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,12:61:99:204,0,1632 -chr1 44120 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=63;Dels=0.00;FS=5.124;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-4.000;QD=2.69;ReadPosRankSum=1.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:198,0,1749 -chr1 44126 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.677;DP=63;Dels=0.00;FS=8.122;HaplotypeScore=17.4822;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=-4.789;QD=6.36;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,21:63:99:429,0,1420 -chr1 44145 . T A 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.048;DP=72;Dels=0.00;FS=14.645;HaplotypeScore=3.9967;MLEAC=1;MLEAF=0.500;MQ=50.27;MQ0=0;MQRankSum=-4.480;QD=6.77;ReadPosRankSum=2.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:516,0,1706 -chr1 44157 . T C 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.780;DP=70;Dels=0.00;FS=5.275;HaplotypeScore=5.7502;MLEAC=1;MLEAF=0.500;MQ=49.89;MQ0=0;MQRankSum=-1.502;QD=1.11;ReadPosRankSum=2.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,10:70:99:106,0,2013 -chr1 44177 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;DP=73;Dels=0.00;FS=7.693;HaplotypeScore=14.5600;MLEAC=1;MLEAF=0.500;MQ=49.07;MQ0=0;MQRankSum=0.080;QD=7.48;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,20:73:99:574,0,1711 -chr1 44183 . T C 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=73;Dels=0.00;FS=3.202;HaplotypeScore=50.8308;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=0;MQRankSum=-1.131;QD=1.08;ReadPosRankSum=-0.425;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:107,0,2164 -chr1 44188 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=74;Dels=0.00;FS=14.435;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=0;MQRankSum=-4.140;QD=6.90;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,24:74:99:539,0,1696 -chr1 44191 . C G 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=78;Dels=0.00;FS=1.989;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=0;MQRankSum=3.081;QD=11.29;ReadPosRankSum=1.210;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,29:78:99:909,0,1490 -chr1 44202 . T C 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=70;Dels=0.00;FS=18.949;HaplotypeScore=45.1512;MLEAC=1;MLEAF=0.500;MQ=50.32;MQ0=0;MQRankSum=-3.780;QD=4.45;ReadPosRankSum=-1.041;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,17:70:99:340,0,1880 -chr1 44205 . T G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.786;DP=71;Dels=0.00;FS=2.009;HaplotypeScore=52.8564;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=2.066;QD=13.29;ReadPosRankSum=0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,30:71:99:972,0,1251 -chr1 44214 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=65;Dels=0.00;FS=6.471;HaplotypeScore=49.1081;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-3.604;QD=0.55;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,8:65:64:64,0,1916 -chr1 44224 . C T 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=65;Dels=0.00;FS=11.066;HaplotypeScore=41.7947;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=3.011;QD=10.97;ReadPosRankSum=-1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:741,0,1311 -chr1 44226 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.161;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=0.468;QD=10.58;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:663,0,1231 -chr1 44227 . T C 1771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=60;Dels=0.00;FS=3.739;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=3.270;QD=29.53;ReadPosRankSum=-1.934;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,52:60:43:1800,0,43 -chr1 44240 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=2.627;HaplotypeScore=23.3747;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=2.800;QD=10.58;ReadPosRankSum=1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:536,0,932 -chr1 44248 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=9.054;HaplotypeScore=23.3746;MLEAC=1;MLEAF=0.500;MQ=50.11;MQ0=0;MQRankSum=-4.405;QD=3.08;ReadPosRankSum=2.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,10:48:99:176,0,1356 -chr1 44249 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.419;DP=49;Dels=0.00;FS=8.239;HaplotypeScore=24.3740;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.565;QD=3.65;ReadPosRankSum=1.809;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:207,0,1354 -chr1 44258 . T A 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.562;DP=54;Dels=0.00;FS=4.366;HaplotypeScore=24.1638;MLEAC=1;MLEAF=0.500;MQ=48.73;MQ0=0;MQRankSum=4.329;QD=10.64;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:603,0,1025 -chr1 44282 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=57;Dels=0.00;FS=1.055;HaplotypeScore=8.1141;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=0;MQRankSum=4.194;QD=11.70;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,24:57:99:695,0,881 -chr1 44304 . T C 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=23.9832;MLEAC=1;MLEAF=0.500;MQ=43.23;MQ0=2;MQRankSum=4.033;QD=11.74;ReadPosRankSum=0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,25:62:99:756,0,963 -chr1 44307 . C G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.815;DP=60;Dels=0.00;FS=6.252;HaplotypeScore=26.1832;MLEAC=1;MLEAF=0.500;MQ=43.38;MQ0=2;MQRankSum=-0.025;QD=7.33;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:468,0,1201 -chr1 44311 . A G 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.265;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=30.9134;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=2;MQRankSum=-2.338;QD=10.90;ReadPosRankSum=-0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,29:60:99:682,0,949 -chr1 44317 . T A 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.835;DP=59;Dels=0.00;FS=4.227;HaplotypeScore=16.7737;MLEAC=1;MLEAF=0.500;MQ=42.80;MQ0=2;MQRankSum=0.606;QD=6.47;ReadPosRankSum=-2.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:410,0,1154 -chr1 44342 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=61;Dels=0.00;FS=4.324;HaplotypeScore=34.0871;MLEAC=1;MLEAF=0.500;MQ=42.11;MQ0=2;MQRankSum=-1.601;QD=6.18;ReadPosRankSum=0.691;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,16:61:99:405,0,1260 -chr1 44367 . C T 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=9.9194;MLEAC=1;MLEAF=0.500;MQ=42.27;MQ0=2;MQRankSum=2.251;QD=15.05;ReadPosRankSum=0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:886,0,731 -chr1 44414 . C T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.135;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=14.3006;MLEAC=1;MLEAF=0.500;MQ=44.91;MQ0=0;MQRankSum=0.590;QD=12.70;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:714,0,919 -chr1 44417 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.333;DP=59;Dels=0.00;FS=7.276;HaplotypeScore=15.3006;MLEAC=1;MLEAF=0.500;MQ=45.19;MQ0=0;MQRankSum=-3.435;QD=2.13;ReadPosRankSum=-2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:154,0,1624 -chr1 44447 . T C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.70;MQ0=0;MQRankSum=-0.207;QD=1.35;ReadPosRankSum=-0.960;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,7:57:99:105,0,1613 -chr1 44452 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=58;Dels=0.00;FS=3.537;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.96;MQ0=0;MQRankSum=-0.530;QD=2.01;ReadPosRankSum=-0.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,8:58:99:145,0,1592 -chr1 44473 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=69;Dels=0.00;FS=9.852;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=-4.187;QD=0.71;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,12:69:77:77,0,2026 -chr1 44477 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.028;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=0;MQRankSum=-0.984;QD=1.30;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:118,0,1985 -chr1 44478 . G C 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.175;DP=70;Dels=0.00;FS=1.536;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.34;MQ0=0;MQRankSum=-0.858;QD=1.21;ReadPosRankSum=2.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,8:70:99:113,0,2020 -chr1 44484 . A G 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=36.7273;MLEAC=1;MLEAF=0.500;MQ=45.51;MQ0=0;MQRankSum=-1.246;QD=1.13;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:106,0,1981 -chr1 44498 . A C 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=59;Dels=0.03;FS=1.285;HaplotypeScore=66.6807;MLEAC=1;MLEAF=0.500;MQ=46.25;MQ0=0;MQRankSum=1.067;QD=5.03;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,12:57:99:325,0,1534 -chr1 44501 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.558;DP=54;Dels=0.00;FS=2.868;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=0.142;QD=6.25;ReadPosRankSum=-0.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,13:54:99:366,0,1280 -chr1 44503 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=55;Dels=0.00;FS=2.476;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=-0.130;QD=18.18;ReadPosRankSum=1.776;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1028,0,672 -chr1 44505 . T C 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.716;DP=56;Dels=0.00;FS=1.565;HaplotypeScore=46.3941;MLEAC=1;MLEAF=0.500;MQ=46.01;MQ0=0;MQRankSum=-0.697;QD=1.69;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:56:99:123,0,1510 -chr1 44517 . G A 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=8.8138;MLEAC=1;MLEAF=0.500;MQ=44.77;MQ0=0;MQRankSum=-3.350;QD=2.42;ReadPosRankSum=2.577;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,11:54:99:159,0,1479 -chr1 44560 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=43;Dels=0.00;FS=9.300;HaplotypeScore=4.7566;MLEAC=1;MLEAF=0.500;MQ=41.88;MQ0=0;MQRankSum=0.807;QD=9.95;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:456,0,729 -chr1 44587 . T C 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.665;DP=38;Dels=0.00;FS=13.265;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=40.46;MQ0=0;MQRankSum=-1.286;QD=9.10;ReadPosRankSum=-0.547;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:374,0,691 -chr1 44614 . C G 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.420;DP=43;Dels=0.00;FS=1.868;HaplotypeScore=14.4733;MLEAC=1;MLEAF=0.500;MQ=42.93;MQ0=0;MQRankSum=0.020;QD=1.11;ReadPosRankSum=0.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,6:43:76:76,0,1119 -chr1 44632 . A T 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=54;Dels=0.00;FS=2.363;HaplotypeScore=21.5373;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=1.153;QD=12.81;ReadPosRankSum=-0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:720,0,934 -chr1 44637 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=22.5160;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=-0.673;QD=1.44;ReadPosRankSum=0.812;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,9:54:99:106,0,1529 -chr1 44657 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=58;Dels=0.00;FS=2.599;HaplotypeScore=22.8584;MLEAC=1;MLEAF=0.500;MQ=44.43;MQ0=0;MQRankSum=2.619;QD=7.03;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:58:99:436,0,1315 -chr1 44666 . T C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=4.523;HaplotypeScore=18.8632;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=0;MQRankSum=-3.198;QD=5.00;ReadPosRankSum=0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,14:51:99:283,0,1321 -chr1 44682 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=48;Dels=0.00;FS=1.217;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=44.53;MQ0=0;MQRankSum=-2.438;QD=21.25;ReadPosRankSum=-0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,34:48:99:1048,0,416 -chr1 44721 . A T 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=38;Dels=0.00;FS=2.913;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=0;MQRankSum=1.227;QD=11.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:471,0,475 -chr1 44722 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=40;Dels=0.00;FS=1.222;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.48;MQ0=0;MQRankSum=0.137;QD=8.77;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:379,0,602 -chr1 44844 . C T 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.998;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=13.6215;MLEAC=1;MLEAF=0.500;MQ=39.32;MQ0=0;MQRankSum=0.233;QD=13.06;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,25:50:99:681,0,649 -chr1 44875 . C T 224.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=6.7552;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=0;MQRankSum=-1.397;QD=3.57;ReadPosRankSum=-1.910;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,14:63:99:253,0,1577 -chr1 44905 . C G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.316;DP=72;Dels=0.00;FS=2.379;HaplotypeScore=14.6636;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=1;MQRankSum=0.928;QD=8.39;ReadPosRankSum=-1.284;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,23:72:99:632,0,1456 -chr1 44912 . A G 1743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677;DP=68;Dels=0.00;FS=1.336;HaplotypeScore=30.8580;MLEAC=1;MLEAF=0.500;MQ=43.96;MQ0=2;MQRankSum=-0.403;QD=25.64;ReadPosRankSum=-1.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,53:68:99:1772,0,267 -chr1 44920 . T C 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.714;DP=73;Dels=0.00;FS=7.931;HaplotypeScore=5.9984;MLEAC=1;MLEAF=0.500;MQ=42.33;MQ0=4;MQRankSum=-0.128;QD=5.48;ReadPosRankSum=1.793;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,21:73:99:428,0,1524 -chr1 44950 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=38.40;MQ0=5;MQRankSum=0.127;QD=7.52;ReadPosRankSum=1.502;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,23:72:99:570,0,1227 -chr1 44980 . T G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=53;Dels=0.00;FS=1.794;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=32.25;MQ0=6;MQRankSum=0.207;QD=17.41;ReadPosRankSum=-1.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,47:53:53:951,0,53 -chr1 44999 . A G 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=6;MQRankSum=-2.111;QD=4.22;ReadPosRankSum=-0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:231,0,671 -chr1 45005 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=44;Dels=0.00;FS=5.608;HaplotypeScore=21.5580;MLEAC=1;MLEAF=0.500;MQ=30.42;MQ0=4;MQRankSum=1.637;QD=10.11;ReadPosRankSum=1.096;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:473,0,341 -chr1 45055 . C T 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.634;DP=71;Dels=0.00;FS=12.767;HaplotypeScore=11.6629;MLEAC=1;MLEAF=0.500;MQ=43.94;MQ0=9;MQRankSum=-0.438;QD=0.94;ReadPosRankSum=-0.182;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:53,15:71:95:95,0,1604 -chr1 45090 . C T 1075.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=87;Dels=0.00;FS=4.246;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=3.081;QD=12.37;ReadPosRankSum=-0.758;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,34:87:99:1104,0,1445 -chr1 45092 . C T 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=86;Dels=0.00;FS=18.933;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=1;MQRankSum=-0.050;QD=0.57;ReadPosRankSum=-0.221;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:77,9:86:77:77,0,2524 -chr1 45093 . A C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=84;Dels=0.04;FS=4.282;HaplotypeScore=44.0211;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=1;MQRankSum=-2.754;QD=0.47;ReadPosRankSum=0.306;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,16:81:68:68,0,2273 -chr1 45100 . A T 1063.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=91;Dels=0.00;FS=1.785;HaplotypeScore=46.2820;MLEAC=1;MLEAF=0.500;MQ=50.63;MQ0=1;MQRankSum=0.114;QD=11.69;ReadPosRankSum=1.119;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,34:91:99:1092,0,1575 -chr1 45104 . C T 1245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.511;DP=93;Dels=0.00;FS=5.290;HaplotypeScore=20.4240;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=1;MQRankSum=1.122;QD=13.40;ReadPosRankSum=-0.845;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1274,0,1627 -chr1 45135 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.219;DP=93;Dels=0.00;FS=0.788;HaplotypeScore=3.1233;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=0.496;QD=15.87;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,46:93:99:1504,0,1552 -chr1 45271 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.331;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=0.761;QD=14.36;ReadPosRankSum=-0.072;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,26:58:99:861,0,1025 -chr1 45286 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7329;MLEAC=1;MLEAF=0.500;MQ=49.43;MQ0=0;MQRankSum=0.497;QD=16.06;ReadPosRankSum=0.752;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,31:64:99:1056,0,1087 -chr1 45290 . T A 1146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;DP=65;Dels=0.00;FS=2.073;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=49.75;MQ0=0;MQRankSum=-0.151;QD=17.64;ReadPosRankSum=0.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1175,0,1019 -chr1 45343 . T A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.611;DP=74;Dels=0.00;FS=3.119;HaplotypeScore=3.9919;MLEAC=1;MLEAF=0.500;MQ=51.54;MQ0=0;MQRankSum=1.189;QD=16.85;ReadPosRankSum=0.605;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,37:74:99:1275,0,1131 -chr1 45377 . C T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=72;Dels=0.00;FS=27.679;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-2.895;QD=0.71;ReadPosRankSum=-1.328;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,9:72:79:79,0,2293 -chr1 45401 . T G 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=75;Dels=0.00;FS=42.438;HaplotypeScore=1.8656;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-2.624;QD=2.74;ReadPosRankSum=2.484;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,13:75:99:234,0,2260 -chr1 45425 . T C 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=62;Dels=0.00;FS=32.888;HaplotypeScore=11.8192;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.715;QD=3.33;ReadPosRankSum=2.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,12:62:99:235,0,1811 -chr1 45430 . C A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.713;DP=50;Dels=0.00;FS=4.121;HaplotypeScore=21.6418;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=0.980;QD=12.74;ReadPosRankSum=0.446;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,20:50:99:665,0,987 -chr1 45436 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.196;DP=48;Dels=0.00;FS=17.629;HaplotypeScore=19.6275;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-3.668;QD=3.45;ReadPosRankSum=0.470;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:38,10:48:99:194,0,1412 -chr1 45442 . G A 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.766;DP=53;Dels=0.00;FS=20.851;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-3.761;QD=3.49;ReadPosRankSum=-0.055;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,11:53:99:213,0,1458 -chr1 45445 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=54;Dels=0.00;FS=3.890;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=0.857;QD=15.44;ReadPosRankSum=-0.441;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,26:54:99:862,0,877 -chr1 45456 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=47;Dels=0.00;FS=15.317;HaplotypeScore=22.9164;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-2.324;QD=20.91;ReadPosRankSum=-1.560;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,31:47:99:1011,0,399 -chr1 45458 . C A 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.943;DP=49;Dels=0.00;FS=1.157;HaplotypeScore=24.9247;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=0.389;QD=9.83;ReadPosRankSum=0.305;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,17:49:99:510,0,1061 -chr1 45460 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.945;DP=51;Dels=0.00;FS=20.268;HaplotypeScore=33.8333;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-2.966;QD=2.00;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,8:51:99:130,0,1482 -chr1 45468 . T C 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.974;DP=54;Dels=0.00;FS=11.572;HaplotypeScore=42.6787;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=3.688;QD=9.07;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,17:54:99:518,0,1120 -chr1 45469 . C G 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=54;Dels=0.00;FS=25.872;HaplotypeScore=26.8594;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-2.910;QD=1.38;ReadPosRankSum=-0.791;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,8:54:99:103,0,1615 -chr1 45473 . G A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.252;DP=57;Dels=0.00;FS=27.090;HaplotypeScore=18.7370;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=0;MQRankSum=-3.140;QD=1.47;ReadPosRankSum=-0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,9:57:99:112,0,1689 -chr1 45486 . T G 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=59;Dels=0.00;FS=26.386;HaplotypeScore=19.2723;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.044;QD=0.72;ReadPosRankSum=-0.122;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:51,8:59:71:71,0,1772 -chr1 45491 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.621;DP=56;Dels=0.00;FS=11.681;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=2.678;QD=7.98;ReadPosRankSum=-0.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:39,16:56:99:475,0,1141 -chr1 45492 . A C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=56;Dels=0.00;FS=36.390;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-3.873;QD=1.34;ReadPosRankSum=-0.513;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,10:56:99:103,0,1545 -chr1 45515 . A C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=55;Dels=0.00;FS=18.588;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.91;MQ0=0;MQRankSum=1.483;QD=4.54;ReadPosRankSum=1.105;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,11:55:99:278,0,1358 -chr1 45516 . T C 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=55;Dels=0.00;FS=32.991;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.72;MQ0=0;MQRankSum=-5.064;QD=1.89;ReadPosRankSum=0.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,12:55:99:132,0,1550 -chr1 45518 . C T 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102;DP=57;Dels=0.00;FS=26.291;HaplotypeScore=37.5622;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-5.240;QD=2.29;ReadPosRankSum=-0.162;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,13:57:99:159,0,1581 -chr1 45530 . G A 1057.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=61;Dels=0.00;FS=1.071;HaplotypeScore=2.8319;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=4.182;QD=17.34;ReadPosRankSum=-0.133;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,32:61:99:1086,0,615 -chr1 45549 . G A 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.457;DP=67;Dels=0.00;FS=21.346;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=45.62;MQ0=1;MQRankSum=1.140;QD=2.58;ReadPosRankSum=0.504;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:58,9:67:99:201,0,1627 -chr1 45550 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.636;DP=67;Dels=0.00;FS=0.940;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=46.27;MQ0=1;MQRankSum=-4.933;QD=9.31;ReadPosRankSum=0.982;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,33:67:99:652,0,1160 -chr1 45576 . A T 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=86;Dels=0.00;FS=0.996;HaplotypeScore=31.9081;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.062;QD=5.30;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,26:86:99:484,0,1787 -chr1 45578 . A G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.189;DP=84;Dels=0.00;FS=6.011;HaplotypeScore=57.3640;MLEAC=1;MLEAF=0.500;MQ=44.80;MQ0=1;MQRankSum=-6.448;QD=10.99;ReadPosRankSum=-1.326;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,44:84:99:951,0,1314 -chr1 45586 . T C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=80;Dels=0.00;FS=1.341;HaplotypeScore=88.2105;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.105;QD=0.92;ReadPosRankSum=-0.165;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:102,0,2084 -chr1 45587 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=80;Dels=0.00;FS=1.232;HaplotypeScore=75.5755;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.092;QD=1.20;ReadPosRankSum=-0.086;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:124,0,2088 -chr1 45588 . A G 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=81;Dels=0.00;FS=1.248;HaplotypeScore=76.3642;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=1;MQRankSum=-4.082;QD=1.15;ReadPosRankSum=0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:67,14:81:99:121,0,2109 -chr1 45600 . G A 1328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=109;Dels=0.00;FS=1.699;HaplotypeScore=36.6790;MLEAC=1;MLEAF=0.500;MQ=42.25;MQ0=2;MQRankSum=-6.013;QD=12.19;ReadPosRankSum=0.815;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,63:109:99:1357,0,1334 -chr1 45609 . A C 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=114;Dels=0.00;FS=0.838;HaplotypeScore=28.9230;MLEAC=1;MLEAF=0.500;MQ=42.08;MQ0=2;MQRankSum=-1.161;QD=6.55;ReadPosRankSum=1.490;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,34:114:99:775,0,2078 -chr1 45619 . C T 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=119;Dels=0.00;FS=2.580;HaplotypeScore=3.6750;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=2;MQRankSum=-0.216;QD=7.02;ReadPosRankSum=1.214;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:83,36:119:99:864,0,1946 -chr1 45632 . G T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=119;Dels=0.00;FS=0.893;HaplotypeScore=6.6304;MLEAC=1;MLEAF=0.500;MQ=40.17;MQ0=2;MQRankSum=-5.708;QD=2.94;ReadPosRankSum=1.745;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,37:119:99:378,0,2346 -chr1 45659 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.317;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=71.6402;MLEAC=1;MLEAF=0.500;MQ=41.20;MQ0=3;MQRankSum=-6.632;QD=3.24;ReadPosRankSum=0.893;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,39:120:99:417,0,2397 -chr1 45660 . A G 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.966;DP=117;Dels=0.00;FS=2.575;HaplotypeScore=63.3294;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=3;MQRankSum=-1.543;QD=0.31;ReadPosRankSum=1.048;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:117:64:64,0,2593 -chr1 45672 . T G 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=105;Dels=0.00;FS=0.751;HaplotypeScore=110.4878;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=2;MQRankSum=-5.196;QD=8.45;ReadPosRankSum=0.761;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,45:105:99:915,0,1759 -chr1 45673 . G A 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=105;Dels=0.00;FS=0.897;HaplotypeScore=111.2217;MLEAC=1;MLEAF=0.500;MQ=43.63;MQ0=2;MQRankSum=-5.747;QD=1.35;ReadPosRankSum=1.937;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,24:105:99:170,0,2516 -chr1 45679 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.082;DP=116;Dels=0.00;FS=2.067;HaplotypeScore=85.5662;MLEAC=1;MLEAF=0.500;MQ=43.87;MQ0=2;MQRankSum=-0.621;QD=3.21;ReadPosRankSum=-0.794;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,23:116:99:401,0,2219 -chr1 45694 . A G 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=125;Dels=0.00;FS=4.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.00;MQ0=2;MQRankSum=-5.132;QD=1.74;ReadPosRankSum=-0.229;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,25:125:99:246,0,3244 -chr1 45707 . T C 2311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=121;Dels=0.00;FS=6.874;HaplotypeScore=39.0259;MLEAC=1;MLEAF=0.500;MQ=45.33;MQ0=2;MQRankSum=-7.286;QD=19.11;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,87:121:99:2340,0,940 -chr1 45717 . G A 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.975;DP=109;Dels=0.00;FS=1.591;HaplotypeScore=73.3895;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=2;MQRankSum=-1.982;QD=6.89;ReadPosRankSum=2.664;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,43:109:99:779,0,1809 -chr1 45724 . C G 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=100;Dels=0.00;FS=0.957;HaplotypeScore=83.7585;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=2;MQRankSum=-1.008;QD=5.78;ReadPosRankSum=1.509;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,25:100:99:606,0,1819 -chr1 45725 . C T 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=98;Dels=0.00;FS=0.966;HaplotypeScore=96.3231;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=5.039;QD=4.35;ReadPosRankSum=-2.841;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,19:98:99:455,0,2414 -chr1 45728 . T C 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;DP=100;Dels=0.00;FS=12.270;HaplotypeScore=130.4542;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=-0.733;QD=1.80;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,13:100:99:208,0,2628 -chr1 45729 . A G 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.199;DP=98;Dels=0.00;FS=7.239;HaplotypeScore=143.0188;MLEAC=1;MLEAF=0.500;MQ=47.26;MQ0=2;MQRankSum=-2.286;QD=9.53;ReadPosRankSum=1.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,35:98:99:962,0,1812 -chr1 45733 . C T 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.767;DP=103;Dels=0.00;FS=11.158;HaplotypeScore=175.1243;MLEAC=1;MLEAF=0.500;MQ=45.48;MQ0=2;MQRankSum=-0.096;QD=2.07;ReadPosRankSum=2.500;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:90,13:103:99:241,0,2768 -chr1 45746 . C G 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.871;DP=98;Dels=0.00;FS=5.658;HaplotypeScore=144.7874;MLEAC=1;MLEAF=0.500;MQ=43.28;MQ0=6;MQRankSum=-2.422;QD=11.04;ReadPosRankSum=-1.217;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,41:98:99:1110,0,1505 -chr1 45749 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.332;DP=105;Dels=0.00;FS=20.438;HaplotypeScore=99.1311;MLEAC=1;MLEAF=0.500;MQ=42.61;MQ0=6;MQRankSum=-1.228;QD=0.58;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:93,12:105:89:89,0,2686 -chr1 45752 . C A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.973;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=60.4379;MLEAC=1;MLEAF=0.500;MQ=42.32;MQ0=7;MQRankSum=3.784;QD=2.22;ReadPosRankSum=3.512;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:91,16:107:99:266,0,2493 -chr1 45756 . T C 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=54.1966;MLEAC=1;MLEAF=0.500;MQ=41.83;MQ0=7;MQRankSum=3.711;QD=3.90;ReadPosRankSum=2.139;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,19:105:99:438,0,2316 -chr1 45792 . A T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=73;Dels=0.00;FS=9.059;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.74;MQ0=7;MQRankSum=-2.340;QD=8.15;ReadPosRankSum=-0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,26:73:99:623,0,946 -chr1 45793 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=74;Dels=0.00;FS=6.479;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=-1.025;QD=10.97;ReadPosRankSum=-1.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,32:74:99:840,0,770 -chr1 45796 . T A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=73;Dels=0.03;FS=11.097;HaplotypeScore=57.0004;MLEAC=1;MLEAF=0.500;MQ=32.88;MQ0=7;MQRankSum=-0.761;QD=2.38;ReadPosRankSum=3.011;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,16:71:99:202,0,1418 -chr1 45826 . A T 1113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=78;Dels=0.01;FS=3.363;HaplotypeScore=5.1586;MLEAC=1;MLEAF=0.500;MQ=36.05;MQ0=3;MQRankSum=-3.121;QD=14.28;ReadPosRankSum=2.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,46:77:99:1142,0,798 -chr1 45844 . T A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.235;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=38.54;MQ0=3;MQRankSum=-3.089;QD=4.97;ReadPosRankSum=0.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,25:96:99:505,0,2123 -chr1 45863 . A T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.601;DP=97;Dels=0.00;FS=0.931;HaplotypeScore=2.8214;MLEAC=1;MLEAF=0.500;MQ=39.70;MQ0=1;MQRankSum=3.322;QD=5.27;ReadPosRankSum=-0.737;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,22:97:99:539,0,2180 -chr1 45895 . C T 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;DP=86;Dels=0.00;FS=3.221;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=40.11;MQ0=2;MQRankSum=2.945;QD=7.57;ReadPosRankSum=1.653;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:61,25:86:99:679,0,1779 -chr1 45899 . T G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=84;Dels=0.00;FS=5.870;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=39.85;MQ0=3;MQRankSum=-2.045;QD=4.13;ReadPosRankSum=-0.184;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,20:84:99:375,0,1957 -chr1 45911 . C T 1407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=77;Dels=0.00;FS=0.933;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.22;MQ0=3;MQRankSum=-3.291;QD=18.28;ReadPosRankSum=1.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,51:77:99:1436,0,660 -chr1 45928 . G A 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364;DP=63;Dels=0.00;FS=1.202;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-2.063;QD=3.84;ReadPosRankSum=-0.054;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,13:63:99:270,0,1333 -chr1 45929 . C G 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=63;Dels=0.00;FS=1.173;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-1.844;QD=3.39;ReadPosRankSum=0.603;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,15:63:99:242,0,1410 -chr1 45934 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=10.8117;MLEAC=1;MLEAF=0.500;MQ=38.27;MQ0=3;MQRankSum=-1.596;QD=3.36;ReadPosRankSum=0.489;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,14:55:99:213,0,1231 -chr1 45957 . T C 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=26;Dels=0.00;FS=2.754;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=3;MQRankSum=-0.385;QD=3.11;ReadPosRankSum=0.385;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,7:26:99:109,0,455 -chr1 46015 . T A 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.89;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:83:83,0,581 -chr1 46016 . G T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.96;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:85:85,0,588 -chr1 46033 . A C 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.857;DP=62;Dels=0.00;FS=17.444;HaplotypeScore=12.6635;MLEAC=1;MLEAF=0.500;MQ=30.48;MQ0=9;MQRankSum=0.683;QD=2.08;ReadPosRankSum=0.683;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,8:62:99:157,0,1251 -chr1 46051 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=90;Dels=0.00;FS=6.369;HaplotypeScore=23.7978;MLEAC=1;MLEAF=0.500;MQ=30.89;MQ0=10;MQRankSum=-1.053;QD=5.56;ReadPosRankSum=1.556;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,26:90:99:529,0,1416 -chr1 46062 . T A 1644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.702;DP=97;Dels=0.00;FS=0.875;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.34;MQ0=10;MQRankSum=2.289;QD=16.96;ReadPosRankSum=2.106;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,62:97:99:1673,0,454 -chr1 46073 . A T 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=18.4418;MLEAC=1;MLEAF=0.500;MQ=30.65;MQ0=10;MQRankSum=3.059;QD=15.41;ReadPosRankSum=3.428;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,64:111:99:1739,0,618 -chr1 46082 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=119;Dels=0.00;FS=2.762;HaplotypeScore=10.8856;MLEAC=1;MLEAF=0.500;MQ=30.51;MQ0=11;MQRankSum=-0.591;QD=0.29;ReadPosRankSum=1.598;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:105,14:119:63:63,0,2389 -chr1 46123 . T A 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=118;Dels=0.00;FS=2.620;HaplotypeScore=14.0204;MLEAC=1;MLEAF=0.500;MQ=29.74;MQ0=16;MQRankSum=0.492;QD=1.49;ReadPosRankSum=-1.118;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:204,0,2132 -chr1 46130 . G C 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.815;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=12.9254;MLEAC=1;MLEAF=0.500;MQ=28.94;MQ0=18;MQRankSum=2.438;QD=9.95;ReadPosRankSum=0.465;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:59,54:113:99:1153,0,946 -chr1 46134 . A C 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=28.45;MQ0=19;MQRankSum=3.071;QD=10.54;ReadPosRankSum=0.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,52:106:99:1146,0,745 -chr1 46151 . A C 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=29.0289;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=23;MQRankSum=2.003;QD=2.89;ReadPosRankSum=2.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,22:96:99:306,0,1339 -chr1 46158 . G C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=96;Dels=0.00;FS=1.341;HaplotypeScore=39.0149;MLEAC=1;MLEAF=0.500;MQ=26.29;MQ0=24;MQRankSum=1.288;QD=2.65;ReadPosRankSum=2.514;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,22:96:99:283,0,1187 -chr1 46169 . C A 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=33.7549;MLEAC=1;MLEAF=0.500;MQ=29.68;MQ0=25;MQRankSum=0.853;QD=1.55;ReadPosRankSum=-0.449;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,14:105:99:191,0,1752 -chr1 46178 . A G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=40.5352;MLEAC=1;MLEAF=0.500;MQ=29.80;MQ0=26;MQRankSum=1.065;QD=5.13;ReadPosRankSum=-0.715;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,32:106:99:572,0,1382 -chr1 46199 . T G 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.172;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=146.8097;MLEAC=1;MLEAF=0.500;MQ=35.49;MQ0=8;MQRankSum=0.538;QD=3.53;ReadPosRankSum=-0.275;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,17:90:99:346,0,1892 -chr1 46203 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=95;Dels=0.00;FS=4.713;HaplotypeScore=115.8313;MLEAC=1;MLEAF=0.500;MQ=36.73;MQ0=7;MQRankSum=2.951;QD=8.13;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,30:95:99:801,0,1544 -chr1 46204 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=99;Dels=0.00;FS=1.263;HaplotypeScore=104.3565;MLEAC=1;MLEAF=0.500;MQ=36.99;MQ0=7;MQRankSum=-3.158;QD=1.27;ReadPosRankSum=2.038;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,14:99:99:154,0,2379 -chr1 46209 . G C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=105;Dels=0.00;FS=2.148;HaplotypeScore=73.4158;MLEAC=1;MLEAF=0.500;MQ=37.74;MQ0=6;MQRankSum=-0.435;QD=4.08;ReadPosRankSum=1.073;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,22:105:99:457,0,2172 -chr1 46217 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=107;Dels=0.00;FS=7.349;HaplotypeScore=36.8004;MLEAC=1;MLEAF=0.500;MQ=38.39;MQ0=6;MQRankSum=2.982;QD=7.89;ReadPosRankSum=-0.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,33:107:99:872,0,1991 -chr1 46223 . A T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=110;Dels=0.00;FS=16.066;HaplotypeScore=84.6532;MLEAC=1;MLEAF=0.500;MQ=39.41;MQ0=4;MQRankSum=3.566;QD=7.08;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,30:110:99:807,0,2258 -chr1 46259 . A C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.583;DP=125;Dels=0.00;FS=8.544;HaplotypeScore=18.7174;MLEAC=1;MLEAF=0.500;MQ=39.29;MQ0=5;MQRankSum=-2.002;QD=5.90;ReadPosRankSum=0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:68,35:125:99:766,0,2032 -chr1 46279 . G T 1314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.148;DP=126;Dels=0.00;FS=16.583;HaplotypeScore=16.7188;MLEAC=1;MLEAF=0.500;MQ=36.95;MQ0=11;MQRankSum=-2.173;QD=10.43;ReadPosRankSum=1.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,64:126:99:1343,0,1687 -chr1 46288 . A T 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=25.9225;MLEAC=1;MLEAF=0.500;MQ=35.56;MQ0=13;MQRankSum=-0.037;QD=2.17;ReadPosRankSum=0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:103,21:124:99:297,0,2552 -chr1 46297 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=123;Dels=0.00;FS=1.177;HaplotypeScore=28.4676;MLEAC=1;MLEAF=0.500;MQ=34.77;MQ0=13;MQRankSum=-1.404;QD=1.19;ReadPosRankSum=0.112;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,15:123:99:174,0,2572 -chr1 46303 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=113;Dels=0.00;FS=5.395;HaplotypeScore=31.8222;MLEAC=1;MLEAF=0.500;MQ=33.25;MQ0=13;MQRankSum=-0.279;QD=4.00;ReadPosRankSum=0.573;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,31:113:99:480,0,1952 -chr1 46311 . T C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=106;Dels=0.00;FS=4.629;HaplotypeScore=71.9889;MLEAC=1;MLEAF=0.500;MQ=31.67;MQ0=13;MQRankSum=-1.015;QD=2.43;ReadPosRankSum=1.472;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,25:106:99:286,0,1902 -chr1 46313 . T A 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=108;Dels=0.00;FS=12.679;HaplotypeScore=73.9836;MLEAC=1;MLEAF=0.500;MQ=31.59;MQ0=13;MQRankSum=-1.299;QD=2.52;ReadPosRankSum=0.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,23:108:99:300,0,1934 -chr1 46345 . G T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;DP=118;Dels=0.00;FS=1.369;HaplotypeScore=15.7222;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=12;MQRankSum=0.291;QD=2.25;ReadPosRankSum=1.341;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:95,23:118:99:294,0,1983 -chr1 46349 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;DP=129;Dels=0.00;FS=0.000;HaplotypeScore=20.2580;MLEAC=1;MLEAF=0.500;MQ=32.38;MQ0=11;MQRankSum=4.078;QD=2.87;ReadPosRankSum=-1.669;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:107,22:129:99:399,0,2225 -chr1 46360 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.738;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=144.3890;MLEAC=1;MLEAF=0.500;MQ=34.17;MQ0=10;MQRankSum=-0.032;QD=2.73;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:96,25:121:99:359,0,2284 -chr1 46365 . G T 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=86.2004;MLEAC=1;MLEAF=0.500;MQ=34.29;MQ0=10;MQRankSum=-0.261;QD=1.43;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:197,0,2403 -chr1 46370 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=121;Dels=0.00;FS=0.988;HaplotypeScore=85.2005;MLEAC=1;MLEAF=0.500;MQ=35.94;MQ0=9;MQRankSum=3.941;QD=2.91;ReadPosRankSum=0.376;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,21:121:99:380,0,2395 -chr1 46385 . A T 1987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=41.86;MQ0=1;MQRankSum=-4.706;QD=15.06;ReadPosRankSum=0.577;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,78:132:99:2016,0,1639 -chr1 46409 . G A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.697;DP=147;Dels=0.00;FS=5.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.328;QD=4.48;ReadPosRankSum=2.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:119,28:147:99:687,0,3761 -chr1 46442 . A T 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=132;Dels=0.00;FS=6.626;HaplotypeScore=24.9609;MLEAC=1;MLEAF=0.500;MQ=46.74;MQ0=1;MQRankSum=0.945;QD=6.40;ReadPosRankSum=2.434;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,31:132:99:873,0,3591 -chr1 46448 . T C 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.670;DP=120;Dels=0.00;FS=1.884;HaplotypeScore=45.9537;MLEAC=1;MLEAF=0.500;MQ=46.81;MQ0=1;MQRankSum=-1.356;QD=4.39;ReadPosRankSum=0.293;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,23:120:99:555,0,3478 -chr1 46453 . T A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=109;Dels=0.00;FS=3.408;HaplotypeScore=1.9892;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=1;MQRankSum=-1.198;QD=4.26;ReadPosRankSum=1.024;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,20:109:99:493,0,3241 -chr1 46466 . T A 1384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.022;DP=98;Dels=0.00;FS=1.650;HaplotypeScore=38.9441;MLEAC=1;MLEAF=0.500;MQ=46.96;MQ0=1;MQRankSum=0.510;QD=14.13;ReadPosRankSum=0.930;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,46:98:99:1413,0,1799 -chr1 46486 . T A 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=62;Dels=0.00;FS=0.975;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=43.40;MQ0=1;MQRankSum=-0.195;QD=14.11;ReadPosRankSum=-0.137;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,29:62:99:903,0,1128 -chr1 46505 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=39.03;MQ0=0;MQRankSum=1.388;QD=8.99;ReadPosRankSum=-1.130;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,8:24:99:244,0,502 -chr1 46511 . G C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=13;Dels=0.00;FS=2.920;HaplotypeScore=1.9890;MLEAC=1;MLEAF=0.500;MQ=36.55;MQ0=0;MQRankSum=0.592;QD=4.06;ReadPosRankSum=-1.099;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,3:13:81:81,0,328 -chr1 46579 . T C 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.651;DP=54;Dels=0.00;FS=2.600;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=0;MQRankSum=-0.248;QD=8.00;ReadPosRankSum=-0.266;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,18:54:99:460,0,1017 -chr1 46608 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=97;Dels=0.00;FS=7.798;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=45.77;MQ0=1;MQRankSum=0.169;QD=6.28;ReadPosRankSum=0.458;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,27:97:99:637,0,2291 -chr1 46649 . C G 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=128;Dels=0.00;FS=5.797;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=1;MQRankSum=0.828;QD=4.14;ReadPosRankSum=-0.170;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,26:128:99:558,0,3425 -chr1 46661 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=1.8874;MLEAC=1;MLEAF=0.500;MQ=52.82;MQ0=1;MQRankSum=-1.890;QD=4.49;ReadPosRankSum=-0.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:98,25:123:99:580,0,3412 -chr1 46669 . T C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=71.8527;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=2;MQRankSum=-1.040;QD=2.79;ReadPosRankSum=0.046;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:94,17:111:99:338,0,3242 -chr1 46672 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.735;DP=101;Dels=0.00;FS=1.153;HaplotypeScore=51.8777;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=2;MQRankSum=0.285;QD=2.14;ReadPosRankSum=1.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,13:101:99:244,0,3052 -chr1 46675 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=49.8785;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=2;MQRankSum=0.732;QD=1.80;ReadPosRankSum=2.032;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,12:100:99:208,0,3050 -chr1 46676 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=65.8754;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=2;MQRankSum=0.553;QD=1.87;ReadPosRankSum=1.978;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:99:213,0,3001 -chr1 46677 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=103;Dels=0.00;FS=3.208;HaplotypeScore=64.9814;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=2;MQRankSum=-2.102;QD=4.91;ReadPosRankSum=0.977;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,24:103:99:534,0,2803 -chr1 46680 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=105;Dels=0.00;FS=3.142;HaplotypeScore=55.7727;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=2;MQRankSum=-1.393;QD=4.65;ReadPosRankSum=1.009;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,23:105:99:516,0,2857 -chr1 46706 . T A 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.654;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=2.7898;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=2;MQRankSum=0.757;QD=2.05;ReadPosRankSum=-0.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,17:91:99:215,0,2448 -chr1 46718 . A C 1001.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.273;DP=81;Dels=0.00;FS=1.893;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.582;QD=12.37;ReadPosRankSum=1.963;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,34:81:99:1030,0,1456 -chr1 46719 . A C 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.250;QD=3.16;ReadPosRankSum=-0.404;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,15:81:99:284,0,2191 -chr1 46829 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=28.31;MQ0=9;MQRankSum=-1.417;QD=3.18;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:165,0,685 -chr1 46863 . T A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6918;MLEAC=1;MLEAF=0.500;MQ=34.16;MQ0=4;MQRankSum=1.021;QD=3.19;ReadPosRankSum=-0.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,10:31:99:127,0,637 -chr1 46875 . C T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=0.391;QD=7.75;ReadPosRankSum=0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:222,0,386 -chr1 46877 . A G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.036;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=-0.391;QD=7.71;ReadPosRankSum=0.675;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:221,0,382 -chr1 46911 . T C 225.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.295;QD=11.88;ReadPosRankSum=1.120;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,13:19:99:254,0,170 -chr1 46912 . T C 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.059;QD=7.36;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:168,0,256 -chr1 46921 . A T 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=1.120;QD=6.94;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:160,0,232 -chr1 46930 . T C 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.382;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=0.382;QD=2.05;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,3:15:59:59,0,224 -chr1 46932 . T G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=-0.278;QD=10.05;ReadPosRankSum=0.597;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,11:15:99:179,0,100 -chr1 47124 . A G 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.189;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=2.616;QD=3.49;ReadPosRankSum=-0.713;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,5:30:99:133,0,417 -chr1 47130 . C A 109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=-0.972;QD=3.54;ReadPosRankSum=-0.417;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,8:31:99:138,0,432 -chr1 47133 . A T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.968;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=15.5825;MLEAC=1;MLEAF=0.500;MQ=29.36;MQ0=5;MQRankSum=2.905;QD=5.37;ReadPosRankSum=-1.743;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,7:32:99:200,0,418 -chr1 47144 . A G 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.060;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.9886;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.440;QD=17.39;ReadPosRankSum=-0.420;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,26:33:45:602,0,45 -chr1 47176 . T C 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.24;MQ0=6;MQRankSum=-3.114;QD=8.56;ReadPosRankSum=-0.467;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,20:32:99:302,0,299 -chr1 47177 . G A 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=6;MQRankSum=0.027;QD=6.93;ReadPosRankSum=0.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,11:31:99:243,0,342 -chr1 47200 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.35;MQ0=1;MQRankSum=0.312;QD=7.13;ReadPosRankSum=1.954;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,7:14:99:128,0,187 -chr1 47234 . T C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.58;MQ0=3;MQRankSum=-1.721;QD=2.61;ReadPosRankSum=1.721;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,13:21:83:83,0,132 -chr1 47250 . G A 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.640;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=5.7510;MLEAC=1;MLEAF=0.500;MQ=21.76;MQ0=5;MQRankSum=-1.456;QD=2.27;ReadPosRankSum=0.646;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,22:66:99:178,0,749 -chr1 47261 . A G 1410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=6.7299;MLEAC=1;MLEAF=0.500;MQ=24.69;MQ0=5;MQRankSum=-5.094;QD=13.44;ReadPosRankSum=1.015;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,92:105:99:1439,0,288 -chr1 47285 . A T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.781;DP=169;Dels=0.00;FS=25.466;HaplotypeScore=47.9098;MLEAC=1;MLEAF=0.500;MQ=25.11;MQ0=7;MQRankSum=-4.336;QD=4.42;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,68:169:99:776,0,2136 -chr1 47310 . A T 485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.824;DP=205;Dels=0.00;FS=0.000;HaplotypeScore=49.7328;MLEAC=1;MLEAF=0.500;MQ=25.09;MQ0=7;MQRankSum=4.634;QD=2.37;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:176,29:205:99:514,0,2996 -chr1 47323 . G A 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.212;DP=211;Dels=0.00;FS=17.070;HaplotypeScore=51.7365;MLEAC=1;MLEAF=0.500;MQ=25.41;MQ0=8;MQRankSum=-0.372;QD=4.96;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:139,72:211:99:1074,0,2488 -chr1 47338 . C T 938.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.180;DP=186;Dels=0.02;FS=12.473;HaplotypeScore=79.8806;MLEAC=1;MLEAF=0.500;MQ=25.59;MQ0=8;MQRankSum=-2.645;QD=5.05;ReadPosRankSum=-1.238;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:110,73:183:99:967,0,2144 -chr1 47343 . A C 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.678;DP=175;Dels=0.00;FS=24.414;HaplotypeScore=63.4079;MLEAC=1;MLEAF=0.500;MQ=25.75;MQ0=8;MQRankSum=-4.741;QD=1.42;ReadPosRankSum=-2.918;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:123,52:175:99:276,0,2689 -chr1 47371 . T C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=89;Dels=0.00;FS=1.351;HaplotypeScore=13.6568;MLEAC=1;MLEAF=0.500;MQ=24.59;MQ0=7;MQRankSum=-0.275;QD=11.91;ReadPosRankSum=-0.593;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,70:89:99:1088,0,261 -chr1 47428 . T C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.940;DP=69;Dels=0.00;FS=2.933;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=23.55;MQ0=5;MQRankSum=3.350;QD=4.91;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,22:69:99:367,0,707 -chr1 47434 . T C 785.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.090;DP=72;Dels=0.00;FS=5.763;HaplotypeScore=21.1457;MLEAC=1;MLEAF=0.500;MQ=23.17;MQ0=5;MQRankSum=-4.249;QD=10.91;ReadPosRankSum=1.041;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,57:72:99:814,0,307 -chr1 47443 . G A 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=18.3434;MLEAC=1;MLEAF=0.500;MQ=20.97;MQ0=15;MQRankSum=-0.420;QD=0.53;ReadPosRankSum=1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,18:99:81:81,0,1206 -chr1 47486 . T C 1453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;DP=155;Dels=0.00;FS=0.000;HaplotypeScore=12.8061;MLEAC=1;MLEAF=0.500;MQ=22.09;MQ0=28;MQRankSum=-5.676;QD=9.38;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,119:155:99:1482,0,780 -chr1 47491 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=17.2378;MLEAC=1;MLEAF=0.500;MQ=22.27;MQ0=26;MQRankSum=5.308;QD=3.06;ReadPosRankSum=-1.409;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:133,23:156:99:506,0,1813 -chr1 47535 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=93;Dels=0.02;FS=0.000;HaplotypeScore=38.1338;MLEAC=1;MLEAF=0.500;MQ=21.13;MQ0=22;MQRankSum=2.066;QD=3.23;ReadPosRankSum=1.772;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,16:91:99:329,0,900 -chr1 47841 . C A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=15.69;MQ0=10;MQRankSum=0.024;QD=2.26;ReadPosRankSum=0.315;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:38:99:114,0,159 -chr1 47868 . A G 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=14.6837;MLEAC=1;MLEAF=0.500;MQ=16.29;MQ0=5;MQRankSum=0.408;QD=1.05;ReadPosRankSum=0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,10:33:63:63,0,165 -chr1 48010 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.5644;MLEAC=1;MLEAF=0.500;MQ=17.06;MQ0=4;MQRankSum=1.490;QD=1.24;ReadPosRankSum=1.149;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,5:32:68:68,0,115 -chr1 48044 . T C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.952;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=15.75;MQ0=6;MQRankSum=0.905;QD=2.20;ReadPosRankSum=1.323;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,12:34:99:103,0,101 -chr1 69699 . C T 41.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.03;MQ0=2;MQRankSum=-0.762;QD=3.81;ReadPosRankSum=1.666;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,9:11:15:70,0,15 -chr1 69764 . A G 449.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=37;Dels=0.00;FS=9.031;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=23.29;MQ0=17;MQRankSum=2.126;QD=12.15;ReadPosRankSum=0.047;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:7:477,0,7 -chr1 69840 . G A 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.6917;MLEAC=1;MLEAF=0.500;MQ=29.33;MQ0=7;MQRankSum=-2.507;QD=16.16;ReadPosRankSum=0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,31:36:55:610,0,55 -chr1 69869 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.277;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.44;MQ0=9;MQRankSum=-2.380;QD=0.76;ReadPosRankSum=1.273;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,11:46:63:63,0,767 -chr1 69912 . A G 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.049;DP=89;Dels=0.00;FS=2.410;HaplotypeScore=43.2151;MLEAC=1;MLEAF=0.500;MQ=28.97;MQ0=20;MQRankSum=-2.202;QD=0.85;ReadPosRankSum=-1.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,18:89:99:104,0,1176 -chr1 69914 . T A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=89;Dels=0.00;FS=2.466;HaplotypeScore=31.1187;MLEAC=1;MLEAF=0.500;MQ=28.72;MQ0=20;MQRankSum=-2.123;QD=0.55;ReadPosRankSum=-0.877;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,15:89:77:77,0,1075 -chr1 69917 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.757;DP=93;Dels=0.00;FS=4.107;HaplotypeScore=21.6983;MLEAC=1;MLEAF=0.500;MQ=28.07;MQ0=21;MQRankSum=6.024;QD=8.30;ReadPosRankSum=3.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,33:93:99:800,0,323 -chr1 69936 . T C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.032;DP=99;Dels=0.00;FS=7.704;HaplotypeScore=13.1641;MLEAC=1;MLEAF=0.500;MQ=29.72;MQ0=22;MQRankSum=-2.828;QD=0.58;ReadPosRankSum=-0.226;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,24:99:86:86,0,1391 -chr1 69952 . G A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=98;Dels=0.00;FS=10.410;HaplotypeScore=7.2476;MLEAC=1;MLEAF=0.500;MQ=31.15;MQ0=22;MQRankSum=-3.094;QD=1.13;ReadPosRankSum=1.550;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,23:98:99:139,0,1447 -chr1 70044 . T C 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.831;DP=64;Dels=0.00;FS=17.302;HaplotypeScore=1.4972;MLEAC=1;MLEAF=0.500;MQ=39.43;MQ0=5;MQRankSum=-6.056;QD=6.00;ReadPosRankSum=-3.773;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,29:64:99:412,0,1246 -chr1 70061 . A T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=133;Dels=0.00;FS=7.265;HaplotypeScore=20.7708;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=7;MQRankSum=-0.379;QD=2.95;ReadPosRankSum=-1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,25:133:99:420,0,2776 -chr1 70083 . T A 2582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=229;Dels=0.00;FS=16.594;HaplotypeScore=75.2516;MLEAC=1;MLEAF=0.500;MQ=35.83;MQ0=10;MQRankSum=-6.665;QD=11.28;ReadPosRankSum=-0.109;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,97:229:99:2611,0,1502 -chr1 70125 . G T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=250;Dels=0.00;FS=22.446;HaplotypeScore=27.9709;MLEAC=1;MLEAF=0.500;MQ=34.24;MQ0=12;MQRankSum=6.009;QD=2.97;ReadPosRankSum=-1.398;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:216,34:250:99:771,0,5278 -chr1 70150 . A T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=239;Dels=0.00;FS=21.127;HaplotypeScore=368.1172;MLEAC=1;MLEAF=0.500;MQ=33.77;MQ0=11;MQRankSum=1.765;QD=9.26;ReadPosRankSum=0.325;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:156,83:239:99:2242,0,3406 -chr1 70216 . A C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=108;Dels=0.00;FS=9.502;HaplotypeScore=1.7297;MLEAC=1;MLEAF=0.500;MQ=29.27;MQ0=14;MQRankSum=-0.174;QD=5.67;ReadPosRankSum=-0.831;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,38:108:99:641,0,1179 -chr1 70250 . G A 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.529;DP=135;Dels=0.00;FS=13.533;HaplotypeScore=55.9122;MLEAC=1;MLEAF=0.500;MQ=30.56;MQ0=13;MQRankSum=-4.770;QD=12.90;ReadPosRankSum=-1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,110:135:99:1770,0,694 -chr1 70260 . T A 1494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=159;Dels=0.00;FS=11.693;HaplotypeScore=60.0297;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=12;MQRankSum=3.229;QD=9.40;ReadPosRankSum=-1.725;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,62:159:99:1523,0,1679 -chr1 70324 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.298;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=36;MQRankSum=-1.206;QD=1.62;ReadPosRankSum=-0.310;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:212,38:250:99:433,0,4781 -chr1 70330 . T C 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;DP=247;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=29.87;MQ0=39;MQRankSum=4.681;QD=4.35;ReadPosRankSum=0.440;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:201,45:247:99:1102,0,3835 -chr1 70352 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.133;DP=231;Dels=0.00;FS=0.000;HaplotypeScore=38.6164;MLEAC=1;MLEAF=0.500;MQ=29.11;MQ0=43;MQRankSum=-0.256;QD=4.09;ReadPosRankSum=1.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:164,67:231:99:973,0,3380 -chr1 70354 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=228;Dels=0.00;FS=0.000;HaplotypeScore=36.7869;MLEAC=1;MLEAF=0.500;MQ=28.93;MQ0=43;MQRankSum=0.019;QD=2.38;ReadPosRankSum=1.450;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:181,47:228:99:571,0,3676 -chr1 70360 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;DP=214;Dels=0.00;FS=0.000;HaplotypeScore=31.5616;MLEAC=1;MLEAF=0.500;MQ=28.34;MQ0=42;MQRankSum=0.615;QD=3.26;ReadPosRankSum=0.618;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:163,51:214:99:725,0,3164 -chr1 70400 . A G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.22;MQ0=0;MQRankSum=-1.795;QD=15.51;ReadPosRankSum=0.535;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,14:23:99:385,0,241 -chr1 70409 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=-2.381;QD=13.95;ReadPosRankSum=0.958;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,14:25:99:377,0,326 -chr1 70454 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=38;Dels=0.00;FS=4.521;HaplotypeScore=2.5142;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=-4.169;QD=10.55;ReadPosRankSum=0.264;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,17:38:99:429,0,678 -chr1 70455 . G C 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=4.198;QD=16.99;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,21:38:99:674,0,427 -chr1 70476 . C T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=28;Dels=0.00;FS=1.583;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=-4.339;QD=6.71;ReadPosRankSum=-2.613;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,10:28:99:216,0,597 -chr1 70481 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.212;DP=29;Dels=0.00;FS=3.696;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.39;MQ0=0;MQRankSum=-4.266;QD=5.23;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:180,0,720 -chr1 70487 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=31;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=0;MQRankSum=-3.992;QD=3.25;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,7:31:99:129,0,866 -chr1 70488 . G C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.493;DP=30;Dels=0.00;FS=12.454;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=-3.759;QD=3.33;ReadPosRankSum=-0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,6:30:99:128,0,824 -chr1 70508 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=31;Dels=0.00;FS=8.915;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.10;MQ0=0;MQRankSum=3.902;QD=21.83;ReadPosRankSum=2.250;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,20:31:99:705,0,304 -chr1 70513 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.673;DP=29;Dels=0.00;FS=6.306;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=0;MQRankSum=-3.512;QD=7.10;ReadPosRankSum=-0.966;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:234,0,716 -chr1 70534 . A T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.500;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=0;MQRankSum=4.082;QD=15.43;ReadPosRankSum=1.082;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:661,0,570 -chr1 70544 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.74;MQ0=0;MQRankSum=-3.969;QD=13.14;ReadPosRankSum=0.202;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,24:47:99:646,0,706 -chr1 70546 . C G 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-3.859;QD=14.29;ReadPosRankSum=0.413;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,25:48:99:714,0,704 -chr1 70565 . A G 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.21;MQ0=0;MQRankSum=-2.949;QD=14.94;ReadPosRankSum=2.436;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:805,0,789 -chr1 70576 . T C 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.260;DP=58;Dels=0.00;FS=5.843;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.49;MQ0=0;MQRankSum=-3.297;QD=14.46;ReadPosRankSum=2.442;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,29:58:99:867,0,930 -chr1 70628 . T G 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.810;DP=62;Dels=0.00;FS=3.540;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-0.331;QD=16.09;ReadPosRankSum=0.416;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,32:62:99:1026,0,961 -chr1 70637 . G A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=57;Dels=0.00;FS=1.010;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=53.93;MQ0=0;MQRankSum=0.813;QD=17.19;ReadPosRankSum=-0.748;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,30:57:99:1008,0,828 -chr1 70655 . A G 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=53;Dels=0.00;FS=1.090;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-0.769;QD=16.79;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:53:99:918,0,834 -chr1 70684 . C T 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=57;Dels=0.00;FS=3.772;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=1;MQRankSum=1.273;QD=17.59;ReadPosRankSum=-0.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1031,0,872 -chr1 70716 . A G 976.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.361;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=1;MQRankSum=-0.680;QD=16.01;ReadPosRankSum=-0.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1005,0,945 -chr1 70722 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=64;Dels=0.00;FS=0.968;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=1;MQRankSum=-0.310;QD=14.48;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,30:64:99:955,0,1044 -chr1 70732 . T G 1039.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=0.419;QD=16.25;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1068,0,1033 -chr1 70757 . A G 1003.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=57;Dels=0.00;FS=2.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=2;MQRankSum=0.704;QD=17.61;ReadPosRankSum=-0.908;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1032,0,802 -chr1 70805 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.701;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=-0.638;QD=11.39;ReadPosRankSum=3.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:427,0,704 -chr1 70806 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=3.192;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,14:36:99:431,0,755 -chr1 70808 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=1;MQRankSum=-0.461;QD=11.99;ReadPosRankSum=2.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,14:34:99:436,0,682 -chr1 70814 . A T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=1;MQRankSum=-0.281;QD=14.22;ReadPosRankSum=1.333;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,779 -chr1 70860 . G C 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.732;QD=15.72;ReadPosRankSum=-0.025;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,28:55:99:893,0,931 -chr1 70872 . A T 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.806;QD=14.49;ReadPosRankSum=-0.247;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,28:57:99:854,0,1019 -chr1 70927 . T A 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.885;QD=15.03;ReadPosRankSum=0.833;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:840,0,984 -chr1 70928 . C T 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.173;QD=14.92;ReadPosRankSum=0.642;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:834,0,975 -chr1 70958 . G A 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=57;Dels=0.00;FS=1.019;HaplotypeScore=3.9961;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.008;QD=15.52;ReadPosRankSum=-0.855;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,27:57:99:913,0,1033 -chr1 71024 . T A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;QD=10.97;ReadPosRankSum=0.418;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,15:38:99:445,0,742 -chr1 71043 . A G 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=38;Dels=0.00;FS=1.271;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.530;QD=10.86;ReadPosRankSum=-0.257;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,14:38:99:441,0,841 -chr1 71062 . G A 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=39;Dels=0.00;FS=9.774;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.61;MQ0=0;MQRankSum=-1.775;QD=10.92;ReadPosRankSum=-1.342;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,15:39:99:454,0,819 -chr1 71078 . A G 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=46;Dels=0.00;FS=9.879;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-2.684;QD=7.15;ReadPosRankSum=1.952;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,13:46:99:357,0,1152 -chr1 71081 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=45;Dels=0.00;FS=9.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-2.992;QD=7.59;ReadPosRankSum=1.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,13:45:99:370,0,1120 -chr1 71151 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=48;Dels=0.00;FS=6.211;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.755;QD=14.79;ReadPosRankSum=0.962;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:738,0,906 -chr1 71164 . T G 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=52;Dels=0.00;FS=5.816;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.829;QD=13.75;ReadPosRankSum=2.635;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,23:52:99:743,0,987 -chr1 71175 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.190;DP=49;Dels=0.00;FS=8.135;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.410;QD=15.79;ReadPosRankSum=2.570;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,24:49:99:802,0,806 -chr1 71183 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=50;Dels=0.00;FS=5.868;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=-0.740;QD=13.42;ReadPosRankSum=3.290;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:699,0,927 -chr1 71188 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=50;Dels=0.00;FS=4.061;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=-1.246;QD=13.50;ReadPosRankSum=2.647;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:703,0,954 -chr1 71229 . C T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.588;QD=9.33;ReadPosRankSum=-2.495;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,14:42:99:420,0,1008 -chr1 71244 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.527;QD=4.99;ReadPosRankSum=-1.716;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,8:37:99:213,0,1037 -chr1 71245 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-3.757;QD=4.10;ReadPosRankSum=-1.239;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,7:36:99:176,0,1059 -chr1 71254 . G T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-3.568;QD=1.91;ReadPosRankSum=-0.412;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,5:36:97:97,0,1070 -chr1 71359 . G T 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=32;Dels=0.00;FS=18.730;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=8.59;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:303,0,699 -chr1 71365 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=15.204;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.18;MQ0=0;MQRankSum=-4.593;QD=9.83;ReadPosRankSum=-1.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:323,0,626 -chr1 71371 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=34;Dels=0.00;FS=14.526;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.775;QD=8.11;ReadPosRankSum=0.414;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:304,0,729 -chr1 71381 . C T 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=32;Dels=0.00;FS=11.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=9.18;ReadPosRankSum=2.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:322,0,668 -chr1 71388 . T C 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=35;Dels=0.00;FS=18.303;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-4.813;QD=8.08;ReadPosRankSum=3.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:311,0,784 -chr1 71631 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.385;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.055;QD=11.37;ReadPosRankSum=-2.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:301,0,519 -chr1 71646 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=21;Dels=0.00;FS=9.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-3.873;QD=13.42;ReadPosRankSum=-0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:310,0,392 -chr1 71649 . C T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=20;Dels=0.00;FS=10.263;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-3.799;QD=14.19;ReadPosRankSum=-0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,9:20:99:312,0,385 -chr1 71668 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.732;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.94;ReadPosRankSum=2.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:181,0,541 -chr1 71670 . C T 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.518;DP=21;Dels=0.00;FS=12.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-3.542;QD=7.42;ReadPosRankSum=2.997;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:184,0,526 -chr1 71673 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.72;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:176,0,563 -chr1 71675 . T C 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.63;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:174,0,568 -chr1 71676 . A G 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.455;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-3.606;QD=5.99;ReadPosRankSum=3.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:166,0,592 -chr1 71693 . T G 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.595;DP=27;Dels=0.00;FS=8.671;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-3.703;QD=4.03;ReadPosRankSum=1.895;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:137,0,745 -chr1 71734 . G A 950.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.031;DP=49;Dels=0.00;FS=6.300;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=2.206;QD=19.40;ReadPosRankSum=2.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:979,0,585 -chr1 71752 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.360;DP=52;Dels=0.00;FS=8.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=1;MQRankSum=-0.751;QD=11.90;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:647,0,1034 -chr1 71768 . T G 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210;DP=50;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=0.630;QD=13.48;ReadPosRankSum=1.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:702,0,834 -chr1 71769 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=6.329;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-0.010;QD=13.47;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,24:48:99:675,0,839 -chr1 71829 . C A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=56;Dels=0.00;FS=2.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=1;MQRankSum=0.563;QD=19.05;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1095,0,684 -chr1 71834 . T C 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=51;Dels=0.00;FS=2.568;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=1;MQRankSum=0.212;QD=20.49;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,33:51:99:1073,0,570 -chr1 71853 . T C 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=55.00;MQ0=1;MQRankSum=-0.422;QD=19.24;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:971,0,612 -chr1 71859 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=49;Dels=0.00;FS=1.079;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=1;MQRankSum=-1.148;QD=16.89;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:856,0,696 -chr1 71860 . A T 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.606;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=1;MQRankSum=-0.374;QD=17.77;ReadPosRankSum=1.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:881,0,668 -chr1 71878 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.614;DP=44;Dels=0.00;FS=2.696;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=1;MQRankSum=-1.741;QD=16.99;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:776,0,611 -chr1 71879 . G T 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.817;DP=45;Dels=0.00;FS=2.750;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.60;MQ0=1;MQRankSum=-1.880;QD=16.79;ReadPosRankSum=1.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:784,0,584 -chr1 71900 . G A 544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=26.2859;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=0.829;QD=13.97;ReadPosRankSum=-0.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:573,0,657 -chr1 71950 . T A 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=28;Dels=0.00;FS=21.924;HaplotypeScore=4.3987;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=2;MQRankSum=-0.462;QD=3.24;ReadPosRankSum=-1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:119,0,331 -chr1 71973 . C A 115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=5.0534;MLEAC=1;MLEAF=0.500;MQ=13.29;MQ0=15;MQRankSum=2.752;QD=1.90;ReadPosRankSum=3.058;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:54,7:61:75:144,0,75 -chr1 71995 . C T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.495;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=22.9908;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=18;MQRankSum=2.453;QD=1.44;ReadPosRankSum=3.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:66,8:74:99:135,0,173 -chr1 72037 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.0800;MLEAC=1;MLEAF=0.500;MQ=11.16;MQ0=17;MQRankSum=2.289;QD=0.63;ReadPosRankSum=2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:61,2:63:68:68,0,74 -chr1 72220 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.1644;MLEAC=1;MLEAF=0.500;MQ=16.77;MQ0=8;MQRankSum=2.009;QD=1.02;ReadPosRankSum=2.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,3:33:62:62,0,141 -chr1 72309 . T G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=9.6153;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=2.041;QD=2.45;ReadPosRankSum=-0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:65:65,0,114 -chr1 72313 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.788;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=12.8714;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=-1.000;QD=4.38;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:6,9:15:86:94,0,86 -chr1 72362 . A G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.15;MQ0=4;MQRankSum=0.000;QD=3.98;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,6:14:61:84,0,61 -chr1 72490 . A G 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=17.81;MQ0=2;MQRankSum=2.538;QD=5.57;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,11:24:54:162,0,54 -chr1 72602 . G A 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=19;Dels=0.00;FS=10.000;HaplotypeScore=6.4109;MLEAC=1;MLEAF=0.500;MQ=20.13;MQ0=4;MQRankSum=1.734;QD=1.88;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:19:64:64,0,89 -chr1 72626 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.482;DP=23;Dels=0.00;FS=3.332;HaplotypeScore=8.3126;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=5;MQRankSum=0.796;QD=2.34;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:82:82,0,124 -chr1 72630 . G A 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=5;MQRankSum=0.787;QD=1.32;ReadPosRankSum=-1.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:60:60,0,147 -chr1 72631 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.646;DP=25;Dels=0.00;FS=2.680;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.06;MQ0=5;MQRankSum=1.905;QD=2.15;ReadPosRankSum=0.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,3:25:82:82,0,124 -chr1 72638 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=22.7383;MLEAC=1;MLEAF=0.500;MQ=17.66;MQ0=5;MQRankSum=-0.417;QD=3.96;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,17:29:95:143,0,95 -chr1 72647 . A T 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.883;DP=33;Dels=0.00;FS=2.141;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=-1.102;QD=2.24;ReadPosRankSum=-1.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,12:33:99:102,0,158 -chr1 72717 . T C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.369;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=16.28;MQ0=1;MQRankSum=0.555;QD=3.41;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:7,7:14:32:76,0,32 -chr1 72825 . G C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.350;QD=1.40;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,4:39:83:83,0,118 -chr1 72829 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.750;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.050;QD=1.40;ReadPosRankSum=1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:35,4:39:83:83,0,121 -chr1 72858 . G A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=11.8688;MLEAC=1;MLEAF=0.500;MQ=16.70;MQ0=9;MQRankSum=1.415;QD=2.30;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,4:26:82:88,0,82 -chr1 73190 . T C 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-0.021;QD=8.71;ReadPosRankSum=4.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:307,0,753 -chr1 73232 . T G 932.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.025;QD=21.20;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:961,0,450 -chr1 73255 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.483;DP=47;Dels=0.00;FS=6.570;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-2.077;QD=9.48;ReadPosRankSum=-0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:474,0,1089 -chr1 73261 . C A 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.379;DP=44;Dels=0.00;FS=4.722;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.183;QD=21.88;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:991,0,472 -chr1 73263 . C G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=44;Dels=0.00;FS=2.932;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.964;QD=21.31;ReadPosRankSum=1.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:966,0,458 -chr1 73275 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.486;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.535;QD=22.72;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:1028,0,450 -chr1 73353 . T C 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.342;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.881;QD=11.40;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:587,0,1121 -chr1 73399 . A G 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.278;DP=55;Dels=0.00;FS=1.104;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.735;QD=9.60;ReadPosRankSum=2.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,18:55:99:556,0,1319 -chr1 73405 . A T 1043.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.503;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.482;QD=21.30;ReadPosRankSum=-0.975;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1072,0,626 -chr1 73409 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=50;Dels=0.00;FS=1.111;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-1.396;QD=19.28;ReadPosRankSum=-0.295;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:992,0,686 -chr1 73415 . A C 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.654;DP=46;Dels=0.00;FS=2.689;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-0.221;QD=17.91;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,629 -chr1 73486 . T A 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.8288;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.472;QD=15.77;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:864,0,913 -chr1 73498 . T G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=60;Dels=0.00;FS=7.060;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.598;QD=16.43;ReadPosRankSum=-1.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1014,0,976 -chr1 73526 . G C 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.141;DP=55;Dels=0.00;FS=5.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.947;QD=18.87;ReadPosRankSum=-1.408;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1066,0,776 -chr1 73533 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.024;DP=53;Dels=0.00;FS=1.107;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.014;QD=17.51;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:956,0,715 -chr1 73559 . G C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.050;QD=12.94;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:753,0,1151 -chr1 73601 . T C 1170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.426;DP=64;Dels=0.00;FS=0.969;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.995;QD=18.29;ReadPosRankSum=-0.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1199,0,892 -chr1 73621 . C T 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=67;Dels=0.00;FS=0.922;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.292;QD=18.98;ReadPosRankSum=-0.019;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,37:67:99:1300,0,965 -chr1 73648 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.955;DP=69;Dels=0.00;FS=2.001;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.776;QD=13.56;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,32:69:99:964,0,1308 -chr1 73726 . T A 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.512;QD=18.38;ReadPosRankSum=1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:800,0,577 -chr1 73823 . G C 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.311;QD=16.01;ReadPosRankSum=1.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:877,0,914 -chr1 73849 . G A 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;DP=62;Dels=0.00;FS=1.017;HaplotypeScore=3.9989;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.015;QD=21.00;ReadPosRankSum=-0.146;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,39:62:99:1330,0,730 -chr1 73870 . G A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=62;Dels=0.00;FS=3.539;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.230;QD=20.11;ReadPosRankSum=0.861;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1275,0,847 -chr1 73877 . A G 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=64;Dels=0.00;FS=3.431;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-0.836;QD=17.84;ReadPosRankSum=1.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1170,0,987 -chr1 73917 . A G 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=2.047;HaplotypeScore=1.9912;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.905;QD=16.80;ReadPosRankSum=-0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1137,0,1083 -chr1 73927 . T C 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.691;DP=59;Dels=0.00;FS=3.614;HaplotypeScore=2.6984;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.812;QD=17.32;ReadPosRankSum=-1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:1050,0,941 -chr1 73941 . C G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6987;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=0.313;QD=14.74;ReadPosRankSum=0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:839,0,1011 -chr1 73956 . A C 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.468;QD=13.53;ReadPosRankSum=0.514;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:637,0,849 -chr1 74024 . G C 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=3;MQRankSum=-2.569;QD=14.19;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:681,0,673 -chr1 74047 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=52;Dels=0.00;FS=6.153;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.43;MQ0=4;MQRankSum=-3.097;QD=12.90;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:699,0,647 -chr1 74080 . G A 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=58;Dels=0.00;FS=2.389;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=48.01;MQ0=4;MQRankSum=-5.098;QD=10.86;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:658,0,902 -chr1 74086 . A T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.43;MQ0=1;MQRankSum=-6.245;QD=9.29;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:530,0,995 -chr1 74089 . T G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-6.297;QD=9.30;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:540,0,1006 -chr1 74105 . G A 433.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=50.74;MQ0=1;MQRankSum=-6.154;QD=8.18;ReadPosRankSum=-0.700;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:462,0,1044 -chr1 74115 . A G 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=1;MQRankSum=-5.772;QD=6.19;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:319,0,952 -chr1 74119 . A G 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.277;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=1;MQRankSum=-5.551;QD=7.02;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:337,0,895 -chr1 74343 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.338;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.918;QD=17.18;ReadPosRankSum=3.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:973,0,882 -chr1 74475 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.652;DP=61;Dels=0.00;FS=12.530;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.79;MQ0=0;MQRankSum=-6.052;QD=16.83;ReadPosRankSum=2.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1055,0,1074 -chr1 74477 . T C 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.511;DP=59;Dels=0.00;FS=10.241;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-5.936;QD=17.84;ReadPosRankSum=2.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1081,0,1017 -chr1 74481 . G A 1104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.304;DP=60;Dels=0.00;FS=7.540;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-5.682;QD=18.41;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,32:60:99:1133,0,933 -chr1 74490 . A G 836.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.635;DP=62;Dels=0.00;FS=5.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=5.728;QD=13.50;ReadPosRankSum=1.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:865,0,1275 -chr1 74532 . C T 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.207;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.874;QD=18.60;ReadPosRankSum=-1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1163,0,974 -chr1 74539 . T A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-2.447;QD=15.63;ReadPosRankSum=0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:935,0,1102 -chr1 74540 . A T 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.639;QD=15.55;ReadPosRankSum=0.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:930,0,1112 -chr1 74544 . T C 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=1.937;QD=16.08;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,30:63:99:1041,0,1120 -chr1 74554 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=62;Dels=0.00;FS=0.939;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.760;QD=15.63;ReadPosRankSum=1.056;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:997,0,1066 -chr1 74559 . A G 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.648;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.806;QD=16.03;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,30:60:99:990,0,1042 -chr1 74590 . G A 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=0.903;QD=14.71;ReadPosRankSum=2.690;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:808,0,980 -chr1 74638 . C T 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=1.355;QD=14.74;ReadPosRankSum=-1.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:839,0,868 -chr1 74648 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=53;Dels=0.00;FS=3.775;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=1.331;QD=14.88;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:817,0,917 -chr1 74652 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.459;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=1.026;QD=14.20;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:738,0,887 -chr1 74732 . C A 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.435;DP=42;Dels=0.00;FS=18.002;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.102;QD=12.26;ReadPosRankSum=-0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:543,0,832 -chr1 74805 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=32;Dels=0.00;FS=11.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.183;QD=8.59;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:303,0,769 -chr1 74809 . A G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.788;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.297;QD=7.10;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:227,0,624 -chr1 74810 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.348;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.687;QD=7.67;ReadPosRankSum=0.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:243,0,706 -chr1 74816 . A T 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.472;DP=30;Dels=0.00;FS=8.475;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=2.064;QD=5.89;ReadPosRankSum=-0.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,7:30:99:205,0,702 -chr1 74826 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9448;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.122;QD=28.38;ReadPosRankSum=2.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:4,19:23:88:681,0,88 -chr1 74921 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-0.573;QD=6.31;ReadPosRankSum=1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:249,0,790 -chr1 75695 . T C 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=34;Dels=0.00;FS=1.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.62;MQ0=1;MQRankSum=-0.738;QD=15.23;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:546,0,545 -chr1 75762 . C T 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=56;Dels=0.00;FS=11.912;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.737;QD=13.66;ReadPosRankSum=-0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:793,0,1062 -chr1 75763 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.486;QD=13.21;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:755,0,1074 -chr1 75764 . A G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.339;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.930;QD=13.14;ReadPosRankSum=-0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:751,0,1072 -chr1 75807 . A C 597.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;DP=47;Dels=0.00;FS=1.116;HaplotypeScore=3.2018;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-0.075;QD=12.72;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:626,0,814 -chr1 75832 . A G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.198;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=13.9498;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-3.243;QD=6.99;ReadPosRankSum=3.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,7:22:99:182,0,490 -chr1 75850 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-1.228;QD=19.73;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:9,14:23:99:482,0,253 -chr1 75905 . T G 911.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.627;DP=45;Dels=0.00;FS=4.849;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=1;MQRankSum=-0.699;QD=20.26;ReadPosRankSum=-0.337;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:940,0,570 -chr1 75930 . T C 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=54;Dels=0.00;FS=8.156;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=1;MQRankSum=-2.270;QD=12.68;ReadPosRankSum=-0.996;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:713,0,1060 -chr1 76013 . T G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.758;DP=38;Dels=0.00;FS=1.402;HaplotypeScore=1.9956;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=1;MQRankSum=0.479;QD=12.73;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,658 -chr1 76032 . A T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.051;DP=43;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=1;MQRankSum=1.973;QD=12.72;ReadPosRankSum=-0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:575,0,722 -chr1 76087 . C A 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=51;Dels=0.00;FS=11.471;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=1.732;QD=14.84;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:785,0,818 -chr1 76168 . T C 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=43;Dels=0.00;FS=2.727;HaplotypeScore=5.8324;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=1;MQRankSum=-0.743;QD=19.58;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:870,0,570 -chr1 76328 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=51;Dels=0.00;FS=4.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.205;QD=10.86;ReadPosRankSum=-2.893;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:582,0,977 -chr1 76334 . A G 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.425;DP=45;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=2.653;QD=12.17;ReadPosRankSum=-1.587;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:576,0,815 -chr1 76427 . A C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.347;DP=54;Dels=0.00;FS=12.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=-0.169;QD=14.07;ReadPosRankSum=0.508;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:788,0,919 -chr1 76443 . T C 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.715;DP=59;Dels=0.00;FS=11.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=1;MQRankSum=0.451;QD=14.91;ReadPosRankSum=-0.513;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:908,0,963 -chr1 76465 . C T 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.671;DP=50;Dels=0.00;FS=19.919;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=-1.733;QD=16.46;ReadPosRankSum=-0.711;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:851,0,769 -chr1 76478 . G T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=48;Dels=0.00;FS=13.782;HaplotypeScore=145.9761;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=-2.207;QD=15.77;ReadPosRankSum=0.565;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:785,0,657 -chr1 76552 . C A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.464;DP=33;Dels=0.00;FS=1.376;HaplotypeScore=16.6986;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-3.019;QD=17.72;ReadPosRankSum=0.524;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:613,0,416 -chr1 76554 . A T 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=14.9106;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.480;QD=15.93;ReadPosRankSum=0.827;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:570,0,574 -chr1 76667 . C A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=50;Dels=0.00;FS=2.539;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.616;QD=22.38;ReadPosRankSum=2.961;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1147,0,573 -chr1 76736 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.2657;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.771;QD=21.09;ReadPosRankSum=-0.603;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:956,0,527 -chr1 76758 . A G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.695;DP=38;Dels=0.00;FS=1.289;HaplotypeScore=16.4637;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.370;QD=19.39;ReadPosRankSum=0.103;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:765,0,537 -chr1 76765 . A T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=38;Dels=0.00;FS=1.281;HaplotypeScore=62.8561;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.219;QD=17.55;ReadPosRankSum=1.535;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:695,0,601 -chr1 76784 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.258;QD=14.59;ReadPosRankSum=-1.433;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:670,0,738 -chr1 76813 . G T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.627;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.777;QD=19.61;ReadPosRankSum=-1.476;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,32:52:99:1048,0,649 -chr1 76827 . C T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.020;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-1.020;QD=19.94;ReadPosRankSum=-1.218;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1025,0,663 -chr1 76831 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-0.124;QD=19.94;ReadPosRankSum=-1.136;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1105,0,628 -chr1 76885 . G C 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.785;DP=51;Dels=0.00;FS=8.452;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.280;QD=21.15;ReadPosRankSum=0.878;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1107,0,632 -chr1 76963 . A G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;QD=19.62;ReadPosRankSum=0.589;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V46A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:715,0,396 -chr1 76964 . C A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.364;QD=19.68;ReadPosRankSum=0.791;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V46L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:717,0,439 -chr1 77028 . G T 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.083;QD=11.11;ReadPosRankSum=-0.305;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S24R|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:15,10:25:99:306,0,525 -chr1 77036 . C G 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=2.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.482;QD=9.75;ReadPosRankSum=1.399;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V22L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,10:29:99:311,0,667 -chr1 77066 . C T 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.686;QD=15.94;ReadPosRankSum=2.051;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A12T|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:18,19:38:99:634,0,588 -chr1 77068 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.131;QD=16.28;ReadPosRankSum=2.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V11A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:647,0,593 -chr1 77072 . G C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.606;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.518;QD=15.65;ReadPosRankSum=2.628;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L10V|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:623,0,636 -chr1 77096 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=45;Dels=0.00;FS=6.823;HaplotypeScore=2.9948;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.215;QD=17.06;ReadPosRankSum=0.534;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2K|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:22,23:45:99:796,0,679 -chr1 77106 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.035;QD=17.26;ReadPosRankSum=-1.240;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,24:45:99:805,0,662 -chr1 77122 . A G 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.595;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-1.700;QD=14.32;ReadPosRankSum=-0.728;EFF=START_GAINED(LOW||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,15:34:99:515,0,632 -chr1 77126 . A T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=37;Dels=0.00;FS=7.143;HaplotypeScore=3.7335;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-1.844;QD=14.97;ReadPosRankSum=-0.808;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:20,17:37:99:582,0,647 -chr1 77144 . A C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;DP=41;Dels=0.00;FS=4.506;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-1.265;QD=15.85;ReadPosRankSum=0.170;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,20:41:99:678,0,682 -chr1 77180 . C A 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.879;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=4.1179;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.179;QD=17.54;ReadPosRankSum=-0.594;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:16,24:40:99:730,0,535 -chr1 77221 . C G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=43;Dels=0.00;FS=14.813;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.319;QD=20.88;ReadPosRankSum=-0.163;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,27:43:99:926,0,502 -chr1 77244 . G C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=39;Dels=0.00;FS=5.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.512;QD=21.81;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:14,25:39:99:879,0,425 -chr1 77298 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.048;DP=35;Dels=0.00;FS=5.506;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.901;QD=23.14;ReadPosRankSum=1.190;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:838,0,318 -chr1 77332 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=32;Dels=0.00;FS=3.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-0.516;QD=22.34;ReadPosRankSum=0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,21:32:99:743,0,352 -chr1 77376 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.170;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=83.6545;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.434;QD=15.40;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:783,0,747 -chr1 77378 . A C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=124.2479;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.053;QD=15.32;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:779,0,892 -chr1 77438 . C T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.363;DP=53;Dels=0.00;FS=15.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.633;QD=16.94;ReadPosRankSum=-2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:926,0,869 -chr1 77442 . T G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=51;Dels=0.00;FS=15.703;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.218;QD=15.02;ReadPosRankSum=3.474;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,934 -chr1 77449 . T C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=48;Dels=0.00;FS=11.196;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.972;QD=13.39;ReadPosRankSum=2.206;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:671,0,945 -chr1 77450 . A G 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.917;DP=46;Dels=0.00;FS=11.459;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.853;QD=14.34;ReadPosRankSum=1.673;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:688,0,862 -chr1 77458 . A T 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=51;Dels=0.00;FS=16.807;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=1;MQRankSum=2.301;QD=15.23;ReadPosRankSum=0.146;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:805,0,791 -chr1 77464 . G A 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=49;Dels=0.00;FS=17.115;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=-0.908;QD=16.95;ReadPosRankSum=-1.610;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:859,0,697 -chr1 77489 . G A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.648;DP=46;Dels=0.00;FS=12.506;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=2;MQRankSum=-0.625;QD=14.45;ReadPosRankSum=2.345;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:693,0,690 -chr1 77491 . A G 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=45;Dels=0.00;FS=15.152;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.71;MQ0=2;MQRankSum=2.203;QD=12.71;ReadPosRankSum=-1.489;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:600,0,730 -chr1 77495 . A G 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.505;DP=41;Dels=0.00;FS=16.483;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=2;MQRankSum=2.237;QD=11.36;ReadPosRankSum=-0.476;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:494,0,766 -chr1 77531 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=49;Dels=0.00;FS=11.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=3;MQRankSum=4.899;QD=15.53;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:789,0,677 -chr1 77535 . C T 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=49;Dels=0.00;FS=13.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=3;MQRankSum=-5.229;QD=14.63;ReadPosRankSum=-2.065;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:745,0,801 -chr1 77544 . C T 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.557;DP=48;Dels=0.00;FS=11.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=3;MQRankSum=-5.517;QD=13.20;ReadPosRankSum=-0.330;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:662,0,770 -chr1 77549 . C G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.738;DP=50;Dels=0.00;FS=10.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=3;MQRankSum=-5.596;QD=12.14;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:635,0,869 -chr1 77557 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.869;DP=45;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=3;MQRankSum=-5.553;QD=14.15;ReadPosRankSum=0.416;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:665,0,732 -chr1 77577 . T G 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=3;MQRankSum=-3.998;QD=6.89;ReadPosRankSum=2.292;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:290,0,880 -chr1 77589 . C T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=42;Dels=0.00;FS=4.743;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=2;MQRankSum=-2.271;QD=11.95;ReadPosRankSum=-0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:530,0,807 -chr1 77592 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=2.439;QD=16.46;ReadPosRankSum=0.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:736,0,657 -chr1 77593 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-1.969;QD=15.04;ReadPosRankSum=-0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:675,0,722 -chr1 77615 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.765;DP=43;Dels=0.00;FS=2.820;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=2;MQRankSum=-0.327;QD=16.53;ReadPosRankSum=-0.327;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:739,0,655 -chr1 77617 . C T 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.975;DP=42;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=2;MQRankSum=0.488;QD=16.40;ReadPosRankSum=0.027;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,22:42:99:717,0,653 -chr1 77620 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.342;DP=43;Dels=0.00;FS=2.687;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=2;MQRankSum=0.013;QD=12.79;ReadPosRankSum=0.781;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:43:99:578,0,822 -chr1 77633 . G A 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=1.015;QD=11.33;ReadPosRankSum=-0.555;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:504,0,850 -chr1 77648 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.970;DP=44;Dels=0.00;FS=1.269;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=1;MQRankSum=0.304;QD=8.81;ReadPosRankSum=-0.569;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:416,0,909 -chr1 77695 . A G 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.171;DP=48;Dels=0.00;FS=11.450;HaplotypeScore=1.9984;MLEAC=1;MLEAF=0.500;MQ=56.59;MQ0=1;MQRankSum=-1.215;QD=11.39;ReadPosRankSum=-2.156;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:575,0,980 -chr1 77798 . A G 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.110;DP=51;Dels=0.00;FS=4.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-0.292;QD=13.56;ReadPosRankSum=-0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:720,0,928 -chr1 77814 . G T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.710;DP=51;Dels=0.00;FS=4.322;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=54.03;MQ0=1;MQRankSum=-1.124;QD=18.72;ReadPosRankSum=0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:983,0,686 -chr1 77873 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=1.065;QD=20.19;ReadPosRankSum=-2.142;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:937,0,508 -chr1 77986 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=56;Dels=0.00;FS=5.494;HaplotypeScore=1.9774;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-1.712;QD=14.80;ReadPosRankSum=0.778;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:857,0,933 -chr1 78007 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.299;DP=43;Dels=0.00;FS=1.315;HaplotypeScore=19.9836;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.842;QD=11.18;ReadPosRankSum=0.565;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:509,0,882 -chr1 78009 . C T 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.704;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.014;QD=19.65;ReadPosRankSum=-0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:893,0,579 -chr1 78012 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.563;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.037;QD=18.65;ReadPosRankSum=-0.185;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:830,0,589 -chr1 78019 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=44;Dels=0.00;FS=3.112;HaplotypeScore=24.9845;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.446;QD=10.13;ReadPosRankSum=2.105;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,15:44:99:474,0,1015 -chr1 78027 . T C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=44;Dels=0.00;FS=12.758;HaplotypeScore=6.9973;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.701;QD=1.72;ReadPosRankSum=-1.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:38,6:44:99:104,0,1372 -chr1 78118 . T A 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.504;DP=54;Dels=0.00;FS=1.040;HaplotypeScore=35.7719;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.892;QD=19.46;ReadPosRankSum=1.994;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1079,0,770 -chr1 78134 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;DP=54;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=0.099;QD=11.72;ReadPosRankSum=-0.958;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:34,20:54:99:661,0,1176 -chr1 78240 . T C 1102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=57;Dels=0.00;FS=3.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.234;QD=19.35;ReadPosRankSum=0.444;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1131,0,782 -chr1 78243 . T A 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=58;Dels=0.00;FS=5.380;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=0.361;QD=19.34;ReadPosRankSum=0.848;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1150,0,823 -chr1 78259 . A G 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=58;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.330;QD=17.05;ReadPosRankSum=0.319;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1017,0,977 -chr1 78296 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=35;Dels=0.00;FS=5.073;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.286;QD=20.34;ReadPosRankSum=1.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:740,0,458 -chr1 78459 . A G 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=56;Dels=0.00;FS=1.071;HaplotypeScore=2.7605;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=4;MQRankSum=1.156;QD=18.75;ReadPosRankSum=1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1078,0,681 -chr1 78480 . G T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=4;MQRankSum=-1.866;QD=7.95;ReadPosRankSum=-1.529;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:418,0,1082 -chr1 78503 . A C 1406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.844;DP=60;Dels=0.00;FS=2.699;HaplotypeScore=42.4334;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=3;MQRankSum=1.437;QD=23.45;ReadPosRankSum=2.809;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,45:60:99:1435,0,403 -chr1 78601 . G A 1151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.289;DP=48;Dels=0.00;FS=5.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=0;MQRankSum=-0.133;QD=24.00;ReadPosRankSum=-0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,33:48:99:1180,0,463 -chr1 78753 . G T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=65;Dels=0.00;FS=0.960;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.007;QD=12.77;ReadPosRankSum=-0.353;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:38,27:65:99:858,0,1336 -chr1 78787 . G A 1365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.554;DP=61;Dels=0.00;FS=1.030;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.660;QD=22.39;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,40:61:99:1394,0,614 -chr1 78815 . A G 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.008;DP=57;Dels=0.00;FS=3.773;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;QD=20.50;ReadPosRankSum=1.320;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,35:57:99:1197,0,695 -chr1 78892 . C T 925.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=15.69;ReadPosRankSum=0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:954,0,1057 -chr1 78931 . G A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.869;DP=63;Dels=0.00;FS=11.290;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.796;QD=16.93;ReadPosRankSum=-1.025;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1095,0,1023 -chr1 78981 . T C 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.954;DP=27;Dels=0.00;FS=12.207;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.904;QD=4.88;ReadPosRankSum=2.537;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:160,0,693 -chr1 78994 . T A 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.138;DP=38;Dels=0.00;FS=22.047;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=2.492;QD=20.10;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,25:38:99:792,0,376 -chr1 79011 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.991;DP=42;Dels=0.00;FS=18.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.654;QD=7.21;ReadPosRankSum=1.573;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:331,0,1024 -chr1 79031 . C A 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=45;Dels=0.00;FS=23.835;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=2.704;QD=20.24;ReadPosRankSum=0.386;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:939,0,503 -chr1 79092 . A C 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=56;Dels=0.00;FS=20.015;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-1.258;QD=7.25;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:41,15:56:99:434,0,1487 -chr1 79155 . A G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.851;DP=43;Dels=0.00;FS=24.229;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.433;QD=4.20;ReadPosRankSum=1.776;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:209,0,1210 -chr1 79211 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=44;Dels=0.00;FS=24.701;HaplotypeScore=3.9990;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-4.230;QD=6.36;ReadPosRankSum=2.095;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,12:44:99:308,0,1153 -chr1 79215 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=46;Dels=0.00;FS=28.108;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-3.940;QD=5.84;ReadPosRankSum=2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,12:46:99:297,0,1207 -chr1 79219 . C T 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=48;Dels=0.00;FS=32.959;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.417;QD=5.62;ReadPosRankSum=2.464;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:298,0,1293 -chr1 79242 . C T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.484;DP=54;Dels=0.00;FS=36.287;HaplotypeScore=13.9681;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-5.699;QD=8.00;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:460,0,1314 -chr1 79253 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.069;DP=49;Dels=0.00;FS=18.054;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=5.556;QD=23.30;ReadPosRankSum=2.594;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,32:49:99:1170,0,488 -chr1 79258 . C T 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=50;Dels=0.00;FS=15.207;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.996;QD=7.74;ReadPosRankSum=-1.397;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:415,0,1279 -chr1 79284 . A T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-4.938;QD=8.83;ReadPosRankSum=1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:452,0,1222 -chr1 79288 . G C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=25.1292;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-5.205;QD=8.68;ReadPosRankSum=1.690;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:445,0,1219 -chr1 79300 . T A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-4.876;QD=8.74;ReadPosRankSum=1.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,14:44:99:413,0,1090 -chr1 79321 . G C 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.836;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-4.816;QD=15.72;ReadPosRankSum=-0.137;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:610,0,654 -chr1 79337 . G A 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-4.610;QD=14.14;ReadPosRankSum=1.392;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:495,0,617 -chr1 79397 . C A 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.587;DP=32;Dels=0.00;FS=32.017;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-4.602;QD=9.12;ReadPosRankSum=-2.420;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,11:32:99:320,0,754 -chr1 79404 . T A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;DP=40;Dels=0.00;FS=20.081;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.252;QD=10.74;ReadPosRankSum=-1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:458,0,853 -chr1 79408 . T A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.460;DP=42;Dels=0.00;FS=18.695;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=0;MQRankSum=-4.894;QD=11.90;ReadPosRankSum=-1.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:528,0,853 -chr1 79425 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.446;DP=44;Dels=0.00;FS=12.871;HaplotypeScore=3.5215;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=-3.990;QD=9.90;ReadPosRankSum=1.522;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,15:44:99:464,0,918 -chr1 79451 . G A 406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.625;DP=45;Dels=0.00;FS=2.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.017;QD=9.04;ReadPosRankSum=1.361;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:435,0,1059 -chr1 79452 . A T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.469;DP=46;Dels=0.00;FS=2.785;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.218;QD=9.36;ReadPosRankSum=1.148;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:459,0,1031 -chr1 79468 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.623;QD=14.00;ReadPosRankSum=-0.748;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:700,0,913 -chr1 79478 . G C 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=1.6648;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.471;QD=16.94;ReadPosRankSum=-1.753;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:926,0,881 -chr1 79598 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.841;DP=38;Dels=0.00;FS=9.653;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-3.061;QD=4.23;ReadPosRankSum=-0.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,8:38:99:189,0,1018 -chr1 79615 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=23.6444;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.17;ReadPosRankSum=0.428;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:475,0,803 -chr1 79617 . T A 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=40;Dels=0.00;FS=9.975;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-4.200;QD=4.77;ReadPosRankSum=0.762;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,8:40:99:219,0,844 -chr1 79618 . G A 138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-3.364;QD=3.47;ReadPosRankSum=0.254;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,8:40:99:167,0,1124 -chr1 79619 . C T 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.201;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.09;ReadPosRankSum=1.256;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:472,0,808 -chr1 79624 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=37;Dels=0.00;FS=12.746;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.605;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,974 -chr1 79626 . G A 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.125;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.83;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:207,0,1010 -chr1 79627 . A G 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.900;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,1015 -chr1 79640 . C T 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=51;Dels=0.00;FS=14.590;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-1.369;QD=9.39;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,17:51:99:507,0,1160 -chr1 79641 . G A 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=51;Dels=0.00;FS=3.858;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-3.463;QD=1.92;ReadPosRankSum=3.189;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:44,7:51:99:126,0,1543 -chr1 79670 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=-3.131;QD=14.97;ReadPosRankSum=1.235;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:717,0,801 -chr1 79675 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=2.704;HaplotypeScore=18.9737;MLEAC=1;MLEAF=0.500;MQ=55.22;MQ0=0;MQRankSum=-2.223;QD=15.51;ReadPosRankSum=0.765;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:695,0,699 -chr1 79753 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.941;DP=37;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.411;QD=13.21;ReadPosRankSum=0.290;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:517,0,675 -chr1 79840 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.767;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.127;QD=12.11;ReadPosRankSum=0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:428,0,660 -chr1 79842 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.492;QD=20.75;ReadPosRankSum=-0.608;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:713,0,391 -chr1 79860 . G A 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.431;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.839;QD=14.44;ReadPosRankSum=0.000;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:577,0,643 -chr1 80017 . T A 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.877;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.458;QD=12.63;ReadPosRankSum=0.340;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:508,0,721 -chr1 80041 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.861;DP=37;Dels=0.00;FS=2.846;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.611;QD=11.24;ReadPosRankSum=-1.174;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:444,0,776 -chr1 80045 . G C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.955;DP=36;Dels=0.00;FS=1.366;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.811;QD=21.47;ReadPosRankSum=1.548;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,23:36:99:801,0,403 -chr1 80079 . G C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.802;DP=36;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.481;QD=12.77;ReadPosRankSum=-2.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,737 -chr1 80184 . G A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.084;QD=20.44;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:846,0,495 -chr1 80244 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=32;Dels=0.00;FS=7.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.62;MQ0=0;MQRankSum=-3.927;QD=16.96;ReadPosRankSum=1.888;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,17:32:99:571,0,493 -chr1 80710 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.494;DP=36;Dels=0.00;FS=5.334;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-1.350;QD=10.69;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:413,0,777 -chr1 80861 . C T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=39;Dels=0.00;FS=2.826;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.328;QD=19.05;ReadPosRankSum=1.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:771,0,477 -chr1 80867 . T C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.071;DP=39;Dels=0.00;FS=2.869;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.827;QD=16.40;ReadPosRankSum=1.374;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,22:39:99:668,0,541 -chr1 80925 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=44;Dels=0.00;FS=22.159;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.041;QD=7.20;ReadPosRankSum=0.203;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:345,0,1053 -chr1 80926 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.372;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-0.744;QD=6.37;ReadPosRankSum=0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:302,0,1088 -chr1 80927 . G A 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.057;QD=6.27;ReadPosRankSum=0.372;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:298,0,1101 -chr1 80933 . T G 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=45;Dels=0.00;FS=23.434;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-1.225;QD=7.17;ReadPosRankSum=0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:351,0,1105 -chr1 80959 . T A 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398;DP=45;Dels=0.00;FS=5.002;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=1;MQRankSum=0.940;QD=10.44;ReadPosRankSum=-0.121;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:498,0,944 -chr1 80967 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=44;Dels=0.00;FS=5.002;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=1;MQRankSum=0.490;QD=11.29;ReadPosRankSum=0.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,17:44:99:525,0,924 -chr1 81012 . C G 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=40;Dels=0.00;FS=4.442;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.019;QD=17.52;ReadPosRankSum=1.672;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:729,0,588 -chr1 81069 . C A 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.275;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.919;QD=12.97;ReadPosRankSum=0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:599,0,905 -chr1 81071 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.373;QD=12.54;ReadPosRankSum=0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:580,0,911 -chr1 81072 . C G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.097;DP=45;Dels=0.00;FS=20.102;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.286;QD=12.66;ReadPosRankSum=-0.081;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:598,0,942 -chr1 81095 . C G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.970;DP=57;Dels=0.00;FS=23.054;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.781;QD=8.77;ReadPosRankSum=-1.073;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:528,0,1396 -chr1 81130 . T G 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.726;QD=8.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:440,0,1117 -chr1 81131 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-1.523;QD=8.78;ReadPosRankSum=0.422;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:432,0,1127 -chr1 81133 . T C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;DP=45;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.951;QD=9.33;ReadPosRankSum=0.349;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,15:45:99:448,0,1081 -chr1 81169 . A G 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.374;DP=49;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.172;QD=13.10;ReadPosRankSum=2.091;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:670,0,987 -chr1 81178 . C A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=50;Dels=0.00;FS=8.297;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-3.555;QD=11.28;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:592,0,991 -chr1 81185 . G A 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.606;DP=41;Dels=0.00;FS=12.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=-3.568;QD=11.26;ReadPosRankSum=1.403;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:490,0,818 -chr1 81371 . G A 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.908;DP=48;Dels=0.00;FS=4.645;HaplotypeScore=1.9957;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.473;QD=6.60;ReadPosRankSum=-2.001;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,16:48:99:345,0,1127 -chr1 81408 . A G 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=53;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=0;MQRankSum=-4.943;QD=8.94;ReadPosRankSum=2.754;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:502,0,1182 -chr1 81418 . C T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.718;DP=50;Dels=0.00;FS=21.604;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=0;MQRankSum=-4.962;QD=9.28;ReadPosRankSum=2.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:492,0,1136 -chr1 81422 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.035;DP=48;Dels=0.00;FS=21.618;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=0;MQRankSum=5.281;QD=21.62;ReadPosRankSum=-2.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1066,0,457 -chr1 81453 . C A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-4.476;QD=8.15;ReadPosRankSum=0.442;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:403,0,1150 -chr1 81455 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.808;QD=8.04;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:398,0,1139 -chr1 81456 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.245;DP=47;Dels=0.00;FS=15.915;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-4.013;QD=8.02;ReadPosRankSum=0.384;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,14:47:99:405,0,1154 -chr1 81457 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.062;DP=46;Dels=0.00;FS=15.915;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=-3.617;QD=8.36;ReadPosRankSum=0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:413,0,1151 -chr1 81482 . G T 1236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.464;DP=50;Dels=0.00;FS=4.620;HaplotypeScore=1.7206;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=2.035;QD=24.74;ReadPosRankSum=0.265;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1265,0,325 -chr1 81544 . A G 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8400;MLEAC=1;MLEAF=0.500;MQ=56.30;MQ0=0;MQRankSum=2.542;QD=8.41;ReadPosRankSum=-0.370;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:415,0,1040 -chr1 81580 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=43;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=1.644;QD=14.60;ReadPosRankSum=-2.471;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:656,0,776 -chr1 81581 . G A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=4.524;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=0.767;QD=15.18;ReadPosRankSum=-2.496;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:681,0,762 -chr1 81594 . G A 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.680;DP=41;Dels=0.00;FS=1.230;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-0.251;QD=19.53;ReadPosRankSum=1.919;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:829,0,565 -chr1 81600 . T G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-2.660;QD=16.65;ReadPosRankSum=2.588;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:744,0,706 -chr1 81638 . C T 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=0;MQRankSum=-2.108;QD=15.37;ReadPosRankSum=-1.219;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:843,0,879 -chr1 81650 . C T 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=59;Dels=0.00;FS=0.989;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=1.677;QD=16.42;ReadPosRankSum=0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:997,0,893 -chr1 81655 . A T 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=50.82;MQ0=1;MQRankSum=-1.189;QD=14.60;ReadPosRankSum=-0.497;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:846,0,959 -chr1 81660 . C G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.26;MQ0=1;MQRankSum=-1.272;QD=14.65;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:834,0,917 -chr1 81684 . T C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.407;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.850;QD=11.40;ReadPosRankSum=1.572;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:450,0,653 -chr1 81688 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.947;QD=10.94;ReadPosRankSum=2.054;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:433,0,686 -chr1 81689 . T C 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=36;Dels=0.00;FS=2.958;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=1;MQRankSum=-3.750;QD=10.77;ReadPosRankSum=1.950;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:416,0,612 -chr1 81693 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=38;Dels=0.00;FS=4.815;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.42;MQ0=1;MQRankSum=-3.581;QD=12.68;ReadPosRankSum=1.143;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:510,0,642 -chr1 81707 . T C 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=47;Dels=0.00;FS=1.176;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.19;MQ0=1;MQRankSum=3.636;QD=11.87;ReadPosRankSum=-0.268;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:586,0,810 -chr1 81724 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.003;DP=44;Dels=0.00;FS=1.986;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=-0.378;QD=1.27;ReadPosRankSum=0.609;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,8:44:84:84,0,1258 -chr1 81739 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.983;QD=19.66;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,28:42:99:854,0,419 -chr1 81778 . A G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.868;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=3;MQRankSum=0.964;QD=8.94;ReadPosRankSum=2.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:493,0,1122 -chr1 81794 . A C 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.402;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=3;MQRankSum=0.029;QD=18.77;ReadPosRankSum=-0.488;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1042,0,496 -chr1 81881 . G A 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=46.68;MQ0=0;MQRankSum=-0.097;QD=21.21;ReadPosRankSum=2.511;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:707,0,302 -chr1 81889 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.311;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=49.01;MQ0=0;MQRankSum=-0.851;QD=9.17;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:340,0,730 -chr1 81914 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.672;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=0;MQRankSum=0.503;QD=17.79;ReadPosRankSum=-3.004;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:740,0,520 -chr1 81935 . A T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.440;DP=43;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-0.335;QD=12.44;ReadPosRankSum=1.279;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:563,0,831 -chr1 81995 . G A 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.114;QD=12.73;ReadPosRankSum=0.458;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,740 -chr1 82003 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.877;QD=9.37;ReadPosRankSum=3.261;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:375,0,858 -chr1 82004 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.910;QD=9.51;ReadPosRankSum=3.326;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:380,0,857 -chr1 82005 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.190;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.358;QD=9.53;ReadPosRankSum=3.293;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:381,0,863 -chr1 82009 . T C 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.836;DP=36;Dels=0.00;FS=3.018;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-3.574;QD=10.05;ReadPosRankSum=2.970;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:390,0,731 -chr1 82011 . G C 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.763;DP=35;Dels=0.00;FS=1.421;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-3.736;QD=10.42;ReadPosRankSum=2.763;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:393,0,756 -chr1 82025 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.275;DP=40;Dels=0.00;FS=4.364;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.59;MQ0=0;MQRankSum=-4.604;QD=16.92;ReadPosRankSum=0.244;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:705,0,617 -chr1 82036 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.13;MQ0=0;MQRankSum=-4.538;QD=19.31;ReadPosRankSum=-0.103;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:762,0,463 -chr1 82050 . C T 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.144;DP=35;Dels=0.00;FS=10.665;HaplotypeScore=49.2919;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-4.080;QD=21.25;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,22:35:99:772,0,401 -chr1 82064 . T C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.141;DP=31;Dels=0.00;FS=8.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.343;QD=19.41;ReadPosRankSum=1.501;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,18:31:99:630,0,427 -chr1 82126 . G A 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.199;DP=37;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-1.977;QD=16.02;ReadPosRankSum=-0.169;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:621,0,501 -chr1 82156 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.862;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-0.011;QD=14.34;ReadPosRankSum=0.990;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:702,0,724 -chr1 82158 . T A 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=0.352;QD=13.81;ReadPosRankSum=1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:705,0,824 -chr1 82161 . C G 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.131;QD=16.63;ReadPosRankSum=-1.578;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:843,0,731 -chr1 82212 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.113;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.113;QD=17.12;ReadPosRankSum=0.788;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:970,0,654 -chr1 82270 . A C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=48;Dels=0.00;FS=7.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=-0.969;QD=11.54;ReadPosRankSum=0.224;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:582,0,945 -chr1 82352 . G C 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.780;QD=14.59;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:787,0,872 -chr1 82367 . G A 907.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.433;DP=60;Dels=0.00;FS=0.988;HaplotypeScore=2.7001;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.509;QD=15.13;ReadPosRankSum=-0.630;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:60:99:936,0,959 -chr1 82434 . T C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-1.087;QD=14.15;ReadPosRankSum=1.842;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:764,0,957 -chr1 82440 . G C 859.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=49;Dels=0.00;FS=1.092;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=0.955;QD=17.55;ReadPosRankSum=-1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:888,0,719 -chr1 82482 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=1.064;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=-1.757;QD=14.52;ReadPosRankSum=-1.194;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,24:51:99:769,0,899 -chr1 82487 . T A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=1;MQRankSum=-0.850;QD=15.32;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:794,0,848 -chr1 82613 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-1.183;QD=12.44;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,964 -chr1 82614 . A G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-0.539;QD=12.44;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,934 -chr1 82616 . G C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=1;MQRankSum=-2.266;QD=11.86;ReadPosRankSum=0.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:657,0,973 -chr1 82648 . A G 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=45;Dels=0.00;FS=5.254;HaplotypeScore=6.9393;MLEAC=1;MLEAF=0.500;MQ=52.78;MQ0=3;MQRankSum=-4.177;QD=3.93;ReadPosRankSum=-0.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,12:45:99:205,0,1095 -chr1 82650 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=43;Dels=0.00;FS=5.772;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=3;MQRankSum=-4.146;QD=2.51;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:136,0,1090 -chr1 82656 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=3;MQRankSum=4.699;QD=22.29;ReadPosRankSum=0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,27:41:99:942,0,189 -chr1 82658 . T G 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=42;Dels=0.00;FS=3.333;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=3;MQRankSum=-4.050;QD=2.66;ReadPosRankSum=-1.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:140,0,1017 -chr1 82690 . G T 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=40;Dels=0.00;FS=5.301;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=1;MQRankSum=-2.041;QD=8.64;ReadPosRankSum=-2.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:374,0,898 -chr1 82792 . T A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.636;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=0.289;QD=19.32;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:743,0,494 -chr1 82795 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.114;QD=11.86;ReadPosRankSum=1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:467,0,769 -chr1 82814 . G A 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.079;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.958;QD=8.48;ReadPosRankSum=0.707;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:359,0,871 -chr1 82878 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=36;Dels=0.00;FS=2.928;HaplotypeScore=2.5775;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.111;QD=15.72;ReadPosRankSum=-2.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:594,0,499 -chr1 82887 . T C 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.631;DP=36;Dels=0.00;FS=1.344;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.257;QD=11.41;ReadPosRankSum=2.246;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:439,0,686 -chr1 82936 . A T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=28;Dels=0.00;FS=10.544;HaplotypeScore=8.7318;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.839;QD=7.03;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:225,0,697 -chr1 82946 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.977;DP=34;Dels=0.00;FS=20.808;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.942;QD=14.52;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:522,0,487 -chr1 83013 . A T 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=48;Dels=0.00;FS=46.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.792;QD=11.70;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:590,0,915 -chr1 83024 . A G 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=42.658;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=1;MQRankSum=-2.045;QD=10.57;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:472,0,804 -chr1 83033 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;DP=39;Dels=0.00;FS=31.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=1;MQRankSum=-3.862;QD=6.79;ReadPosRankSum=2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:293,0,843 -chr1 83044 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.349;DP=37;Dels=0.00;FS=27.416;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=1;MQRankSum=-4.362;QD=6.40;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,11:37:99:265,0,839 -chr1 83337 . A C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.588;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=1;MQRankSum=-2.646;QD=10.34;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:9,8:17:99:204,0,330 -chr1 83398 . G T 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.192;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=0.778;QD=6.32;ReadPosRankSum=2.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:11,4:15:99:123,0,311 -chr1 83404 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=45.65;MQ0=1;MQRankSum=-1.157;QD=4.34;ReadPosRankSum=-1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:9,5:14:89:89,0,317 -chr1 83532 . G T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.264;DP=30;Dels=0.00;FS=5.946;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.56;MQ0=2;MQRankSum=-3.188;QD=6.56;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83509_83569) GT:AD:DP:GQ:PL 0/1:18,12:30:99:225,0,597 -chr1 83605 . A G 62.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=24;Dels=0.00;FS=7.799;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.85;MQ0=0;MQRankSum=-2.167;QD=2.62;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,6:24:91:91,0,606 -chr1 83629 . T G 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=19;Dels=0.00;FS=4.713;HaplotypeScore=1.7880;MLEAC=1;MLEAF=0.500;MQ=41.28;MQ0=0;MQRankSum=-2.268;QD=2.04;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,5:19:67:67,0,465 -chr1 83691 . T G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=35;Dels=0.00;FS=8.175;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=42.05;MQ0=0;MQRankSum=-0.020;QD=5.51;ReadPosRankSum=-1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,8:35:99:221,0,947 -chr1 83837 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.636;DP=30;Dels=0.00;FS=14.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.28;MQ0=2;MQRankSum=-3.738;QD=5.23;ReadPosRankSum=-0.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83730_84064) GT:AD:DP:GQ:PL 0/1:20,10:30:99:185,0,667 -chr1 84090 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.235;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.8663;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.440;QD=13.44;ReadPosRankSum=-0.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:539,0,732 -chr1 84156 . C T 1240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=56;Dels=0.00;FS=6.157;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-1.818;QD=22.16;ReadPosRankSum=0.463;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,39:56:99:1269,0,542 -chr1 84266 . A C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.232;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.392;QD=11.12;ReadPosRankSum=-0.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:484,0,881 -chr1 84467 . C A 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.341;DP=48;Dels=0.00;FS=5.874;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.321;QD=14.87;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,877 -chr1 84548 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=61;Dels=0.00;FS=3.670;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=2.402;QD=16.54;ReadPosRankSum=1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1037,0,988 -chr1 84601 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.270;DP=65;Dels=0.00;FS=2.135;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.172;QD=19.63;ReadPosRankSum=-0.797;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,39:65:99:1304,0,773 -chr1 84805 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.168;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.505;QD=19.46;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S113|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1001,0,641 -chr1 84858 . A C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.541;DP=42;Dels=0.00;FS=8.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.322;QD=16.95;ReadPosRankSum=1.876;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K131T|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,22:42:99:740,0,673 -chr1 84886 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.437;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.521;QD=14.58;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V140|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:21,18:39:99:597,0,712 -chr1 85016 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.347;QD=17.45;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:988,0,847 -chr1 85055 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.450;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.599;QD=16.34;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:992,0,999 -chr1 85064 . T C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=54;Dels=0.00;FS=3.998;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.488;QD=14.61;ReadPosRankSum=0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:817,0,887 -chr1 85114 . A G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.117;DP=47;Dels=0.00;FS=2.488;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=-1.011;QD=16.40;ReadPosRankSum=-0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:799,0,742 -chr1 85206 . A G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=-0.412;QD=14.65;ReadPosRankSum=-1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:834,0,932 -chr1 85259 . T C 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.311;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=26.7919;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.070;QD=17.50;ReadPosRankSum=0.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,924 -chr1 85388 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=56;Dels=0.00;FS=2.338;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.972;QD=17.91;ReadPosRankSum=2.060;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1031,0,826 -chr1 85403 . A G 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.803;DP=53;Dels=0.00;FS=3.822;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.045;QD=20.00;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1088,0,713 -chr1 85460 . A C 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=4.180;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=17.87;ReadPosRankSum=-2.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:886,0,741 -chr1 85658 . T A 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.2566;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.933;QD=12.97;ReadPosRankSum=2.850;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:560,0,680 -chr1 85709 . T A 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=30;Dels=0.00;FS=3.431;HaplotypeScore=15.9845;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.209;QD=17.76;ReadPosRankSum=1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:561,0,349 -chr1 85779 . A G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.928;DP=32;Dels=0.00;FS=10.207;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.042;QD=6.27;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,9:32:99:229,0,795 -chr1 85866 . G A 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=15.4975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.788;QD=15.93;ReadPosRankSum=-1.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:506,0,472 -chr1 85928 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=31;Dels=0.00;FS=1.566;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.021;QD=22.54;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,21:31:99:727,0,300 -chr1 85964 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=32;Dels=0.00;FS=3.848;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.936;QD=26.59;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,24:32:99:879,0,222 -chr1 85983 . T C 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;QD=24.67;ReadPosRankSum=-0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:793,0,280 -chr1 85984 . A T 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.413;QD=24.19;ReadPosRankSum=-0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:778,0,283 -chr1 86057 . T A 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.117;QD=16.34;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:796,0,802 -chr1 86096 . T C 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.383;DP=47;Dels=0.00;FS=6.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.171;QD=18.42;ReadPosRankSum=0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:894,0,583 -chr1 86197 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.775;QD=15.83;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:614,0,592 -chr1 86283 . T G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=81;Dels=0.00;FS=11.183;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-1.581;QD=7.98;ReadPosRankSum=-5.926;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:45,36:81:99:675,0,1045 -chr1 86295 . G A 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-0.694;QD=2.69;ReadPosRankSum=-1.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,17:79:99:241,0,1690 -chr1 86334 . C T 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=-1.600;QD=18.65;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:942,0,629 -chr1 86368 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.010;QD=17.87;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:904,0,769 -chr1 86487 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.006;DP=60;Dels=0.00;FS=3.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-2.588;QD=18.93;ReadPosRankSum=1.410;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1164,0,811 -chr1 86494 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.597;DP=62;Dels=0.00;FS=1.012;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.077;QD=11.83;ReadPosRankSum=-0.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:762,0,1311 -chr1 86710 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.161;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=15.58;ReadPosRankSum=-1.135;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:667,0,725 -chr1 86783 . T C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.254;DP=51;Dels=0.00;FS=1.083;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.98;ReadPosRankSum=0.141;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:843,0,891 -chr1 86874 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.055;DP=46;Dels=0.00;FS=2.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.587;QD=18.63;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,605 -chr1 86945 . C T 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.551;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.651;QD=15.59;ReadPosRankSum=-1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:792,0,917 -chr1 87016 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.274;DP=53;Dels=0.00;FS=2.380;HaplotypeScore=46.7458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.134;QD=15.01;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,910 -chr1 87182 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=65.7226;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.562;QD=16.77;ReadPosRankSum=-1.948;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:716,0,647 -chr1 87257 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.809;DP=42;Dels=0.00;FS=2.756;HaplotypeScore=3.9986;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.202;QD=14.71;ReadPosRankSum=-0.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:646,0,809 -chr1 87282 . C T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=11.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;QD=17.97;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:783,0,641 -chr1 87399 . T A 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.840;DP=43;Dels=0.00;FS=4.388;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.426;QD=15.41;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:691,0,818 -chr1 88214 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.856;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4710;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.316;QD=17.04;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,23:45:99:795,0,623 -chr1 88243 . G A 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.274;DP=40;Dels=0.00;FS=2.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.465;QD=19.67;ReadPosRankSum=-2.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:815,0,487 -chr1 88460 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.222;DP=41;Dels=0.00;FS=4.561;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.874;QD=15.80;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:676,0,700 -chr1 88534 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=50;Dels=0.00;FS=13.391;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.545;QD=14.54;ReadPosRankSum=-1.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1964|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_88510_88890) GT:AD:DP:GQ:PL 0/1:27,23:50:99:755,0,913 -chr1 88912 . A C 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.131;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-1.268;QD=13.31;ReadPosRankSum=-0.971;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:627,0,862 -chr1 88959 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.476;DP=56;Dels=0.00;FS=9.559;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.590;QD=15.78;ReadPosRankSum=0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:912,0,1002 -chr1 88961 . C G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=58;Dels=0.00;FS=11.723;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.661;QD=17.50;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,950 -chr1 89344 . G C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=61;Dels=0.00;FS=5.322;HaplotypeScore=2.9937;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=1;MQRankSum=-0.052;QD=16.77;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1051,0,895 -chr1 89418 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.659;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=0.521;QD=18.45;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1793|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89391_89495) GT:AD:DP:GQ:PL 0/1:19,25:44:99:840,0,514 -chr1 89522 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.620;DP=45;Dels=0.00;FS=11.478;HaplotypeScore=103.5819;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.517;QD=13.15;ReadPosRankSum=-1.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:620,0,881 -chr1 89531 . A G 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=114.0798;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=1;MQRankSum=-0.041;QD=1.14;ReadPosRankSum=-1.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,9:50:85:85,0,1381 -chr1 89635 . T G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.207;DP=56;Dels=0.00;FS=7.797;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.737;QD=18.12;ReadPosRankSum=0.339;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N1762H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1043,0,749 -chr1 89954 . T C 1227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.449;DP=64;Dels=0.00;FS=2.069;HaplotypeScore=2.6551;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.884;QD=19.18;ReadPosRankSum=1.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,37:64:99:1256,0,894 -chr1 90005 . A G 1150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=58;Dels=0.00;FS=3.623;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.523;QD=19.84;ReadPosRankSum=0.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1179,0,842 -chr1 90303 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.343;DP=46;Dels=0.00;FS=5.030;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.388;QD=13.49;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I1592T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 0/1:26,20:46:99:649,0,883 -chr1 90520 . C T 496.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=7.375;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-0.693;QD=23.66;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:18:525,0,18 -chr1 90521 . C T 488.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;DP=21;Dels=0.00;FS=8.316;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-1.197;QD=23.24;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:12:516,0,12 -chr1 90588 . A G 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.589;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.768;QD=8.06;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:262,0,686 -chr1 90591 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.430;DP=30;Dels=0.00;FS=1.987;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.387;QD=21.59;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,19:30:99:676,0,304 -chr1 90977 . G T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.999;DP=45;Dels=0.00;FS=4.453;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.857;QD=13.48;ReadPosRankSum=-1.633;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:635,0,845 -chr1 90985 . T C 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=47;Dels=0.00;FS=4.385;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.160;QD=12.29;ReadPosRankSum=0.228;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:606,0,909 -chr1 91526 . G C 509.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=2.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.065;QD=12.14;ReadPosRankSum=-0.842;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:538,0,882 -chr1 91614 . A C 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.445;QD=17.90;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:1013,0,821 -chr1 91617 . T A 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.288;QD=18.19;ReadPosRankSum=1.043;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1047,0,834 -chr1 91650 . C A 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=42;Dels=0.00;FS=1.831;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.893;QD=0.88;ReadPosRankSum=-2.796;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q1346H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:37,5:42:65:65,0,1325 -chr1 91722 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.741;DP=50;Dels=0.00;FS=4.367;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.000;QD=10.08;ReadPosRankSum=0.676;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1322|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:33,17:50:99:532,0,996 -chr1 91774 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.765;QD=13.25;ReadPosRankSum=-1.230;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:823,0,1195 -chr1 91973 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.239;QD=15.71;ReadPosRankSum=-1.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1269|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:20,22:42:99:688,0,658 -chr1 91976 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.609;DP=46;Dels=0.00;FS=6.133;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.277;QD=12.97;ReadPosRankSum=2.338;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1268|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:26,20:46:99:625,0,846 -chr1 92011 . A C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=56;Dels=0.00;FS=7.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.813;QD=19.53;ReadPosRankSum=1.995;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1257A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1122,0,788 -chr1 92186 . G A 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;DP=35;Dels=0.00;FS=5.368;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.083;QD=16.51;ReadPosRankSum=-0.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1198|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:16,19:35:99:606,0,541 -chr1 92279 . A G 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=41;Dels=0.00;FS=6.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.090;QD=18.92;ReadPosRankSum=0.775;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:804,0,592 -chr1 92325 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.810;DP=44;Dels=0.00;FS=6.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.692;QD=16.40;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:750,0,740 -chr1 92362 . A G 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.701;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.214;QD=14.48;ReadPosRankSum=0.097;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:752,0,920 -chr1 92420 . A C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=46;Dels=0.00;FS=6.635;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.404;QD=10.39;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,16:46:99:506,0,1054 -chr1 92426 . C T 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=42;Dels=0.00;FS=9.664;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.680;QD=9.99;ReadPosRankSum=0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:448,0,1021 -chr1 92459 . G A 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=41;Dels=0.00;FS=2.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.521;QD=11.87;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:515,0,892 -chr1 92463 . G A 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=43;Dels=0.00;FS=2.743;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.406;QD=12.99;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:587,0,880 -chr1 92529 . T A 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=1.253;QD=16.77;ReadPosRankSum=0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:984,0,918 -chr1 92647 . A G 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.840;QD=9.40;ReadPosRankSum=0.680;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:423,0,976 -chr1 92758 . T A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.338;DP=53;Dels=0.00;FS=3.955;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.930;QD=10.18;ReadPosRankSum=1.380;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:568,0,1136 -chr1 92787 . A G 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=68;Dels=0.00;FS=3.335;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.142;QD=13.50;ReadPosRankSum=0.377;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:946,0,1223 -chr1 92881 . G T 1034.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.472;DP=57;Dels=0.00;FS=9.783;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=1.051;QD=18.15;ReadPosRankSum=-0.803;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1063,0,740 -chr1 92887 . A G 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.408;DP=56;Dels=0.00;FS=2.506;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=1;MQRankSum=0.126;QD=15.62;ReadPosRankSum=0.008;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:903,0,715 -chr1 92906 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=64;Dels=0.00;FS=2.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=2;MQRankSum=1.450;QD=13.48;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,30:64:99:891,0,1127 -chr1 93051 . G C 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=67;Dels=0.00;FS=0.945;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.436;QD=19.41;ReadPosRankSum=-0.576;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,38:67:99:1329,0,959 -chr1 93126 . T G 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.349;QD=21.83;ReadPosRankSum=-0.099;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1207,0,605 -chr1 93129 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=0.905;QD=22.01;ReadPosRankSum=0.242;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1217,0,604 -chr1 93143 . G C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.109;DP=51;Dels=0.00;FS=2.448;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.287;QD=11.86;ReadPosRankSum=-1.357;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:51:99:633,0,1071 -chr1 93221 . G C 960.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=59;Dels=0.00;FS=0.998;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.371;QD=16.28;ReadPosRankSum=0.387;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:989,0,965 -chr1 93235 . G A 1138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=63;Dels=0.00;FS=2.089;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=1.110;QD=18.08;ReadPosRankSum=-0.779;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,34:63:99:1167,0,900 -chr1 93280 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.487;DP=52;Dels=0.00;FS=4.010;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.194;QD=13.11;ReadPosRankSum=3.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:710,0,1066 -chr1 93282 . G C 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.616;DP=49;Dels=0.00;FS=4.055;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.636;QD=14.02;ReadPosRankSum=3.222;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:715,0,961 -chr1 93283 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.394;DP=50;Dels=0.00;FS=2.447;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.10;MQ0=0;MQRankSum=-1.065;QD=14.36;ReadPosRankSum=2.746;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:746,0,976 -chr1 93333 . C T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.258;DP=53;Dels=0.00;FS=5.940;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=0.454;QD=15.32;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:840,0,924 -chr1 93352 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=57;Dels=0.00;FS=11.817;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.745;QD=15.03;ReadPosRankSum=1.402;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:885,0,1090 -chr1 93358 . A C 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.132;DP=56;Dels=0.00;FS=12.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.231;QD=14.50;ReadPosRankSum=1.615;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,1093 -chr1 93504 . G A 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.233;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.560;QD=16.00;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,29:59:99:972,0,962 -chr1 93567 . A G 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=59;Dels=0.00;FS=2.347;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.177;QD=9.56;ReadPosRankSum=0.344;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,20:59:99:592,0,1326 -chr1 93595 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=4.620;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=7.95;ReadPosRankSum=-0.586;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,14:49:99:418,0,1282 -chr1 93676 . A G 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.019;QD=17.14;ReadPosRankSum=1.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1167|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93628_93699) GT:AD:DP:GQ:PL 0/1:27,28:55:99:971,0,908 -chr1 93754 . T A 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.413;DP=58;Dels=0.00;FS=5.597;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=11.58;ReadPosRankSum=-0.111;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,23:58:99:700,0,1216 -chr1 93903 . G T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.782;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.011;QD=16.62;ReadPosRankSum=-0.261;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I1129|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:22,23:45:99:776,0,668 -chr1 93906 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=1.9830;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.098;QD=14.46;ReadPosRankSum=0.309;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1128|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:25,22:47:99:708,0,860 -chr1 94001 . A G 893.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=53;Dels=0.00;FS=2.323;HaplotypeScore=1.5782;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.240;QD=16.86;ReadPosRankSum=0.827;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:922,0,890 -chr1 94020 . G C 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.912;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.331;QD=15.44;ReadPosRankSum=1.733;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:785,0,888 -chr1 94164 . A G 839.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.879;QD=15.00;ReadPosRankSum=-0.501;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1084|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94102_94193) GT:AD:DP:GQ:PL 0/1:30,26:56:99:868,0,1033 -chr1 94307 . G A 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.403;QD=17.66;ReadPosRankSum=-0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:876,0,754 -chr1 94331 . G T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.887;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.692;QD=15.95;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:714,0,748 -chr1 94476 . G T 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.404;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=1;MQRankSum=0.350;QD=18.87;ReadPosRankSum=-1.498;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1047,0,739 -chr1 94499 . C T 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.740;DP=55;Dels=0.00;FS=1.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.531;QD=13.83;ReadPosRankSum=0.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:789,0,1061 -chr1 94679 . A G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.046;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.70;ReadPosRankSum=-0.198;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1005|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94543_94708) GT:AD:DP:GQ:PL 0/1:26,25:51:99:829,0,859 -chr1 94743 . G A 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.225;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-1.258;QD=9.38;ReadPosRankSum=3.272;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:366,0,807 -chr1 94753 . A C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.8896;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-0.225;QD=9.94;ReadPosRankSum=0.898;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:386,0,718 -chr1 94840 . A C 753.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.135;DP=58;Dels=0.00;FS=0.999;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.272;QD=13.00;ReadPosRankSum=-0.455;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S985A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:33,25:58:99:782,0,1167 -chr1 94856 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.040;QD=18.01;ReadPosRankSum=0.523;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L979|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1055,0,767 -chr1 94898 . G A 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.088;DP=57;Dels=0.00;FS=2.219;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.679;QD=16.35;ReadPosRankSum=-2.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L965|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:27,30:57:99:960,0,917 -chr1 94963 . C A 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.668;QD=16.69;ReadPosRankSum=-0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:896,0,874 -chr1 95594 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;DP=53;Dels=0.00;FS=5.738;HaplotypeScore=2.6552;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=0.085;QD=17.22;ReadPosRankSum=0.349;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G817|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95323_95596) GT:AD:DP:GQ:PL 0/1:24,28:53:99:941,0,742 -chr1 96214 . A T 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.364;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.622;QD=15.04;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1036,0,1067 -chr1 96224 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.656;QD=15.16;ReadPosRankSum=-2.171;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:953,0,1050 -chr1 96309 . A G 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.522;DP=54;Dels=0.00;FS=7.971;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.262;QD=13.66;ReadPosRankSum=-2.029;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:766,0,1037 -chr1 96360 . G A 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.447;DP=58;Dels=0.00;FS=3.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=1.081;QD=15.86;ReadPosRankSum=-0.864;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,883 -chr1 96399 . T G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=51;Dels=0.00;FS=8.273;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.902;QD=17.76;ReadPosRankSum=1.618;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:934,0,788 -chr1 96448 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.536;DP=51;Dels=0.00;FS=4.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.121;QD=17.09;ReadPosRankSum=-1.479;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:900,0,792 -chr1 96485 . A T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=44;Dels=0.00;FS=2.672;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=0.141;QD=15.77;ReadPosRankSum=0.987;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T806|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:23,21:44:99:722,0,775 -chr1 96530 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.746;QD=18.04;ReadPosRankSum=0.526;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N791|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:19,24:43:99:804,0,602 -chr1 96637 . G A 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.628;QD=15.17;ReadPosRankSum=-1.798;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:741,0,788 -chr1 96789 . C T 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;DP=69;Dels=0.00;FS=0.918;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=1;MQRankSum=0.417;QD=15.65;ReadPosRankSum=1.436;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1108,0,1126 -chr1 96791 . T C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=1.110;QD=15.59;ReadPosRankSum=1.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:1057,0,1086 -chr1 96822 . T G 1272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=73;Dels=0.00;FS=1.969;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=1;MQRankSum=-0.475;QD=17.44;ReadPosRankSum=-0.328;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,40:73:99:1301,0,1128 -chr1 96868 . A T 1270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=72;Dels=0.00;FS=7.826;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.620;QD=17.65;ReadPosRankSum=0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1299,0,1177 -chr1 96880 . C T 1144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;DP=65;Dels=0.00;FS=3.414;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.795;QD=17.61;ReadPosRankSum=-0.729;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1173,0,1062 -chr1 96881 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.233;DP=62;Dels=0.00;FS=4.010;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.752;QD=8.00;ReadPosRankSum=0.101;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,18:62:99:524,0,1555 -chr1 96885 . G T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=2.212;HaplotypeScore=11.9973;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.053;QD=17.23;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1045,0,994 -chr1 97080 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.185;DP=53;Dels=0.00;FS=3.844;HaplotypeScore=4.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.312;QD=15.58;ReadPosRankSum=-1.630;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L759S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:28,25:53:99:854,0,987 -chr1 97141 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.017;DP=35;Dels=0.00;FS=7.260;HaplotypeScore=3.5776;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.183;QD=19.31;ReadPosRankSum=2.450;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P739S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:15,20:35:99:704,0,461 -chr1 97145 . G A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=37;Dels=0.00;FS=2.995;HaplotypeScore=5.4724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.461;QD=20.48;ReadPosRankSum=1.021;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P737|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:13,23:37:99:786,0,395 -chr1 97223 . A C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=0.412;QD=14.31;ReadPosRankSum=0.443;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,28:58:99:858,0,1018 -chr1 97268 . G T 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.938;DP=63;Dels=0.00;FS=2.132;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.326;QD=12.76;ReadPosRankSum=-0.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:832,0,1288 -chr1 97299 . A G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.648;QD=14.48;ReadPosRankSum=-0.290;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,28:62:99:926,0,1199 -chr1 97312 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.498;DP=67;Dels=0.00;FS=0.988;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.608;QD=13.74;ReadPosRankSum=1.761;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1344 -chr1 97631 . G C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.243;DP=55;Dels=0.00;FS=2.478;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.377;QD=11.76;ReadPosRankSum=-0.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A723G|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97615_97666) GT:AD:DP:GQ:PL 0/1:34,21:55:99:675,0,1153 -chr1 97696 . C T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.902;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.101;QD=12.26;ReadPosRankSum=1.362;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,18:46:99:592,0,888 -chr1 97749 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.914;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.748;QD=13.02;ReadPosRankSum=-0.831;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:653,0,801 -chr1 97919 . A T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=46;Dels=0.00;FS=4.288;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.066;QD=16.41;ReadPosRankSum=-0.945;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:783,0,771 -chr1 97946 . C G 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.771;DP=41;Dels=0.00;FS=2.814;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.879;QD=14.68;ReadPosRankSum=-1.799;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,20:41:99:630,0,670 -chr1 98038 . A G 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.277;DP=50;Dels=0.00;FS=1.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.019;QD=17.68;ReadPosRankSum=0.564;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:912,0,770 -chr1 98179 . G T 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.164;DP=54;Dels=0.00;FS=3.840;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.099;QD=16.44;ReadPosRankSum=1.013;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:916,0,864 -chr1 98294 . A G 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=52;Dels=0.00;FS=8.574;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-1.000;QD=15.21;ReadPosRankSum=0.707;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:819,0,922 -chr1 98466 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.245;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.607;QD=15.61;ReadPosRankSum=-2.224;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:762,0,808 -chr1 98495 . G A 994.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.390;QD=19.51;ReadPosRankSum=-1.113;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:1023,0,696 -chr1 98562 . A C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=55;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.698;QD=12.67;ReadPosRankSum=-0.572;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:725,0,1123 -chr1 98613 . T C 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=41;Dels=0.00;FS=4.457;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.327;QD=14.31;ReadPosRankSum=1.011;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:615,0,801 -chr1 98666 . A T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.742;DP=47;Dels=0.00;FS=2.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=1.116;QD=18.97;ReadPosRankSum=-3.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:920,0,631 -chr1 98933 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=1;MQRankSum=-0.034;QD=16.22;ReadPosRankSum=0.612;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1066,0,1072 -chr1 99114 . A T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.229;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.092;QD=14.05;ReadPosRankSum=-1.037;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I608|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:28,24:52:99:759,0,894 -chr1 99351 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=45;Dels=0.00;FS=2.527;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.683;QD=11.93;ReadPosRankSum=0.637;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L529|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,18:45:99:565,0,935 -chr1 99567 . T G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=12.036;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=0;MQRankSum=0.412;QD=14.02;ReadPosRankSum=-0.533;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E457D|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,22:49:99:715,0,877 -chr1 99633 . A G 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.770;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9944;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=1.259;QD=13.09;ReadPosRankSum=-0.599;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S435|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,731 -chr1 99642 . C T 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.702;QD=11.25;ReadPosRankSum=-0.579;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V432|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:25,18:43:99:512,0,818 -chr1 99729 . G A 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.652;DP=53;Dels=0.00;FS=3.841;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.298;QD=18.45;ReadPosRankSum=-1.670;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G403|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1006,0,723 -chr1 99861 . A G 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.654;DP=48;Dels=0.00;FS=2.555;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.822;QD=18.89;ReadPosRankSum=-1.581;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S359|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:19,29:48:99:935,0,572 -chr1 100026 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=-0.156;QD=20.77;ReadPosRankSum=-0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:859,0,407 -chr1 100660 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.981;QD=10.20;ReadPosRankSum=1.005;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:569,0,1225 -chr1 100710 . A C 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.633;DP=58;Dels=0.00;FS=1.023;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.213;QD=16.46;ReadPosRankSum=-1.944;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F235C|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,29:58:99:983,0,1001 -chr1 100778 . A T 1005.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=60;Dels=0.00;FS=2.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.139;QD=16.76;ReadPosRankSum=0.888;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A212|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1034,0,964 -chr1 100875 . C A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=46;Dels=0.00;FS=1.178;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.963;QD=14.84;ReadPosRankSum=-0.794;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:711,0,861 -chr1 100917 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.969;DP=54;Dels=0.00;FS=3.266;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.189;QD=3.81;ReadPosRankSum=-3.129;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:234,0,1538 -chr1 101397 . A G 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.492;QD=15.28;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:899,0,799 -chr1 101547 . A G 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=65;Dels=0.00;FS=10.521;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.833;QD=15.89;ReadPosRankSum=-0.151;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1061,0,1064 -chr1 101683 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.992;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.040;QD=12.41;ReadPosRankSum=0.437;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:537,0,822 -chr1 101684 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.439;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.910;QD=13.31;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:534,0,741 -chr1 101745 . G A 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.536;DP=56;Dels=0.00;FS=3.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.107;QD=15.39;ReadPosRankSum=0.715;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:890,0,1039 -chr1 101797 . C A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=66;Dels=0.00;FS=0.940;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.032;QD=16.34;ReadPosRankSum=-0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1107,0,1179 -chr1 101798 . C T 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=69;Dels=0.00;FS=1.986;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=16.27;ReadPosRankSum=-0.582;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:69:99:1151,0,1212 -chr1 101901 . C T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.165;DP=38;Dels=0.00;FS=6.942;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.407;QD=20.49;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:807,0,440 -chr1 101943 . G C 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.433;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.144;QD=21.97;ReadPosRankSum=-0.445;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,30:45:99:1017,0,464 -chr1 101964 . A T 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.379;QD=14.30;ReadPosRankSum=-0.037;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:643,0,818 -chr1 102084 . T C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.787;DP=61;Dels=0.00;FS=0.974;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.816;QD=16.77;ReadPosRankSum=0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1051,0,930 -chr1 102113 . A C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=-1.220;QD=15.40;ReadPosRankSum=0.579;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:860,0,828 -chr1 102117 . C A 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=55;Dels=0.00;FS=2.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=1;MQRankSum=-1.307;QD=14.85;ReadPosRankSum=1.030;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:845,0,861 -chr1 102158 . T C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=54;Dels=0.00;FS=2.323;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=1;MQRankSum=1.951;QD=15.22;ReadPosRankSum=0.526;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:850,0,846 -chr1 102167 . G A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=57;Dels=0.00;FS=5.494;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=2;MQRankSum=0.806;QD=16.59;ReadPosRankSum=-2.418;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:974,0,828 -chr1 102205 . T C 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=59;Dels=0.00;FS=1.030;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-0.661;QD=15.50;ReadPosRankSum=0.770;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:943,0,978 -chr1 102214 . G C 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-2.208;QD=15.30;ReadPosRankSum=-1.135;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:931,0,1005 -chr1 102348 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=44;Dels=0.00;FS=11.766;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.295;QD=18.20;ReadPosRankSum=-0.554;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:829,0,650 -chr1 102411 . T A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.145;DP=43;Dels=0.00;FS=2.999;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.308;QD=18.02;ReadPosRankSum=-0.382;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:803,0,602 -chr1 102454 . T A 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.682;DP=46;Dels=0.00;FS=19.456;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=1.572;QD=16.93;ReadPosRankSum=-1.352;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:807,0,705 -chr1 102506 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.117;DP=36;Dels=0.00;FS=5.231;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=-1.950;QD=17.69;ReadPosRankSum=0.317;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:665,0,522 -chr1 102514 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;DP=39;Dels=0.00;FS=7.216;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=1;MQRankSum=0.617;QD=14.10;ReadPosRankSum=-0.264;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:578,0,741 -chr1 102597 . T A 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.154;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=-0.495;QD=17.25;ReadPosRankSum=1.374;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:839,0,693 -chr1 102685 . T C 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=48;Dels=0.00;FS=11.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-2.270;QD=15.41;ReadPosRankSum=-0.310;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:768,0,789 -chr1 102745 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=57;Dels=0.00;FS=1.037;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.626;QD=12.54;ReadPosRankSum=0.203;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:743,0,1192 -chr1 102828 . T A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.556;QD=13.44;ReadPosRankSum=-1.748;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:687,0,969 -chr1 102840 . C T 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.773;DP=49;Dels=0.00;FS=2.600;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.317;QD=11.49;ReadPosRankSum=-0.425;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:591,0,1069 -chr1 102853 . A T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=51;Dels=0.00;FS=4.012;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.453;QD=20.98;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1098,0,644 -chr1 103138 . A T 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=57;Dels=0.00;FS=3.801;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.010;QD=17.93;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1050,0,812 -chr1 103150 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=53;Dels=0.00;FS=2.466;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=2;MQRankSum=0.274;QD=14.58;ReadPosRankSum=-0.632;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:801,0,943 -chr1 103189 . A G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=55;Dels=0.00;FS=4.291;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=1;MQRankSum=0.854;QD=12.70;ReadPosRankSum=1.329;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:727,0,1140 -chr1 103225 . G A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.322;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=1;MQRankSum=1.023;QD=15.72;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:877,0,949 -chr1 103405 . C T 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=57;Dels=0.00;FS=2.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.280;QD=17.24;ReadPosRankSum=1.223;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1011,0,920 -chr1 103515 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=2.536;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.222;QD=13.79;ReadPosRankSum=-0.778;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:704,0,944 -chr1 103542 . G C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229;DP=44;Dels=0.00;FS=2.800;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=19.31;ReadPosRankSum=-1.492;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:878,0,558 -chr1 103599 . C G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.7842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.583;QD=15.71;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,22:46:99:751,0,773 -chr1 103609 . A C 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=48;Dels=0.00;FS=4.201;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.330;QD=16.89;ReadPosRankSum=-1.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:839,0,793 -chr1 103612 . C T 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=49;Dels=0.00;FS=1.101;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.130;QD=17.30;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:876,0,826 -chr1 103621 . G T 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;QD=17.70;ReadPosRankSum=-1.915;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:931,0,802 -chr1 103691 . C A 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=60;Dels=0.00;FS=2.252;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.061;QD=21.20;ReadPosRankSum=2.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,37:60:99:1300,0,754 -chr1 103828 . C G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=55;Dels=0.00;FS=7.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=0.227;QD=17.23;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:976,0,894 -chr1 103856 . C T 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=49;Dels=0.00;FS=16.948;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=-1.149;QD=12.02;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:617,0,1000 -chr1 103995 . G A 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.761;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.440;QD=12.81;ReadPosRankSum=-0.510;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,26:63:99:835,0,1325 -chr1 104120 . C G 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=54;Dels=0.00;FS=5.785;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.227;QD=12.09;ReadPosRankSum=-1.032;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:681,0,1040 -chr1 104149 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=51;Dels=0.00;FS=2.555;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.048;QD=19.29;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1012,0,605 -chr1 104155 . A G 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.401;DP=49;Dels=0.00;FS=4.412;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.798;QD=10.73;ReadPosRankSum=2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,17:49:99:554,0,1041 -chr1 104159 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=51;Dels=0.00;FS=4.244;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-1.120;QD=11.25;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:602,0,1079 -chr1 104167 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=2.473;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.109;QD=12.25;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,20:51:99:653,0,1056 -chr1 104213 . C T 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.709;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.104;QD=13.73;ReadPosRankSum=-1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:756,0,1034 -chr1 104376 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=53;Dels=0.00;FS=10.088;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.367;QD=18.28;ReadPosRankSum=-1.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,29:53:99:997,0,714 -chr1 104545 . A C 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.847;QD=17.70;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1108,0,937 -chr1 104570 . G T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.314;DP=66;Dels=0.00;FS=2.084;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.212;QD=16.97;ReadPosRankSum=0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1148,0,1049 -chr1 104631 . T A 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.341;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.7461;MLEAC=1;MLEAF=0.500;MQ=60.16;MQ0=0;MQRankSum=-1.676;QD=15.18;ReadPosRankSum=-0.596;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:1045,0,1181 -chr1 104738 . A T 1287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=70;Dels=0.00;FS=10.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.242;QD=18.40;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1316,0,1019 -chr1 104775 . C A 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=61;Dels=0.00;FS=2.287;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.380;QD=20.29;ReadPosRankSum=0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,37:61:99:1266,0,700 -chr1 104901 . T G 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.076;DP=55;Dels=0.00;FS=2.401;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.582;QD=18.03;ReadPosRankSum=0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1020,0,851 -chr1 104914 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.187;QD=15.35;ReadPosRankSum=-0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,26:54:99:857,0,929 -chr1 105276 . A G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=49;Dels=0.02;FS=1.174;HaplotypeScore=2.9659;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.120;QD=20.71;ReadPosRankSum=0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:48:99:1043,0,542 -chr1 105289 . C A 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=0.027;QD=19.57;ReadPosRankSum=0.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1085,0,685 -chr1 105391 . A G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=59;Dels=0.00;FS=7.470;HaplotypeScore=3.5213;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=12.00;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,23:59:99:736,0,1250 -chr1 105636 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=70;Dels=0.00;FS=8.071;HaplotypeScore=4.6697;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.786;QD=15.83;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:70:99:1136,0,1128 -chr1 105656 . G A 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;DP=63;Dels=0.00;FS=6.709;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-1.218;QD=15.63;ReadPosRankSum=-0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1013,0,1033 -chr1 105769 . C G 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=68;Dels=0.00;FS=3.397;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.071;QD=13.58;ReadPosRankSum=1.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,31:68:99:952,0,1291 -chr1 105775 . A G 1185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=2.634;QD=17.97;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1214,0,951 -chr1 105776 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.385;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.105;QD=13.42;ReadPosRankSum=0.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:914,0,1186 -chr1 105815 . C A 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;DP=65;Dels=0.00;FS=2.177;HaplotypeScore=2.3346;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=0.388;QD=17.30;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1153,0,982 -chr1 105914 . A G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.125;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.402;QD=19.33;ReadPosRankSum=1.939;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1014,0,607 -chr1 105940 . A G 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.169;DP=55;Dels=0.00;FS=1.036;HaplotypeScore=6.1984;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.580;QD=11.83;ReadPosRankSum=1.117;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,21:55:99:679,0,1160 -chr1 106000 . G A 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.619;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.475;QD=15.08;ReadPosRankSum=-0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,23:48:99:752,0,840 -chr1 106003 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.730;QD=15.87;ReadPosRankSum=-0.650;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,24:49:99:806,0,839 -chr1 106222 . A T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.445;DP=56;Dels=0.00;FS=3.858;HaplotypeScore=2.9889;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.294;QD=10.64;ReadPosRankSum=-1.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,22:56:99:624,0,1107 -chr1 106301 . G A 1226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=76;Dels=0.00;FS=3.172;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.057;QD=16.14;ReadPosRankSum=-0.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,38:76:99:1255,0,1277 -chr1 106304 . C T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.244;DP=75;Dels=0.00;FS=3.136;HaplotypeScore=1.6988;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.178;QD=14.90;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,36:75:99:1146,0,1287 -chr1 106447 . C A 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;DP=58;Dels=0.00;FS=3.667;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=1.169;QD=15.17;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:908,0,1064 -chr1 106476 . T G 1349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=77;Dels=0.00;FS=16.431;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=1.137;QD=17.53;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,40:77:99:1378,0,1148 -chr1 106481 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=76;Dels=0.00;FS=14.274;HaplotypeScore=3.8312;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.091;QD=12.37;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,32:76:99:968,0,1489 -chr1 106482 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=76;Dels=0.00;FS=17.089;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.404;QD=12.63;ReadPosRankSum=0.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,32:76:99:988,0,1538 -chr1 106502 . C T 1216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=80;Dels=0.00;FS=9.385;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.833;QD=15.21;ReadPosRankSum=0.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,38:80:99:1245,0,1351 -chr1 106522 . G C 1262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=73;Dels=0.00;FS=7.905;HaplotypeScore=3.1224;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.745;QD=17.30;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,37:73:99:1291,0,1178 -chr1 106546 . A T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=68;Dels=0.00;FS=21.595;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.577;QD=16.29;ReadPosRankSum=0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,35:68:99:1136,0,1064 -chr1 106547 . T A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.040;DP=65;Dels=0.00;FS=19.861;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.581;QD=13.38;ReadPosRankSum=0.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,32:65:99:898,0,1081 -chr1 106583 . A C 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=51;Dels=0.00;FS=1.066;HaplotypeScore=1.8313;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.161;QD=18.17;ReadPosRankSum=-1.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:955,0,750 -chr1 106636 . C G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.551;DP=53;Dels=0.00;FS=4.175;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.208;QD=12.96;ReadPosRankSum=0.713;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:715,0,996 -chr1 106713 . G T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.015;DP=52;Dels=0.00;FS=10.628;HaplotypeScore=24.7277;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.007;QD=15.17;ReadPosRankSum=0.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:817,0,902 -chr1 106817 . C T 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=40;Dels=0.00;FS=2.928;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.801;QD=23.29;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:960,0,454 -chr1 106840 . C T 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.801;QD=25.20;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,31:44:99:1137,0,394 -chr1 106843 . G C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.852;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.206;QD=8.09;ReadPosRankSum=-1.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:384,0,1140 -chr1 106885 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.646;QD=22.57;ReadPosRankSum=0.921;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,23:33:99:773,0,304 -chr1 107234 . T C 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.256;DP=34;Dels=0.00;FS=10.000;HaplotypeScore=3.3679;MLEAC=1;MLEAF=0.500;MQ=15.56;MQ0=13;MQRankSum=2.161;QD=1.99;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,4:34:58:96,0,58 -chr1 108057 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=2.204;QD=13.15;ReadPosRankSum=3.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:620,0,784 -chr1 108058 . C T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=-1.780;QD=17.55;ReadPosRankSum=-2.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:818,0,619 -chr1 108104 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.48;MQ0=0;MQRankSum=-4.097;QD=14.00;ReadPosRankSum=-5.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:686,0,806 -chr1 108111 . A G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.878;QD=9.97;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:427,0,745 -chr1 108112 . G A 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.496;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.793;QD=9.94;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:426,0,750 -chr1 108120 . A C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=48;Dels=0.00;FS=2.509;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.28;MQ0=0;MQRankSum=-2.348;QD=14.56;ReadPosRankSum=0.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:727,0,612 -chr1 108125 . T C 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=46;Dels=0.00;FS=2.597;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=33.80;MQ0=0;MQRankSum=1.807;QD=11.10;ReadPosRankSum=-1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:539,0,755 -chr1 108131 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.573;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.012;QD=13.32;ReadPosRankSum=2.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:721,0,597 -chr1 108137 . T A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.072;QD=13.30;ReadPosRankSum=4.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:720,0,593 -chr1 108138 . G C 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.272;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=0.952;QD=10.88;ReadPosRankSum=-4.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:594,0,722 -chr1 108170 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQ0=3;MQRankSum=0.019;QD=7.68;ReadPosRankSum=2.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:297,0,467 -chr1 108172 . A T 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.052;DP=34;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=3;MQRankSum=0.020;QD=7.99;ReadPosRankSum=2.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:300,0,431 -chr1 108179 . A T 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=31;Dels=0.00;FS=1.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.94;MQ0=3;MQRankSum=-0.092;QD=7.67;ReadPosRankSum=3.271;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:266,0,355 -chr1 108237 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.136;DP=52;Dels=0.00;FS=1.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=0.076;QD=2.84;ReadPosRankSum=-3.358;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:176,0,1420 -chr1 108244 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.012;DP=52;Dels=0.00;FS=3.548;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.507;QD=3.19;ReadPosRankSum=-2.533;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:194,0,1435 -chr1 108245 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=52;Dels=0.00;FS=3.605;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.358;QD=3.17;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:193,0,1432 -chr1 108320 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.061;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=0;MQRankSum=-1.995;QD=13.85;ReadPosRankSum=-0.737;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:804,0,1051 -chr1 108356 . C A 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=72;Dels=0.00;FS=1.099;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=1.076;QD=7.89;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:596,0,1658 -chr1 108358 . G C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.113;DP=72;Dels=0.00;FS=2.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=0.603;QD=8.11;ReadPosRankSum=-0.180;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:612,0,1682 -chr1 108381 . C G 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=57;Dels=0.00;FS=2.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=1.583;QD=9.47;ReadPosRankSum=-0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,19:57:99:568,0,1331 -chr1 108383 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.245;DP=59;Dels=0.00;FS=2.367;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.657;QD=10.86;ReadPosRankSum=-0.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:669,0,1309 -chr1 108421 . T C 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=54;Dels=0.00;FS=5.922;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.455;QD=12.48;ReadPosRankSum=-1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:702,0,1090 -chr1 108425 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.158;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.604;QD=12.76;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:666,0,1049 -chr1 108449 . A G 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.445;DP=52;Dels=0.00;FS=6.027;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=1.139;QD=12.59;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:683,0,1017 -chr1 108459 . T C 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=57;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=1;MQRankSum=-0.379;QD=17.36;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1018,0,841 -chr1 108482 . T C 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=70;Dels=0.00;FS=6.663;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=1;MQRankSum=-0.510;QD=11.90;ReadPosRankSum=-0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,28:70:99:861,0,1470 -chr1 108528 . T A 1085.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.439;DP=90;Dels=0.00;FS=2.962;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=3;MQRankSum=-0.509;QD=12.06;ReadPosRankSum=-0.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,37:90:99:1114,0,1842 -chr1 108603 . T C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=72;Dels=0.00;FS=5.096;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-1.165;QD=10.07;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:48,24:72:99:753,0,1647 -chr1 108612 . T C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=75;Dels=0.00;FS=7.991;HaplotypeScore=66.7830;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.528;QD=11.52;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:46,29:75:99:892,0,1572 -chr1 108628 . A C 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.110;DP=62;Dels=0.00;FS=2.268;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-0.346;QD=10.00;ReadPosRankSum=1.802;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:648,0,1375 -chr1 108660 . G A 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.575;QD=16.15;ReadPosRankSum=-1.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:852,0,837 -chr1 108664 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=49;Dels=0.00;FS=2.568;HaplotypeScore=1.7820;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.551;QD=15.63;ReadPosRankSum=-1.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:794,0,758 -chr1 108698 . C G 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=38;Dels=0.00;FS=8.656;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.27;MQ0=0;MQRankSum=0.998;QD=13.70;ReadPosRankSum=-4.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:549,0,669 -chr1 108709 . A C 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=37;Dels=0.00;FS=12.587;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=0.442;QD=13.97;ReadPosRankSum=-0.411;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:545,0,634 -chr1 108759 . T A 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.087;DP=55;Dels=0.00;FS=33.086;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.45;MQ0=0;MQRankSum=1.155;QD=14.38;ReadPosRankSum=0.868;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:819,0,968 -chr1 108772 . G A 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=54;Dels=0.00;FS=28.588;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-1.120;QD=13.33;ReadPosRankSum=-0.805;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:748,0,1076 -chr1 108796 . C T 1158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176;DP=42;Dels=0.00;FS=2.508;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.950;QD=27.59;ReadPosRankSum=-0.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,33:42:99:1187,0,248 -chr1 108799 . G A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.972;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.684;QD=26.97;ReadPosRankSum=-0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,31:40:99:1107,0,249 -chr1 108827 . C T 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074;DP=32;Dels=0.00;FS=27.227;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-3.223;QD=11.99;ReadPosRankSum=-0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:412,0,643 -chr1 108889 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=18;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-1.616;QD=26.71;ReadPosRankSum=-1.335;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,16:18:33:509,0,33 -chr1 108893 . A G 636.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.770;DP=22;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.400;QD=28.95;ReadPosRankSum=-1.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,20:22:18:665,0,18 -chr1 108940 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=35;Dels=0.00;FS=14.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.160;QD=22.74;ReadPosRankSum=1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:824,0,345 -chr1 108956 . G A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=38;Dels=0.00;FS=10.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.354;QD=23.86;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,27:38:99:935,0,334 -chr1 108987 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=30;Dels=0.00;FS=5.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.022;QD=9.69;ReadPosRankSum=-0.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:319,0,707 -chr1 109006 . G A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.423;DP=30;Dels=0.00;FS=9.472;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.963;QD=18.89;ReadPosRankSum=2.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:595,0,411 -chr1 109022 . A G 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=22;Dels=0.00;FS=2.126;HaplotypeScore=3.9974;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.672;QD=19.94;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,14:22:99:467,0,255 -chr1 109058 . A C 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=6.641;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-4.308;QD=19.07;ReadPosRankSum=0.467;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:524,0,360 -chr1 109062 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=27;Dels=0.00;FS=9.864;HaplotypeScore=13.9930;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=0;MQRankSum=-4.440;QD=16.55;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:475,0,443 -chr1 109083 . T C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.570;DP=34;Dels=0.00;FS=14.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=-3.295;QD=14.64;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:526,0,626 -chr1 109085 . G A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.173;DP=37;Dels=0.00;FS=16.965;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-3.692;QD=15.80;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:613,0,599 -chr1 109091 . G A 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=18.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-1.845;QD=17.92;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:781,0,633 -chr1 109097 . T A 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.958;DP=44;Dels=0.00;FS=18.557;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.652;QD=15.47;ReadPosRankSum=-1.072;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:709,0,666 -chr1 109115 . C T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=42;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=-1.862;QD=16.52;ReadPosRankSum=-1.233;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:722,0,721 -chr1 109169 . G C 974.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=21.19;ReadPosRankSum=-0.979;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:1003,0,590 -chr1 109252 . C T 1130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.266;DP=54;Dels=0.00;FS=7.888;HaplotypeScore=2.6437;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.461;QD=20.94;ReadPosRankSum=-0.763;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1159,0,672 -chr1 109269 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.574;DP=54;Dels=0.00;FS=15.735;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.175;QD=11.68;ReadPosRankSum=0.455;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:659,0,1060 -chr1 109311 . T A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.952;QD=14.86;ReadPosRankSum=-0.651;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,26:50:99:771,0,715 -chr1 109317 . T C 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=48;Dels=0.00;FS=1.079;HaplotypeScore=2.3119;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.702;QD=13.12;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:658,0,763 -chr1 109405 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=42;Dels=0.00;FS=6.930;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=2;MQRankSum=-0.585;QD=15.68;ReadPosRankSum=-0.938;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:687,0,600 -chr1 109412 . C A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.217;DP=47;Dels=0.00;FS=6.249;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.422;QD=16.31;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:795,0,679 -chr1 109420 . A T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=50;Dels=0.00;FS=1.145;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=2;MQRankSum=1.148;QD=15.90;ReadPosRankSum=-0.010;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:823,0,754 -chr1 109464 . C T 986.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=60;Dels=0.00;FS=7.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=3;MQRankSum=-1.214;QD=16.45;ReadPosRankSum=-0.217;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1015,0,831 -chr1 109479 . G A 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=53;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=3;MQRankSum=2.123;QD=17.43;ReadPosRankSum=-1.356;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:952,0,701 -chr1 109539 . T C 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=51;Dels=0.00;FS=2.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=1.378;QD=17.49;ReadPosRankSum=-0.518;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:920,0,726 -chr1 109549 . C T 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.389;DP=60;Dels=0.00;FS=1.044;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-0.603;QD=13.80;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1084 -chr1 109646 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.471;QD=16.52;ReadPosRankSum=0.311;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:970,0,961 -chr1 109673 . A T 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.120;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.499;QD=14.44;ReadPosRankSum=1.382;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:909,0,993 -chr1 109734 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.181;DP=56;Dels=0.00;FS=2.436;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=0.033;QD=14.01;ReadPosRankSum=0.115;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:813,0,1012 -chr1 109767 . C T 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=-0.035;QD=13.44;ReadPosRankSum=1.596;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:754,0,928 -chr1 109788 . T C 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-3.116;QD=5.73;ReadPosRankSum=2.141;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:269,0,1133 -chr1 109814 . C T 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.124;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.18;MQ0=0;MQRankSum=-4.437;QD=10.59;ReadPosRankSum=-1.494;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,18:47:99:526,0,933 -chr1 109855 . C G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1986;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-5.305;QD=11.95;ReadPosRankSum=1.686;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:542,0,816 -chr1 109898 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.567;DP=42;Dels=0.00;FS=4.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=-4.596;QD=14.49;ReadPosRankSum=-0.038;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:637,0,754 -chr1 109948 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.655;DP=45;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.56;MQ0=0;MQRankSum=-4.171;QD=13.66;ReadPosRankSum=-0.931;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,26:45:99:643,0,655 -chr1 110000 . T C 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.991;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=3.3547;MLEAC=1;MLEAF=0.500;MQ=40.16;MQ0=0;MQRankSum=-3.699;QD=6.42;ReadPosRankSum=0.672;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:330,0,703 -chr1 110006 . A G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.955;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.5657;MLEAC=1;MLEAF=0.500;MQ=41.04;MQ0=0;MQRankSum=-3.990;QD=5.89;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:317,0,813 -chr1 110176 . A G 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=39;Dels=0.00;FS=2.780;HaplotypeScore=3.5109;MLEAC=1;MLEAF=0.500;MQ=46.75;MQ0=0;MQRankSum=-0.407;QD=13.61;ReadPosRankSum=-0.014;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T411|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:559,0,657 -chr1 110245 . A G 456.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.065;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=-0.531;QD=10.88;ReadPosRankSum=-0.142;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y388|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:485,0,885 -chr1 110253 . A C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.29;MQ0=0;MQRankSum=-0.744;QD=10.27;ReadPosRankSum=0.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S386A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,16:44:99:480,0,992 -chr1 110499 . C A 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.668;DP=57;Dels=0.00;FS=7.487;HaplotypeScore=1.9858;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.040;QD=15.54;ReadPosRankSum=1.365;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:914,0,969 -chr1 110567 . C A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=12.462;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.072;QD=17.29;ReadPosRankSum=-0.965;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1152,0,1057 -chr1 110655 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=49;Dels=0.00;FS=10.545;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.344;QD=18.79;ReadPosRankSum=-0.414;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:949,0,664 -chr1 110836 . G C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.256;QD=13.11;ReadPosRankSum=0.128;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:579,0,858 -chr1 110841 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=42;Dels=0.00;FS=1.210;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.025;QD=14.76;ReadPosRankSum=-0.783;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,793 -chr1 110897 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.379;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=-0.138;QD=16.14;ReadPosRankSum=-0.344;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:577,0,566 -chr1 110902 . G A 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=36;Dels=0.00;FS=1.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.792;QD=15.33;ReadPosRankSum=-0.032;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:580,0,630 -chr1 110931 . T A 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=46;Dels=0.00;FS=4.246;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.242;QD=17.30;ReadPosRankSum=-1.440;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:824,0,677 -chr1 110948 . T A 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=55;Dels=0.00;FS=1.028;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=0;MQRankSum=0.416;QD=17.70;ReadPosRankSum=-0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|atA/atT|I314|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:1002,0,664 -chr1 110974 . T G 1390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=77;Dels=0.00;FS=4.904;HaplotypeScore=1.9464;MLEAC=1;MLEAF=0.500;MQ=54.88;MQ0=3;MQRankSum=-1.165;QD=18.06;ReadPosRankSum=-0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R306|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,49:77:99:1419,0,866 -chr1 111012 . A G 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.621;DP=99;Dels=0.00;FS=4.879;HaplotypeScore=1.9775;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=2;MQRankSum=-2.017;QD=1.50;ReadPosRankSum=1.985;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I293T|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:177,0,2833 -chr1 111037 . C T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.209;DP=91;Dels=0.00;FS=27.980;HaplotypeScore=5.8656;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=1;MQRankSum=-5.776;QD=7.67;ReadPosRankSum=1.097;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G285R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,30:91:99:726,0,2033 -chr1 111047 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.018;DP=95;Dels=0.00;FS=36.143;HaplotypeScore=18.9090;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=2;MQRankSum=-6.952;QD=8.96;ReadPosRankSum=-0.167;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L281|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,39:95:99:879,0,1831 -chr1 111053 . G A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.068;DP=94;Dels=0.00;FS=22.160;HaplotypeScore=52.4073;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=2;MQRankSum=2.884;QD=5.07;ReadPosRankSum=-0.550;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y279|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:75,19:94:99:505,0,2239 -chr1 111063 . G A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=88;Dels=0.00;FS=26.842;HaplotypeScore=20.7019;MLEAC=1;MLEAF=0.500;MQ=49.44;MQ0=2;MQRankSum=-5.090;QD=3.58;ReadPosRankSum=-0.104;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,21:88:99:343,0,2305 -chr1 111093 . T G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;DP=72;Dels=0.00;FS=18.592;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.32;MQ0=2;MQRankSum=-5.719;QD=9.66;ReadPosRankSum=1.059;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:72:99:724,0,1232 -chr1 111097 . C T 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.318;DP=72;Dels=0.00;FS=35.215;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.27;MQ0=2;MQRankSum=-6.753;QD=9.77;ReadPosRankSum=1.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,35:72:99:732,0,1245 -chr1 111100 . A G 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=71;Dels=0.00;FS=28.661;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.11;MQ0=2;MQRankSum=-5.937;QD=9.72;ReadPosRankSum=0.950;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:71:99:718,0,1230 -chr1 111136 . T C 1449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=59.2005;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-5.507;QD=20.14;ReadPosRankSum=1.606;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,49:72:99:1478,0,710 -chr1 111137 . T A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=58.2007;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=5.353;QD=9.45;ReadPosRankSum=-1.274;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:49,22:71:99:699,0,1451 -chr1 111146 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=19.0679;MLEAC=1;MLEAF=0.500;MQ=51.24;MQ0=1;MQRankSum=-5.478;QD=4.65;ReadPosRankSum=0.664;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:372,0,1862 -chr1 111162 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=77;Dels=0.00;FS=4.192;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=1;MQRankSum=-4.854;QD=3.78;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:57,20:77:99:319,0,1968 -chr1 111178 . A G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.787;DP=88;Dels=0.00;FS=4.774;HaplotypeScore=23.6084;MLEAC=1;MLEAF=0.500;MQ=51.68;MQ0=1;MQRankSum=-2.409;QD=9.66;ReadPosRankSum=0.590;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:878,0,1739 -chr1 111187 . C T 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713;DP=91;Dels=0.00;FS=21.798;HaplotypeScore=61.2603;MLEAC=1;MLEAF=0.500;MQ=52.52;MQ0=1;MQRankSum=-5.366;QD=4.35;ReadPosRankSum=-0.991;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),SPLICE_SITE_DONOR(HIGH||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:69,22:91:99:424,0,2409 -chr1 111193 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=1;MQRankSum=-4.830;QD=5.18;ReadPosRankSum=-0.680;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Agg|W268R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:479,0,2299 -chr1 111194 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=1;MQRankSum=-4.830;QD=5.11;ReadPosRankSum=-0.649;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y267|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:473,0,2303 -chr1 111218 . A G 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.345;DP=85;Dels=0.00;FS=28.288;HaplotypeScore=40.8045;MLEAC=1;MLEAF=0.500;MQ=53.15;MQ0=1;MQRankSum=-6.832;QD=18.02;ReadPosRankSum=0.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D259|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,50:85:99:1560,0,1149 -chr1 111221 . A G 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.974;DP=85;Dels=0.00;FS=2.368;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-0.591;QD=5.79;ReadPosRankSum=0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G258|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,21:85:99:520,0,2174 -chr1 111222 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=85;Dels=0.00;FS=52.665;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-6.297;QD=9.76;ReadPosRankSum=-0.509;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G258D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,30:85:99:858,0,1882 -chr1 111233 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=8.074;HaplotypeScore=21.7535;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=0.985;QD=6.33;ReadPosRankSum=-0.484;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P254|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:554,0,2166 -chr1 111239 . C T 1826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=83;Dels=0.00;FS=18.536;HaplotypeScore=20.7540;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-5.866;QD=22.01;ReadPosRankSum=-0.753;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,56:83:99:1855,0,817 -chr1 111265 . T C 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=74;Dels=0.00;FS=53.983;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.93;MQ0=0;MQRankSum=-6.988;QD=12.77;ReadPosRankSum=2.319;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,32:74:99:973,0,1429 -chr1 111274 . T C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=65;Dels=0.00;FS=22.427;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=4.440;QD=9.60;ReadPosRankSum=-1.326;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:652,0,1525 -chr1 111296 . T A 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.855;DP=60;Dels=0.00;FS=47.063;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-6.194;QD=11.68;ReadPosRankSum=-0.038;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:729,0,1223 -chr1 111307 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.080;DP=61;Dels=0.00;FS=45.484;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-6.030;QD=8.75;ReadPosRankSum=-0.269;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:562,0,1377 -chr1 111315 . A T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.943;DP=53;Dels=0.00;FS=25.441;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-4.672;QD=4.07;ReadPosRankSum=-2.694;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:244,0,1509 -chr1 111318 . C T 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=50;Dels=0.00;FS=22.968;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-4.247;QD=3.04;ReadPosRankSum=-2.686;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,8:50:99:180,0,1475 -chr1 111485 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.983;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=-1.024;QD=15.81;ReadPosRankSum=1.190;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q223|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111401_111565) GT:AD:DP:GQ:PL 0/1:23,26:49:99:803,0,742 -chr1 111592 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=60;Dels=0.00;FS=3.582;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.112;QD=13.36;ReadPosRankSum=-0.246;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:830,0,1146 -chr1 111732 . A G 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.751;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=-1.026;QD=14.15;ReadPosRankSum=1.868;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:764,0,902 -chr1 111733 . G A 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.217;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=2.274;QD=17.17;ReadPosRankSum=-2.142;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:904,0,661 -chr1 111744 . G A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.681;DP=48;Dels=0.00;FS=2.691;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=0.557;QD=16.14;ReadPosRankSum=-0.227;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:803,0,707 -chr1 111927 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;DP=61;Dels=0.00;FS=8.983;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.791;QD=18.34;ReadPosRankSum=0.399;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q139|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1147,0,896 -chr1 111933 . G A 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=59;Dels=0.00;FS=11.534;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.586;QD=18.06;ReadPosRankSum=0.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I137|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,32:59:99:1094,0,890 -chr1 112145 . T C 969.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=47;Dels=0.00;FS=8.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-2.922;QD=20.63;ReadPosRankSum=0.908;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:998,0,587 -chr1 112214 . G A 579.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.778;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=2;MQRankSum=0.106;QD=14.87;ReadPosRankSum=-2.021;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:608,0,645 -chr1 112312 . C G 1042.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=44;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.391;QD=23.70;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,30:44:99:1071,0,416 -chr1 112332 . G A 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.961;QD=7.80;ReadPosRankSum=-0.320;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:356,0,1063 -chr1 112390 . A T 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.639;DP=47;Dels=0.00;FS=2.499;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.835;QD=11.10;ReadPosRankSum=-0.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:550,0,929 -chr1 112486 . A C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.749;DP=57;Dels=0.00;FS=12.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.008;QD=12.10;ReadPosRankSum=-1.976;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:718,0,1139 -chr1 112608 . A G 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.596;QD=13.66;ReadPosRankSum=-0.185;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,27:62:99:875,0,1208 -chr1 112726 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=45;Dels=0.00;FS=1.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.059;QD=10.97;ReadPosRankSum=-0.925;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:522,0,972 -chr1 112792 . A G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=41;Dels=0.00;FS=7.053;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.535;QD=16.53;ReadPosRankSum=0.561;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L68|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:20,21:41:99:706,0,681 -chr1 112926 . A T 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.603;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=24.1961;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.021;QD=14.43;ReadPosRankSum=-3.139;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V23D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,16:30:99:461,0,376 -chr1 112990 . T C 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.3109;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.352;QD=7.05;ReadPosRankSum=-0.185;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T2A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:24,12:36:99:282,0,828 -chr1 112999 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.4558;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.333;QD=22.16;ReadPosRankSum=-0.622;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:11,24:35:99:804,0,241 -chr1 113028 . T C 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.3184;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.835;QD=9.35;ReadPosRankSum=0.000;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:17,11:28:99:290,0,593 -chr1 113037 . G T 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.102;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=20.2844;MLEAC=1;MLEAF=0.500;MQ=56.42;MQ0=0;MQRankSum=-2.110;QD=8.84;ReadPosRankSum=-0.220;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,9:25:99:258,0,479 -chr1 113038 . A T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.888;DP=25;Dels=0.04;FS=0.000;HaplotypeScore=19.2851;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-0.827;QD=7.51;ReadPosRankSum=0.582;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:16,8:24:99:216,0,560 -chr1 113092 . C T 1222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.600;DP=42;Dels=0.00;FS=2.442;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=2;MQRankSum=-1.195;QD=29.11;ReadPosRankSum=0.789;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:4,38:42:40:1251,0,40 -chr1 113115 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=2;MQRankSum=1.145;QD=17.44;ReadPosRankSum=-0.628;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,27:45:99:813,0,572 -chr1 113119 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=45;Dels=0.00;FS=2.776;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=2;MQRankSum=0.335;QD=11.11;ReadPosRankSum=0.907;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:28,17:45:99:528,0,850 -chr1 113173 . T C 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.461;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=1.037;QD=10.59;ReadPosRankSum=0.148;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,12:30:99:346,0,540 -chr1 113190 . C G 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=1.585;HaplotypeScore=1.7883;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.665;QD=8.34;ReadPosRankSum=-1.996;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:19,10:29:99:270,0,614 -chr1 113238 . G A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.041;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=20.8374;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.586;QD=3.57;ReadPosRankSum=2.277;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,5:26:99:121,0,747 -chr1 113268 . T G 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=36;Dels=0.00;FS=5.290;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.353;QD=10.83;ReadPosRankSum=-0.257;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,15:36:99:418,0,717 -chr1 113324 . C A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=34;Dels=0.00;FS=1.524;HaplotypeScore=1.9977;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.248;QD=20.79;ReadPosRankSum=0.071;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:13,21:34:99:735,0,408 -chr1 113358 . G A 385.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.134;QD=29.68;ReadPosRankSum=1.470;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:1,12:13:2:412,0,2 -chr1 113431 . A G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=0;MQRankSum=1.920;QD=18.85;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,5:8:82:179,0,82 -chr1 114304 . A G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;DP=21;Dels=0.00;FS=5.898;HaplotypeScore=11.6441;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-2.064;QD=10.66;ReadPosRankSum=-1.195;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,8:21:99:252,0,383 -chr1 114312 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.329;DP=16;Dels=0.00;FS=6.726;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-2.223;QD=11.05;ReadPosRankSum=-1.799;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:205,0,294 -chr1 114313 . G C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=0.722;QD=13.40;ReadPosRankSum=2.646;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:256,0,295 -chr1 114326 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=0.249;QD=12.27;ReadPosRankSum=0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:286,0,380 -chr1 114330 . T C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-0.462;QD=16.94;ReadPosRankSum=-0.320;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,12:21:99:384,0,253 -chr1 114353 . C A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.002;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-1.591;QD=11.18;ReadPosRankSum=-0.648;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:196,0,307 -chr1 114354 . A T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.945;QD=18.85;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:311,0,195 -chr1 114356 . G T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.120;QD=18.92;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:312,0,191 -chr1 114371 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.9971;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.899;QD=13.75;ReadPosRankSum=0.417;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:427,0,524 -chr1 114439 . T C 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.119;DP=37;Dels=0.00;FS=3.179;HaplotypeScore=1.5781;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=0.445;QD=17.07;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:660,0,452 -chr1 114460 . C A 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.748;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.398;QD=13.74;ReadPosRankSum=-1.894;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:523,0,607 -chr1 114463 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.778;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.579;QD=14.34;ReadPosRankSum=2.434;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,19:35:99:530,0,535 -chr1 114470 . T G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.856;DP=26;Dels=0.00;FS=7.707;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=1.004;QD=4.38;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,6:26:99:142,0,623 -chr1 114475 . A G 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.177;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.350;QD=5.47;ReadPosRankSum=1.813;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:165,0,582 -chr1 114476 . G C 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.686;DP=25;Dels=0.00;FS=7.908;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.223;QD=5.75;ReadPosRankSum=2.004;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:172,0,560 -chr1 114480 . C A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.623;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-1.304;QD=5.71;ReadPosRankSum=2.450;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:171,0,583 -chr1 114486 . T G 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.268;DP=31;Dels=0.00;FS=17.994;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=0.434;QD=8.86;ReadPosRankSum=0.681;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:303,0,607 -chr1 114552 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=25;Dels=0.00;FS=11.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=0.245;QD=17.19;ReadPosRankSum=1.006;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:458,0,356 -chr1 114578 . T C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=4.533;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=0;MQRankSum=0.381;QD=7.32;ReadPosRankSum=1.778;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:204,0,601 -chr1 114645 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=37.7265;MLEAC=1;MLEAF=0.500;MQ=45.53;MQ0=0;MQRankSum=-1.288;QD=20.49;ReadPosRankSum=1.767;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,23:34:99:725,0,274 -chr1 115081 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=17;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=0.433;QD=16.63;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,275 -chr1 115249 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=53;Dels=0.00;FS=9.816;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.278;QD=13.15;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:725,0,1025 -chr1 115271 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.303;DP=57;Dels=0.00;FS=11.864;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.031;QD=16.42;ReadPosRankSum=-3.364;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:964,0,858 -chr1 115276 . G T 881.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;DP=60;Dels=0.00;FS=6.930;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=0.956;QD=14.70;ReadPosRankSum=-2.838;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:910,0,1060 -chr1 115305 . A G 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;DP=56;Dels=0.00;FS=5.501;HaplotypeScore=51.1251;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=3.741;QD=14.66;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:849,0,1091 -chr1 115360 . T C 783.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=-1.129;QD=31.34;ReadPosRankSum=1.965;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,22:25:7:811,0,7 -chr1 115381 . A G 1182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.28;MQ0=1;MQRankSum=4.365;QD=21.12;ReadPosRankSum=5.503;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1211,0,406 -chr1 115399 . G T 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.993;DP=58;Dels=0.00;FS=5.640;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-3.684;QD=11.55;ReadPosRankSum=-2.448;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:698,0,1158 -chr1 115400 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.919;DP=58;Dels=0.00;FS=5.893;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-2.871;QD=11.38;ReadPosRankSum=-2.415;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:688,0,1133 -chr1 115414 . A G 1203.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=64;Dels=0.00;FS=3.517;HaplotypeScore=52.2248;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=2.511;QD=18.81;ReadPosRankSum=-0.519;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1232,0,864 -chr1 115418 . T C 1129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.624;DP=66;Dels=0.00;FS=0.952;HaplotypeScore=30.9607;MLEAC=1;MLEAF=0.500;MQ=55.61;MQ0=1;MQRankSum=3.185;QD=17.12;ReadPosRankSum=0.112;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1158,0,983 -chr1 115440 . A C 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.049;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=0.387;QD=14.95;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:970,0,1095 -chr1 115476 . T C 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.880;QD=13.59;ReadPosRankSum=1.676;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:735,0,938 -chr1 115485 . T C 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.179;QD=16.48;ReadPosRankSum=0.288;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:984,0,900 -chr1 115540 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=54;Dels=0.00;FS=4.135;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=-0.444;QD=11.44;ReadPosRankSum=-1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:646,0,1164 -chr1 115574 . C T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=37;Dels=0.00;FS=4.170;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.454;QD=3.64;ReadPosRankSum=1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,7:37:99:163,0,1074 -chr1 115730 . A G 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;DP=35;Dels=0.00;FS=8.346;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.007;QD=16.96;ReadPosRankSum=-1.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:622,0,576 -chr1 115732 . G A 512.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;DP=34;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.103;QD=15.08;ReadPosRankSum=-1.033;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:541,0,583 -chr1 115738 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.838;DP=37;Dels=0.00;FS=5.540;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-0.229;QD=16.99;ReadPosRankSum=-2.088;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:657,0,575 -chr1 115746 . A C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=38;Dels=0.00;FS=7.279;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.905;QD=15.23;ReadPosRankSum=-1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:607,0,655 -chr1 115811 . T G 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.283;QD=12.62;ReadPosRankSum=2.897;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1114 -chr1 115814 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.500;QD=12.67;ReadPosRankSum=2.987;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:700,0,1111 -chr1 115817 . A C 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.839;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.670;QD=12.35;ReadPosRankSum=3.005;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:683,0,1076 -chr1 115818 . G A 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.244;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.507;QD=12.73;ReadPosRankSum=2.771;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:703,0,1078 -chr1 115819 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.977;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.995;QD=12.52;ReadPosRankSum=2.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:692,0,1062 -chr1 115824 . T C 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=64;Dels=0.00;FS=0.970;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=3.857;QD=14.17;ReadPosRankSum=1.430;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,29:64:99:935,0,1177 -chr1 115872 . T C 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=37;Dels=0.00;FS=13.443;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=56.26;MQ0=0;MQRankSum=-0.564;QD=17.59;ReadPosRankSum=2.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:679,0,570 -chr1 115884 . G T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=32;Dels=0.00;FS=10.606;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.397;QD=13.49;ReadPosRankSum=-2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:460,0,582 -chr1 115887 . A T 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.104;DP=30;Dels=0.00;FS=8.202;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.395;QD=16.23;ReadPosRankSum=2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:515,0,435 -chr1 115890 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.658;DP=29;Dels=0.00;FS=5.988;HaplotypeScore=5.4965;MLEAC=1;MLEAF=0.500;MQ=56.14;MQ0=0;MQRankSum=-1.060;QD=15.58;ReadPosRankSum=2.211;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,15:29:99:480,0,414 -chr1 115900 . C A 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.934;DP=29;Dels=0.00;FS=2.129;HaplotypeScore=9.4946;MLEAC=1;MLEAF=0.500;MQ=56.43;MQ0=0;MQRankSum=0.375;QD=1.51;ReadPosRankSum=-2.050;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,5:29:72:72,0,793 -chr1 115966 . T A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=2;MQRankSum=0.798;QD=14.42;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:735,0,712 -chr1 115983 . T C 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=55;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.139;QD=17.10;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:969,0,769 -chr1 115998 . C G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=62;Dels=0.00;FS=5.215;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=0.776;QD=15.22;ReadPosRankSum=-0.747;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:972,0,1040 -chr1 116012 . A T 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=65;Dels=0.00;FS=1.013;HaplotypeScore=4.5213;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=1;MQRankSum=0.189;QD=14.12;ReadPosRankSum=0.486;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:946,0,1099 -chr1 116026 . T A 1054.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.724;DP=65;Dels=0.00;FS=2.157;HaplotypeScore=2.6644;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=1;MQRankSum=-0.182;QD=16.23;ReadPosRankSum=-0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1083,0,932 -chr1 116068 . A G 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.699;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-1.678;QD=17.75;ReadPosRankSum=-0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:898,0,730 -chr1 116073 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.379;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=0;MQRankSum=-1.194;QD=15.54;ReadPosRankSum=0.884;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:805,0,790 -chr1 116191 . G A 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.858;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=3.7255;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=0.684;QD=10.49;ReadPosRankSum=-2.599;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:448,0,731 -chr1 116284 . G T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.326;DP=43;Dels=0.00;FS=1.216;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.07;MQ0=2;MQRankSum=-1.787;QD=15.72;ReadPosRankSum=-0.352;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,696 -chr1 116327 . C T 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=46.31;MQ0=1;MQRankSum=-3.916;QD=5.32;ReadPosRankSum=0.305;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:193,0,788 -chr1 116368 . G T 687.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=24;Dels=0.00;FS=2.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.36;MQ0=0;MQRankSum=2.706;QD=28.66;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,21:24:26:716,0,26 -chr1 116391 . T A 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.605;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-2.880;QD=4.61;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:162,0,816 -chr1 116393 . A T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.688;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-3.134;QD=4.65;ReadPosRankSum=-0.127;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:163,0,804 -chr1 116422 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.301;DP=31;Dels=0.00;FS=12.035;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-3.613;QD=9.83;ReadPosRankSum=1.590;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:333,0,662 -chr1 116436 . T G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;DP=37;Dels=0.00;FS=10.037;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.32;MQ0=0;MQRankSum=-1.109;QD=14.97;ReadPosRankSum=-0.957;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:582,0,665 -chr1 116493 . C T 555.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.670;QD=13.56;ReadPosRankSum=-2.010;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:584,0,810 -chr1 116506 . A G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=41;Dels=0.00;FS=2.694;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-2.600;QD=16.68;ReadPosRankSum=-2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,21:41:99:712,0,659 -chr1 116529 . G A 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-3.948;QD=16.90;ReadPosRankSum=2.053;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:755,0,724 -chr1 116532 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=3.827;QD=15.97;ReadPosRankSum=-2.199;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:715,0,752 -chr1 116554 . A C 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.179;DP=42;Dels=0.00;FS=9.199;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.68;MQ0=0;MQRankSum=-3.792;QD=19.64;ReadPosRankSum=0.436;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:853,0,555 -chr1 116565 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=41;Dels=0.00;FS=6.909;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-3.782;QD=20.31;ReadPosRankSum=-0.628;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:861,0,489 -chr1 116576 . G A 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=44;Dels=0.02;FS=4.546;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-3.188;QD=18.47;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:841,0,592 -chr1 116582 . A T 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=48;Dels=0.00;FS=2.552;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=0;MQRankSum=-2.973;QD=19.66;ReadPosRankSum=-0.611;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:972,0,614 -chr1 116621 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.163;DP=41;Dels=0.00;FS=2.820;HaplotypeScore=1.9914;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=1.938;QD=12.04;ReadPosRankSum=-1.029;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:522,0,880 -chr1 116708 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.97;MQ0=0;MQRankSum=-0.735;QD=6.64;ReadPosRankSum=0.035;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:181,0,612 -chr1 116724 . T A 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.705;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-0.054;QD=21.55;ReadPosRankSum=-2.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,10:16:99:373,0,200 -chr1 116749 . A T 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.553;QD=15.18;ReadPosRankSum=0.456;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:787,0,824 -chr1 116757 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.743;QD=12.68;ReadPosRankSum=1.259;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:637,0,796 -chr1 116804 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.704;QD=12.06;ReadPosRankSum=0.418;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:559,0,846 -chr1 116822 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.282;DP=39;Dels=0.00;FS=1.310;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.493;QD=13.92;ReadPosRankSum=1.507;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:571,0,715 -chr1 116906 . C A 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.149;QD=12.02;ReadPosRankSum=-2.562;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:569,0,916 -chr1 116917 . A G 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610;DP=47;Dels=0.00;FS=1.154;HaplotypeScore=1.9931;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-0.501;QD=12.89;ReadPosRankSum=-2.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:634,0,880 -chr1 116943 . A G 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.102;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.695;QD=18.14;ReadPosRankSum=-2.536;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:881,0,663 -chr1 116949 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=0.854;QD=13.97;ReadPosRankSum=3.146;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:713,0,926 -chr1 116959 . G A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=55;Dels=0.00;FS=1.029;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.355;QD=14.94;ReadPosRankSum=2.113;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:850,0,924 -chr1 116971 . G A 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.651;DP=50;Dels=0.00;FS=2.386;HaplotypeScore=3.2789;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-0.283;QD=17.90;ReadPosRankSum=0.870;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:923,0,717 -chr1 117050 . G A 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.324;QD=6.57;ReadPosRankSum=-1.528;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,5:19:99:153,0,501 -chr1 117051 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.267;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.099;QD=7.10;ReadPosRankSum=-1.971;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:156,0,470 -chr1 117054 . T G 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.971;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.887;QD=7.26;ReadPosRankSum=-1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:159,0,429 -chr1 117071 . G A 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.080;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.164;QD=9.79;ReadPosRankSum=0.783;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:322,0,621 -chr1 117077 . G C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=33;Dels=0.00;FS=1.434;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=1.029;QD=10.75;ReadPosRankSum=1.740;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:383,0,738 -chr1 117104 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-2.211;QD=13.17;ReadPosRankSum=-0.335;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:700,0,1034 -chr1 117130 . C A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.251;DP=72;Dels=0.00;FS=18.205;HaplotypeScore=5.9991;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=4;MQRankSum=-4.097;QD=0.80;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:61,11:72:86:86,0,2246 -chr1 117148 . G T 1083.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.492;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=1;MQRankSum=0.824;QD=14.65;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:39,35:74:99:1112,0,1310 -chr1 117150 . C T 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=75;Dels=0.00;FS=0.883;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.114;QD=14.84;ReadPosRankSum=1.763;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:40,35:75:99:1141,0,1350 -chr1 117157 . A G 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=75;Dels=0.00;FS=1.938;HaplotypeScore=5.7880;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.827;QD=16.04;ReadPosRankSum=2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:38,37:75:99:1231,0,1283 -chr1 117161 . G A 1326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=76;Dels=0.00;FS=3.158;HaplotypeScore=3.9994;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.545;QD=17.46;ReadPosRankSum=0.900;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,40:76:99:1355,0,1228 -chr1 117175 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=78;Dels=0.00;FS=22.021;HaplotypeScore=9.9969;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.164;QD=3.19;ReadPosRankSum=-2.376;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:58,12:78:99:277,0,2135 -chr1 117193 . G A 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=65;Dels=0.00;FS=7.705;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.404;QD=13.73;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,28:65:99:921,0,1261 -chr1 117202 . G T 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=61;Dels=0.00;FS=10.025;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=1.292;QD=12.16;ReadPosRankSum=0.170;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,24:61:99:770,0,1299 -chr1 117350 . A T 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.016;DP=63;Dels=0.00;FS=4.058;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-6.819;QD=13.96;ReadPosRankSum=-3.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,30:63:99:908,0,1176 -chr1 117353 . G A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.169;DP=62;Dels=0.00;FS=6.115;HaplotypeScore=4.6334;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=6.744;QD=18.04;ReadPosRankSum=2.271;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,33:62:99:1147,0,898 -chr1 117361 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.041;DP=50;Dels=0.00;FS=2.729;HaplotypeScore=10.5317;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-5.755;QD=9.76;ReadPosRankSum=1.270;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:516,0,1175 -chr1 117411 . T C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=23;Dels=0.00;FS=39.846;HaplotypeScore=10.9973;MLEAC=1;MLEAF=0.500;MQ=46.04;MQ0=1;MQRankSum=-3.989;QD=6.82;ReadPosRankSum=-2.011;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,11:23:99:185,0,421 -chr1 117420 . A T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=-0.092;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,370 -chr1 117422 . G T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.523;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=0.215;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,369 -chr1 117438 . G C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.413;DP=32;Dels=0.00;FS=52.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.12;MQ0=1;MQRankSum=-3.851;QD=17.24;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,23:32:99:580,0,237 -chr1 117461 . G C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.770;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.298;QD=9.92;ReadPosRankSum=1.591;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,309 -chr1 117462 . T C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.123;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.887;QD=9.92;ReadPosRankSum=1.827;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117464 . C T 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.652;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.652;QD=9.92;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117465 . T A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.416;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.062;QD=9.86;ReadPosRankSum=1.355;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:186,0,295 -chr1 117467 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.550;DP=18;Dels=0.00;FS=28.543;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=1;MQRankSum=-3.224;QD=12.82;ReadPosRankSum=0.241;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,9:18:99:259,0,257 -chr1 117527 . C A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.031;DP=38;Dels=0.00;FS=14.618;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=2;MQRankSum=-4.256;QD=7.26;ReadPosRankSum=2.631;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:304,0,852 -chr1 117551 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.950;DP=19;Dels=0.00;FS=5.815;HaplotypeScore=15.9941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.750;QD=3.88;ReadPosRankSum=-1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:15,4:19:99:102,0,544 -chr1 117967 . C T 371.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.351;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.465;QD=11.99;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:400,0,581 -chr1 117972 . C G 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.218;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.686;QD=12.02;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:401,0,578 -chr1 117996 . T C 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.341;DP=34;Dels=0.00;FS=8.609;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=2;MQRankSum=-1.468;QD=9.26;ReadPosRankSum=0.635;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:343,0,658 -chr1 118063 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=3.026;QD=21.04;ReadPosRankSum=3.377;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,13:19:36:428,0,36 -chr1 118067 . T A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.792;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.566;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:60:418,0,60 -chr1 118068 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.426;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.487;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:69:418,0,69 -chr1 118098 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=17.1556;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=3.923;QD=21.06;ReadPosRankSum=-0.468;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:10,22:32:99:702,0,186 -chr1 118118 . A G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.220;DP=42;Dels=0.00;FS=2.745;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.888;QD=19.30;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:839,0,403 -chr1 118122 . C A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.130;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-1.111;QD=9.81;ReadPosRankSum=-0.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:411,0,831 -chr1 118131 . A G 556.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;DP=44;Dels=0.00;FS=2.548;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.24;MQ0=0;MQRankSum=-0.837;QD=12.65;ReadPosRankSum=-1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:585,0,736 -chr1 118140 . T A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-3.047;QD=12.91;ReadPosRankSum=-0.299;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:622,0,857 -chr1 118262 . C A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;QD=21.49;ReadPosRankSum=2.452;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:974,0,497 -chr1 118324 . A G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-1.355;QD=10.63;ReadPosRankSum=-2.135;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:528,0,851 -chr1 118347 . T A 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=42;Dels=0.00;FS=5.576;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.125;QD=22.54;ReadPosRankSum=0.181;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,30:42:99:975,0,281 -chr1 118394 . C G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=43;Dels=0.00;FS=9.242;HaplotypeScore=4.1872;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=1.960;QD=15.99;ReadPosRankSum=0.524;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:716,0,621 -chr1 118436 . T A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.005;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=2.6648;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.756;QD=14.47;ReadPosRankSum=-1.770;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,26:53:99:795,0,854 -chr1 118461 . T C 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=3;MQRankSum=1.167;QD=15.68;ReadPosRankSum=-1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,27:47:99:765,0,667 -chr1 118483 . G C 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=44;Dels=0.00;FS=4.457;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=3;MQRankSum=-1.011;QD=12.18;ReadPosRankSum=0.197;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,21:44:99:564,0,783 -chr1 118577 . A G 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.12;MQ0=0;MQRankSum=-3.972;QD=1.53;ReadPosRankSum=-1.520;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,7:30:74:74,0,821 -chr1 118586 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.704;DP=28;Dels=0.00;FS=1.906;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-4.094;QD=3.21;ReadPosRankSum=-0.992;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,8:28:99:118,0,717 -chr1 118591 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;DP=26;Dels=0.00;FS=4.471;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=3.972;QD=23.84;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,18:26:99:648,0,124 -chr1 118613 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.81;MQ0=0;MQRankSum=-3.748;QD=6.56;ReadPosRankSum=3.244;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:179,0,510 -chr1 118618 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=-3.181;QD=6.60;ReadPosRankSum=3.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:180,0,492 -chr1 118625 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=18;Dels=0.00;FS=4.708;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-2.950;QD=6.32;ReadPosRankSum=2.763;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,6:18:99:142,0,434 -chr1 118868 . G A 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.576;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-4.743;QD=17.09;ReadPosRankSum=1.211;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,17:31:99:558,0,461 -chr1 118885 . A G 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=1.002;QD=15.42;ReadPosRankSum=-0.530;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,9:16:99:275,0,201 -chr1 118973 . C T 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.10;MQ0=1;MQRankSum=-0.456;QD=17.38;ReadPosRankSum=2.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,13:15:48:289,0,48 -chr1 119028 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.598;DP=28;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.29;MQ0=5;MQRankSum=2.693;QD=1.21;ReadPosRankSum=-2.784;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,3:28:62:62,0,217 -chr1 119038 . C G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.913;DP=27;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.72;MQ0=5;MQRankSum=2.679;QD=2.07;ReadPosRankSum=-2.775;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,3:27:84:84,0,217 -chr1 119044 . T A 84.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.19;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:27:113,0,27 -chr1 119050 . A T 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28 -chr1 119961 . G C 77.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=65.19;MQ0=0;MQRankSum=0.727;QD=19.44;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:26:106,0,26 -chr1 119977 . T G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=13;Dels=0.00;FS=9.792;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.49;MQ0=0;MQRankSum=-1.466;QD=19.52;ReadPosRankSum=0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,9:13:99:282,0,121 -chr1 120103 . C G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=41;Dels=0.00;FS=9.770;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.26;MQ0=0;MQRankSum=0.468;QD=3.29;ReadPosRankSum=1.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,7:41:99:163,0,1266 -chr1 120119 . G A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=37;Dels=0.00;FS=4.862;HaplotypeScore=2.9458;MLEAC=1;MLEAF=0.500;MQ=60.29;MQ0=0;MQRankSum=0.258;QD=14.67;ReadPosRankSum=-0.623;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,19:37:99:571,0,599 -chr1 120128 . T C 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=1.9459;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=1.099;QD=15.88;ReadPosRankSum=-0.594;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,18:34:99:568,0,540 -chr1 120143 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=27;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=1;MQRankSum=1.487;QD=14.95;ReadPosRankSum=0.154;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:432,0,438 -chr1 120179 . C T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=1;MQRankSum=-0.517;QD=13.45;ReadPosRankSum=0.680;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:378,0,440 -chr1 120186 . T C 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.610;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=1;MQRankSum=-0.268;QD=12.74;ReadPosRankSum=0.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,12:28:99:385,0,463 -chr1 120227 . C T 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140;DP=38;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=1;MQRankSum=1.322;QD=15.28;ReadPosRankSum=-1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,18:38:99:609,0,620 -chr1 120238 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=41;Dels=0.00;FS=7.160;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.231;QD=16.41;ReadPosRankSum=0.177;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,23:41:99:701,0,597 -chr1 120278 . C A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=49;Dels=0.00;FS=4.269;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=1;MQRankSum=0.282;QD=18.55;ReadPosRankSum=-0.366;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,29:49:99:937,0,665 -chr1 120311 . T C 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.855;DP=42;Dels=0.00;FS=1.163;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.780;QD=16.54;ReadPosRankSum=0.101;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:723,0,713 -chr1 120315 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.036;QD=15.72;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,762 -chr1 120437 . C T 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.001;DP=32;Dels=0.00;FS=22.212;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=0;MQRankSum=-1.284;QD=14.02;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:477,0,541 -chr1 120513 . C G 436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=35;Dels=0.00;FS=5.287;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-1.317;QD=12.48;ReadPosRankSum=0.883;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:35:99:465,0,629 -chr1 120525 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=32;Dels=0.00;FS=5.486;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=55.77;MQ0=1;MQRankSum=0.337;QD=12.46;ReadPosRankSum=0.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:427,0,557 -chr1 120532 . T A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=34;Dels=0.00;FS=7.806;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=55.37;MQ0=1;MQRankSum=-0.055;QD=11.26;ReadPosRankSum=0.856;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,15:34:99:411,0,622 -chr1 120550 . C G 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.115;DP=33;Dels=0.00;FS=3.269;HaplotypeScore=2.4595;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-0.422;QD=10.60;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:378,0,603 -chr1 120567 . A T 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=25;Dels=0.00;FS=2.671;HaplotypeScore=15.7066;MLEAC=1;MLEAF=0.500;MQ=53.60;MQ0=1;MQRankSum=-2.312;QD=2.43;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,5:25:89:89,0,628 -chr1 120698 . C T 666.53 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.689;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=2.693;QD=28.98;ReadPosRankSum=0.959;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,20:23:3:693,0,3 -chr1 120722 . T C 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=3.000;QD=28.23;ReadPosRankSum=-0.403;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,17:21:43:621,0,43 -chr1 120730 . T C 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;DP=23;Dels=0.00;FS=1.935;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.58;MQ0=0;MQRankSum=-2.065;QD=3.77;ReadPosRankSum=-0.805;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,6:23:99:115,0,600 -chr1 120744 . C A 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.752;DP=27;Dels=0.00;FS=1.574;HaplotypeScore=6.9985;MLEAC=1;MLEAF=0.500;MQ=46.78;MQ0=0;MQRankSum=1.604;QD=19.32;ReadPosRankSum=0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,16:27:99:550,0,301 -chr1 120759 . T C 295.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.164;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-0.367;QD=15.57;ReadPosRankSum=-1.347;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:324,0,285 -chr1 120764 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=0;MQRankSum=-0.599;QD=13.70;ReadPosRankSum=0.951;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,10:21:99:316,0,375 -chr1 120777 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.459;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=1.257;QD=12.14;ReadPosRankSum=-0.018;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:429,0,613 -chr1 120780 . G A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.623;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=0;MQRankSum=0.960;QD=11.94;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:446,0,633 -chr1 120787 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.328;DP=39;Dels=0.00;FS=1.273;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=0;MQRankSum=-1.898;QD=14.64;ReadPosRankSum=2.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,19:39:99:599,0,603 -chr1 120802 . T C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=45;Dels=0.00;FS=2.555;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=0;MQRankSum=-3.970;QD=16.39;ReadPosRankSum=1.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,24:45:99:766,0,656 -chr1 120813 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=4.507;QD=14.68;ReadPosRankSum=-0.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,22:45:99:689,0,762 -chr1 120816 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=51.82;MQ0=0;MQRankSum=-4.264;QD=15.31;ReadPosRankSum=0.639;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:656,0,729 -chr1 120820 . T C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=40;Dels=0.00;FS=2.785;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-4.361;QD=15.12;ReadPosRankSum=1.517;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,684 -chr1 120875 . C T 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.870;DP=43;Dels=0.00;FS=4.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=1;MQRankSum=-5.022;QD=11.48;ReadPosRankSum=2.076;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,18:43:99:522,0,781 -chr1 120891 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.826;DP=23;Dels=0.00;FS=9.132;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=0;MQRankSum=-3.019;QD=3.16;ReadPosRankSum=1.155;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,5:23:99:101,0,602 -chr1 120925 . T A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.177;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.81;MQ0=1;MQRankSum=-1.123;QD=12.24;ReadPosRankSum=0.578;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:99:481,0,688 -chr1 120960 . G C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.936;DP=43;Dels=0.00;FS=2.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=1;MQRankSum=-1.055;QD=18.34;ReadPosRankSum=-1.309;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:817,0,617 -chr1 120966 . T C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=-1.213;QD=16.55;ReadPosRankSum=-0.480;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:740,0,631 -chr1 120969 . G A 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.851;DP=43;Dels=0.00;FS=1.149;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=1.322;QD=15.13;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:679,0,731 -chr1 121015 . T C 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.582;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.989;QD=17.38;ReadPosRankSum=0.659;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:932,0,820 -chr1 121034 . T C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.450;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.850;QD=16.97;ReadPosRankSum=0.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,25:49:99:860,0,817 -chr1 121052 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=46;Dels=0.00;FS=8.862;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.022;QD=16.80;ReadPosRankSum=0.681;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,23:46:99:801,0,734 -chr1 121087 . G T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=40;Dels=0.00;FS=5.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.924;QD=8.42;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,16:40:99:365,0,767 -chr1 121118 . T A 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=7.025;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-0.692;QD=16.94;ReadPosRankSum=0.890;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,12:22:99:401,0,296 -chr1 121148 . G A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=27;Dels=0.00;FS=9.204;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.655;QD=15.92;ReadPosRankSum=-0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:458,0,425 -chr1 121152 . T C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.256;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.923;QD=15.84;ReadPosRankSum=-0.821;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:440,0,417 -chr1 121153 . C T 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.615;QD=15.76;ReadPosRankSum=-0.872;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:438,0,430 -chr1 121415 . G A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.544;DP=32;Dels=0.00;FS=8.557;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-2.657;QD=11.24;ReadPosRankSum=-0.094;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,16:32:99:388,0,539 -chr1 121448 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=3.811;QD=14.79;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,20:43:99:664,0,751 -chr1 121451 . G A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=-3.859;QD=16.34;ReadPosRankSum=0.816;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:731,0,659 -chr1 121462 . T A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=40;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-4.391;QD=16.62;ReadPosRankSum=0.204;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,22:40:99:693,0,595 -chr1 122173 . G T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.745;DP=41;Dels=0.00;FS=1.248;HaplotypeScore=3.6993;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=0.176;QD=15.77;ReadPosRankSum=0.311;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,20:41:99:675,0,610 -chr1 122179 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=44;Dels=0.00;FS=2.744;HaplotypeScore=2.7126;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-0.813;QD=14.45;ReadPosRankSum=1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:664,0,726 -chr1 122203 . A C 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.560;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.51;MQ0=0;MQRankSum=-2.415;QD=16.76;ReadPosRankSum=0.352;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:732,0,674 -chr1 122216 . C G 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.587;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=32.8942;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-1.343;QD=15.60;ReadPosRankSum=-0.117;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:668,0,646 -chr1 122277 . T C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.946;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.4826;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.650;QD=9.49;ReadPosRankSum=2.750;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,10:30:99:313,0,658 -chr1 122297 . G A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.136;DP=32;Dels=0.00;FS=3.151;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.564;QD=11.15;ReadPosRankSum=2.511;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,12:32:99:385,0,654 -chr1 122415 . G A 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=43;Dels=0.00;FS=2.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.30;MQ0=0;MQRankSum=-0.135;QD=13.41;ReadPosRankSum=-0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:605,0,828 -chr1 122430 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=43;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.37;MQ0=1;MQRankSum=0.216;QD=18.23;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:812,0,558 -chr1 122456 . G T 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=37;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=2;MQRankSum=-0.480;QD=12.51;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,20:37:99:491,0,496 -chr1 122471 . G A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=26;Dels=0.00;FS=3.892;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=37.29;MQ0=2;MQRankSum=1.101;QD=11.64;ReadPosRankSum=-0.811;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:331,0,295 -chr1 122483 . G A 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.303;DP=23;Dels=0.00;FS=4.036;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=35.66;MQ0=2;MQRankSum=-2.429;QD=8.34;ReadPosRankSum=2.429;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,12:23:99:220,0,312 -chr1 122487 . T A 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=20;Dels=0.05;FS=1.957;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=31.84;MQ0=2;MQRankSum=-2.454;QD=6.64;ReadPosRankSum=2.742;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:161,0,242 -chr1 122498 . T C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.9968;MLEAC=1;MLEAF=0.500;MQ=48.55;MQ0=1;MQRankSum=0.407;QD=14.02;ReadPosRankSum=-0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,19:42:99:617,0,646 -chr1 122548 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=35;Dels=0.00;FS=1.445;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.791;QD=19.42;ReadPosRankSum=2.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,21:35:99:708,0,420 -chr1 122565 . A T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.454;DP=37;Dels=0.00;FS=7.957;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.391;QD=20.07;ReadPosRankSum=-0.673;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,23:37:99:771,0,457 -chr1 122594 . G T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=54;Dels=0.00;FS=2.373;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=0.177;QD=12.25;ReadPosRankSum=2.129;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,21:54:99:690,0,1043 -chr1 122607 . G C 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=3.662;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.387;QD=15.56;ReadPosRankSum=-0.751;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,28:59:99:946,0,1029 -chr1 122655 . T G 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=64;Dels=0.00;FS=1.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.915;QD=9.84;ReadPosRankSum=1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,21:64:99:658,0,1417 -chr1 122658 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=63;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.303;QD=9.33;ReadPosRankSum=1.676;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,20:63:99:616,0,1391 -chr1 122661 . C T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=59;Dels=0.00;FS=3.946;HaplotypeScore=7.7321;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-0.511;QD=9.88;ReadPosRankSum=1.371;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,19:59:99:611,0,1272 -chr1 122767 . A C 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-5.113;QD=8.09;ReadPosRankSum=2.844;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:360,0,994 -chr1 122789 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-4.915;QD=8.73;ReadPosRankSum=1.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,12:38:99:360,0,925 -chr1 122826 . G A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.987;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.84;MQ0=0;MQRankSum=-3.853;QD=3.02;ReadPosRankSum=1.957;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,6:37:99:140,0,1158 -chr1 122828 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=40;Dels=0.00;FS=1.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.688;QD=4.42;ReadPosRankSum=0.423;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,8:40:99:205,0,1171 -chr1 122865 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=49;Dels=0.00;FS=14.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=0.373;QD=9.81;ReadPosRankSum=0.501;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,16:49:99:509,0,1184 -chr1 122905 . C T 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.019;DP=42;Dels=0.00;FS=5.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.989;QD=6.14;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,10:42:99:286,0,1168 -chr1 122938 . C T 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.284;DP=41;Dels=0.00;FS=5.664;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=1;MQRankSum=-4.235;QD=7.65;ReadPosRankSum=-3.497;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:342,0,1011 -chr1 122969 . T C 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=52;Dels=0.00;FS=11.610;HaplotypeScore=2.8266;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=-5.166;QD=13.00;ReadPosRankSum=1.641;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,21:52:99:704,0,1092 -chr1 122976 . C T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=49;Dels=0.00;FS=12.245;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-3.283;QD=13.83;ReadPosRankSum=2.879;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:706,0,952 -chr1 122990 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.759;DP=52;Dels=0.00;FS=15.894;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-4.241;QD=12.23;ReadPosRankSum=3.207;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:664,0,1073 -chr1 123012 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.417;DP=52;Dels=0.00;FS=6.555;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-3.786;QD=11.46;ReadPosRankSum=0.019;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:624,0,1045 -chr1 123034 . T C 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.523;DP=46;Dels=0.00;FS=4.428;HaplotypeScore=3.8314;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-1.707;QD=10.23;ReadPosRankSum=-1.707;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,17:46:99:499,0,1020 -chr1 123098 . A G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=38;Dels=0.00;FS=7.718;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=1;MQRankSum=1.769;QD=9.86;ReadPosRankSum=-1.613;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:403,0,787 -chr1 123121 . C T 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.802;DP=35;Dels=0.00;FS=3.247;HaplotypeScore=1.8273;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=1;MQRankSum=-1.207;QD=9.59;ReadPosRankSum=-1.907;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:364,0,645 -chr1 123294 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=22;Dels=0.00;FS=6.897;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.901;QD=10.03;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:249,0,484 -chr1 123320 . T A 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.094;DP=23;Dels=0.00;FS=7.060;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.409;QD=11.56;ReadPosRankSum=2.425;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,9:23:99:294,0,487 -chr1 123328 . G C 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=25;Dels=0.00;FS=6.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.878;QD=9.19;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:258,0,573 -chr1 123730 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=23;Dels=0.00;FS=5.969;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.502;QD=1.34;ReadPosRankSum=-0.411;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,3:23:59:59,0,664 -chr1 123755 . C A 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=28;Dels=0.00;FS=5.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=0.624;QD=2.21;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,4:28:90:90,0,768 -chr1 123843 . T C 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=0.889;QD=7.57;ReadPosRankSum=-0.191;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:210,0,577 -chr1 123903 . T A 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.580;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.500;QD=11.77;ReadPosRankSum=1.221;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:393,0,627 -chr1 123904 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.941;QD=11.67;ReadPosRankSum=1.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:390,0,619 -chr1 123916 . T G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.496;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.276;QD=10.49;ReadPosRankSum=0.390;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:385,0,693 -chr1 123923 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.329;QD=9.32;ReadPosRankSum=-0.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:373,0,791 -chr1 123947 . C A 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=1.259;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.321;QD=9.66;ReadPosRankSum=-0.867;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:434,0,970 -chr1 123966 . G A 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=11.9954;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.893;QD=8.91;ReadPosRankSum=-0.275;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:349,0,885 -chr1 123975 . T A 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=41;Dels=0.00;FS=1.345;HaplotypeScore=13.9928;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.124;QD=9.60;ReadPosRankSum=1.113;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:422,0,967 -chr1 124035 . T C 365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.216;DP=34;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-0.378;QD=10.76;ReadPosRankSum=1.423;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:394,0,689 -chr1 124057 . G A 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=38;Dels=0.00;FS=1.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.990;QD=12.70;ReadPosRankSum=0.754;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:511,0,655 -chr1 124075 . T G 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-0.800;QD=11.92;ReadPosRankSum=1.082;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:362,0,542 -chr1 124090 . T C 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.741;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-3.362;QD=13.27;ReadPosRankSum=0.703;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:453,0,623 -chr1 124097 . G A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=-3.549;QD=10.19;ReadPosRankSum=0.669;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:344,0,678 -chr1 124108 . A G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=29;Dels=0.00;FS=3.834;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.061;QD=9.68;ReadPosRankSum=1.124;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,669 -chr1 124113 . C A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.297;DP=32;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.25;MQ0=0;MQRankSum=-3.923;QD=8.52;ReadPosRankSum=1.159;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:301,0,784 -chr1 124123 . A C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.866;DP=31;Dels=0.00;FS=6.205;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.867;QD=8.61;ReadPosRankSum=-0.063;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:295,0,742 -chr1 124134 . C T 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=29;Dels=0.00;FS=10.056;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=3.001;QD=23.82;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:8,21:29:99:719,0,221 -chr1 124151 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=0;MQRankSum=1.104;QD=10.27;ReadPosRankSum=1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:285,0,486 -chr1 124494 . G A 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.11;MQ0=0;MQRankSum=2.064;QD=19.94;ReadPosRankSum=4.069;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1025,0,663 -chr1 124512 . A C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.557;QD=13.28;ReadPosRankSum=1.261;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:692,0,960 -chr1 124607 . T C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.445;DP=50;Dels=0.00;FS=19.947;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.175;QD=16.82;ReadPosRankSum=1.106;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:869,0,855 -chr1 124731 . C A 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=30;Dels=0.00;FS=18.572;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.727;QD=1.29;ReadPosRankSum=-2.688;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,4:30:67:67,0,818 -chr1 124820 . A T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.600;QD=13.31;ReadPosRankSum=1.683;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:667,0,918 -chr1 124864 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.180;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.318;QD=14.06;ReadPosRankSum=-2.039;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:647,0,835 -chr1 124901 . T G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.761;QD=16.06;ReadPosRankSum=0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:751,0,736 -chr1 124917 . A T 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.090;DP=40;Dels=0.00;FS=2.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=0.251;QD=11.29;ReadPosRankSum=-1.145;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:480,0,891 -chr1 124920 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.054;QD=10.47;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:405,0,807 -chr1 125002 . T C 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.594;DP=49;Dels=0.00;FS=1.202;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.069;QD=9.57;ReadPosRankSum=-1.460;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:497,0,1178 -chr1 125004 . A G 1137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.804;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=1.148;QD=23.22;ReadPosRankSum=1.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,32:49:99:1166,0,460 -chr1 125020 . A T 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.617;DP=46;Dels=0.00;FS=1.204;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-1.547;QD=9.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:486,0,1126 -chr1 125046 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=1.788;QD=12.74;ReadPosRankSum=0.293;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:627,0,985 -chr1 125096 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.345;HaplotypeScore=2.7212;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.887;QD=16.57;ReadPosRankSum=0.553;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:724,0,731 -chr1 125124 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.683;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=3.985;QD=26.36;ReadPosRankSum=0.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:7,26:33:99:898,0,147 -chr1 125126 . T C 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.859;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.029;QD=3.63;ReadPosRankSum=0.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:148,0,866 -chr1 125128 . G A 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.011;QD=2.63;ReadPosRankSum=2.370;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,7:33:99:115,0,854 -chr1 125133 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.992;QD=3.99;ReadPosRankSum=2.622;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:152,0,843 -chr1 125142 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=52.83;MQ0=0;MQRankSum=4.377;QD=22.16;ReadPosRankSum=-1.254;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,20:30:99:693,0,230 -chr1 125149 . G A 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=28;Dels=0.00;FS=1.690;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=50.58;MQ0=0;MQRankSum=-4.514;QD=12.42;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:376,0,460 -chr1 125166 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=-4.339;QD=9.10;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:283,0,577 -chr1 125168 . C T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=1.805;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.84;MQ0=0;MQRankSum=4.551;QD=18.83;ReadPosRankSum=0.826;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,18:30:99:593,0,339 -chr1 125190 . C T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=37;Dels=0.00;FS=4.233;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=0;MQRankSum=-5.120;QD=10.53;ReadPosRankSum=0.820;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:418,0,736 -chr1 125207 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.99;ReadPosRankSum=2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:379,0,880 -chr1 125210 . C T 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.89;ReadPosRankSum=2.309;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:375,0,828 -chr1 125216 . G C 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.307;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.26;MQ0=0;MQRankSum=-5.080;QD=8.81;ReadPosRankSum=1.918;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:372,0,862 -chr1 125248 . T C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=49;Dels=0.00;FS=1.304;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=1;MQRankSum=-3.990;QD=12.14;ReadPosRankSum=-0.686;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:623,0,932 -chr1 125250 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.022;DP=47;Dels=0.00;FS=2.895;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.33;MQ0=1;MQRankSum=4.261;QD=18.97;ReadPosRankSum=0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:920,0,541 -chr1 125274 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=3.553;QD=15.80;ReadPosRankSum=0.624;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:755,0,576 -chr1 125306 . A T 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=36;Dels=0.00;FS=1.377;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=1;MQRankSum=-2.732;QD=11.44;ReadPosRankSum=1.772;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:440,0,654 -chr1 125310 . C T 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.769;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=1;MQRankSum=3.388;QD=16.64;ReadPosRankSum=-1.600;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:544,0,362 -chr1 125319 . C T 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.05;MQ0=1;MQRankSum=-3.282;QD=8.96;ReadPosRankSum=2.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:279,0,506 -chr1 125345 . C T 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=23;Dels=0.00;FS=1.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.96;MQ0=0;MQRankSum=-3.132;QD=9.86;ReadPosRankSum=-0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:255,0,427 -chr1 125441 . A G 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=24;Dels=0.00;FS=1.760;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=1;MQRankSum=-3.324;QD=4.32;ReadPosRankSum=-3.905;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:132,0,545 -chr1 125444 . C T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=26;Dels=0.00;FS=1.697;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.30;MQ0=1;MQRankSum=3.652;QD=21.11;ReadPosRankSum=2.746;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:577,0,160 -chr1 125447 . G A 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.535;DP=24;Dels=0.00;FS=1.744;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.32;MQ0=1;MQRankSum=-3.937;QD=6.12;ReadPosRankSum=-2.551;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:175,0,501 -chr1 125453 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.271;DP=24;Dels=0.00;FS=3.963;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.60;MQ0=1;MQRankSum=-4.062;QD=7.91;ReadPosRankSum=-2.946;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,11:24:99:218,0,462 -chr1 125481 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.995;DP=33;Dels=0.00;FS=3.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.76;MQ0=1;MQRankSum=-4.758;QD=8.93;ReadPosRankSum=2.724;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:323,0,666 -chr1 125491 . G C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.31;ReadPosRankSum=1.104;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:286,0,566 -chr1 125495 . G A 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.953;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.43;ReadPosRankSum=1.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:289,0,560 -chr1 125497 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.689;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.55;ReadPosRankSum=1.274;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:292,0,557 -chr1 125498 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.19;ReadPosRankSum=1.387;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:283,0,571 -chr1 125503 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=26;Dels=0.00;FS=1.657;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=0;MQRankSum=-4.042;QD=10.14;ReadPosRankSum=1.294;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:292,0,609 -chr1 125548 . C A 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=29;Dels=0.00;FS=9.640;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=2.073;QD=16.13;ReadPosRankSum=0.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,15:29:99:496,0,417 -chr1 125582 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.929;DP=28;Dels=0.00;FS=3.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=1;MQRankSum=0.386;QD=21.10;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,18:28:99:619,0,268 -chr1 125622 . A C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.336;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=1;MQRankSum=-0.542;QD=19.26;ReadPosRankSum=-0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:837,0,537 -chr1 125640 . G T 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=41;Dels=0.00;FS=2.681;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-1.405;QD=14.29;ReadPosRankSum=3.533;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:614,0,776 -chr1 125691 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=44;Dels=0.00;FS=4.165;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-2.085;QD=13.79;ReadPosRankSum=-0.308;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:635,0,863 -chr1 125721 . T G 219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=36;Dels=0.00;FS=1.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-1.754;QD=6.10;ReadPosRankSum=0.913;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,9:36:99:248,0,910 -chr1 125736 . T C 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-1.023;QD=7.61;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:264,0,762 -chr1 125740 . A G 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.249;QD=8.20;ReadPosRankSum=-1.014;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:266,0,653 -chr1 125759 . T C 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.697;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.079;QD=11.06;ReadPosRankSum=-0.652;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:349,0,542 -chr1 125772 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.466;DP=26;Dels=0.00;FS=8.852;HaplotypeScore=17.6766;MLEAC=1;MLEAF=0.500;MQ=55.71;MQ0=0;MQRankSum=-4.089;QD=13.88;ReadPosRankSum=-0.489;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:389,0,400 -chr1 125794 . C T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.246;DP=25;Dels=0.00;FS=1.697;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-4.243;QD=12.43;ReadPosRankSum=1.670;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:339,0,466 -chr1 125810 . G T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.808;QD=9.17;ReadPosRankSum=1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:331,0,680 -chr1 126059 . T C 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.273;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.52;ReadPosRankSum=-2.721;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:590,0,540 -chr1 126061 . T A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.514;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.40;ReadPosRankSum=-3.341;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:586,0,522 -chr1 126072 . G A 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.927;DP=28;Dels=0.00;FS=6.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.25;MQ0=0;MQRankSum=-4.480;QD=11.53;ReadPosRankSum=1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:351,0,542 -chr1 126082 . A T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310;DP=19;Dels=0.00;FS=7.701;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=0;MQRankSum=-3.592;QD=9.46;ReadPosRankSum=1.479;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,7:19:99:208,0,430 -chr1 126547 . G A 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=25;Dels=0.00;FS=13.262;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.44;MQ0=0;MQRankSum=0.082;QD=16.95;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:452,0,359 -chr1 126551 . A G 380.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=25;Dels=0.00;FS=13.829;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.34;MQ0=0;MQRankSum=0.027;QD=15.23;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,12:25:99:409,0,391 -chr1 126556 . T C 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=24;Dels=0.00;FS=26.945;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-0.381;QD=12.41;ReadPosRankSum=4.070;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:326,0,444 -chr1 126572 . G C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=49;Dels=0.00;FS=4.366;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=0;MQRankSum=-3.829;QD=8.40;ReadPosRankSum=0.618;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,15:49:99:440,0,1091 -chr1 126583 . C T 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-1.853;QD=19.55;ReadPosRankSum=5.365;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:947,0,591 -chr1 126584 . G A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=47;Dels=0.00;FS=2.763;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-4.028;QD=8.53;ReadPosRankSum=1.677;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,15:47:99:429,0,1116 -chr1 126595 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=52;Dels=0.00;FS=2.606;HaplotypeScore=22.9737;MLEAC=1;MLEAF=0.500;MQ=51.73;MQ0=0;MQRankSum=-4.709;QD=8.67;ReadPosRankSum=2.092;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:479,0,1271 -chr1 126599 . G T 1355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=50;Dels=0.00;FS=1.289;HaplotypeScore=32.9690;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-2.510;QD=27.12;ReadPosRankSum=-1.715;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,38:50:99:1384,0,313 -chr1 126603 . A G 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=50;Dels=0.00;FS=2.527;HaplotypeScore=32.7034;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-4.690;QD=8.90;ReadPosRankSum=4.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:473,0,1206 -chr1 126605 . C T 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.369;HaplotypeScore=32.7046;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=3.501;QD=15.29;ReadPosRankSum=-4.331;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:808,0,893 -chr1 126609 . C T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.515;DP=50;Dels=0.00;FS=2.429;HaplotypeScore=30.7052;MLEAC=1;MLEAF=0.500;MQ=52.80;MQ0=0;MQRankSum=-2.243;QD=17.32;ReadPosRankSum=3.641;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:894,0,800 -chr1 126615 . T A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.333;DP=53;Dels=0.00;FS=8.297;HaplotypeScore=11.7855;MLEAC=1;MLEAF=0.500;MQ=54.30;MQ0=0;MQRankSum=-5.840;QD=8.94;ReadPosRankSum=4.602;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:502,0,1303 -chr1 126645 . G A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.603;HaplotypeScore=100.5169;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-5.977;QD=5.77;ReadPosRankSum=-1.607;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,16:65:99:403,0,1747 -chr1 126670 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=54;Dels=0.00;FS=1.105;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-1.100;QD=11.75;ReadPosRankSum=-0.710;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:663,0,1180 -chr1 126698 . T C 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.857;DP=55;Dels=0.00;FS=8.472;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=2.036;QD=22.43;ReadPosRankSum=2.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1262,0,539 -chr1 126702 . T C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=58;Dels=0.00;FS=16.756;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.515;QD=9.98;ReadPosRankSum=-2.609;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:38,20:58:99:607,0,1364 -chr1 126709 . C T 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=54;Dels=0.00;FS=4.827;HaplotypeScore=4.9981;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.447;QD=5.42;ReadPosRankSum=-0.697;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:42,12:54:99:321,0,1519 -chr1 126725 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=57;Dels=0.00;FS=9.993;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.729;QD=12.00;ReadPosRankSum=-1.418;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:35,22:57:99:712,0,1228 -chr1 126730 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=53;Dels=0.00;FS=6.032;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.467;QD=9.18;ReadPosRankSum=-2.601;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:515,0,1208 -chr1 126761 . C A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=1.910;QD=16.77;ReadPosRankSum=-0.350;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:850,0,808 -chr1 126795 . T A 1211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=58;Dels=0.00;FS=1.054;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.462;QD=20.89;ReadPosRankSum=1.685;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1240,0,735 -chr1 126808 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=61;Dels=0.00;FS=3.491;HaplotypeScore=16.9835;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-3.792;QD=1.68;ReadPosRankSum=-0.502;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:53,8:61:99:131,0,1927 -chr1 126813 . C A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=62;Dels=0.00;FS=3.493;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.433;QD=1.59;ReadPosRankSum=0.304;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,8:62:99:127,0,1961 -chr1 126818 . A T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=60;Dels=0.00;FS=3.656;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=-1.381;QD=19.81;ReadPosRankSum=-0.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1217,0,765 -chr1 126828 . G A 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.847;DP=64;Dels=0.00;FS=3.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.035;QD=18.39;ReadPosRankSum=0.616;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1205,0,913 -chr1 126853 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=65;Dels=0.00;FS=24.367;HaplotypeScore=18.9957;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-2.099;QD=2.83;ReadPosRankSum=-0.102;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,11:65:99:212,0,1982 -chr1 126860 . A C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.719;DP=68;Dels=0.00;FS=20.308;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=1;MQRankSum=-1.259;QD=2.08;ReadPosRankSum=0.450;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,10:68:99:170,0,2073 -chr1 126861 . T A 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=69;Dels=0.00;FS=6.505;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=0.043;QD=15.01;ReadPosRankSum=1.333;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1064,0,1239 -chr1 126865 . G C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;DP=69;Dels=0.00;FS=24.072;HaplotypeScore=18.9966;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-0.684;QD=2.62;ReadPosRankSum=0.043;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,11:69:99:209,0,2116 -chr1 126883 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.091;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=0.724;QD=7.50;ReadPosRankSum=0.943;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:50,19:69:99:546,0,1802 -chr1 126896 . G T 1175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.676;DP=66;Dels=0.00;FS=6.828;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=1;MQRankSum=0.099;QD=17.81;ReadPosRankSum=-1.057;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1204,0,1011 -chr1 126923 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=68;Dels=0.00;FS=11.174;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=1;MQRankSum=1.555;QD=9.54;ReadPosRankSum=-1.395;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:46,22:68:99:677,0,1574 -chr1 126945 . A T 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.121;DP=63;Dels=0.00;FS=9.115;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.380;QD=4.79;ReadPosRankSum=0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,14:63:99:330,0,1740 -chr1 126957 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.697;DP=59;Dels=0.00;FS=5.370;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=0.773;QD=2.47;ReadPosRankSum=1.289;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,10:59:99:174,0,1767 -chr1 126959 . A G 174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=55;Dels=0.00;FS=5.678;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-0.116;QD=3.18;ReadPosRankSum=0.812;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:45,10:55:99:203,0,1601 -chr1 126963 . C A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=54;Dels=0.00;FS=19.876;HaplotypeScore=17.9934;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-0.135;QD=13.01;ReadPosRankSum=0.695;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:731,0,1059 -chr1 126974 . G A 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;DP=53;Dels=0.00;FS=4.336;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=1;MQRankSum=-0.448;QD=19.37;ReadPosRankSum=-0.858;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:1055,0,636 -chr1 126988 . T C 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=1;MQRankSum=-0.179;QD=1.42;ReadPosRankSum=-0.636;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:40,7:47:95:95,0,1426 -chr1 127338 . C T 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.92;MQ0=0;MQRankSum=0.731;QD=15.01;ReadPosRankSum=0.731;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:1,4:5:12:103,0,12 -chr1 127348 . G A 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=6;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.23;MQ0=0;MQRankSum=0.720;QD=12.51;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:2,4:6:12:103,0,12 -chr1 127382 . C T 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;DP=10;Dels=0.00;FS=11.181;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=35.14;MQ0=0;MQRankSum=2.383;QD=9.08;ReadPosRankSum=-0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:6,4:10:43:119,0,43 -chr1 127438 . G T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=27;Dels=0.00;FS=15.441;HaplotypeScore=6.0290;MLEAC=1;MLEAF=0.500;MQ=25.45;MQ0=5;MQRankSum=2.404;QD=11.51;ReadPosRankSum=1.469;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,14:27:56:339,0,56 -chr1 127567 . G A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=35;Dels=0.00;FS=6.623;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=2;MQRankSum=-4.564;QD=1.99;ReadPosRankSum=-3.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,12:35:98:98,0,737 -chr1 127579 . G C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=39;Dels=0.00;FS=3.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=2;MQRankSum=-4.786;QD=2.30;ReadPosRankSum=-2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:118,0,827 -chr1 127590 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=42;Dels=0.00;FS=4.107;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.59;MQ0=2;MQRankSum=-4.885;QD=1.95;ReadPosRankSum=1.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,13:42:99:110,0,969 -chr1 127637 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.819;DP=40;Dels=0.00;FS=12.746;HaplotypeScore=2.4098;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-4.973;QD=2.04;ReadPosRankSum=-1.284;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:110,0,984 -chr1 127648 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.114;DP=35;Dels=0.00;FS=12.225;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=4.397;QD=25.96;ReadPosRankSum=3.076;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,26:35:99:937,0,111 -chr1 128373 . T A 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.675;DP=31;Dels=0.00;FS=10.328;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=0;MQRankSum=-3.475;QD=1.64;ReadPosRankSum=-1.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,6:31:79:79,0,886 -chr1 128434 . A G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=34;Dels=0.00;FS=10.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=-4.271;QD=13.76;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:496,0,567 -chr1 128435 . C A 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.620;DP=34;Dels=0.00;FS=13.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=4.202;QD=15.61;ReadPosRankSum=-1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:559,0,495 -chr1 128484 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.879;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-4.478;QD=17.06;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:540,0,432 -chr1 128493 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.90;MQ0=0;MQRankSum=-4.008;QD=15.96;ReadPosRankSum=0.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,15:28:99:475,0,439 -chr1 128534 . G T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=28;Dels=0.00;FS=5.632;HaplotypeScore=18.3580;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.821;QD=1.99;ReadPosRankSum=-2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,4:28:84:84,0,841 -chr1 128588 . C T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=37;Dels=0.00;FS=28.800;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.381;QD=17.89;ReadPosRankSum=1.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:690,0,561 -chr1 128691 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.043;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=4;MQRankSum=-0.764;QD=6.66;ReadPosRankSum=-0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:288,0,846 -chr1 128700 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=5;MQRankSum=-1.458;QD=4.21;ReadPosRankSum=-0.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:184,0,862 -chr1 128703 . A G 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.686;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-0.441;QD=4.19;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:175,0,799 -chr1 128705 . C T 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=5;MQRankSum=-0.969;QD=4.27;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:182,0,890 -chr1 128706 . A G 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.275;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-1.471;QD=4.59;ReadPosRankSum=0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:189,0,851 -chr1 128741 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=49;Dels=0.00;FS=18.338;HaplotypeScore=2.9979;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=3;MQRankSum=-1.889;QD=10.67;ReadPosRankSum=2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:551,0,903 -chr1 128751 . A G 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.379;DP=53;Dels=0.00;FS=22.251;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=3;MQRankSum=-1.700;QD=9.75;ReadPosRankSum=3.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:545,0,1055 -chr1 128795 . G A 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.675;DP=55;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-3.881;QD=14.92;ReadPosRankSum=-1.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:849,0,927 -chr1 128807 . T C 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=57;Dels=0.00;FS=5.835;HaplotypeScore=10.9974;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.485;QD=12.96;ReadPosRankSum=3.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:767,0,1052 -chr1 128816 . A G 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=56;Dels=0.00;FS=11.033;HaplotypeScore=23.9742;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.409;QD=5.35;ReadPosRankSum=-2.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:328,0,1466 -chr1 128821 . G T 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=54;Dels=0.00;FS=1.128;HaplotypeScore=13.9934;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=0;MQRankSum=-1.961;QD=19.50;ReadPosRankSum=3.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1081,0,641 -chr1 128823 . C T 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;DP=51;Dels=0.00;FS=1.146;HaplotypeScore=22.8239;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-0.718;QD=18.68;ReadPosRankSum=2.727;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:981,0,699 -chr1 128833 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.443;DP=53;Dels=0.00;FS=6.025;HaplotypeScore=10.8296;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=0;MQRankSum=-0.580;QD=3.51;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:214,0,1479 -chr1 128853 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=49;Dels=0.00;FS=11.665;HaplotypeScore=1.6634;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.294;QD=3.67;ReadPosRankSum=1.902;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:39,9:49:99:208,0,1382 -chr1 128899 . G A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.178;DP=38;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-3.084;QD=11.84;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:478,0,618 -chr1 128911 . T C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=51;Dels=0.00;FS=1.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.607;QD=3.39;ReadPosRankSum=-3.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:201,0,1364 -chr1 128916 . G A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-1.816;QD=3.41;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:202,0,1455 -chr1 128946 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=60;Dels=0.00;FS=2.267;HaplotypeScore=13.9962;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.741;QD=9.48;ReadPosRankSum=1.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:597,0,1331 -chr1 128948 . A C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.669;DP=62;Dels=0.00;FS=1.018;HaplotypeScore=31.9736;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-2.302;QD=9.50;ReadPosRankSum=1.640;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:617,0,1424 -chr1 128956 . C G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=47.9525;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=0.097;QD=7.15;ReadPosRankSum=1.620;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:493,0,1642 -chr1 128957 . T G 1312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=33.9668;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.149;QD=20.84;ReadPosRankSum=1.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1341,0,755 -chr1 128961 . G A 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.577;QD=19.96;ReadPosRankSum=1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1286,0,756 -chr1 128975 . G T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=33.8278;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.350;QD=10.39;ReadPosRankSum=-0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,23:68:99:735,0,1596 -chr1 128988 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.066;DP=73;Dels=0.00;FS=12.861;HaplotypeScore=23.3284;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.345;QD=5.52;ReadPosRankSum=1.976;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:55,17:73:99:431,0,2010 -chr1 129160 . A T 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-5.688;QD=4.52;ReadPosRankSum=-1.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,15:63:99:313,0,1702 -chr1 129165 . G T 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-5.619;QD=4.83;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,15:61:99:323,0,1605 -chr1 129168 . A G 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-5.671;QD=4.71;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:47,15:62:99:320,0,1616 -chr1 129174 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.686;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-5.798;QD=4.36;ReadPosRankSum=1.384;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:50,16:66:99:316,0,1690 -chr1 129186 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.619;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQ0=1;MQRankSum=-6.469;QD=6.53;ReadPosRankSum=1.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,23:69:99:479,0,1553 -chr1 129201 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=58;Dels=0.00;FS=2.756;HaplotypeScore=12.9038;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=1;MQRankSum=1.307;QD=5.62;ReadPosRankSum=1.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,14:58:99:354,0,1347 -chr1 129215 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088;DP=44;Dels=0.00;FS=1.218;HaplotypeScore=9.9234;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.732;QD=10.43;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:487,0,829 -chr1 129227 . T C 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.3660;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=1;MQRankSum=-4.330;QD=5.34;ReadPosRankSum=1.719;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:199,0,742 -chr1 129279 . T G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;DP=43;Dels=0.00;FS=7.514;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=55.76;MQ0=2;MQRankSum=-0.257;QD=20.27;ReadPosRankSum=-4.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,28:43:99:900,0,484 -chr1 129287 . G A 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=45;Dels=0.00;FS=10.631;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.96;MQ0=2;MQRankSum=-1.076;QD=22.04;ReadPosRankSum=-3.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:14,31:45:99:1020,0,440 -chr1 129320 . T A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=51;Dels=0.00;FS=20.436;HaplotypeScore=2.9997;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=3;MQRankSum=0.864;QD=22.03;ReadPosRankSum=3.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1152,0,502 -chr1 129323 . A G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.889;DP=48;Dels=0.00;FS=17.838;HaplotypeScore=3.9996;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=0.605;QD=21.10;ReadPosRankSum=3.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1041,0,518 -chr1 129341 . C G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=57;Dels=0.00;FS=17.030;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=6;MQRankSum=-1.618;QD=3.28;ReadPosRankSum=-3.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,14:57:99:215,0,1547 -chr1 129364 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.104;DP=53;Dels=0.00;FS=30.019;HaplotypeScore=14.7852;MLEAC=1;MLEAF=0.500;MQ=56.85;MQ0=5;MQRankSum=-1.619;QD=5.17;ReadPosRankSum=0.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:37,16:53:99:302,0,1331 -chr1 129366 . C T 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.951;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=12.7857;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=5;MQRankSum=2.207;QD=16.03;ReadPosRankSum=-0.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,729 -chr1 129393 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=49;Dels=0.00;FS=6.439;HaplotypeScore=51.4904;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=-1.665;QD=10.87;ReadPosRankSum=1.560;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:561,0,1020 -chr1 129409 . C T 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=52;Dels=0.00;FS=15.514;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-1.292;QD=7.01;ReadPosRankSum=2.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:393,0,1247 -chr1 129415 . T G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=10.402;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-1.083;QD=4.57;ReadPosRankSum=1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,13:49:99:252,0,1255 -chr1 129421 . A G 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=47;Dels=0.00;FS=10.402;HaplotypeScore=14.7307;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.163;QD=4.36;ReadPosRankSum=1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,11:47:99:233,0,1272 -chr1 129428 . T A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=47;Dels=0.00;FS=11.605;HaplotypeScore=14.5195;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=0.749;QD=1.72;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:109,0,1365 -chr1 129430 . T C 1335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.868;DP=47;Dels=0.00;FS=14.700;HaplotypeScore=13.5208;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.941;QD=28.42;ReadPosRankSum=-1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,40:47:99:1364,0,151 -chr1 129470 . A G 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=34;Dels=0.00;FS=6.431;HaplotypeScore=3.9295;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=3.106;QD=26.23;ReadPosRankSum=3.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,26:34:99:920,0,161 -chr1 129499 . G A 154.94 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=4.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.736;QD=25.82;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:1,5:6:14:183,0,14 -chr1 129600 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.9992;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=1.557;QD=13.22;ReadPosRankSum=-0.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:372,0,498 -chr1 129610 . G T 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.411;DP=28;Dels=0.00;FS=28.641;HaplotypeScore=3.7875;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=-2.006;QD=30.10;ReadPosRankSum=0.446;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:3,25:28:36:871,0,36 -chr1 129625 . G A 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.306;DP=29;Dels=0.00;FS=12.308;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.476;QD=13.10;ReadPosRankSum=1.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,12:29:99:408,0,556 -chr1 130382 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.395;DP=19;Dels=0.00;FS=9.745;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=0;MQRankSum=-1.395;QD=20.51;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:418,0,230 -chr1 130392 . G A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=16;Dels=0.00;FS=10.532;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=0;MQRankSum=-1.059;QD=17.24;ReadPosRankSum=1.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:304,0,242 -chr1 130395 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=17;Dels=0.00;FS=10.843;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.81;MQ0=0;MQRankSum=-1.107;QD=16.63;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,277 -chr1 130428 . C T 234.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=20;Dels=0.00;FS=13.778;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=0;MQRankSum=0.501;QD=11.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:12,8:20:99:263,0,382 -chr1 130463 . T A 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.131;DP=33;Dels=0.00;FS=33.092;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=1.767;QD=13.30;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:467,0,604 -chr1 130464 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.665;DP=34;Dels=0.00;FS=25.025;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-1.006;QD=16.52;ReadPosRankSum=-0.104;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:590,0,499 -chr1 130471 . G T 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=36;Dels=0.00;FS=24.517;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.430;QD=13.85;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:527,0,659 -chr1 130515 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.442;DP=43;Dels=0.00;FS=6.930;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.717;QD=16.53;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:739,0,723 -chr1 130542 . C T 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.025;DP=53;Dels=0.00;FS=1.790;HaplotypeScore=19.9950;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.161;QD=1.77;ReadPosRankSum=-3.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,8:53:99:122,0,1658 -chr1 130586 . C T 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.100;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.060;QD=18.68;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:962,0,598 -chr1 130630 . G A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=19.8889;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=0;MQRankSum=0.154;QD=17.07;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:745,0,563 -chr1 130682 . A C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.407;QD=11.69;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,21:55:99:671,0,1176 -chr1 130699 . G A 1434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.851;QD=23.14;ReadPosRankSum=-0.956;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,42:62:99:1463,0,623 -chr1 130768 . C T 1247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=53;Dels=0.00;FS=14.260;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.41;MQ0=0;MQRankSum=0.829;QD=23.54;ReadPosRankSum=-1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1276,0,522 -chr1 130839 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=2.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.222;QD=17.69;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:665,0,568 -chr1 130914 . A G 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.017;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.258;QD=22.52;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1109,0,452 -chr1 130927 . A C 1100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;DP=48;Dels=0.00;FS=6.248;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.498;QD=22.93;ReadPosRankSum=2.329;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1129,0,467 -chr1 130951 . A G 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.242;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=26.1290;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.231;QD=23.90;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:1056,0,426 -chr1 130966 . A T 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=53;Dels=0.00;FS=6.248;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.819;QD=24.73;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,38:53:99:1339,0,440 -chr1 130976 . G C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.645;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-0.337;QD=9.57;ReadPosRankSum=1.048;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:526,0,1151 -chr1 130992 . C T 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.042;DP=57;Dels=0.00;FS=3.924;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.112;QD=21.72;ReadPosRankSum=-1.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,37:57:99:1266,0,611 -chr1 131017 . C G 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=49;Dels=0.00;FS=19.446;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.850;QD=16.36;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:830,0,803 -chr1 131080 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=9.7317;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-0.662;QD=13.66;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:561,0,711 -chr1 131092 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=2.039;QD=20.12;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,25:40:99:833,0,436 -chr1 131093 . A T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.421;DP=40;Dels=0.00;FS=5.618;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.234;QD=5.22;ReadPosRankSum=1.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:237,0,1057 -chr1 131106 . A G 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.361;DP=32;Dels=0.00;FS=8.080;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-2.945;QD=13.59;ReadPosRankSum=-0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:463,0,546 -chr1 131121 . C T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.467;DP=34;Dels=0.00;FS=5.188;HaplotypeScore=15.7761;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.640;QD=15.90;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:569,0,510 -chr1 131132 . C A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.426;DP=44;Dels=0.00;FS=15.097;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.78;MQ0=0;MQRankSum=4.844;QD=17.24;ReadPosRankSum=-1.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:787,0,609 -chr1 131154 . A T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=44;Dels=0.00;FS=23.397;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-4.184;QD=14.54;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:668,0,759 -chr1 131158 . C T 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.954;DP=41;Dels=0.00;FS=21.509;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.27;MQ0=0;MQRankSum=-3.830;QD=13.41;ReadPosRankSum=2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:578,0,692 -chr1 131170 . T G 560.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=49;Dels=0.00;FS=38.825;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=-3.211;QD=11.44;ReadPosRankSum=1.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:589,0,938 -chr1 131184 . G A 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.436;DP=49;Dels=0.00;FS=38.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=2;MQRankSum=-3.020;QD=8.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:461,0,1001 -chr1 131207 . G T 418.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.185;DP=42;Dels=0.00;FS=27.416;HaplotypeScore=4.4038;MLEAC=1;MLEAF=0.500;MQ=48.07;MQ0=2;MQRankSum=-3.576;QD=9.97;ReadPosRankSum=-4.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:447,0,821 -chr1 131225 . C G 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.578;DP=40;Dels=0.00;FS=16.577;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.44;MQ0=3;MQRankSum=-2.808;QD=6.19;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:276,0,822 -chr1 131301 . T C 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.737;DP=31;Dels=0.00;FS=14.239;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=3;MQRankSum=0.331;QD=6.41;ReadPosRankSum=-2.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:227,0,719 -chr1 131355 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=32;Dels=0.00;FS=6.200;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=1;MQRankSum=0.099;QD=15.24;ReadPosRankSum=0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:516,0,481 -chr1 131363 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.895;DP=30;Dels=0.00;FS=4.091;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=1;MQRankSum=-1.768;QD=15.03;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:479,0,438 -chr1 131370 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=35;Dels=0.00;FS=6.017;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=1;MQRankSum=2.012;QD=12.54;ReadPosRankSum=0.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:467,0,650 -chr1 131393 . T A 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.277;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-1.006;QD=16.68;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:612,0,506 -chr1 131394 . T G 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-2.497;QD=16.71;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:613,0,502 -chr1 131432 . G C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=42;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=1;MQRankSum=-1.274;QD=17.66;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:770,0,563 -chr1 131475 . G T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=48;Dels=0.00;FS=2.505;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.99;MQ0=1;MQRankSum=0.096;QD=15.00;ReadPosRankSum=0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:748,0,812 -chr1 131486 . C G 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=50;Dels=0.00;FS=2.434;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.59;MQ0=0;MQRankSum=0.601;QD=16.58;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:857,0,830 -chr1 131561 . A G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=33.7934;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=4.289;QD=12.63;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,25:63:99:824,0,1054 -chr1 131579 . T A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.134;DP=55;Dels=0.00;FS=1.050;HaplotypeScore=2.6642;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=3.452;QD=14.49;ReadPosRankSum=-1.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:825,0,902 -chr1 131720 . T C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.158;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.715;QD=13.65;ReadPosRankSum=4.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:779,0,1056 -chr1 131760 . C T 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=39;Dels=0.00;FS=7.125;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=2;MQRankSum=1.717;QD=15.71;ReadPosRankSum=0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:641,0,573 -chr1 131775 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080;DP=35;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQ0=2;MQRankSum=-1.927;QD=13.85;ReadPosRankSum=-1.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:513,0,603 -chr1 131776 . G A 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.441;DP=33;Dels=0.00;FS=3.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQ0=2;MQRankSum=-2.203;QD=12.42;ReadPosRankSum=-0.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:438,0,599 -chr1 131796 . A G 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.532;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.71;MQ0=2;MQRankSum=-2.445;QD=10.05;ReadPosRankSum=0.780;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,14:36:99:390,0,704 -chr1 131801 . A G 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.91;MQ0=2;MQRankSum=2.114;QD=19.39;ReadPosRankSum=-1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:707,0,371 -chr1 131805 . G C 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=2.434;QD=19.64;ReadPosRankSum=-1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:39:99:794,0,392 -chr1 131806 . A G 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.239;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=-2.752;QD=9.10;ReadPosRankSum=1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:383,0,799 -chr1 131818 . T C 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=39;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.16;MQ0=2;MQRankSum=-2.677;QD=7.05;ReadPosRankSum=0.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:303,0,803 -chr1 131851 . A G 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=41;Dels=0.00;FS=5.599;HaplotypeScore=20.1968;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-3.302;QD=7.48;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:41:99:335,0,851 -chr1 131940 . C T 523.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=33;Dels=0.00;FS=13.038;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.25;MQ0=1;MQRankSum=0.537;QD=15.87;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:552,0,366 -chr1 131946 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.071;DP=33;Dels=0.00;FS=13.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.15;MQ0=1;MQRankSum=-0.754;QD=7.81;ReadPosRankSum=-0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:286,0,622 -chr1 131950 . G A 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.061;DP=33;Dels=0.00;FS=9.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=1;MQRankSum=-0.793;QD=6.69;ReadPosRankSum=-0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:249,0,652 -chr1 131964 . T C 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.757;DP=27;Dels=0.00;FS=4.809;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.64;MQ0=1;MQRankSum=-0.976;QD=1.70;ReadPosRankSum=-2.017;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,5:27:74:74,0,639 -chr1 132327 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.844;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.266;QD=7.82;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,314 -chr1 132328 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.532;QD=7.82;ReadPosRankSum=1.644;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,315 -chr1 132332 . A T 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.400;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.355;QD=7.65;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:166,0,314 -chr1 132348 . G A 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=0;MQRankSum=1.431;QD=8.74;ReadPosRankSum=1.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:238,0,433 -chr1 132356 . A C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.968;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=14.3879;MLEAC=1;MLEAF=0.500;MQ=45.87;MQ0=0;MQRankSum=-2.087;QD=16.82;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,15:24:99:432,0,228 -chr1 132369 . A T 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.273;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.53;MQ0=0;MQRankSum=-0.634;QD=1.95;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,5:23:73:73,0,558 -chr1 132456 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=28;Dels=0.00;FS=1.941;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=50.78;MQ0=2;MQRankSum=0.212;QD=22.35;ReadPosRankSum=0.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,18:28:99:654,0,184 -chr1 132478 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.382;DP=36;Dels=0.00;FS=3.155;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=2;MQRankSum=0.673;QD=9.83;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:382,0,743 -chr1 132730 . G C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=40;Dels=0.00;FS=1.399;HaplotypeScore=2.7317;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=1;MQRankSum=-4.323;QD=6.12;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:273,0,1019 -chr1 132737 . C T 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=48;Dels=0.00;FS=1.273;HaplotypeScore=23.7282;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=2;MQRankSum=-4.842;QD=7.04;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,14:48:99:366,0,1103 -chr1 132780 . A G 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.056;DP=55;Dels=0.00;FS=28.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=1;MQRankSum=2.043;QD=6.52;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:387,0,1434 -chr1 132838 . G A 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;DP=60;Dels=0.00;FS=19.671;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.32;MQ0=0;MQRankSum=-0.669;QD=14.03;ReadPosRankSum=1.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:870,0,1128 -chr1 132922 . T C 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.652;QD=17.87;ReadPosRankSum=1.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:600,0,462 -chr1 132923 . G T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.842;QD=17.65;ReadPosRankSum=1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:593,0,451 -chr1 133059 . C T 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;DP=46;Dels=0.00;FS=11.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=0;MQRankSum=-2.139;QD=15.34;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:734,0,651 -chr1 133068 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.081;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=0;MQRankSum=-2.420;QD=14.97;ReadPosRankSum=-0.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:687,0,652 -chr1 133104 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=47;Dels=0.00;FS=4.125;HaplotypeScore=2.9633;MLEAC=1;MLEAF=0.500;MQ=52.43;MQ0=0;MQRankSum=1.309;QD=14.85;ReadPosRankSum=-0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:726,0,732 -chr1 133115 . C G 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=46;Dels=0.00;FS=2.550;HaplotypeScore=2.9394;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-1.164;QD=15.49;ReadPosRankSum=0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:741,0,689 -chr1 133160 . A T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=24.1627;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=2.042;QD=14.09;ReadPosRankSum=0.744;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:592,0,613 -chr1 133344 . T C 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.230;QD=15.59;ReadPosRankSum=0.150;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:792,0,735 -chr1 133404 . G T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=49;Dels=0.00;FS=1.131;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=3.143;QD=19.20;ReadPosRankSum=0.559;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:20,29:49:99:969,0,589 -chr1 133433 . G A 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-4.245;QD=8.51;ReadPosRankSum=0.593;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:27,12:39:99:360,0,943 -chr1 133448 . C A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.362;DP=47;Dels=0.00;FS=1.146;HaplotypeScore=1.5317;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-4.461;QD=10.08;ReadPosRankSum=-0.365;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,17:47:99:502,0,1052 -chr1 133453 . C T 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.012;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=16.0294;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-4.142;QD=10.85;ReadPosRankSum=-0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,18:48:99:549,0,976 -chr1 133553 . A G 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.865;DP=46;Dels=0.00;FS=8.994;HaplotypeScore=2.6278;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-4.347;QD=9.08;ReadPosRankSum=0.657;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,16:46:99:446,0,1041 -chr1 133580 . G T 655.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=46;Dels=0.00;FS=8.283;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=0;MQRankSum=-5.226;QD=14.26;ReadPosRankSum=-1.808;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,21:46:99:684,0,798 -chr1 133584 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=4.288;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-5.037;QD=13.24;ReadPosRankSum=-1.450;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,20:45:99:624,0,830 -chr1 133629 . G A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=53;Dels=0.00;FS=2.379;HaplotypeScore=3.9941;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.817;QD=14.45;ReadPosRankSum=0.793;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:28,25:53:99:794,0,922 -chr1 133703 . G A 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.177;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-5.657;QD=8.59;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:29,18:47:99:432,0,1026 -chr1 133708 . C T 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-4.162;QD=6.83;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:34,14:48:99:356,0,1139 -chr1 133768 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.666;DP=35;Dels=0.00;FS=3.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-3.499;QD=9.74;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:22,13:35:99:369,0,766 -chr1 133772 . T A 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.647;DP=31;Dels=0.00;FS=1.503;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.798;QD=11.86;ReadPosRankSum=-0.258;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:17,14:31:99:396,0,591 -chr1 133877 . G C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=64;Dels=0.00;FS=2.113;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=0;MQRankSum=-3.336;QD=12.97;ReadPosRankSum=1.698;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V19|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:858,0,1194 -chr1 133880 . T G 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.53;MQ0=0;MQRankSum=-1.770;QD=2.61;ReadPosRankSum=2.191;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S20|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,10:62:99:190,0,1843 -chr1 133924 . C T 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.234;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=14.4642;MLEAC=1;MLEAF=0.500;MQ=50.02;MQ0=1;MQRankSum=-2.145;QD=5.48;ReadPosRankSum=0.419;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P35L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:302,0,1267 -chr1 133955 . C G 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;DP=31;Dels=0.00;FS=1.768;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.62;MQ0=0;MQRankSum=-2.415;QD=5.06;ReadPosRankSum=-1.377;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D45E|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:185,0,789 -chr1 134007 . G T 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.146;DP=26;Dels=0.00;FS=3.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=1;MQRankSum=-3.466;QD=6.64;ReadPosRankSum=-0.903;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V63L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:201,0,596 -chr1 134011 . C T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=30;Dels=0.00;FS=3.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-3.372;QD=7.46;ReadPosRankSum=-0.619;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A64V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:252,0,660 -chr1 134148 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.729;DP=60;Dels=0.00;FS=15.632;HaplotypeScore=2.9570;MLEAC=1;MLEAF=0.500;MQ=39.89;MQ0=8;MQRankSum=1.349;QD=8.15;ReadPosRankSum=0.912;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R110C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,19:60:99:517,0,973 -chr1 134280 . A C 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=91;Dels=0.00;FS=2.074;HaplotypeScore=10.4073;MLEAC=1;MLEAF=0.500;MQ=34.28;MQ0=7;MQRankSum=1.802;QD=10.80;ReadPosRankSum=-0.414;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K154Q|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,38:91:99:1011,0,1041 -chr1 134333 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.529;DP=65;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.88;MQ0=7;MQRankSum=0.576;QD=10.38;ReadPosRankSum=0.734;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y171|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:703,0,1008 -chr1 134354 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.63;MQ0=7;MQRankSum=0.036;QD=9.56;ReadPosRankSum=-0.060;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A178|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:516,0,788 -chr1 134514 . T C 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.7876;MLEAC=1;MLEAF=0.500;MQ=37.13;MQ0=3;MQRankSum=-2.851;QD=7.28;ReadPosRankSum=-0.527;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C232R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:392,0,878 -chr1 134570 . T C 854.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.49;MQ0=0;MQRankSum=3.436;QD=19.43;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F250|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:883,0,419 -chr1 134603 . G T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.9762;MLEAC=1;MLEAF=0.500;MQ=42.98;MQ0=0;MQRankSum=-4.437;QD=12.42;ReadPosRankSum=-1.075;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T261|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:612,0,769 -chr1 134696 . G A 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;DP=25;Dels=0.00;FS=7.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.51;MQ0=1;MQRankSum=1.217;QD=13.63;ReadPosRankSum=-3.187;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R292|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:11,14:25:99:369,0,240 -chr1 134730 . T G 147.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=17;Dels=0.00;FS=9.031;HaplotypeScore=3.8313;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=6;MQRankSum=0.715;QD=8.70;ReadPosRankSum=1.931;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F304V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:3,14:17:2:174,0,2 -chr1 134780 . T C 422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=42;Dels=0.00;FS=7.420;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=0.050;QD=10.07;ReadPosRankSum=1.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C320|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:451,0,502 -chr1 134807 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=53;Dels=0.00;FS=2.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.74;MQ0=5;MQRankSum=-1.432;QD=14.07;ReadPosRankSum=0.010;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I329|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:774,0,584 -chr1 134822 . T C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=52;Dels=0.00;FS=4.058;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=36.11;MQ0=1;MQRankSum=-2.231;QD=16.55;ReadPosRankSum=0.789;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I334|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,33:52:99:889,0,575 -chr1 134927 . G C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=5.3557;MLEAC=1;MLEAF=0.500;MQ=26.60;MQ0=9;MQRankSum=1.588;QD=7.44;ReadPosRankSum=-0.677;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E369D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:415,0,456 -chr1 135029 . G C 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=68;Dels=0.00;FS=9.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=1;MQRankSum=-1.650;QD=2.79;ReadPosRankSum=-0.245;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L403F|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,11:68:99:218,0,1758 -chr1 135042 . A G 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.577;DP=75;Dels=0.00;FS=8.931;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=39.96;MQ0=1;MQRankSum=3.045;QD=8.50;ReadPosRankSum=0.420;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N408D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,22:75:99:666,0,1347 -chr1 135055 . A G 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.310;DP=84;Dels=0.00;FS=10.873;HaplotypeScore=9.3239;MLEAC=1;MLEAF=0.500;MQ=36.61;MQ0=3;MQRankSum=0.553;QD=3.71;ReadPosRankSum=1.854;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E412G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:340,0,1652 -chr1 135124 . A G 1965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.982;DP=84;Dels=0.00;FS=3.513;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=2.897;QD=23.40;ReadPosRankSum=0.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q435R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,68:84:99:1994,0,139 -chr1 135152 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.499;DP=86;Dels=0.00;FS=1.215;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=3;MQRankSum=-0.614;QD=1.25;ReadPosRankSum=0.942;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D444|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:136,0,2271 -chr1 135153 . G A 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.997;DP=87;Dels=0.00;FS=1.186;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=3;MQRankSum=-0.409;QD=1.65;ReadPosRankSum=0.537;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V445M|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:172,0,2269 -chr1 135160 . C G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.067;DP=80;Dels=0.00;FS=2.719;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=38.64;MQ0=3;MQRankSum=0.297;QD=2.51;ReadPosRankSum=1.116;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S447C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:229,0,2067 -chr1 135180 . T A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.230;DP=74;Dels=0.00;FS=21.668;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.55;MQ0=0;MQRankSum=1.094;QD=3.70;ReadPosRankSum=1.690;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Att|F454I|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,13:74:99:302,0,1980 -chr1 135182 . T C 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=73;Dels=0.00;FS=22.648;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.76;MQ0=0;MQRankSum=-0.479;QD=10.89;ReadPosRankSum=1.077;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F454|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,29:73:99:823,0,1443 -chr1 135209 . A G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.127;DP=78;Dels=0.00;FS=18.781;HaplotypeScore=10.8281;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-2.484;QD=12.02;ReadPosRankSum=0.229;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A463|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:966,0,1557 -chr1 135218 . T C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=76;Dels=0.00;FS=7.732;HaplotypeScore=20.2693;MLEAC=1;MLEAF=0.500;MQ=49.54;MQ0=0;MQRankSum=-1.200;QD=6.59;ReadPosRankSum=-0.624;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S466|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,19:76:99:529,0,1942 -chr1 135220 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=77;Dels=0.00;FS=5.434;HaplotypeScore=9.4397;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-0.384;QD=6.30;ReadPosRankSum=-0.821;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E467G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:58,19:77:99:513,0,1945 -chr1 135242 . G T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;DP=84;Dels=0.00;FS=4.355;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-2.169;QD=10.69;ReadPosRankSum=-0.189;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P474|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,32:84:99:926,0,1735 -chr1 135249 . C A 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=83;Dels=0.00;FS=0.951;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=3.080;QD=7.48;ReadPosRankSum=1.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P477T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:649,0,2002 -chr1 135260 . G C 1586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=1.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=-0.838;QD=20.61;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A480|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,50:77:99:1615,0,861 -chr1 135276 . C T 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=78;Dels=0.00;FS=3.392;HaplotypeScore=25.9840;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=0.021;QD=9.15;ReadPosRankSum=0.503;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,25:78:99:742,0,1838 -chr1 135284 . A G 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;DP=83;Dels=0.00;FS=0.867;HaplotypeScore=45.6804;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=2.555;QD=10.96;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,30:83:99:938,0,1841 -chr1 135290 . A G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.543;DP=80;Dels=0.00;FS=3.316;HaplotypeScore=43.6813;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.055;QD=11.50;ReadPosRankSum=-0.730;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:948,0,1404 -chr1 135296 . T A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=77;Dels=0.00;FS=3.797;HaplotypeScore=25.7468;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.051;QD=7.83;ReadPosRankSum=0.366;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,22:77:99:631,0,2017 -chr1 135305 . C A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.358;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=18.7849;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.819;QD=2.55;ReadPosRankSum=-4.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:77,14:91:99:260,0,2802 -chr1 135319 . A G 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=101;Dels=0.00;FS=0.864;HaplotypeScore=3.9995;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.932;QD=7.50;ReadPosRankSum=-0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,27:101:99:786,0,2632 -chr1 135362 . G C 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;DP=104;Dels=0.00;FS=0.933;HaplotypeScore=3.5999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.569;QD=5.02;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,21:104:99:550,0,2813 -chr1 135376 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=104;Dels=0.00;FS=0.969;HaplotypeScore=2.8632;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-2.044;QD=4.12;ReadPosRankSum=0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:85,19:104:99:457,0,2999 -chr1 135391 . T G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.718;DP=103;Dels=0.00;FS=2.944;HaplotypeScore=27.2496;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-0.169;QD=7.15;ReadPosRankSum=0.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:103:99:765,0,2417 -chr1 135400 . G A 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=108;Dels=0.00;FS=6.146;HaplotypeScore=26.0389;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-2.758;QD=15.78;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,52:108:99:1732,0,1799 -chr1 135425 . T C 2440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=100;Dels=0.00;FS=5.702;HaplotypeScore=37.9722;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-2.038;QD=24.41;ReadPosRankSum=-0.257;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,72:100:99:2469,0,843 -chr1 135428 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=96;Dels=0.00;FS=3.339;HaplotypeScore=38.9718;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-1.010;QD=4.73;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:482,0,2684 -chr1 135433 . G T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=100;Dels=0.00;FS=5.032;HaplotypeScore=76.9445;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-4.688;QD=4.05;ReadPosRankSum=0.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:433,0,2862 -chr1 135440 . A T 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=97;Dels=0.00;FS=0.920;HaplotypeScore=61.9081;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.804;QD=5.41;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:553,0,2671 -chr1 135443 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.451;DP=97;Dels=0.00;FS=2.004;HaplotypeScore=60.8069;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.533;QD=5.00;ReadPosRankSum=-0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:513,0,2730 -chr1 135446 . C T 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.176;DP=97;Dels=0.00;FS=2.653;HaplotypeScore=42.8139;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-7.372;QD=12.97;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,42:97:99:1286,0,1882 -chr1 135450 . C T 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=94;Dels=0.00;FS=2.740;HaplotypeScore=39.6045;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-7.169;QD=13.13;ReadPosRankSum=-0.593;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:54,40:94:99:1262,0,1853 -chr1 135469 . C T 1458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=101;Dels=0.00;FS=3.736;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-8.200;QD=14.44;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1487,0,1800 -chr1 135483 . A C 2726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.152;DP=96;Dels=0.00;FS=0.981;HaplotypeScore=66.5358;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=0;MQRankSum=-3.811;QD=28.40;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,75:96:99:2755,0,482 -chr1 135489 . T G 1566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;DP=97;Dels=0.00;FS=12.274;HaplotypeScore=43.2734;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-7.619;QD=16.15;ReadPosRankSum=1.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,47:97:99:1595,0,1719 -chr1 135492 . A G 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=97;Dels=0.00;FS=1.972;HaplotypeScore=44.2721;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-4.134;QD=6.52;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:661,0,2654 -chr1 135504 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.723;DP=98;Dels=0.00;FS=21.343;HaplotypeScore=21.9832;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-6.623;QD=15.06;ReadPosRankSum=2.581;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,45:98:99:1504,0,1796 -chr1 135514 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=97;Dels=0.00;FS=12.661;HaplotypeScore=41.9659;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=0;MQRankSum=-5.004;QD=6.73;ReadPosRankSum=0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:681,0,2606 -chr1 135517 . C T 1587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.502;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=21.9725;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=2.170;QD=16.71;ReadPosRankSum=1.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,48:95:99:1616,0,1560 -chr1 135527 . T C 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.045;DP=85;Dels=0.00;FS=8.852;HaplotypeScore=80.9742;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-4.243;QD=2.79;ReadPosRankSum=1.642;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,13:85:99:265,0,2552 -chr1 135535 . G A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.892;DP=82;Dels=0.00;FS=8.551;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-5.078;QD=3.08;ReadPosRankSum=1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,13:82:99:281,0,2484 -chr1 135536 . C T 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=79;Dels=0.00;FS=4.308;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=-1.623;QD=4.20;ReadPosRankSum=1.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,14:79:99:360,0,1863 -chr1 135537 . A G 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.307;DP=78;Dels=0.00;FS=9.867;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.630;QD=11.14;ReadPosRankSum=1.297;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,28:78:99:897,0,1742 -chr1 135551 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=91;Dels=0.00;FS=9.889;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=-4.719;QD=8.24;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:63,27:91:99:778,0,2232 -chr1 135557 . A C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.109;DP=92;Dels=0.00;FS=11.651;HaplotypeScore=3.9926;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-3.944;QD=8.20;ReadPosRankSum=-1.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:783,0,2240 -chr1 135582 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.013;DP=97;Dels=0.00;FS=10.159;HaplotypeScore=29.4167;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-4.142;QD=6.48;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,24:97:99:657,0,2497 -chr1 135587 . G C 2286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.678;DP=96;Dels=0.00;FS=0.869;HaplotypeScore=28.5846;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=0.144;QD=23.82;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,67:96:99:2315,0,856 -chr1 135606 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.585;DP=96;Dels=0.00;FS=2.045;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.629;QD=4.78;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:487,0,2576 -chr1 135609 . C A 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.944;DP=93;Dels=0.00;FS=7.797;HaplotypeScore=83.8468;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=-3.424;QD=7.92;ReadPosRankSum=-0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,27:93:99:765,0,2259 -chr1 135618 . C T 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.853;DP=89;Dels=0.00;FS=1.036;HaplotypeScore=65.8507;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.727;QD=3.94;ReadPosRankSum=2.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,17:89:99:379,0,2429 -chr1 135632 . G C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=89;Dels=0.00;FS=3.725;HaplotypeScore=67.7422;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-1.496;QD=4.58;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,18:89:99:436,0,2397 -chr1 135637 . A C 1811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.105;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=83.6799;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.341;QD=22.65;ReadPosRankSum=-0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,56:80:99:1840,0,664 -chr1 135639 . T G 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.448;DP=83;Dels=0.00;FS=11.996;HaplotypeScore=104.6691;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.923;QD=4.39;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,18:83:99:393,0,2312 -chr1 135641 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.648;QD=6.67;ReadPosRankSum=-0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:602,0,2169 -chr1 135642 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.954;QD=6.71;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:605,0,2180 -chr1 135643 . C T 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=90;Dels=0.00;FS=9.549;HaplotypeScore=115.6735;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-2.215;QD=4.20;ReadPosRankSum=0.801;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,19:90:99:406,0,2519 -chr1 135648 . G C 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=94;Dels=0.00;FS=0.939;HaplotypeScore=81.8473;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.363;QD=6.44;ReadPosRankSum=-0.062;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,23:94:99:634,0,2439 -chr1 135650 . G A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=98;Dels=0.00;FS=0.925;HaplotypeScore=85.9035;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.805;QD=6.04;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:620,0,2541 -chr1 135660 . T G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=101;Dels=0.00;FS=0.897;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.059;QD=6.71;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,25:101:99:706,0,2603 -chr1 135662 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.122;QD=6.70;ReadPosRankSum=0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,26:101:99:705,0,2524 -chr1 135693 . G A 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;DP=102;Dels=0.00;FS=1.895;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=1.915;QD=7.13;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:102:99:756,0,2603 -chr1 135705 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.990;QD=6.44;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,26:103:99:692,0,2558 -chr1 135725 . C A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=2;MQRankSum=0.224;QD=6.62;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:677,0,2539 -chr1 135734 . C T 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=84;Dels=0.00;FS=9.368;HaplotypeScore=43.9728;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=3;MQRankSum=-0.578;QD=2.59;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:246,0,2508 -chr1 135736 . C G 2208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=87;Dels=0.00;FS=2.092;HaplotypeScore=32.9825;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=3;MQRankSum=-1.198;QD=25.39;ReadPosRankSum=-0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,66:87:99:2237,0,546 -chr1 135750 . A G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.586;DP=76;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=3;MQRankSum=-1.757;QD=1.50;ReadPosRankSum=2.431;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,10:76:99:142,0,2292 -chr1 135758 . G T 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=79;Dels=0.00;FS=5.453;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.66;MQ0=3;MQRankSum=-3.574;QD=4.98;ReadPosRankSum=-1.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:422,0,2063 -chr1 135778 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.029;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=-4.222;QD=5.93;ReadPosRankSum=2.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:224,0,882 -chr1 135782 . G T 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.47;MQ0=0;MQRankSum=-3.992;QD=5.41;ReadPosRankSum=3.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:196,0,843 -chr1 135800 . C T 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.440;DP=36;Dels=0.00;FS=3.702;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-4.077;QD=3.97;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:171,0,1061 -chr1 135819 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=52;Dels=0.00;FS=6.289;HaplotypeScore=11.8640;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.616;QD=8.25;ReadPosRankSum=-2.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:457,0,1294 -chr1 135828 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.663;DP=51;Dels=0.00;FS=8.174;HaplotypeScore=22.8565;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.593;QD=4.52;ReadPosRankSum=-0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,11:51:99:259,0,1414 -chr1 135836 . G T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.890;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=12.5980;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=4.353;QD=12.80;ReadPosRankSum=2.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:796,0,1231 -chr1 135848 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.467;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.656;QD=13.62;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1249 -chr1 135855 . T G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.541;DP=69;Dels=0.00;FS=0.917;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=1.635;QD=13.33;ReadPosRankSum=-2.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,29:69:99:948,0,1381 -chr1 135865 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=67;Dels=0.00;FS=2.217;HaplotypeScore=55.9758;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.993;QD=8.09;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,20:67:99:570,0,1674 -chr1 135868 . A T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.045;DP=65;Dels=0.00;FS=1.000;HaplotypeScore=20.9924;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.676;QD=9.50;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:646,0,1554 -chr1 135874 . T C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.590;DP=70;Dels=0.00;FS=0.954;HaplotypeScore=19.9927;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-2.097;QD=10.60;ReadPosRankSum=-0.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2S|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,26:70:99:770,0,1499 -chr1 135880 . T G 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.422;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-1.102;QD=10.01;ReadPosRankSum=0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F4C|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:45,24:69:99:719,0,1540 -chr1 135884 . T C 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.749;DP=70;Dels=0.00;FS=2.105;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.179;QD=10.03;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,24:70:99:730,0,1622 -chr1 135900 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.045;DP=74;Dels=0.00;FS=1.994;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.685;QD=10.38;ReadPosRankSum=0.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R11*|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,27:74:99:796,0,1573 -chr1 135922 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=92;Dels=0.00;FS=1.814;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.479;QD=9.52;ReadPosRankSum=0.760;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I18T|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,31:92:99:904,0,2103 -chr1 135936 . A G 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=84;Dels=0.00;FS=4.645;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=1.810;QD=9.10;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T23A|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,27:84:99:793,0,1944 -chr1 135937 . C T 1766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.487;QD=21.55;ReadPosRankSum=-0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T23I|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1795,0,896 -chr1 135938 . A G 1781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.486;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.699;QD=21.73;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T23|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1810,0,895 -chr1 135950 . G A 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.094;DP=83;Dels=0.00;FS=4.423;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.851;QD=9.73;ReadPosRankSum=-0.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K27|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,27:83:99:836,0,1943 -chr1 135990 . T G 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.534;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=18.3925;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.628;QD=8.58;ReadPosRankSum=0.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,21:67:99:603,0,1660 -chr1 136009 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=44;Dels=0.00;FS=6.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.106;QD=14.20;ReadPosRankSum=-2.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:653,0,848 -chr1 136065 . A T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=46;Dels=0.00;FS=1.150;HaplotypeScore=1.7675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.035;QD=12.34;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,18:46:99:596,0,963 -chr1 136086 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.177;DP=51;Dels=0.00;FS=2.381;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.043;QD=12.07;ReadPosRankSum=0.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:644,0,1054 -chr1 136090 . A G 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.098;DP=50;Dels=0.00;FS=2.463;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-1.042;QD=12.52;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:654,0,1012 -chr1 136102 . G A 1209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=59;Dels=0.00;FS=2.203;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.365;QD=20.50;ReadPosRankSum=0.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,36:59:99:1238,0,690 -chr1 136134 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=52;Dels=0.00;FS=11.273;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.346;QD=8.28;ReadPosRankSum=1.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,17:52:99:459,0,1143 -chr1 136138 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=12.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-0.829;QD=7.34;ReadPosRankSum=1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:417,0,1249 -chr1 136150 . G C 528.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.335;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=17.3638;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-0.945;QD=10.37;ReadPosRankSum=-0.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:557,0,1120 -chr1 136165 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.333;DP=49;Dels=0.00;FS=8.545;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.736;QD=9.87;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:512,0,993 -chr1 136178 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=49;Dels=0.00;FS=8.560;HaplotypeScore=1.9248;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.250;QD=9.83;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:510,0,1040 -chr1 136208 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=40;Dels=0.00;FS=5.407;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-2.022;QD=7.12;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:313,0,1004 -chr1 136237 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.694;QD=3.25;ReadPosRankSum=1.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:142,0,1006 -chr1 136238 . T A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.197;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.423;QD=3.16;ReadPosRankSum=1.242;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:139,0,998 -chr1 136245 . A G 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.130;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.151;QD=3.26;ReadPosRankSum=1.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:152,0,1108 -chr1 136246 . G A 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.054;QD=3.39;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:157,0,1099 -chr1 136281 . A G 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=2.132;QD=20.72;ReadPosRankSum=1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1064,0,533 -chr1 136286 . T A 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=50;Dels=0.00;FS=1.154;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=1.147;QD=9.96;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:526,0,1136 -chr1 136296 . T C 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.294;DP=57;Dels=0.00;FS=2.395;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.166;QD=8.75;ReadPosRankSum=1.526;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:527,0,1372 -chr1 136297 . A C 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=57;Dels=0.00;FS=1.124;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.951;QD=8.80;ReadPosRankSum=1.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:530,0,1359 -chr1 136349 . A G 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.221;DP=55;Dels=0.00;FS=4.256;HaplotypeScore=2.8244;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.501;QD=7.32;ReadPosRankSum=-2.806;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:431,0,1458 -chr1 136407 . T A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.022;DP=36;Dels=0.00;FS=1.438;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-4.739;QD=7.63;ReadPosRankSum=1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:303,0,897 -chr1 136411 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.363;DP=35;Dels=0.00;FS=3.074;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-4.708;QD=7.94;ReadPosRankSum=1.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,11:35:99:306,0,864 -chr1 136414 . A G 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.761;DP=34;Dels=0.00;FS=1.456;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-4.675;QD=8.23;ReadPosRankSum=1.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:308,0,808 -chr1 136416 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.63;MQ0=0;MQRankSum=-4.640;QD=8.57;ReadPosRankSum=1.814;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:311,0,783 -chr1 136425 . A G 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=37;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-5.166;QD=12.29;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:483,0,735 -chr1 136429 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=39;Dels=0.00;FS=6.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=-5.339;QD=12.84;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:529,0,713 -chr1 136439 . C T 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-5.553;QD=13.61;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A37V|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:600,0,750 -chr1 136450 . C G 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.709;DP=44;Dels=0.00;FS=8.887;HaplotypeScore=14.9765;MLEAC=1;MLEAF=0.500;MQ=51.92;MQ0=0;MQRankSum=-5.669;QD=12.77;ReadPosRankSum=0.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H41D|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:590,0,832 -chr1 136462 . G A 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;DP=37;Dels=0.00;FS=5.041;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=51.93;MQ0=0;MQRankSum=-4.995;QD=9.59;ReadPosRankSum=1.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E45K|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:383,0,810 -chr1 136465 . T A 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.278;DP=36;Dels=0.00;FS=5.077;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.37;MQ0=0;MQRankSum=-5.070;QD=11.02;ReadPosRankSum=1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_LOST(HIGH|MISSENSE|Tga/Aga|*46R|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:425,0,704 -chr1 136487 . G T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.53;ReadPosRankSum=1.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:361,0,895 -chr1 136488 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.143;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.66;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:366,0,788 -chr1 136547 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.519;DP=52;Dels=0.00;FS=24.103;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=0.123;QD=15.98;ReadPosRankSum=1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I7M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,28:52:99:859,0,785 -chr1 136596 . A C 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-0.139;QD=18.76;ReadPosRankSum=-0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K24Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1004,0,696 -chr1 136655 . T A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.512;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.278;QD=15.84;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H43Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:18,20:38:99:630,0,576 -chr1 136742 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.161;DP=48;Dels=0.00;FS=11.641;HaplotypeScore=1.8937;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.635;QD=17.29;ReadPosRankSum=-0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F72|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,27:48:99:858,0,624 -chr1 136752 . C T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=43;Dels=0.00;FS=4.498;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.528;QD=15.37;ReadPosRankSum=0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P76S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,24:43:99:689,0,591 -chr1 136754 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=45;Dels=0.00;FS=8.549;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.808;QD=15.51;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P76|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,24:45:99:726,0,665 -chr1 136841 . A G 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.684;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.110;QD=17.34;ReadPosRankSum=0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E105|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,25:46:99:826,0,691 -chr1 136902 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.935;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.194;QD=13.13;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L126|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,20:46:99:632,0,609 -chr1 136996 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.141;HaplotypeScore=2.5774;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.082;QD=14.73;ReadPosRankSum=0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K157R|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:647,0,707 -chr1 137035 . T C 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.623;QD=14.32;ReadPosRankSum=1.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V170A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:29,27:56:99:830,0,902 -chr1 137064 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=65;Dels=0.00;FS=3.370;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;QD=16.57;ReadPosRankSum=0.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V180I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1105,0,993 -chr1 137119 . A G 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=59;Dels=0.00;FS=0.985;HaplotypeScore=3.6004;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.388;QD=18.93;ReadPosRankSum=-0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N198S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,34:59:99:1145,0,816 -chr1 137153 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.416;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=1;MQRankSum=2.932;QD=17.69;ReadPosRankSum=-0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S209|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1001,0,825 -chr1 137179 . A G 799.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=1.7878;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=-3.289;QD=13.79;ReadPosRankSum=-0.603;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E218G|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:828,0,1091 -chr1 137275 . G A 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=55;Dels=0.00;FS=4.048;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-2.535;QD=20.30;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R250K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,35:55:99:1145,0,643 -chr1 137372 . C T 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.028;QD=13.71;ReadPosRankSum=0.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V282|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1029,0,1332 -chr1 137373 . A G 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-2.632;QD=14.48;ReadPosRankSum=0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T283A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1085,0,1343 -chr1 137483 . G A 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-0.043;QD=11.64;ReadPosRankSum=-0.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M319I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,16:39:99:482,0,810 -chr1 137571 . A G 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=61;Dels=0.00;FS=1.046;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=55.97;MQ0=0;MQRankSum=-2.341;QD=13.06;ReadPosRankSum=-0.022;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N349D|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:35,26:61:99:825,0,1208 -chr1 137613 . C T 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.184;DP=57;Dels=0.00;FS=4.341;HaplotypeScore=3.9492;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-2.620;QD=14.84;ReadPosRankSum=-0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L363F|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:31,26:57:99:874,0,1052 -chr1 137666 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.663;DP=44;Dels=0.00;FS=1.184;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-0.687;QD=17.20;ReadPosRankSum=1.422;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C380|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,25:44:99:785,0,643 -chr1 137873 . T C 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=-1.416;QD=15.98;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V449|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,25:50:99:827,0,840 -chr1 137891 . C T 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.27;MQ0=0;MQRankSum=1.660;QD=16.26;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I455|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,26:50:99:841,0,766 -chr1 137927 . A T 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.120;QD=12.43;ReadPosRankSum=-0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P467|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:749,0,1114 -chr1 138034 . T C 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8939;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=0.781;QD=7.54;ReadPosRankSum=-1.513;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V503A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:33,13:46:99:375,0,1176 -chr1 138075 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;DP=48;Dels=0.00;FS=2.557;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.500;QD=14.02;ReadPosRankSum=-0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L517|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,22:48:99:701,0,894 -chr1 138170 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-3.956;QD=13.84;ReadPosRankSum=-0.258;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K548|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,18:40:99:582,0,750 -chr1 138221 . G A 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=49;Dels=0.00;FS=4.125;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=-4.650;QD=14.73;ReadPosRankSum=1.474;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K565|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,24:49:99:750,0,740 -chr1 138281 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.653;DP=47;Dels=0.00;FS=8.620;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-4.611;QD=12.82;ReadPosRankSum=0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T585|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,21:47:99:631,0,882 -chr1 138362 . T C 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.377;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-3.648;QD=16.45;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A612|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:719,0,680 -chr1 138386 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.181;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.153;QD=15.48;ReadPosRankSum=0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F620|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,20:43:99:694,0,739 -chr1 138609 . G A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.214;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-4.884;QD=12.04;ReadPosRankSum=0.573;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E695K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,24:50:99:630,0,897 -chr1 138660 . C A 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=0;MQRankSum=4.417;QD=18.88;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1010,0,467 -chr1 138683 . G T 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;DP=56;Dels=0.00;FS=2.284;HaplotypeScore=2.8620;MLEAC=1;MLEAF=0.500;MQ=46.57;MQ0=0;MQRankSum=-4.417;QD=10.00;ReadPosRankSum=-2.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:588,0,1019 -chr1 138698 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=58;Dels=0.00;FS=2.144;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-3.995;QD=10.77;ReadPosRankSum=-1.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:653,0,1080 -chr1 138718 . T C 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=53;Dels=0.00;FS=5.608;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=0;MQRankSum=-4.422;QD=13.60;ReadPosRankSum=-0.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:749,0,948 -chr1 138736 . T C 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=50;Dels=0.00;FS=10.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=-4.540;QD=16.34;ReadPosRankSum=-0.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:845,0,811 -chr1 138777 . T A 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.575;DP=53;Dels=0.00;FS=2.347;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=0;MQRankSum=-4.937;QD=16.24;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:889,0,952 -chr1 138922 . A T 728.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417;DP=57;Dels=0.00;FS=1.039;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=1;MQRankSum=-0.363;QD=12.79;ReadPosRankSum=-1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:757,0,1026 -chr1 138982 . C A 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.642;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=1;MQRankSum=0.793;QD=17.38;ReadPosRankSum=0.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1036,0,849 -chr1 139024 . A T 1024.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=56;Dels=0.00;FS=5.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.72;MQ0=0;MQRankSum=-1.928;QD=18.30;ReadPosRankSum=0.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1053,0,858 -chr1 139066 . A G 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-3.328;QD=16.55;ReadPosRankSum=-0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:988,0,1020 -chr1 139093 . A G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=47;Dels=0.00;FS=4.452;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=-4.267;QD=16.85;ReadPosRankSum=-1.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:820,0,809 -chr1 139143 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=38;Dels=0.00;FS=2.742;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-4.926;QD=17.57;ReadPosRankSum=1.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:696,0,605 -chr1 139149 . A G 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=38;Dels=0.00;FS=2.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.61;MQ0=0;MQRankSum=-4.932;QD=18.23;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,21:38:99:721,0,567 -chr1 139163 . C T 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.156;QD=14.30;ReadPosRankSum=1.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:586,0,689 -chr1 139224 . A G 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=58;Dels=0.00;FS=3.833;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.755;QD=12.22;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:737,0,1030 -chr1 139254 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=60;Dels=0.00;FS=3.815;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.339;QD=14.35;ReadPosRankSum=-0.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:889,0,1036 -chr1 139269 . A G 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=58;Dels=0.00;FS=1.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-4.651;QD=14.17;ReadPosRankSum=0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:850,0,1089 -chr1 139286 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.863;DP=56;Dels=0.00;FS=3.856;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.836;QD=15.19;ReadPosRankSum=0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:879,0,1015 -chr1 139341 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=0;MQRankSum=-2.059;QD=15.48;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:725,0,819 -chr1 139358 . A T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.459;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.28;MQ0=0;MQRankSum=-2.238;QD=14.18;ReadPosRankSum=-0.694;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:737,0,962 -chr1 139417 . A C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.696;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.263;QD=8.24;ReadPosRankSum=-1.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:440,0,1164 -chr1 139435 . T G 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.343;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.55;MQ0=0;MQRankSum=-5.052;QD=4.45;ReadPosRankSum=0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:255,0,1407 -chr1 139441 . G A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.092;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=0;MQRankSum=-5.283;QD=5.05;ReadPosRankSum=0.845;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,13:52:99:291,0,1353 -chr1 139480 . A G 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-4.475;QD=2.29;ReadPosRankSum=1.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,9:47:99:136,0,1324 -chr1 139483 . T C 1251.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=5.087;QD=25.04;ReadPosRankSum=0.863;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1280,0,278 -chr1 139488 . T A 312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.71;MQ0=0;MQRankSum=-5.373;QD=6.01;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:341,0,1293 -chr1 139495 . G T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=50;Dels=0.00;FS=1.248;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=-5.314;QD=6.36;ReadPosRankSum=-1.207;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,1235 -chr1 139501 . T G 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.434;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.62;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:326,0,1098 -chr1 139502 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.066;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.55;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:323,0,1098 -chr1 139534 . T C 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=0;MQRankSum=-5.026;QD=15.83;ReadPosRankSum=-0.795;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,24:43:99:709,0,616 -chr1 139556 . A G 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=5.120;QD=12.09;ReadPosRankSum=-2.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:560,0,740 -chr1 139563 . T C 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-5.014;QD=18.81;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:856,0,472 -chr1 139576 . C A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.257;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=19.9086;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-4.247;QD=21.52;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:846,0,350 -chr1 139610 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=8.3569;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=-4.699;QD=13.06;ReadPosRankSum=-1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:603,0,686 -chr1 139650 . C A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=0;MQRankSum=-3.849;QD=15.37;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:720,0,755 -chr1 139700 . T C 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.796;DP=42;Dels=0.00;FS=2.709;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=1;MQRankSum=-4.603;QD=15.66;ReadPosRankSum=-0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:686,0,746 -chr1 139730 . T C 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;DP=44;Dels=0.00;FS=2.648;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.08;MQ0=1;MQRankSum=-5.150;QD=13.86;ReadPosRankSum=0.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:638,0,806 -chr1 139736 . A G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=47;Dels=0.00;FS=4.288;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=1;MQRankSum=-4.921;QD=13.97;ReadPosRankSum=-0.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:685,0,804 -chr1 139754 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=44;Dels=0.00;FS=9.774;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=1;MQRankSum=-5.101;QD=14.49;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:666,0,663 -chr1 139766 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.920;DP=47;Dels=0.00;FS=19.585;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=2;MQRankSum=-4.394;QD=11.61;ReadPosRankSum=0.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:574,0,790 -chr1 139816 . T A 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=40;Dels=0.00;FS=36.168;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.812;QD=18.44;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:766,0,353 -chr1 139888 . A G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.061;DP=34;Dels=0.00;FS=8.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.243;QD=5.49;ReadPosRankSum=-1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,8:34:99:215,0,931 -chr1 142437 . C T 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.548;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=-4.440;QD=13.66;ReadPosRankSum=-4.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:397,0,497 -chr1 142438 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=4.392;QD=16.73;ReadPosRankSum=4.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:480,0,389 -chr1 142776 . G A 1396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=67;Dels=0.00;FS=3.384;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.34;MQ0=0;MQRankSum=-3.183;QD=20.85;ReadPosRankSum=1.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,42:67:99:1425,0,774 -chr1 142821 . T A 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.014;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=43.83;MQ0=0;MQRankSum=-1.966;QD=20.30;ReadPosRankSum=-0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1287,0,713 -chr1 142863 . G A 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=51;Dels=0.00;FS=2.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.90;MQ0=0;MQRankSum=-0.161;QD=16.58;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:874,0,753 -chr1 142891 . A T 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=2.468;QD=17.49;ReadPosRankSum=-0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:955,0,777 -chr1 142898 . A G 956.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=0.197;QD=17.09;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,29:56:99:985,0,879 -chr1 142936 . A C 1403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=77;Dels=0.00;FS=0.875;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.936;QD=18.23;ReadPosRankSum=-0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,42:77:99:1432,0,1097 -chr1 142944 . T C 1485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.608;DP=75;Dels=0.00;FS=1.980;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.683;QD=19.81;ReadPosRankSum=-1.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,44:75:99:1514,0,922 -chr1 142972 . C T 1381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=75;Dels=0.00;FS=0.882;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.585;QD=18.42;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,42:75:99:1410,0,1088 -chr1 143047 . G C 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=57;Dels=0.00;FS=5.471;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=2;MQRankSum=-0.379;QD=14.84;ReadPosRankSum=0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:874,0,913 -chr1 143077 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=43;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.876;QD=14.32;ReadPosRankSum=-0.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:644,0,718 -chr1 143079 . T A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=44;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=1;MQRankSum=-1.497;QD=13.54;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:624,0,799 -chr1 143101 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.221;DP=58;Dels=0.00;FS=5.324;HaplotypeScore=5.2545;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.582;QD=15.00;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,28:58:99:898,0,920 -chr1 143121 . C T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.297;DP=78;Dels=0.00;FS=16.462;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-4.301;QD=1.05;ReadPosRankSum=-3.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:69,9:78:99:110,0,2263 -chr1 143129 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=82;Dels=0.00;FS=21.866;HaplotypeScore=20.8424;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-4.844;QD=1.53;ReadPosRankSum=-2.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,11:82:99:154,0,2388 -chr1 143138 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=85;Dels=0.00;FS=19.743;HaplotypeScore=26.7703;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.325;QD=10.00;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:51,34:85:99:878,0,1589 -chr1 143140 . C T 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=85;Dels=0.00;FS=27.442;HaplotypeScore=15.7969;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-4.591;QD=3.11;ReadPosRankSum=-1.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,14:85:99:293,0,2284 -chr1 143161 . G A 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=78;Dels=0.00;FS=0.906;HaplotypeScore=32.9944;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=1.886;QD=11.66;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:938,0,1383 -chr1 143163 . C A 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=33.0925;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.100;QD=10.32;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,31:78:99:833,0,1525 -chr1 143164 . G T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.056;DP=79;Dels=0.00;FS=32.060;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-4.706;QD=4.33;ReadPosRankSum=2.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:370,0,2093 -chr1 143165 . G A 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=79;Dels=0.00;FS=28.863;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-3.856;QD=3.93;ReadPosRankSum=2.881;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:339,0,2068 -chr1 143178 . C A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.003;DP=76;Dels=0.00;FS=33.120;HaplotypeScore=44.4775;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=-4.295;QD=4.14;ReadPosRankSum=3.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:62,14:76:99:343,0,1910 -chr1 143221 . A T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.319;DP=63;Dels=0.00;FS=19.029;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=2;MQRankSum=-2.568;QD=1.30;ReadPosRankSum=-0.916;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,9:63:99:110,0,1876 -chr1 143376 . C G 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=51;Dels=0.00;FS=6.452;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=6;MQRankSum=2.251;QD=20.51;ReadPosRankSum=-0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1074,0,461 -chr1 143406 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=55;Dels=0.00;FS=3.966;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=2;MQRankSum=-1.903;QD=13.47;ReadPosRankSum=0.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:769,0,1020 -chr1 143414 . A G 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=56;Dels=0.00;FS=5.804;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-0.572;QD=12.89;ReadPosRankSum=1.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:750,0,1015 -chr1 143459 . G T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.432;DP=56;Dels=0.00;FS=5.668;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=2;MQRankSum=1.522;QD=11.17;ReadPosRankSum=0.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:654,0,1069 -chr1 143490 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-1.155;QD=11.50;ReadPosRankSum=0.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:649,0,1103 -chr1 143531 . G A 1174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=61;Dels=0.00;FS=2.178;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.591;QD=19.26;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,35:61:99:1203,0,835 -chr1 143603 . C T 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-1.269;QD=15.61;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:918,0,950 -chr1 143650 . T C 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.267;QD=17.93;ReadPosRankSum=1.209;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:871,0,713 -chr1 143705 . G A 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.934;DP=50;Dels=0.00;FS=10.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=1.538;QD=15.12;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:784,0,957 -chr1 143726 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=51;Dels=0.00;FS=4.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=0.349;QD=15.19;ReadPosRankSum=-1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:803,0,907 -chr1 143837 . A G 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.74;MQ0=0;MQRankSum=-3.207;QD=15.49;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:880,0,915 -chr1 143843 . G T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.62;MQ0=0;MQRankSum=-2.653;QD=15.86;ReadPosRankSum=1.953;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,954 -chr1 143851 . A T 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=55;Dels=0.00;FS=2.282;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=0;MQRankSum=-2.639;QD=17.25;ReadPosRankSum=0.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:977,0,823 -chr1 143867 . T A 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.451;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-2.076;QD=17.19;ReadPosRankSum=-0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1111,0,885 -chr1 143879 . A C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=66;Dels=0.00;FS=0.942;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.64;MQ0=0;MQRankSum=-1.603;QD=16.06;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,36:66:99:1088,0,1011 -chr1 143887 . C G 1133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=70;Dels=0.00;FS=0.918;HaplotypeScore=4.7286;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-0.633;QD=16.20;ReadPosRankSum=-1.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,38:70:99:1162,0,1037 -chr1 143960 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=49;Dels=0.00;FS=2.555;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.728;QD=12.06;ReadPosRankSum=-0.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:619,0,1001 -chr1 144130 . G A 1136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=62;Dels=0.00;FS=5.270;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.014;QD=18.33;ReadPosRankSum=-1.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1165,0,864 -chr1 144149 . G A 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=1.013;QD=17.25;ReadPosRankSum=-1.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1029,0,881 -chr1 144222 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.87;MQ0=0;MQRankSum=-2.776;QD=15.38;ReadPosRankSum=-0.729;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R143|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:859,0,804 -chr1 144255 . A G 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=54;Dels=0.00;FS=10.821;HaplotypeScore=2.7619;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=-5.069;QD=15.64;ReadPosRankSum=1.367;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T132|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:873,0,825 -chr1 144286 . C G 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=45;Dels=0.00;FS=1.238;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=-5.256;QD=15.22;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G122A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:713,0,730 -chr1 144294 . T A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.317;QD=16.47;ReadPosRankSum=0.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E119D|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:786,0,731 -chr1 144318 . G T 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=40;Dels=0.00;FS=5.217;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQ0=0;MQRankSum=-5.240;QD=14.62;ReadPosRankSum=-1.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R111|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:613,0,598 -chr1 144319 . C T 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=40;Dels=0.00;FS=2.910;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-5.180;QD=14.67;ReadPosRankSum=-1.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R111H|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:615,0,628 -chr1 144346 . G C 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-4.374;QD=17.19;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T102S|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:802,0,630 -chr1 144351 . A C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-4.499;QD=15.33;ReadPosRankSum=1.692;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P100|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:764,0,687 -chr1 144382 . T G 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=53;Dels=0.00;FS=2.371;HaplotypeScore=4.8928;MLEAC=1;MLEAF=0.500;MQ=56.28;MQ0=0;MQRankSum=-2.346;QD=14.58;ReadPosRankSum=2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D90A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:53:99:801,0,829 -chr1 144385 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.198;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=6.8884;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-2.125;QD=15.05;ReadPosRankSum=2.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D89G|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:811,0,831 -chr1 144434 . T A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=55;Dels=0.00;FS=1.039;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.232;QD=12.49;ReadPosRankSum=-0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N73Y|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:715,0,1146 -chr1 144525 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.856;QD=18.21;ReadPosRankSum=-0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R42|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:629,0,394 -chr1 144561 . C G 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.186;QD=18.71;ReadPosRankSum=1.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R30|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:758,0,482 -chr1 144564 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.541;QD=19.10;ReadPosRankSum=0.943;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q29|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:735,0,466 -chr1 144606 . G C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.165;DP=54;Dels=0.00;FS=2.347;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.276;QD=16.09;ReadPosRankSum=-0.898;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S15|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,27:54:99:897,0,877 -chr1 144686 . T C 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=54;Dels=0.00;FS=1.047;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.788;QD=16.87;ReadPosRankSum=-1.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:26,28:54:99:939,0,867 -chr1 144759 . C G 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.336;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.833;QD=14.26;ReadPosRankSum=1.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:20,18:38:99:570,0,686 -chr1 144778 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=-1.949;QD=17.02;ReadPosRankSum=-1.535;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),START_GAINED(LOW||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:607,0,531 -chr1 144839 . C T 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-3.678;QD=8.56;ReadPosRankSum=-2.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:24,11:35:99:328,0,819 -chr1 144909 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=44;Dels=0.00;FS=4.590;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=0.603;QD=20.77;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:942,0,494 -chr1 144934 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=38;Dels=0.00;FS=17.088;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.893;QD=21.31;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:838,0,442 -chr1 144950 . G A 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=38;Dels=0.00;FS=11.386;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.801;QD=22.23;ReadPosRankSum=0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,25:38:99:873,0,375 -chr1 144960 . A G 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=31;Dels=0.00;FS=13.484;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=0.675;QD=23.61;ReadPosRankSum=-0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:760,0,270 -chr1 144980 . T G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.632;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.879;QD=10.70;ReadPosRankSum=-0.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:317,0,537 -chr1 145002 . C G 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.427;QD=8.92;ReadPosRankSum=0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:269,0,580 -chr1 145030 . C T 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=27;Dels=0.00;FS=7.832;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-0.704;QD=15.14;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:437,0,486 -chr1 145051 . C T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=26;Dels=0.00;FS=10.770;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-0.571;QD=19.38;ReadPosRankSum=-1.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:532,0,376 -chr1 145056 . T C 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=25;Dels=0.00;FS=10.578;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.248;QD=12.11;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:331,0,511 -chr1 145137 . A G 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=17.5729;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-3.783;QD=5.84;ReadPosRankSum=-3.420;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,7:26:99:180,0,645 -chr1 145196 . A T 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=31;Dels=0.00;FS=4.262;HaplotypeScore=15.6286;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=3;MQRankSum=-2.370;QD=20.54;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,19:31:99:665,0,196 -chr1 145230 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=40;Dels=0.00;FS=9.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=2;MQRankSum=1.303;QD=8.29;ReadPosRankSum=2.151;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:360,0,901 -chr1 145381 . T C 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.906;DP=37;Dels=0.03;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=1;MQRankSum=0.283;QD=22.64;ReadPosRankSum=-0.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,27:36:99:866,0,203 -chr1 145385 . A T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-0.159;QD=5.89;ReadPosRankSum=0.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,9:38:99:252,0,952 -chr1 145429 . C T 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=33;Dels=0.00;FS=4.709;HaplotypeScore=14.4456;MLEAC=1;MLEAF=0.500;MQ=53.98;MQ0=1;MQRankSum=-2.077;QD=14.17;ReadPosRankSum=1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:496,0,578 -chr1 145442 . C T 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.854;DP=28;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=1;MQRankSum=2.415;QD=17.49;ReadPosRankSum=-2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,16:28:99:518,0,409 -chr1 145509 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=1.970;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.472;QD=23.26;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:633,0,240 -chr1 145512 . C T 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.259;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.711;QD=9.29;ReadPosRankSum=-1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:242,0,524 -chr1 145513 . G A 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.226;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-1.904;QD=20.90;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:509,0,246 -chr1 145515 . G A 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.013;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.126;QD=10.13;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:251,0,503 -chr1 145531 . A G 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.177;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.288;QD=17.10;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,10:18:99:336,0,240 -chr1 145534 . C T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=2.518;QD=11.41;ReadPosRankSum=2.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,8:19:99:245,0,339 -chr1 145538 . T C 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.376;QD=16.92;ReadPosRankSum=-2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:299,0,219 -chr1 145544 . T C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=1.134;QD=11.81;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:99:170,0,230 -chr1 145555 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.470;QD=12.78;ReadPosRankSum=-2.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,5:10:99:156,0,173 -chr1 145654 . T C 490.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=1;MQRankSum=-2.198;QD=15.83;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:519,0,451 -chr1 145666 . G A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=33;Dels=0.00;FS=1.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.78;MQ0=2;MQRankSum=-1.364;QD=13.72;ReadPosRankSum=1.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:481,0,521 -chr1 145673 . T C 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=35;Dels=0.00;FS=1.624;HaplotypeScore=15.4641;MLEAC=1;MLEAF=0.500;MQ=52.28;MQ0=2;MQRankSum=0.955;QD=13.76;ReadPosRankSum=-0.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:510,0,570 -chr1 145676 . A G 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.570;DP=36;Dels=0.00;FS=1.666;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=2;MQRankSum=0.707;QD=13.02;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:497,0,607 -chr1 145688 . A G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.302;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=-0.944;QD=15.17;ReadPosRankSum=-0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:544,0,419 -chr1 145689 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=1.171;QD=11.67;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:425,0,541 -chr1 145783 . G A 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=19;Dels=0.00;FS=2.199;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.549;QD=19.15;ReadPosRankSum=2.409;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:392,0,216 -chr1 145926 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.984;DP=43;Dels=0.00;FS=1.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=2.423;QD=15.23;ReadPosRankSum=0.621;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:683,0,719 -chr1 145928 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=41;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-0.745;QD=16.12;ReadPosRankSum=-0.588;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:689,0,634 -chr1 145949 . T C 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.879;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.907;QD=16.95;ReadPosRankSum=0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:791,0,650 -chr1 145957 . T C 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-2.937;QD=19.86;ReadPosRankSum=0.461;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:942,0,588 -chr1 145961 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=47;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=-3.067;QD=19.74;ReadPosRankSum=1.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:956,0,621 -chr1 145991 . T C 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=40;Dels=0.00;FS=2.157;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-0.969;QD=31.44;ReadPosRankSum=2.998;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,36:40:39:1286,0,39 -chr1 146053 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=42;Dels=0.00;FS=1.216;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.654;QD=14.85;ReadPosRankSum=-1.484;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:652,0,659 -chr1 146141 . G C 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.379;QD=16.12;ReadPosRankSum=0.093;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:915,0,948 -chr1 146183 . C T 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=61;Dels=0.00;FS=13.794;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=0.166;QD=14.73;ReadPosRankSum=1.165;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:927,0,1096 -chr1 146259 . G A 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;DP=50;Dels=0.00;FS=1.112;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.160;QD=13.60;ReadPosRankSum=0.225;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:708,0,962 -chr1 146273 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=47;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=-0.672;QD=14.27;ReadPosRankSum=0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:699,0,859 -chr1 146296 . T C 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123;DP=51;Dels=0.00;FS=2.461;HaplotypeScore=1.7074;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.406;QD=13.64;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:724,0,886 -chr1 146334 . G A 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.744;DP=54;Dels=0.00;FS=15.099;HaplotypeScore=4.3788;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=0.234;QD=13.53;ReadPosRankSum=-0.892;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:759,0,888 -chr1 146352 . A C 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.498;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.008;QD=16.62;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:876,0,875 -chr1 146412 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.096;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.487;QD=17.29;ReadPosRankSum=-0.974;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:841,0,718 -chr1 146446 . G T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-3.670;QD=13.83;ReadPosRankSum=-0.730;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:706,0,869 -chr1 146451 . T C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.785;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-1.455;QD=13.94;ReadPosRankSum=-0.796;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:725,0,868 -chr1 146456 . G C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.9978;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-3.167;QD=10.90;ReadPosRankSum=0.452;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:44:99:508,0,846 -chr1 146467 . C T 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=55.70;MQ0=0;MQRankSum=-3.722;QD=12.56;ReadPosRankSum=-0.562;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:493,0,671 -chr1 146489 . T A 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=6.7989;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-3.721;QD=8.78;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:362,0,945 -chr1 146502 . C T 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.559;DP=40;Dels=0.00;FS=2.861;HaplotypeScore=82.1865;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.486;QD=11.52;ReadPosRankSum=2.989;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:489,0,888 -chr1 146626 . C A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=0.151;QD=9.56;ReadPosRankSum=-0.179;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:420,0,892 -chr1 146707 . A T 748.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=51.1918;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-0.045;QD=14.13;ReadPosRankSum=-0.846;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:777,0,951 -chr1 146722 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.569;DP=53;Dels=0.00;FS=2.427;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-0.514;QD=12.00;ReadPosRankSum=0.966;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:664,0,1073 -chr1 146734 . G A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.057;QD=8.69;ReadPosRankSum=2.226;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:489,0,1193 -chr1 146736 . C T 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.906;QD=9.05;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:508,0,1187 -chr1 146737 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.038;QD=9.15;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:513,0,1186 -chr1 146738 . G A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.005;QD=8.94;ReadPosRankSum=2.470;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:502,0,1205 -chr1 146751 . T C 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.546;DP=56;Dels=0.00;FS=8.313;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=2.036;QD=19.41;ReadPosRankSum=-0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1115,0,613 -chr1 146757 . T C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=54;Dels=0.00;FS=8.599;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=1;MQRankSum=-1.537;QD=11.00;ReadPosRankSum=-0.118;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:622,0,1058 -chr1 146765 . T C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=50;Dels=0.00;FS=2.814;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.67;MQ0=1;MQRankSum=-1.838;QD=9.12;ReadPosRankSum=0.011;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:484,0,1120 -chr1 146805 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.862;DP=39;Dels=0.00;FS=3.130;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=0.738;QD=8.51;ReadPosRankSum=0.585;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:360,0,832 -chr1 146811 . A T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860;DP=41;Dels=0.00;FS=1.258;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.246;QD=10.92;ReadPosRankSum=-0.821;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:476,0,771 -chr1 146917 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=34;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.919;QD=22.14;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,22:34:99:781,0,382 -chr1 146962 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.455;DP=33;Dels=0.00;FS=8.473;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.387;QD=12.14;ReadPosRankSum=-0.387;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:429,0,656 -chr1 147074 . G A 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=4.7802;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=1;MQRankSum=2.617;QD=5.25;ReadPosRankSum=-1.880;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:149,0,214 -chr1 147113 . A C 82.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=27.3842;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=3;MQRankSum=1.937;QD=2.30;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,6:36:99:111,0,296 -chr1 147139 . G A 323.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.091;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=16.6145;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=11;MQRankSum=2.940;QD=6.11;ReadPosRankSum=1.127;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:53:99:352,0,249 -chr1 147150 . T G 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=10.0978;MLEAC=1;MLEAF=0.500;MQ=26.62;MQ0=11;MQRankSum=-1.429;QD=2.04;ReadPosRankSum=-1.554;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:128,0,456 -chr1 147170 . G A 326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=42.8592;MLEAC=1;MLEAF=0.500;MQ=26.42;MQ0=13;MQRankSum=3.898;QD=6.95;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,13:47:99:355,0,181 -chr1 147223 . T C 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=20.60;MQ0=4;MQRankSum=-2.013;QD=3.22;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:112,0,126 -chr1 147226 . G C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.109;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=1.702;QD=2.41;ReadPosRankSum=1.702;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,8:24:86:86,0,115 -chr1 147243 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=22.90;MQ0=2;MQRankSum=0.755;QD=3.39;ReadPosRankSum=1.200;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,8:20:96:96,0,131 -chr1 147246 . A T 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.236;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=24.50;MQ0=1;MQRankSum=1.559;QD=2.56;ReadPosRankSum=-2.126;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,4:21:82:82,0,176 -chr1 147272 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=16;Dels=0.00;FS=3.522;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=31.58;MQ0=1;MQRankSum=2.298;QD=9.11;ReadPosRankSum=-2.062;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,6:16:99:174,0,100 -chr1 147296 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=18;Dels=0.00;FS=7.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=3.532;QD=16.93;ReadPosRankSum=-0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:51:333,0,51 -chr1 147357 . A T 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=30;Dels=0.00;FS=28.709;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.13;MQ0=6;MQRankSum=-3.766;QD=4.79;ReadPosRankSum=-1.133;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,14:30:99:172,0,529 -chr1 147416 . T C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=10;Dels=0.00;FS=15.441;HaplotypeScore=26.0957;MLEAC=1;MLEAF=0.500;MQ=30.35;MQ0=3;MQRankSum=-1.754;QD=3.98;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,4:10:68:68,0,134 -chr1 147424 . A G 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=8;Dels=0.00;FS=11.761;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=30.85;MQ0=2;MQRankSum=1.380;QD=13.85;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,4:8:31:139,0,31 -chr1 147440 . C T 145.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=2;MQRankSum=2.219;QD=13.27;ReadPosRankSum=-0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,5:11:5:173,0,5 -chr1 147461 . G A 174.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=8.9694;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=2;MQRankSum=3.016;QD=11.65;ReadPosRankSum=-1.493;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,6:15:24:203,0,24 -chr1 147474 . C T 286.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=10.9207;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=2;MQRankSum=3.281;QD=15.94;ReadPosRankSum=-2.752;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:15:315,0,15 -chr1 147490 . G A 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=23;Dels=0.00;FS=3.834;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=2.760;QD=12.95;ReadPosRankSum=3.318;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:326,0,430 -chr1 147522 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=30;Dels=0.00;FS=1.449;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.65;MQ0=0;MQRankSum=-3.516;QD=17.83;ReadPosRankSum=-0.963;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:563,0,394 -chr1 147529 . T C 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.492;DP=27;Dels=0.00;FS=1.598;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=3.380;QD=12.77;ReadPosRankSum=0.962;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,11:27:99:373,0,495 -chr1 147542 . C T 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=33;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.17;MQ0=0;MQRankSum=-2.900;QD=17.30;ReadPosRankSum=-0.234;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:599,0,528 -chr1 147543 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=34;Dels=0.00;FS=3.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=0;MQRankSum=-1.639;QD=17.52;ReadPosRankSum=-0.535;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:624,0,489 -chr1 147546 . G A 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=35;Dels=0.00;FS=3.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.560;QD=12.42;ReadPosRankSum=0.248;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:463,0,624 -chr1 147575 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=4.613;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-2.836;QD=20.26;ReadPosRankSum=-0.194;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:879,0,470 -chr1 147578 . A C 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=2.964;QD=10.43;ReadPosRankSum=0.744;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:456,0,851 -chr1 147591 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=35;Dels=0.00;FS=1.344;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-2.317;QD=18.31;ReadPosRankSum=0.850;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:669,0,479 -chr1 147598 . G A 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=33;Dels=0.00;FS=5.093;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-2.045;QD=19.33;ReadPosRankSum=0.166;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:666,0,407 -chr1 147636 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.792;DP=26;Dels=0.00;FS=1.796;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.40;MQ0=0;MQRankSum=-2.081;QD=23.18;ReadPosRankSum=1.272;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,19:26:99:631,0,203 -chr1 147641 . T A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.241;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=0;MQRankSum=-1.623;QD=24.39;ReadPosRankSum=1.241;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,19:25:99:638,0,170 -chr1 147665 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.781;DP=31;Dels=0.00;FS=11.051;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.68;MQ0=0;MQRankSum=2.182;QD=11.86;ReadPosRankSum=-1.741;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:396,0,590 -chr1 147671 . C T 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=30;Dels=0.00;FS=8.496;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-1.517;QD=15.93;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:506,0,416 -chr1 147698 . T C 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=29;Dels=0.00;FS=11.831;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.240;QD=15.47;ReadPosRankSum=-2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:477,0,517 -chr1 147730 . T C 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=24.449;HaplotypeScore=2.5770;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.345;QD=13.02;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:523,0,753 -chr1 147815 . G A 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.116;DP=38;Dels=0.00;FS=5.625;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.779;QD=10.52;ReadPosRankSum=1.129;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S6N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:428,0,860 -chr1 147816 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=38;Dels=0.00;FS=5.221;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.154;QD=10.44;ReadPosRankSum=1.292;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S6|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:425,0,850 -chr1 147861 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-2.322;QD=18.06;ReadPosRankSum=-0.782;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S21|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:823,0,602 -chr1 147863 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.540;QD=18.84;ReadPosRankSum=-0.782;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S22T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:857,0,597 -chr1 147893 . A C 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=28;Dels=0.00;FS=12.411;HaplotypeScore=17.4716;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.534;QD=13.31;ReadPosRankSum=1.694;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y32S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:401,0,517 -chr1 147940 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992;DP=60;Dels=0.00;FS=5.651;HaplotypeScore=4.9890;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=1;MQRankSum=2.013;QD=2.28;ReadPosRankSum=0.601;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E48K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,9:60:99:165,0,1548 -chr1 147980 . T C 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=60;Dels=0.00;FS=2.594;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=1;MQRankSum=-5.013;QD=5.68;ReadPosRankSum=2.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L61S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:369,0,1413 -chr1 148008 . T G 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.047;DP=70;Dels=0.00;FS=5.868;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-4.821;QD=6.14;ReadPosRankSum=0.000;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T70|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:458,0,1746 -chr1 148023 . G A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=65;Dels=0.00;FS=8.565;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-4.083;QD=6.41;ReadPosRankSum=0.082;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V75|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:445,0,1615 -chr1 148028 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=60;Dels=0.00;FS=14.560;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.07;MQ0=0;MQRankSum=-4.165;QD=5.43;ReadPosRankSum=0.768;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S77L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,15:60:99:354,0,1522 -chr1 148029 . G A 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=57;Dels=0.00;FS=9.963;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-2.445;QD=5.21;ReadPosRankSum=1.708;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S77|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:43,13:57:99:325,0,1421 -chr1 148050 . T C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=2.073;QD=10.00;ReadPosRankSum=-0.265;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I84|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:678,0,1415 -chr1 148077 . T G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.434;DP=53;Dels=0.00;FS=12.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-4.267;QD=7.07;ReadPosRankSum=0.313;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H93Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,14:53:99:403,0,1389 -chr1 148078 . C A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.438;DP=54;Dels=0.00;FS=12.716;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=-4.017;QD=6.61;ReadPosRankSum=0.365;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P94T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,14:54:99:385,0,1444 -chr1 148095 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=44;Dels=0.00;FS=14.379;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.117;QD=6.61;ReadPosRankSum=1.003;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A99|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:319,0,1163 -chr1 148104 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=48;Dels=0.00;FS=16.904;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-4.176;QD=7.10;ReadPosRankSum=-0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A102|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,13:48:99:369,0,1201 -chr1 148117 . T C 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=50;Dels=0.00;FS=18.397;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=-3.965;QD=4.16;ReadPosRankSum=1.152;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S107P|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,10:50:99:236,0,1399 -chr1 148124 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=49;Dels=0.00;FS=20.451;HaplotypeScore=1.8499;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.155;QD=3.73;ReadPosRankSum=0.409;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T109I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:211,0,1394 -chr1 148128 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=48;Dels=0.00;FS=20.451;HaplotypeScore=45.3427;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-4.649;QD=3.72;ReadPosRankSum=0.608;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A110|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,9:48:99:207,0,1389 -chr1 148133 . A G 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=46;Dels=0.00;FS=20.653;HaplotypeScore=118.8295;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-4.624;QD=3.82;ReadPosRankSum=-0.194;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D112G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,9:46:99:204,0,1210 -chr1 148165 . C G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=43;Dels=0.00;FS=1.213;HaplotypeScore=4.9810;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.859;QD=11.99;ReadPosRankSum=-1.096;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P123A|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:544,0,806 -chr1 148218 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.156;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=0.826;QD=13.38;ReadPosRankSum=0.216;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S140|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:590,0,747 -chr1 148366 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=46;Dels=0.00;FS=2.594;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=1;MQRankSum=0.742;QD=18.06;ReadPosRankSum=0.811;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:859,0,635 -chr1 148435 . A C 1097.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=54;Dels=0.00;FS=9.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.801;QD=20.33;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,32:54:99:1126,0,692 -chr1 148463 . A G 1201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268;DP=54;Dels=0.00;FS=1.155;HaplotypeScore=28.9952;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.199;QD=22.25;ReadPosRankSum=0.507;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,35:54:99:1230,0,586 -chr1 148468 . A G 1266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.651;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=15.2316;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.761;QD=23.46;ReadPosRankSum=0.615;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,36:54:99:1295,0,544 -chr1 148595 . C T 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.094;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.341;QD=12.88;ReadPosRankSum=-0.048;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:685,0,1002 -chr1 148617 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.242;DP=50;Dels=0.00;FS=1.142;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.203;QD=15.00;ReadPosRankSum=-1.901;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:778,0,841 -chr1 148704 . G C 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.330;QD=17.33;ReadPosRankSum=-0.481;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,798 -chr1 148761 . A T 1165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.413;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.244;QD=17.66;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1194,0,997 -chr1 148794 . T C 1570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.757;DP=84;Dels=0.00;FS=0.829;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.198;QD=18.70;ReadPosRankSum=-0.117;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,47:84:99:1599,0,1205 -chr1 148795 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=81;Dels=0.00;FS=0.833;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.043;QD=14.77;ReadPosRankSum=-0.327;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:44,37:81:99:1225,0,1499 -chr1 148840 . T A 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.283;DP=67;Dels=0.00;FS=6.538;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.018;QD=15.13;ReadPosRankSum=0.094;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1042,0,1215 -chr1 148975 . A T 1278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=70;Dels=0.00;FS=2.050;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.446;QD=18.27;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1307,0,1024 -chr1 149029 . T C 1230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=64;Dels=0.00;FS=7.922;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=4;MQRankSum=-3.991;QD=19.23;ReadPosRankSum=0.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,40:64:99:1259,0,799 -chr1 149049 . C T 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=53;Dels=0.00;FS=4.125;HaplotypeScore=3.9326;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.050;QD=15.88;ReadPosRankSum=0.650;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:870,0,827 -chr1 149054 . T A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.693;DP=53;Dels=0.00;FS=1.097;HaplotypeScore=2.9329;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.556;QD=14.32;ReadPosRankSum=1.012;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:787,0,898 -chr1 149065 . C T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.38;MQ0=4;MQRankSum=3.705;QD=16.74;ReadPosRankSum=-1.056;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:748,0,583 -chr1 149083 . G A 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=1.535;QD=16.43;ReadPosRankSum=1.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:636,0,597 -chr1 149099 . C T 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.884;DP=40;Dels=0.00;FS=2.794;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-0.095;QD=14.47;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,754 -chr1 149156 . G A 46.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;DP=52;Dels=0.00;FS=6.760;HaplotypeScore=3.3564;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.965;QD=0.90;ReadPosRankSum=-3.566;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R158|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,7:52:75:75,0,1569 -chr1 149174 . A G 793.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.409;DP=60;Dels=0.00;FS=14.447;HaplotypeScore=10.5956;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.030;QD=13.23;ReadPosRankSum=0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P164|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:822,0,1037 -chr1 149224 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=47;Dels=0.00;FS=19.146;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.421;QD=14.51;ReadPosRankSum=-0.769;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I181T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,21:47:99:710,0,673 -chr1 149225 . C G 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=47;Dels=0.00;FS=6.565;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.526;QD=1.55;ReadPosRankSum=1.164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I181M|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:101,0,1493 -chr1 149237 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=43;Dels=0.00;FS=4.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.284;QD=0.81;ReadPosRankSum=1.118;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L185|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:38,5:43:63:63,0,1390 -chr1 149279 . G A 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.121;DP=34;Dels=0.00;FS=8.198;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;QD=14.85;ReadPosRankSum=0.155;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S199|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:533,0,627 -chr1 149379 . T C 993.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.329;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=2.8936;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.187;QD=20.28;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:1022,0,551 -chr1 149421 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.477;DP=43;Dels=0.00;FS=1.218;HaplotypeScore=3.8299;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.086;QD=13.09;ReadPosRankSum=0.037;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,836 -chr1 149472 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.074;QD=12.76;ReadPosRankSum=-0.015;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:513,0,690 -chr1 149514 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.243;QD=12.10;ReadPosRankSum=1.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:464,0,734 -chr1 149713 . T G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=42;Dels=0.00;FS=1.480;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.750;QD=12.83;ReadPosRankSum=0.496;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:567,0,822 -chr1 149716 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.591;DP=44;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.177;QD=14.22;ReadPosRankSum=-0.365;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,836 -chr1 149737 . A G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.238;QD=16.15;ReadPosRankSum=1.192;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:755,0,792 -chr1 149745 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.697;QD=13.88;ReadPosRankSum=1.519;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:653,0,850 -chr1 149746 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.247;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.420;QD=13.21;ReadPosRankSum=1.732;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:649,0,910 -chr1 149780 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=33;Dels=0.00;FS=3.967;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.998;QD=11.84;ReadPosRankSum=-1.803;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,13:33:99:419,0,669 -chr1 149946 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.827;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=-1.482;QD=12.69;ReadPosRankSum=0.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:701,0,1128 -chr1 149962 . T C 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=50;Dels=0.00;FS=1.172;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.553;QD=10.14;ReadPosRankSum=-0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:535,0,1193 -chr1 150069 . A G 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-1.083;QD=17.49;ReadPosRankSum=0.217;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I248V|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:19,21:40:99:728,0,642 -chr1 150083 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=42;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=2.679;QD=14.76;ReadPosRankSum=0.859;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,802 -chr1 150236 . G A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.696;DP=55;Dels=0.00;FS=5.672;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.713;QD=12.12;ReadPosRankSum=0.850;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:695,0,1131 -chr1 150249 . C G 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.844;QD=13.76;ReadPosRankSum=2.150;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,24:55:99:785,0,958 -chr1 150265 . C T 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=57;Dels=0.00;FS=2.302;HaplotypeScore=2.8318;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.049;QD=11.47;ReadPosRankSum=2.072;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,22:57:99:682,0,1070 -chr1 150375 . T G 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.134;DP=48;Dels=0.00;FS=14.013;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.610;QD=14.87;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,881 -chr1 150494 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.680;DP=38;Dels=0.00;FS=1.849;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.182;QD=25.63;ReadPosRankSum=1.541;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,28:38:99:1002,0,268 -chr1 150499 . C A 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.340;DP=37;Dels=0.00;FS=1.885;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=1;MQRankSum=-0.698;QD=5.89;ReadPosRankSum=-1.378;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,10:37:99:246,0,955 -chr1 150581 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.334;DP=28;Dels=0.00;FS=7.346;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.220;QD=6.46;ReadPosRankSum=-0.318;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:209,0,766 -chr1 150838 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.568;DP=52;Dels=0.00;FS=6.106;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.029;QD=10.65;ReadPosRankSum=1.741;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:582,0,1173 -chr1 150953 . C A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.538;DP=60;Dels=0.00;FS=31.975;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.044;QD=16.33;ReadPosRankSum=-0.680;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1008,0,1004 -chr1 150957 . T C 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.859;DP=61;Dels=0.00;FS=31.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.888;QD=17.03;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1067,0,979 -chr1 151074 . A T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=1.9853;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.650;QD=16.10;ReadPosRankSum=-0.550;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:817,0,821 -chr1 151153 . T A 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=58;Dels=0.00;FS=7.584;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.355;QD=13.15;ReadPosRankSum=-0.087;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:791,0,1148 -chr1 151277 . G C 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.054;DP=35;Dels=0.00;FS=8.547;HaplotypeScore=3.9810;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.126;QD=9.39;ReadPosRankSum=0.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P284|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_151216_151324) GT:AD:DP:GQ:PL 0/1:22,12:35:99:357,0,750 -chr1 151351 . A G 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.257;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=5.9768;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.771;QD=21.17;ReadPosRankSum=-0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:1150,0,663 -chr1 151391 . T A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.522;DP=43;Dels=0.00;FS=1.286;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.140;QD=10.46;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,15:43:99:478,0,965 -chr1 151489 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=1.065;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.773;QD=17.41;ReadPosRankSum=-0.401;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:951,0,823 -chr1 151542 . C T 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.309;DP=63;Dels=0.00;FS=30.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.313;QD=17.04;ReadPosRankSum=-0.351;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1102,0,1065 -chr1 151610 . C A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.325;DP=59;Dels=0.00;FS=9.684;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.218;QD=14.40;ReadPosRankSum=1.356;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:878,0,1066 -chr1 151618 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=61;Dels=0.00;FS=5.239;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.094;QD=16.44;ReadPosRankSum=0.815;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,31:61:99:1031,0,1031 -chr1 151695 . T G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.206;DP=51;Dels=0.00;FS=1.161;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.688;QD=20.33;ReadPosRankSum=2.209;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1065,0,641 -chr1 151923 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=42;Dels=0.00;FS=6.816;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.225;QD=12.64;ReadPosRankSum=-0.225;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,17:42:99:559,0,782 -chr1 151972 . A G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.562;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.876;QD=17.48;ReadPosRankSum=-0.614;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:745,0,597 -chr1 152290 . A G 1160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=72;Dels=0.00;FS=4.729;HaplotypeScore=2.7880;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.788;QD=16.12;ReadPosRankSum=1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,35:72:99:1189,0,1208 -chr1 152381 . C A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.235;QD=10.50;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:595,0,1229 -chr1 152382 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.305;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.873;QD=10.07;ReadPosRankSum=-0.009;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:562,0,1258 -chr1 152658 . A T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=65;Dels=0.00;FS=3.385;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.165;QD=14.69;ReadPosRankSum=-0.574;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:983,0,1258 -chr1 152720 . A G 1186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.563;QD=18.84;ReadPosRankSum=0.826;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1215,0,861 -chr1 152741 . G T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=61;Dels=0.00;FS=3.616;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=0.365;QD=13.05;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:824,0,1171 -chr1 152755 . T C 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=55;Dels=0.00;FS=3.860;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=1;MQRankSum=2.481;QD=17.30;ReadPosRankSum=1.370;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:980,0,789 -chr1 153166 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=5.7547;MLEAC=1;MLEAF=0.500;MQ=18.57;MQ0=5;MQRankSum=1.137;QD=2.93;ReadPosRankSum=1.137;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,10:30:92:116,0,92 -chr1 153200 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=33;Dels=0.00;FS=3.979;HaplotypeScore=1.7046;MLEAC=1;MLEAF=0.500;MQ=15.76;MQ0=8;MQRankSum=0.670;QD=1.11;ReadPosRankSum=1.136;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,10:33:65:65,0,140 -chr1 153381 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=68;Dels=0.00;FS=15.911;HaplotypeScore=21.0001;MLEAC=1;MLEAF=0.500;MQ=12.66;MQ0=25;MQRankSum=0.041;QD=0.61;ReadPosRankSum=0.528;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,13:68:70:70,0,248 -chr1 153445 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=-0.451;QD=0.83;ReadPosRankSum=0.239;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,12:67:84:84,0,310 -chr1 153446 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.512;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=1.877;QD=0.65;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:59,8:67:72:72,0,323 -chr1 153476 . C T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=14.6632;MLEAC=1;MLEAF=0.500;MQ=16.01;MQ0=39;MQRankSum=1.279;QD=5.89;ReadPosRankSum=0.316;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,35:76:79:476,0,79 -chr1 153481 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=79;Dels=0.00;FS=2.335;HaplotypeScore=14.5114;MLEAC=1;MLEAF=0.500;MQ=15.99;MQ0=39;MQRankSum=0.178;QD=0.62;ReadPosRankSum=-0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:67,12:79:77:77,0,497 -chr1 153516 . G T 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.961;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=40;MQRankSum=1.294;QD=0.37;ReadPosRankSum=0.222;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,8:86:60:60,0,573 -chr1 153518 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=17.03;MQ0=39;MQRankSum=1.715;QD=0.41;ReadPosRankSum=-1.174;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,12:84:63:63,0,569 -chr1 153554 . T C 71.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.458;DP=51;Dels=0.00;FS=5.129;HaplotypeScore=5.7732;MLEAC=1;MLEAF=0.500;MQ=14.69;MQ0=20;MQRankSum=0.275;QD=1.41;ReadPosRankSum=-1.078;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,19:51:99:100,0,209 -chr1 153590 . T C 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=7.8158;MLEAC=1;MLEAF=0.500;MQ=13.34;MQ0=22;MQRankSum=0.750;QD=1.69;ReadPosRankSum=0.824;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,41:74:99:153,0,172 -chr1 153593 . T A 267.79 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=73;Dels=0.00;FS=12.430;HaplotypeScore=16.3870;MLEAC=1;MLEAF=0.500;MQ=13.50;MQ0=20;MQRankSum=-2.002;QD=3.67;ReadPosRankSum=0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,65:73:23:296,0,23 -chr1 153603 . C T 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.475;DP=131;Dels=0.00;FS=1.943;HaplotypeScore=7.3720;MLEAC=1;MLEAF=0.500;MQ=19.19;MQ0=28;MQRankSum=1.316;QD=3.97;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:83,47:131:99:548,0,748 -chr1 153634 . C T 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.160;DP=250;Dels=0.00;FS=8.821;HaplotypeScore=55.7961;MLEAC=1;MLEAF=0.500;MQ=21.90;MQ0=51;MQRankSum=-0.113;QD=0.76;ReadPosRankSum=2.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:217,33:250:99:218,0,3652 -chr1 153635 . A T 2861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.523;DP=250;Dels=0.00;FS=76.787;HaplotypeScore=57.8078;MLEAC=1;MLEAF=0.500;MQ=22.51;MQ0=49;MQRankSum=3.056;QD=11.45;ReadPosRankSum=2.693;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:101,149:250:99:2890,0,1044 -chr1 153682 . C T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=249;Dels=0.00;FS=4.305;HaplotypeScore=56.1815;MLEAC=1;MLEAF=0.500;MQ=24.41;MQ0=45;MQRankSum=2.445;QD=0.69;ReadPosRankSum=1.423;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,20:249:99:200,0,3583 -chr1 153722 . G A 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=245;Dels=0.00;FS=1.279;HaplotypeScore=60.2739;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=46;MQRankSum=2.339;QD=0.86;ReadPosRankSum=1.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:218,26:245:99:239,0,3144 -chr1 153768 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=106;Dels=0.00;FS=2.104;HaplotypeScore=3.8507;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=30;MQRankSum=-0.643;QD=1.08;ReadPosRankSum=0.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,30:106:99:143,0,668 -chr1 153796 . G A 1945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=209;Dels=0.00;FS=0.000;HaplotypeScore=23.0694;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=44;MQRankSum=4.401;QD=9.31;ReadPosRankSum=0.585;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:85,120:209:99:1974,0,350 -chr1 153928 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=177;Dels=0.00;FS=70.822;HaplotypeScore=49.5301;MLEAC=1;MLEAF=0.500;MQ=19.80;MQ0=52;MQRankSum=2.469;QD=0.32;ReadPosRankSum=1.151;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:165,11:177:84:84,0,1870 -chr1 153931 . G C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.672;DP=171;Dels=0.00;FS=63.103;HaplotypeScore=41.3083;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=50;MQRankSum=3.349;QD=7.01;ReadPosRankSum=-0.504;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:103,67:171:99:1227,0,745 -chr1 153947 . A G 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=117;Dels=0.00;FS=16.425;HaplotypeScore=22.7832;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=38;MQRankSum=2.093;QD=2.57;ReadPosRankSum=-1.715;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:97,20:117:99:329,0,946 -chr1 153962 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.029;DP=76;Dels=0.00;FS=28.843;HaplotypeScore=13.6296;MLEAC=1;MLEAF=0.500;MQ=17.52;MQ0=25;MQRankSum=3.039;QD=5.14;ReadPosRankSum=-2.479;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,22:76:99:419,0,279 -chr1 153982 . C G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=27;Dels=0.00;FS=10.000;HaplotypeScore=2.6670;MLEAC=1;MLEAF=0.500;MQ=11.06;MQ0=11;MQRankSum=2.285;QD=1.36;ReadPosRankSum=2.415;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,5:27:29:65,0,29 -chr1 154089 . C T 246.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.061;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9468;MLEAC=1;MLEAF=0.500;MQ=27.14;MQ0=4;MQRankSum=2.003;QD=16.41;ReadPosRankSum=2.003;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,10:15:11:274,0,11 -chr1 154133 . C T 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.115;DP=35;Dels=0.00;FS=9.558;HaplotypeScore=3.5584;MLEAC=1;MLEAF=0.500;MQ=18.65;MQ0=14;MQRankSum=2.353;QD=3.25;ReadPosRankSum=1.445;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:142,0,207 -chr1 154140 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.372;QD=0.88;ReadPosRankSum=0.501;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,368 -chr1 154141 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.501;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.238;QD=0.88;ReadPosRankSum=0.167;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,372 -chr1 154150 . C T 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;DP=52;Dels=0.00;FS=11.840;HaplotypeScore=12.4214;MLEAC=1;MLEAF=0.500;MQ=19.66;MQ0=15;MQRankSum=1.795;QD=3.11;ReadPosRankSum=-1.146;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,11:52:99:190,0,332 -chr1 154162 . G A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.044;DP=55;Dels=0.00;FS=11.710;HaplotypeScore=10.1969;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=15;MQRankSum=2.642;QD=4.32;ReadPosRankSum=-0.664;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:43,12:55:99:266,0,265 -chr1 154178 . A T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=57;Dels=0.00;FS=12.518;HaplotypeScore=35.4325;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=14;MQRankSum=0.047;QD=0.65;ReadPosRankSum=0.421;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:49,8:57:65:65,0,554 -chr1 154186 . C T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;DP=56;Dels=0.00;FS=6.576;HaplotypeScore=25.1706;MLEAC=1;MLEAF=0.500;MQ=19.31;MQ0=13;MQRankSum=2.199;QD=5.50;ReadPosRankSum=1.671;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,16:56:99:336,0,269 -chr1 154212 . G A 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=58;Dels=0.00;FS=23.517;HaplotypeScore=19.0376;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=0.000;QD=0.77;ReadPosRankSum=-1.855;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:48,10:58:73:73,0,611 -chr1 154215 . A G 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=11.7095;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=12;MQRankSum=-0.934;QD=0.60;ReadPosRankSum=2.084;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:45,10:55:61:61,0,555 -chr1 154233 . T A 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.328;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=4.6866;MLEAC=1;MLEAF=0.500;MQ=22.49;MQ0=0;MQRankSum=-1.708;QD=3.52;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:148,0,338 -chr1 154253 . T G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=0;MQRankSum=0.174;QD=6.85;ReadPosRankSum=0.637;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,7:15:99:131,0,128 -chr1 154334 . G A 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=29;Dels=0.00;FS=9.558;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=23.50;MQ0=4;MQRankSum=-0.028;QD=4.34;ReadPosRankSum=-1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:154,0,227 -chr1 154426 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=49;Dels=0.00;FS=2.566;HaplotypeScore=5.9227;MLEAC=1;MLEAF=0.500;MQ=20.19;MQ0=9;MQRankSum=-0.765;QD=0.85;ReadPosRankSum=-0.359;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,10:49:70:70,0,505 -chr1 154501 . C T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=30;Dels=0.00;FS=2.793;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=20.43;MQ0=7;MQRankSum=2.328;QD=1.86;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,3:30:84:84,0,237 -chr1 154559 . G A 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.761;DP=30;Dels=0.00;FS=8.741;HaplotypeScore=6.7678;MLEAC=1;MLEAF=0.500;MQ=21.74;MQ0=1;MQRankSum=1.761;QD=2.36;ReadPosRankSum=0.953;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,5:30:99:99,0,279 -chr1 154731 . T A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=3.8976;MLEAC=1;MLEAF=0.500;MQ=22.58;MQ0=0;MQRankSum=1.214;QD=3.78;ReadPosRankSum=-1.214;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,3:10:66:66,0,111 -chr1 154748 . G C 40.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.185;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=1.664;QD=3.40;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,3:12:69:69,0,77 -chr1 154754 . C T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=7.8245;MLEAC=1;MLEAF=0.500;MQ=21.59;MQ0=0;MQRankSum=1.246;QD=2.34;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,3:14:61:61,0,161 -chr1 154802 . G A 95.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.831;DP=13;Dels=0.00;FS=2.533;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=17.54;MQ0=1;MQRankSum=2.367;QD=7.38;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,7:13:5:123,0,5 -chr1 155280 . G A 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=11.9766;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=12;MQRankSum=3.514;QD=1.38;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:118,13:131:99:209,0,2278 -chr1 155314 . T C 2942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=180;Dels=0.00;FS=0.919;HaplotypeScore=9.2358;MLEAC=1;MLEAF=0.500;MQ=31.00;MQ0=20;MQRankSum=-4.581;QD=16.35;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,153:180:99:2971,0,552 -chr1 155368 . C T 1195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=116;Dels=0.00;FS=10.244;HaplotypeScore=19.2230;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=28;MQRankSum=-3.527;QD=10.31;ReadPosRankSum=-0.904;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,89:116:99:1224,0,527 -chr1 155372 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=110;Dels=0.00;FS=21.794;HaplotypeScore=22.7736;MLEAC=1;MLEAF=0.500;MQ=26.51;MQ0=28;MQRankSum=-2.154;QD=5.63;ReadPosRankSum=-1.004;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,56:110:99:648,0,967 -chr1 155396 . T C 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=11.0107;MLEAC=1;MLEAF=0.500;MQ=20.74;MQ0=18;MQRankSum=0.787;QD=6.88;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,42:60:99:441,0,159 -chr1 155402 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.238;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=14.3324;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=15;MQRankSum=0.120;QD=0.70;ReadPosRankSum=1.919;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,7:51:64:64,0,412 -chr1 155404 . G A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.763;DP=50;Dels=0.00;FS=2.315;HaplotypeScore=14.9975;MLEAC=1;MLEAF=0.500;MQ=18.26;MQ0=14;MQRankSum=-0.535;QD=2.86;ReadPosRankSum=0.049;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:171,0,293 -chr1 155496 . C T 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.978;DP=159;Dels=0.00;FS=16.800;HaplotypeScore=104.1353;MLEAC=1;MLEAF=0.500;MQ=28.15;MQ0=19;MQRankSum=4.281;QD=1.63;ReadPosRankSum=-1.263;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:142,17:159:99:287,0,2754 -chr1 155542 . G A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=109;Dels=0.00;FS=13.436;HaplotypeScore=10.2277;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=23;MQRankSum=3.323;QD=2.63;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:93,16:109:99:315,0,1464 -chr1 155558 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=83;Dels=0.00;FS=2.807;HaplotypeScore=16.4098;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=22;MQRankSum=-3.424;QD=6.50;ReadPosRankSum=-1.063;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,48:83:99:568,0,598 -chr1 155561 . G A 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.883;DP=74;Dels=0.00;FS=6.505;HaplotypeScore=10.4277;MLEAC=1;MLEAF=0.500;MQ=24.10;MQ0=19;MQRankSum=3.377;QD=3.31;ReadPosRankSum=0.558;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:273,0,780 -chr1 155711 . T C 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006;DP=48;Dels=0.00;FS=10.017;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=5;MQRankSum=-2.049;QD=6.66;ReadPosRankSum=2.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:348,0,395 -chr1 156547 . A G 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=56;Dels=0.00;FS=5.379;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.83;MQ0=1;MQRankSum=0.887;QD=14.50;ReadPosRankSum=1.631;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,999 -chr1 156554 . T G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.004;DP=67;Dels=0.00;FS=4.974;HaplotypeScore=1.7313;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=1;MQRankSum=-1.187;QD=13.74;ReadPosRankSum=2.549;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1225 -chr1 156606 . A C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.388;QD=20.16;ReadPosRankSum=2.689;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,39:67:99:1379,0,939 -chr1 156782 . C T 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=67;Dels=0.00;FS=3.401;HaplotypeScore=3.7879;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.087;QD=13.65;ReadPosRankSum=-1.036;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:943,0,1345 -chr1 156846 . T A 1011.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=63;Dels=0.00;FS=3.924;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=2;MQRankSum=0.166;QD=16.06;ReadPosRankSum=2.460;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1040,0,959 -chr1 156855 . T C 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.634;DP=65;Dels=0.00;FS=9.722;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=2;MQRankSum=-0.848;QD=17.73;ReadPosRankSum=1.937;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1181,0,930 -chr1 156873 . C A 440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.088;DP=54;Dels=0.00;FS=4.462;HaplotypeScore=1.7781;MLEAC=1;MLEAF=0.500;MQ=57.51;MQ0=2;MQRankSum=-0.709;QD=8.16;ReadPosRankSum=0.210;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:54:99:469,0,1228 -chr1 156909 . G C 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.429;DP=59;Dels=0.00;FS=5.572;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=4;MQRankSum=0.042;QD=13.79;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:842,0,823 -chr1 156944 . G A 1215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=65;Dels=0.00;FS=0.962;HaplotypeScore=1.8316;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=2;MQRankSum=-0.243;QD=18.70;ReadPosRankSum=1.160;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,37:65:99:1244,0,895 -chr1 157008 . C T 1261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=79;Dels=0.00;FS=7.743;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.24;MQ0=0;MQRankSum=1.211;QD=15.97;ReadPosRankSum=-0.240;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,39:79:99:1290,0,1323 -chr1 157058 . G A 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=69;Dels=0.00;FS=2.053;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.597;QD=14.53;ReadPosRankSum=0.814;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E323K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 0/1:38,31:69:99:1031,0,1223 -chr1 157169 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=58;Dels=0.00;FS=2.379;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.173;QD=13.27;ReadPosRankSum=0.973;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:798,0,1053 -chr1 157239 . C T 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.399;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=14.77;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:885,0,1106 -chr1 157240 . T A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.086;QD=14.63;ReadPosRankSum=1.196;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:877,0,1125 -chr1 157449 . C G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.059;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=0.040;QD=18.19;ReadPosRankSum=-0.929;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1065,0,774 -chr1 157515 . T A 1070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.511;DP=64;Dels=0.00;FS=5.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.17;MQ0=0;MQRankSum=-0.839;QD=16.73;ReadPosRankSum=0.879;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1099,0,1080 -chr1 157636 . T G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.591;QD=13.12;ReadPosRankSum=0.988;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,29:71:99:960,0,1393 -chr1 157961 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.614;DP=56;Dels=0.00;FS=2.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.124;QD=14.01;ReadPosRankSum=0.654;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:813,0,1117 -chr1 158261 . T A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=23.67;MQ0=3;MQRankSum=1.231;QD=5.72;ReadPosRankSum=-1.231;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,2:8:28:74,0,28 -chr1 158283 . C T 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.77;ReadPosRankSum=-1.733;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:62:62,0,105 -chr1 158288 . C T 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.898;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.3135;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.81;ReadPosRankSum=-0.898;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:64:64,0,104 -chr1 159489 . A C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=35;Dels=0.00;FS=5.503;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.782;QD=9.99;ReadPosRankSum=0.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:378,0,778 -chr1 159490 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.923;DP=36;Dels=0.00;FS=5.305;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.017;QD=8.80;ReadPosRankSum=0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:345,0,811 -chr1 159582 . A C 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.531;QD=16.89;ReadPosRankSum=0.155;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,34:64:99:1109,0,986 -chr1 159628 . G A 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.490;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.246;QD=12.01;ReadPosRankSum=1.624;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:689,0,1123 -chr1 159860 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=31;Dels=0.00;FS=1.455;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=1;MQRankSum=1.161;QD=15.99;ReadPosRankSum=-0.581;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:524,0,479 -chr1 160064 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=44;Dels=0.00;FS=4.575;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.662;QD=13.65;ReadPosRankSum=2.440;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:629,0,815 -chr1 160220 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.049;DP=63;Dels=0.00;FS=8.766;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=1;MQRankSum=0.585;QD=15.46;ReadPosRankSum=0.275;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1002,0,1082 -chr1 160312 . T C 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=0.460;QD=18.96;ReadPosRankSum=0.700;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,32:51:99:995,0,618 -chr1 160344 . G T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=1;MQRankSum=-0.844;QD=17.19;ReadPosRankSum=-1.600;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1025,0,815 -chr1 160346 . C T 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.698;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=1;MQRankSum=-1.756;QD=18.01;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1109,0,813 -chr1 160403 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=47;Dels=0.00;FS=2.597;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=0.187;QD=15.87;ReadPosRankSum=1.792;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:774,0,801 -chr1 160457 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.631;DP=50;Dels=0.00;FS=6.171;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=-1.072;QD=15.06;ReadPosRankSum=-0.691;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:781,0,825 -chr1 160628 . A G 1125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.790;DP=56;Dels=0.00;FS=3.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.486;QD=20.10;ReadPosRankSum=0.964;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1154,0,734 -chr1 160653 . T C 936.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.121;DP=49;Dels=0.00;FS=2.547;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;QD=19.12;ReadPosRankSum=1.337;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:965,0,743 -chr1 160771 . A G 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=0.483;QD=11.82;ReadPosRankSum=0.983;EFF=SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R393|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160727_160819) GT:AD:DP:GQ:PL 0/1:20,15:35:99:442,0,684 -chr1 160855 . T G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.510;QD=16.59;ReadPosRankSum=0.790;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:841,0,789 -chr1 160924 . A T 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.068;DP=45;Dels=0.00;FS=4.461;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=1;MQRankSum=0.305;QD=15.66;ReadPosRankSum=2.608;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:733,0,738 -chr1 161085 . T C 995.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=50;Dels=0.00;FS=4.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.708;QD=19.92;ReadPosRankSum=0.314;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1024,0,658 -chr1 161127 . C T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.700;DP=43;Dels=0.00;FS=2.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.281;QD=14.51;ReadPosRankSum=0.159;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:652,0,837 -chr1 161227 . G A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=54;Dels=0.00;FS=1.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.588;QD=17.01;ReadPosRankSum=1.522;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M421I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161192_161296) GT:AD:DP:GQ:PL 0/1:27,27:54:99:947,0,859 -chr1 161350 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.657;DP=58;Dels=0.00;FS=2.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=1;MQRankSum=-1.366;QD=13.12;ReadPosRankSum=0.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:789,0,1101 -chr1 161518 . G T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.065;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.343;QD=20.21;ReadPosRankSum=0.639;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1079,0,713 -chr1 161583 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=48;Dels=0.00;FS=1.275;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.066;QD=17.70;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:878,0,744 -chr1 161598 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.505;QD=16.36;ReadPosRankSum=-0.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:748,0,762 -chr1 161607 . G A 761.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.527;QD=16.56;ReadPosRankSum=0.154;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:790,0,787 -chr1 161743 . A C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.492;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=57.06;MQ0=1;MQRankSum=0.379;QD=15.60;ReadPosRankSum=-1.327;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K479Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,22:41:99:668,0,538 -chr1 161769 . A T 896.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=46;Dels=0.00;FS=9.187;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=1;MQRankSum=0.471;QD=19.49;ReadPosRankSum=0.172;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K487N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,27:46:99:925,0,511 -chr1 161794 . A C 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.236;DP=52;Dels=0.00;FS=10.280;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.58;MQ0=1;MQRankSum=-0.009;QD=11.69;ReadPosRankSum=-2.236;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I496L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,25:52:99:636,0,971 -chr1 161795 . T A 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.758;DP=53;Dels=0.00;FS=10.399;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=-0.513;QD=12.26;ReadPosRankSum=-2.363;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I496K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,26:53:99:678,0,963 -chr1 161822 . C T 899.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.364;DP=66;Dels=0.00;FS=11.007;HaplotypeScore=3.5506;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=1;MQRankSum=-1.119;QD=13.63;ReadPosRankSum=1.484;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P505L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:35,30:66:99:928,0,1200 -chr1 162022 . A G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.438;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.169;QD=11.01;ReadPosRankSum=1.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:744,0,1397 -chr1 162353 . G C 1411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.839;QD=20.46;ReadPosRankSum=0.322;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,42:69:99:1440,0,796 -chr1 162433 . T G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.759;DP=62;Dels=0.00;FS=3.875;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.175;QD=11.56;ReadPosRankSum=0.455;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:745,0,1353 -chr1 162535 . G T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=48;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.094;QD=13.18;ReadPosRankSum=0.596;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:661,0,948 -chr1 162739 . G T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=6;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.406;QD=11.29;ReadPosRankSum=-1.537;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:6:45:96,0,45 -chr1 162750 . G T 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=8;Dels=0.00;FS=7.068;HaplotypeScore=2.9939;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.517;QD=14.97;ReadPosRankSum=-1.920;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,5:8:77:148,0,77 -chr1 162820 . T C 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=28;Dels=0.00;FS=7.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.539;QD=5.78;ReadPosRankSum=-2.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:190,0,773 -chr1 162833 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.944;DP=31;Dels=0.00;FS=12.129;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.218;QD=26.80;ReadPosRankSum=0.130;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,24:31:99:859,0,157 -chr1 163152 . G C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=54;Dels=0.00;FS=5.807;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.98;MQ0=0;MQRankSum=0.996;QD=10.96;ReadPosRankSum=-0.127;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1162 -chr1 163218 . T G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.806;QD=15.84;ReadPosRankSum=-0.456;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:820,0,917 -chr1 163281 . T A 1020.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=49;Dels=0.00;FS=5.959;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.365;QD=20.83;ReadPosRankSum=-0.133;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1049,0,617 -chr1 163602 . A T 1204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=60;Dels=0.00;FS=1.004;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.135;QD=20.08;ReadPosRankSum=-1.080;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1233,0,823 -chr1 163615 . A C 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=61;Dels=0.00;FS=0.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.905;QD=15.06;ReadPosRankSum=0.485;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:947,0,1113 -chr1 163628 . T C 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=65;Dels=0.00;FS=0.942;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.992;QD=16.09;ReadPosRankSum=0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:1074,0,1122 -chr1 163725 . C T 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=1.996;QD=17.52;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1027,0,891 -chr1 163736 . G C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-0.360;QD=17.74;ReadPosRankSum=-0.280;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1057,0,874 -chr1 163777 . C A 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.340;DP=58;Dels=0.00;FS=2.434;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=2;MQRankSum=0.445;QD=18.15;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1081,0,777 -chr1 163806 . C T 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=52;Dels=0.00;FS=4.176;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=0.386;QD=15.90;ReadPosRankSum=0.763;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:855,0,885 -chr1 163808 . A G 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;DP=49;Dels=0.00;FS=2.654;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=1;MQRankSum=-2.064;QD=17.10;ReadPosRankSum=0.186;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:866,0,770 -chr1 163854 . A G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-1.274;QD=13.14;ReadPosRankSum=0.742;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:646,0,892 -chr1 163894 . A C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.626;QD=14.66;ReadPosRankSum=0.011;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:688,0,813 -chr1 163957 . T A 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.596;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.570;QD=15.70;ReadPosRankSum=-1.105;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,29:61:99:986,0,1103 -chr1 163980 . A G 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=63;Dels=0.00;FS=3.778;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.763;QD=16.33;ReadPosRankSum=-1.010;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1057,0,1126 -chr1 164203 . T G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.489;DP=77;Dels=0.00;FS=0.917;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.110;QD=13.15;ReadPosRankSum=1.352;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:44,33:77:99:1041,0,1470 -chr1 164252 . A C 1239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.049;DP=65;Dels=0.00;FS=3.361;HaplotypeScore=3.6644;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.297;QD=19.07;ReadPosRankSum=-0.284;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1268,0,967 -chr1 164282 . T G 1111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=64;Dels=0.00;FS=8.767;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.443;QD=17.37;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1140,0,1007 -chr1 164379 . G A 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.789;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.7845;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.487;QD=17.46;ReadPosRankSum=0.834;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1285,0,1107 -chr1 164494 . T C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.288;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.082;QD=11.78;ReadPosRankSum=2.323;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:641,0,1102 -chr1 164861 . T C 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=68;Dels=0.00;FS=4.986;HaplotypeScore=1.9732;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.679;QD=18.48;ReadPosRankSum=-1.576;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,40:68:99:1285,0,918 -chr1 164958 . A G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.907;DP=50;Dels=0.00;FS=1.129;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.295;QD=12.86;ReadPosRankSum=-1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:671,0,981 -chr1 165095 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.531;QD=16.03;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,944 -chr1 165389 . T G 915.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=62;Dels=0.00;FS=5.213;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-2.850;QD=14.77;ReadPosRankSum=-1.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,29:62:99:944,0,1149 -chr1 165407 . C A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.847;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.97;MQ0=0;MQRankSum=-5.528;QD=13.62;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1192 -chr1 165447 . A G 873.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=5.913;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=4.271;QD=17.83;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:902,0,692 -chr1 165482 . G T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-0.596;QD=13.47;ReadPosRankSum=0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:42:99:594,0,720 -chr1 165483 . G T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.222;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-1.082;QD=15.12;ReadPosRankSum=0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,21:41:99:648,0,635 -chr1 165526 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.764;QD=21.70;ReadPosRankSum=0.631;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,30:47:99:1048,0,485 -chr1 165678 . C T 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;DP=56;Dels=0.00;FS=5.297;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.10;MQ0=0;MQRankSum=-3.048;QD=17.67;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1018,0,833 -chr1 165701 . T A 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.17;MQ0=0;MQRankSum=-1.305;QD=19.86;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1061,0,610 -chr1 165957 . G A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=42;Dels=0.00;FS=6.343;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.657;QD=17.66;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:770,0,629 -chr1 165982 . T G 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.314;DP=35;Dels=0.00;FS=1.320;HaplotypeScore=2.6981;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.007;QD=15.28;ReadPosRankSum=-0.677;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:563,0,552 -chr1 166129 . A T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.425;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.719;QD=14.24;ReadPosRankSum=2.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:612,0,716 -chr1 166135 . T G 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=40;Dels=0.00;FS=4.837;HaplotypeScore=2.7214;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.300;QD=15.12;ReadPosRankSum=1.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,714 -chr1 166157 . C T 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.204;DP=19;Dels=0.00;FS=17.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=1.592;QD=16.30;ReadPosRankSum=-0.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:9,10:19:99:338,0,285 -chr1 166214 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.550;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.69;MQ0=0;MQRankSum=-5.017;QD=10.28;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:388,0,673 -chr1 166219 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-5.166;QD=12.70;ReadPosRankSum=-0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:498,0,722 -chr1 166226 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=35;Dels=0.00;FS=1.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-5.050;QD=14.16;ReadPosRankSum=1.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:524,0,649 -chr1 166233 . G A 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=-4.961;QD=13.89;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:556,0,691 -chr1 166248 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=-3.398;QD=13.51;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,645 -chr1 166255 . A C 437.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=13.4643;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-3.919;QD=12.88;ReadPosRankSum=2.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:466,0,539 -chr1 166256 . C T 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=35;Dels=0.00;FS=2.984;HaplotypeScore=14.4309;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-3.394;QD=13.59;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:504,0,583 -chr1 166297 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=52;Dels=0.00;FS=1.203;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-0.194;QD=19.76;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1056,0,614 -chr1 166322 . T A 1149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=19.16;ReadPosRankSum=0.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1178,0,786 -chr1 166453 . A G 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.040;DP=55;Dels=0.00;FS=9.665;HaplotypeScore=2.6999;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.583;QD=17.09;ReadPosRankSum=-2.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:968,0,816 -chr1 166585 . G A 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;DP=56;Dels=0.00;FS=2.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.945;QD=13.09;ReadPosRankSum=0.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:761,0,1060 -chr1 166654 . A T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=46;Dels=0.00;FS=4.286;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=-1.445;QD=16.45;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:785,0,700 -chr1 166658 . T G 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.864;DP=44;Dels=0.00;FS=9.040;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=-2.277;QD=15.95;ReadPosRankSum=0.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:730,0,641 -chr1 166669 . G C 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=42;Dels=0.00;FS=15.562;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=1;MQRankSum=-0.595;QD=17.68;ReadPosRankSum=-0.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:771,0,549 -chr1 166716 . A G 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.762;DP=46;Dels=0.00;FS=4.124;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=2;MQRankSum=-1.715;QD=15.93;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:761,0,715 -chr1 166733 . T G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.886;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=1.7337;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=2;MQRankSum=-1.925;QD=13.15;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:712,0,936 -chr1 166734 . G T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.213;DP=54;Dels=0.00;FS=5.816;HaplotypeScore=3.7324;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=2;MQRankSum=-2.232;QD=12.46;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:701,0,1010 -chr1 166737 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=56;Dels=0.00;FS=5.681;HaplotypeScore=4.7320;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=2;MQRankSum=-1.928;QD=11.89;ReadPosRankSum=1.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:694,0,1084 -chr1 166751 . A C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=57;Dels=0.00;FS=2.274;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=1;MQRankSum=-0.813;QD=14.42;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:850,0,1009 -chr1 166834 . G A 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=38;Dels=0.00;FS=25.349;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=0.410;QD=15.34;ReadPosRankSum=0.167;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:611,0,646 -chr1 166877 . T A 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=32;Dels=0.00;FS=21.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.083;QD=13.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:468,0,592 -chr1 166961 . T C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=32;Dels=0.00;FS=15.187;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.468;QD=8.99;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:316,0,780 -chr1 167208 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.357;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.870;QD=12.28;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:593,0,944 -chr1 167228 . C G 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=45;Dels=0.00;FS=2.529;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.633;QD=18.57;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:864,0,666 -chr1 167283 . A G 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.416;DP=47;Dels=0.00;FS=13.823;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.906;QD=17.55;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:853,0,735 -chr1 167371 . G A 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.387;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.897;QD=17.33;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,760 -chr1 167399 . G T 890.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.694;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.632;QD=16.20;ReadPosRankSum=-0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:919,0,873 -chr1 167568 . C T 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.926;QD=14.91;ReadPosRankSum=-1.266;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:729,0,770 -chr1 167574 . G T 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.580;QD=14.26;ReadPosRankSum=-1.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:670,0,813 -chr1 167672 . C G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.527;QD=11.41;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:496,0,851 -chr1 167681 . A T 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-0.635;QD=12.42;ReadPosRankSum=-1.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:649,0,985 -chr1 168087 . G A 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7985;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.503;QD=14.59;ReadPosRankSum=0.781;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:714,0,900 -chr1 168095 . G C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.150;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.112;QD=17.61;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:891,0,777 -chr1 168096 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.232;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.551;QD=14.46;ReadPosRankSum=-0.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:737,0,907 -chr1 168153 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=44;Dels=0.00;FS=6.747;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=1.608;QD=15.79;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,22:44:99:723,0,628 -chr1 168196 . G A 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=34;Dels=0.00;FS=3.353;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=0.659;QD=13.11;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:474,0,581 -chr1 168341 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=58;Dels=0.00;FS=1.012;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.993;QD=13.50;ReadPosRankSum=-0.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:811,0,1056 -chr1 168360 . G T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648;DP=55;Dels=0.00;FS=2.266;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.955;QD=12.69;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:726,0,991 -chr1 168533 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=0.230;QD=11.62;ReadPosRankSum=-1.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P42L|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:21,16:37:99:458,0,718 -chr1 168548 . A T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=0.239;QD=11.20;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y47F|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:23,15:38:99:454,0,793 -chr1 168693 . T C 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.458;DP=42;Dels=0.00;FS=4.987;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=2;MQRankSum=-0.505;QD=10.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S95|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:26,15:42:99:483,0,823 -chr1 168747 . A T 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=48;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=1;MQRankSum=0.649;QD=14.06;ReadPosRankSum=-0.309;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G113|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:25,23:48:99:703,0,783 -chr1 168840 . T C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.320;DP=52;Dels=0.00;FS=5.785;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=1.858;QD=15.55;ReadPosRankSum=0.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:837,0,857 -chr1 168897 . T C 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.871;DP=57;Dels=0.00;FS=5.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.07;MQ0=0;MQRankSum=0.583;QD=14.80;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:872,0,987 -chr1 168963 . A C 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.126;DP=70;Dels=0.00;FS=0.909;HaplotypeScore=4.3674;MLEAC=1;MLEAF=0.500;MQ=61.66;MQ0=1;MQRankSum=1.602;QD=15.61;ReadPosRankSum=0.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,35:70:99:1121,0,1161 -chr1 168974 . T C 245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=49;Dels=0.00;FS=5.429;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-4.252;QD=5.02;ReadPosRankSum=2.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:274,0,1377 -chr1 168984 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=50;Dels=0.00;FS=1.222;HaplotypeScore=2.6583;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-3.464;QD=8.06;ReadPosRankSum=1.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:431,0,1261 -chr1 169059 . T C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=48;Dels=0.00;FS=1.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=9.25;ReadPosRankSum=2.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:472,0,1188 -chr1 169061 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.503;QD=10.74;ReadPosRankSum=0.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,18:51:99:576,0,1182 -chr1 169185 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=50;Dels=0.00;FS=4.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.980;QD=11.94;ReadPosRankSum=-1.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:625,0,1008 -chr1 169423 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.535;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.324;QD=14.74;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:618,0,620 -chr1 169424 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.169;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.690;QD=14.42;ReadPosRankSum=0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:605,0,616 -chr1 169456 . C G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.543;DP=47;Dels=0.00;FS=13.725;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=-1.163;QD=13.68;ReadPosRankSum=0.388;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:671,0,799 -chr1 169607 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.477;DP=58;Dels=0.00;FS=3.625;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.227;QD=14.24;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:854,0,1075 -chr1 169642 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.356;DP=58;Dels=0.00;FS=3.717;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.639;QD=14.27;ReadPosRankSum=-0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:856,0,1091 -chr1 169648 . A G 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=59;Dels=0.00;FS=5.223;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.312;QD=14.28;ReadPosRankSum=-0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:871,0,1059 -chr1 169705 . C T 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=63;Dels=0.00;FS=0.971;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.354;QD=12.92;ReadPosRankSum=0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:842,0,1216 -chr1 169719 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.216;DP=60;Dels=0.00;FS=0.971;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.529;QD=13.80;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1191 -chr1 169815 . T C 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.744;DP=85;Dels=0.00;FS=5.036;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=1;MQRankSum=-0.413;QD=6.71;ReadPosRankSum=-0.785;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:63,22:85:99:599,0,2148 -chr1 169830 . T G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;DP=82;Dels=0.00;FS=5.065;HaplotypeScore=4.3793;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=1;MQRankSum=0.781;QD=7.48;ReadPosRankSum=-0.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:58,24:82:99:642,0,1903 -chr1 169867 . A T 1602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.283;DP=92;Dels=0.00;FS=3.988;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=57.78;MQ0=0;MQRankSum=0.596;QD=17.42;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,51:92:99:1631,0,1086 -chr1 169896 . A G 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=92;Dels=0.00;FS=1.896;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-1.080;QD=8.30;ReadPosRankSum=0.557;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:792,0,2212 -chr1 169909 . A G 1909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=89;Dels=0.00;FS=2.916;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.306;QD=21.46;ReadPosRankSum=-1.499;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,54:89:99:1938,0,1053 -chr1 169968 . C T 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.404;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.734;QD=6.51;ReadPosRankSum=1.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,23:95:99:647,0,2530 -chr1 169972 . T C 2032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.409;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.407;QD=20.53;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,62:99:99:2061,0,1189 -chr1 169997 . G T 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.396;DP=92;Dels=0.00;FS=3.217;HaplotypeScore=46.8443;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=1.054;QD=7.27;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:68,24:92:99:697,0,2342 -chr1 170001 . A C 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.420;DP=93;Dels=0.00;FS=3.202;HaplotypeScore=65.8412;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.583;QD=6.35;ReadPosRankSum=-0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:619,0,2321 -chr1 170005 . T A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=62.8400;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=0.339;QD=9.09;ReadPosRankSum=1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:60,31:91:99:855,0,2167 -chr1 170011 . T A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.010;DP=90;Dels=0.00;FS=3.403;HaplotypeScore=40.8458;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.801;QD=6.26;ReadPosRankSum=0.496;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,21:90:99:592,0,2430 -chr1 170043 . G T 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=92;Dels=0.00;FS=6.914;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.005;QD=5.60;ReadPosRankSum=0.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,20:92:99:543,0,2449 -chr1 170079 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=84;Dels=0.00;FS=36.316;HaplotypeScore=155.6412;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.479;QD=3.88;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:354,0,2529 -chr1 170134 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.806;DP=84;Dels=0.00;FS=25.920;HaplotypeScore=2.3987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.915;QD=2.15;ReadPosRankSum=1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:71,13:84:99:209,0,2556 -chr1 170169 . T A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=75;Dels=0.00;FS=22.598;HaplotypeScore=2.7329;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.239;QD=2.08;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,10:75:99:184,0,2327 -chr1 170210 . A C 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=80;Dels=0.00;FS=12.034;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=-0.591;QD=11.07;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:914,0,1744 -chr1 170224 . G A 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=77;Dels=0.00;FS=12.005;HaplotypeScore=3.7332;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=1;MQRankSum=-0.353;QD=11.24;ReadPosRankSum=-0.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,29:77:99:894,0,1620 -chr1 170239 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.912;DP=71;Dels=0.00;FS=8.610;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=1;MQRankSum=-0.098;QD=11.11;ReadPosRankSum=1.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:45,26:71:99:817,0,1578 -chr1 170266 . C T 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.026;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=4.0879;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.051;QD=9.33;ReadPosRankSum=0.076;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:709,0,1696 -chr1 170289 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=2.006;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.339;QD=9.96;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:51,26:77:99:795,0,1734 -chr1 170303 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=63;Dels=0.00;FS=33.610;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.166;QD=5.60;ReadPosRankSum=2.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:381,0,1693 -chr1 170304 . A G 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=63;Dels=0.00;FS=8.306;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.545;QD=6.76;ReadPosRankSum=0.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:454,0,1606 -chr1 170360 . C T 818.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.394;DP=63;Dels=0.00;FS=0.955;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.256;QD=13.00;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:847,0,1189 -chr1 170364 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=59;Dels=0.00;FS=2.175;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=0.510;QD=14.08;ReadPosRankSum=0.936;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:859,0,1076 -chr1 170366 . C T 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=59;Dels=0.00;FS=1.010;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.234;QD=14.39;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:877,0,1076 -chr1 170381 . C T 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=59;Dels=0.00;FS=9.493;HaplotypeScore=9.7866;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.356;QD=11.00;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:677,0,1290 -chr1 170382 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=59;Dels=0.00;FS=7.433;HaplotypeScore=10.7863;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.341;QD=3.44;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:231,0,1765 -chr1 170393 . T A 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=67;Dels=0.00;FS=1.050;HaplotypeScore=21.7756;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.059;QD=12.73;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,26:67:99:881,0,961 -chr1 170403 . C A 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=68;Dels=0.00;FS=2.482;HaplotypeScore=25.9777;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.799;QD=5.08;ReadPosRankSum=0.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:374,0,1880 -chr1 170482 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=57;Dels=0.00;FS=11.052;HaplotypeScore=19.8261;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=-0.166;QD=8.54;ReadPosRankSum=0.166;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:515,0,1440 -chr1 170483 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.764;DP=54;Dels=0.00;FS=14.133;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.397;QD=9.20;ReadPosRankSum=-0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:525,0,1294 -chr1 170487 . A G 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.892;QD=3.05;ReadPosRankSum=-0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,9:56:99:199,0,1721 -chr1 170502 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=57;Dels=0.00;FS=1.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.354;QD=4.54;ReadPosRankSum=-1.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,11:57:99:287,0,1595 -chr1 170515 . G C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.903;DP=63;Dels=0.00;FS=10.967;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.124;QD=6.27;ReadPosRankSum=1.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:423,0,1617 -chr1 170578 . C G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.493;QD=8.29;ReadPosRankSum=-0.627;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,19:65:99:567,0,1665 -chr1 170582 . C T 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=65;Dels=0.00;FS=12.918;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.097;QD=7.18;ReadPosRankSum=2.829;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:495,0,1695 -chr1 170584 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=66;Dels=0.00;FS=3.389;HaplotypeScore=31.9744;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.899;QD=17.30;ReadPosRankSum=2.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1170,0,1057 -chr1 170628 . C T 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.299;DP=67;Dels=0.00;FS=2.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=0.483;QD=13.62;ReadPosRankSum=0.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:941,0,1173 -chr1 170648 . G A 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=67;Dels=0.00;FS=6.632;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=0;MQRankSum=-1.055;QD=1.77;ReadPosRankSum=1.823;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:55,12:67:99:147,0,1992 -chr1 170807 . C G 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.270;DP=63;Dels=0.00;FS=8.737;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.906;QD=13.71;ReadPosRankSum=-0.546;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:892,0,1101 -chr1 170817 . G A 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=59;Dels=0.00;FS=3.720;HaplotypeScore=21.9878;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.618;QD=13.42;ReadPosRankSum=0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,26:59:99:820,0,1062 -chr1 170849 . A T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=51;Dels=0.00;FS=13.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.123;QD=15.02;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,925 -chr1 170873 . A T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.666;DP=58;Dels=0.00;FS=17.770;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.826;QD=17.91;ReadPosRankSum=-1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1067,0,865 -chr1 170879 . G A 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.614;DP=59;Dels=0.00;FS=14.005;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.493;QD=16.74;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1016,0,929 -chr1 170937 . C G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.022;DP=60;Dels=0.00;FS=5.062;HaplotypeScore=3.7392;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=1.504;QD=15.53;ReadPosRankSum=-1.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:960,0,1076 -chr1 170995 . G T 921.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.784;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=-1.752;QD=18.44;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:950,0,694 -chr1 171012 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.147;DP=55;Dels=0.00;FS=2.354;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-2.330;QD=21.27;ReadPosRankSum=1.308;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1198,0,645 -chr1 171029 . C T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.183;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.183;QD=20.21;ReadPosRankSum=2.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,34:52:99:1079,0,514 -chr1 171034 . A G 1294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-1.803;QD=23.54;ReadPosRankSum=1.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1323,0,554 -chr1 171062 . A G 1228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=52;Dels=0.00;FS=2.506;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.024;QD=23.63;ReadPosRankSum=-0.527;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,35:52:99:1257,0,545 -chr1 171065 . C A 1210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.009;DP=51;Dels=0.00;FS=2.449;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.908;QD=23.74;ReadPosRankSum=-0.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1239,0,544 -chr1 171068 . G T 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.744;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.725;QD=23.96;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1298,0,506 -chr1 171215 . C T 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;DP=66;Dels=0.00;FS=2.128;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.155;QD=18.66;ReadPosRankSum=1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,37:66:99:1260,0,877 -chr1 171546 . A T 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=52;Dels=0.00;FS=1.174;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.350;QD=17.88;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,29:52:99:958,0,752 -chr1 171611 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.465;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=15.99;ReadPosRankSum=-0.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:748,0,784 -chr1 171685 . A G 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.679;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.182;QD=15.73;ReadPosRankSum=1.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:689,0,730 -chr1 171706 . C G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=45;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.351;QD=15.73;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:736,0,753 -chr1 172009 . G A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.720;DP=61;Dels=0.00;FS=11.177;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.109;QD=12.93;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:817,0,1209 -chr1 172061 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.707;DP=51;Dels=0.00;FS=18.810;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.159;QD=15.94;ReadPosRankSum=1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:841,0,812 -chr1 172093 . C T 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=35;Dels=0.00;FS=3.303;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=0.728;QD=22.02;ReadPosRankSum=0.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:799,0,305 -chr1 172108 . C T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.397;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=32.9713;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-1.397;QD=2.10;ReadPosRankSum=-0.826;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,7:27:85:85,0,539 -chr1 172179 . G C 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.716;QD=12.55;ReadPosRankSum=1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P815R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:505,0,656 -chr1 172203 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.094;DP=46;Dels=0.00;FS=11.390;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-2.028;QD=12.73;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S807L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:614,0,792 -chr1 172283 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.164;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-0.747;QD=9.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G780|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,14:33:99:332,0,598 -chr1 172319 . A G 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=1;MQRankSum=0.833;QD=22.99;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S768|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,23:33:99:787,0,281 -chr1 172364 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=0.201;QD=23.02;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P753|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,26:36:99:857,0,295 -chr1 172459 . T C 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=43;Dels=0.00;FS=14.539;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=1;MQRankSum=0.000;QD=20.90;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I722V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:16,27:43:99:927,0,470 -chr1 172721 . A G 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=52;Dels=0.00;FS=10.166;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.276;QD=14.23;ReadPosRankSum=-0.958;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D634|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,23:52:99:768,0,1005 -chr1 172810 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.584;DP=54;Dels=0.00;FS=5.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=0.733;QD=10.96;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S605G|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1125 -chr1 173004 . G A 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.007;QD=16.90;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T540I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,22:41:99:721,0,631 -chr1 173180 . C T 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.132;QD=14.91;ReadPosRankSum=1.155;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S481|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:595,0,656 -chr1 173273 . A C 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.237;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.026;QD=19.10;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgG|R450|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1079,0,685 -chr1 173338 . C G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=53;Dels=0.00;FS=1.043;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.759;QD=14.54;ReadPosRankSum=-1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V429L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,24:53:99:799,0,968 -chr1 173346 . C T 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.210;QD=13.37;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G426E|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,23:54:99:750,0,981 -chr1 173348 . A G 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=12.61;ReadPosRankSum=-0.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N425|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:32,22:54:99:709,0,1099 -chr1 173405 . A G 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=42;Dels=0.00;FS=9.292;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.162;QD=12.76;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L406|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,19:42:99:564,0,777 -chr1 173410 . C T 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.566;DP=46;Dels=0.00;FS=8.606;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.794;QD=17.91;ReadPosRankSum=0.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V405I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,607 -chr1 173421 . C A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=45;Dels=0.00;FS=11.272;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.582;QD=13.37;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W401L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,20:45:99:630,0,843 -chr1 173444 . G A 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.970;QD=10.77;ReadPosRankSum=0.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I393|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,19:48:99:545,0,1014 -chr1 173446 . T C 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.885;DP=49;Dels=0.00;FS=2.535;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-1.190;QD=11.95;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I393V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,20:49:99:614,0,949 -chr1 173462 . A G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=52;Dels=0.00;FS=5.860;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.951;QD=11.80;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N387|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,21:52:99:642,0,1078 -chr1 173510 . C T 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000;DP=53;Dels=0.00;FS=1.110;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=2;MQRankSum=-0.086;QD=9.45;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P371|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,23:53:99:529,0,994 -chr1 173561 . T C 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=55;Dels=0.00;FS=1.072;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=2;MQRankSum=0.864;QD=14.30;ReadPosRankSum=0.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K354|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:28,27:55:99:815,0,864 -chr1 173585 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=52;Dels=0.00;FS=2.386;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-1.379;QD=11.82;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I346|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,22:52:99:643,0,934 -chr1 173596 . C A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.149;DP=52;Dels=0.00;FS=1.065;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-0.331;QD=17.67;ReadPosRankSum=0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A343S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:947,0,721 -chr1 173627 . A G 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=52;Dels=0.00;FS=1.082;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=0.180;QD=16.84;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L332|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:904,0,775 -chr1 173642 . A T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.002;DP=46;Dels=0.00;FS=6.250;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.935;QD=13.82;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A327|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:24,22:46:99:664,0,819 -chr1 173687 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.658;QD=14.97;ReadPosRankSum=0.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G312|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,21:44:99:687,0,788 -chr1 173717 . A G 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=4.925;HaplotypeScore=1.7323;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.982;QD=17.52;ReadPosRankSum=0.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D302|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:17,19:36:99:659,0,518 -chr1 173759 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=6.309;HaplotypeScore=1.8237;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.154;QD=15.46;ReadPosRankSum=-0.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E288|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:22,21:43:99:693,0,696 -chr1 173818 . C A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.603;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-1.032;QD=15.94;ReadPosRankSum=-1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A269S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,27:50:99:825,0,741 -chr1 173991 . T A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.550;QD=13.08;ReadPosRankSum=0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q211L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,15:35:99:486,0,659 -chr1 174026 . G T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.138;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.579;QD=14.71;ReadPosRankSum=1.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S199R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,21:42:99:646,0,703 -chr1 174172 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.056;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.622;QD=1.68;ReadPosRankSum=-3.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S151C|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:43,7:50:99:112,0,1507 -chr1 174192 . G A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-1.855;QD=3.51;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T144M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,8:45:99:186,0,1296 -chr1 174204 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.410;DP=46;Dels=0.00;FS=1.159;HaplotypeScore=5.9821;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=1.606;QD=12.86;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H140R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:620,0,865 -chr1 174214 . T G 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DP=37;Dels=0.00;FS=1.982;HaplotypeScore=7.7151;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.595;QD=1.37;ReadPosRankSum=2.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K137Q|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,5:37:79:79,0,1105 -chr1 174232 . C T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.406;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.789;QD=3.93;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G131S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,7:34:99:162,0,947 -chr1 174240 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.038;DP=32;Dels=0.00;FS=1.814;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-2.100;QD=2.99;ReadPosRankSum=0.941;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P128L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,6:32:99:124,0,917 -chr1 174248 . G A 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.044;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.194;QD=1.13;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G125|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,4:29:61:61,0,891 -chr1 174253 . G T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-3.037;QD=1.88;ReadPosRankSum=0.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q124K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:79:79,0,826 -chr1 174257 . G A 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-3.037;QD=1.77;ReadPosRankSum=1.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H122|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:76:76,0,816 -chr1 174272 . G A 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.316;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-3.196;QD=2.54;ReadPosRankSum=1.370;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D117|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:107,0,934 -chr1 174280 . G T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.297;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-3.218;QD=2.37;ReadPosRankSum=1.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L115M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,5:32:99:104,0,957 -chr1 174286 . G C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.671;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-3.303;QD=2.44;ReadPosRankSum=0.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L113V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:104,0,936 -chr1 174310 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.07;MQ0=0;MQRankSum=-2.399;QD=19.31;ReadPosRankSum=-1.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A105T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:11,24:35:99:704,0,322 -chr1 174343 . C T 49.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=0;MQRankSum=-3.088;QD=1.11;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D94N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:40,5:45:78:78,0,1238 -chr1 174344 . A C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.079;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=0;MQRankSum=3.308;QD=9.99;ReadPosRankSum=-2.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T93|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,16:45:99:478,0,949 -chr1 174366 . A G 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.432;QD=2.63;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L86P|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:178,0,1581 -chr1 174384 . G A 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=12.0923;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-4.975;QD=3.53;ReadPosRankSum=0.848;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P80L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,11:62:99:247,0,1745 -chr1 174411 . C T 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.738;QD=2.14;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C71Y|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:150,0,1746 -chr1 174419 . C T 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-4.754;QD=1.78;ReadPosRankSum=1.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R68|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:50,9:59:99:133,0,1748 -chr1 174420 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.019;DP=60;Dels=0.00;FS=1.030;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=2.493;QD=11.21;ReadPosRankSum=-0.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R68K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,23:60:99:701,0,1219 -chr1 174490 . C T 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=53;Dels=0.00;FS=8.491;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-3.764;QD=2.13;ReadPosRankSum=-0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D45N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:45,8:53:99:141,0,1535 -chr1 174501 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=50;Dels=0.00;FS=5.507;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-3.283;QD=3.02;ReadPosRankSum=-0.808;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R41H|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:41,9:50:99:179,0,1448 -chr1 174565 . T C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;DP=66;Dels=0.00;FS=2.875;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=57.27;MQ0=0;MQRankSum=-1.776;QD=3.19;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T20A|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:54,11:66:99:239,0,1827 -chr1 174590 . C A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=58;Dels=0.00;FS=6.430;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.01;MQ0=0;MQRankSum=-2.077;QD=1.20;ReadPosRankSum=-0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L11F|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,7:58:98:98,0,1786 -chr1 174616 . C T 904.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.4534;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-0.293;QD=18.46;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A3T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,28:49:99:933,0,662 -chr1 174675 . G A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=42;Dels=0.00;FS=11.439;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.088;QD=15.57;ReadPosRankSum=0.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:682,0,737 -chr1 174689 . G A 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=47;Dels=0.00;FS=8.283;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-0.221;QD=14.08;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,21:47:99:690,0,836 -chr1 174766 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=2.107;QD=3.74;ReadPosRankSum=-1.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:193,0,1204 -chr1 174767 . G A 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-1.576;QD=3.65;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:189,0,1253 -chr1 174776 . G T 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=30;Dels=0.00;FS=12.809;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=1;MQRankSum=-0.811;QD=17.13;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:542,0,441 -chr1 174825 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.264;DP=30;Dels=0.00;FS=5.710;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.260;QD=18.79;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:592,0,412 -chr1 174856 . T C 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=9.9864;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=-3.069;QD=13.77;ReadPosRankSum=-2.821;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:455,0,505 -chr1 174866 . G T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=1;MQRankSum=-2.467;QD=18.28;ReadPosRankSum=-2.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:668,0,443 -chr1 174896 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.059;DP=36;Dels=0.00;FS=7.563;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-1.893;QD=18.63;ReadPosRankSum=2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:699,0,483 -chr1 174908 . G A 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.143;DP=36;Dels=0.00;FS=7.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.525;QD=14.19;ReadPosRankSum=-1.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:539,0,683 -chr1 174931 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;DP=33;Dels=0.00;FS=7.712;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.630;QD=15.27;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,16:33:99:532,0,597 -chr1 174937 . T C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=33;Dels=0.00;FS=7.702;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.284;QD=14.39;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:503,0,630 -chr1 174946 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.250;DP=35;Dels=0.00;FS=10.992;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.150;QD=13.19;ReadPosRankSum=0.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:490,0,676 -chr1 174949 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=37;Dels=0.00;FS=16.331;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.751;QD=13.40;ReadPosRankSum=-0.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:524,0,731 -chr1 174959 . A C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.957;DP=36;Dels=0.00;FS=23.979;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.535;QD=11.58;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:445,0,733 -chr1 174965 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.564;DP=38;Dels=0.00;FS=25.258;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.777;QD=15.76;ReadPosRankSum=1.173;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:38:99:627,0,565 -chr1 175000 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=31;Dels=0.00;FS=19.167;HaplotypeScore=3.5778;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.048;QD=16.86;ReadPosRankSum=0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:551,0,513 -chr1 175050 . C T 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.635;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=-3.633;QD=11.15;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:307,0,488 -chr1 175051 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.191;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-4.077;QD=10.91;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:301,0,523 -chr1 175057 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.016;DP=23;Dels=0.00;FS=1.713;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-3.752;QD=12.08;ReadPosRankSum=1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:306,0,446 -chr1 175059 . A G 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;DP=24;Dels=0.00;FS=3.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.91;MQ0=0;MQRankSum=3.766;QD=15.28;ReadPosRankSum=-1.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:395,0,347 -chr1 175061 . C T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=26;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-3.944;QD=10.22;ReadPosRankSum=1.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:294,0,532 -chr1 175067 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=4.465;QD=14.78;ReadPosRankSum=1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:516,0,577 -chr1 175070 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.850;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=-4.501;QD=17.05;ReadPosRankSum=-1.284;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:591,0,501 -chr1 175078 . G T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.051;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.709;QD=17.24;ReadPosRankSum=-1.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:666,0,570 -chr1 175079 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.800;QD=17.35;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:670,0,560 -chr1 175082 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.533;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=4.587;QD=14.75;ReadPosRankSum=1.082;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:574,0,663 -chr1 175088 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.728;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.931;QD=16.17;ReadPosRankSum=-0.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:659,0,646 -chr1 175118 . A G 626.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.220;DP=33;Dels=0.00;FS=1.402;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.45;MQ0=0;MQRankSum=4.681;QD=18.99;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:655,0,376 -chr1 175131 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=32;Dels=0.00;FS=1.440;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-4.457;QD=11.06;ReadPosRankSum=1.226;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:382,0,689 -chr1 175191 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.635;DP=24;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.412;QD=1.41;ReadPosRankSum=-1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,5:24:62:62,0,696 -chr1 175195 . A G 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=24;Dels=0.00;FS=2.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=3.341;QD=27.91;ReadPosRankSum=0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:5,19:24:71:698,0,71 -chr1 175196 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.932;DP=23;Dels=0.00;FS=2.671;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.391;QD=1.90;ReadPosRankSum=-0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,5:23:72:72,0,661 -chr1 175215 . A C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=15.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-4.028;QD=6.64;ReadPosRankSum=-0.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:201,0,652 -chr1 175270 . T G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.924;DP=54;Dels=0.00;FS=2.436;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-5.061;QD=12.94;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:727,0,1094 -chr1 175316 . G A 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=-3.991;QD=13.74;ReadPosRankSum=1.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:674,0,909 -chr1 175333 . A G 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=41;Dels=0.00;FS=1.298;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=-4.353;QD=11.17;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:486,0,819 -chr1 175342 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.626;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-4.498;QD=9.69;ReadPosRankSum=0.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:416,0,840 -chr1 175343 . A G 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.450;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=-4.561;QD=9.21;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:406,0,870 -chr1 175351 . C T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.893;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-4.553;QD=8.76;ReadPosRankSum=-0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:370,0,874 -chr1 175354 . T A 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.347;QD=8.35;ReadPosRankSum=-0.626;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:329,0,790 -chr1 175364 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=34;Dels=0.00;FS=1.879;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=0;MQRankSum=-4.021;QD=4.35;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:176,0,882 -chr1 175462 . C T 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.111;DP=54;Dels=0.00;FS=9.949;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-4.141;QD=7.07;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:410,0,1172 -chr1 175465 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;DP=52;Dels=0.00;FS=7.479;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=50.66;MQ0=2;MQRankSum=-4.022;QD=7.53;ReadPosRankSum=-0.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,15:52:99:420,0,1104 -chr1 175476 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.975;DP=49;Dels=0.00;FS=9.035;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-4.277;QD=8.16;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:428,0,984 -chr1 175478 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.647;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-5.820;QD=8.67;ReadPosRankSum=4.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:453,0,901 -chr1 175489 . G A 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;DP=42;Dels=0.00;FS=4.393;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.18;MQ0=2;MQRankSum=-3.213;QD=10.16;ReadPosRankSum=4.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:455,0,695 -chr1 175502 . C T 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=37;Dels=0.00;FS=3.650;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=1;MQRankSum=-5.014;QD=10.10;ReadPosRankSum=3.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:402,0,770 -chr1 175510 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.695;DP=29;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=-4.339;QD=8.82;ReadPosRankSum=1.942;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:284,0,642 -chr1 175518 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.414;DP=29;Dels=0.00;FS=2.032;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=4.291;QD=21.16;ReadPosRankSum=-0.791;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:642,0,280 -chr1 175519 . T C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.728;DP=26;Dels=0.00;FS=1.927;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.53;MQ0=1;MQRankSum=-3.990;QD=6.95;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:209,0,614 -chr1 175583 . C G 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.905;DP=43;Dels=0.00;FS=3.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.67;MQ0=0;MQRankSum=-4.384;QD=4.32;ReadPosRankSum=-4.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:214,0,1136 -chr1 175588 . A T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=44;Dels=0.00;FS=1.379;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-4.418;QD=4.88;ReadPosRankSum=-2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:243,0,1139 -chr1 175611 . A C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=48;Dels=0.00;FS=1.311;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-4.679;QD=4.64;ReadPosRankSum=1.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:251,0,1281 -chr1 175833 . C A 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.203;QD=19.75;ReadPosRankSum=-1.203;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:3,6:9:88:206,0,88 -chr1 175887 . T A 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=31;Dels=0.00;FS=11.982;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=-0.104;QD=15.86;ReadPosRankSum=0.894;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:520,0,468 -chr1 175892 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=30;Dels=0.00;FS=11.831;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.240;QD=15.53;ReadPosRankSum=2.859;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:494,0,466 -chr1 175895 . T A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=30;Dels=0.00;FS=8.557;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=-0.982;QD=14.76;ReadPosRankSum=2.990;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,475 -chr1 175993 . C A 385.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.200;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=0;MQRankSum=-0.646;QD=16.77;ReadPosRankSum=0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:414,0,304 -chr1 176009 . T C 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=0.380;QD=16.09;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:350,0,229 -chr1 176036 . A T 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=21;Dels=0.00;FS=4.419;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=0.187;QD=19.32;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:7,14:21:99:434,0,213 -chr1 176158 . C G 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=26;Dels=0.00;FS=24.095;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=1.397;QD=10.95;ReadPosRankSum=-0.079;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:313,0,559 -chr1 176165 . T C 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=27;Dels=0.00;FS=25.156;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=0.979;QD=10.81;ReadPosRankSum=-0.226;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:320,0,588 -chr1 176174 . T C 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=23.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-0.381;QD=7.07;ReadPosRankSum=-0.064;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:198,0,602 -chr1 176293 . G A 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=17;Dels=0.00;FS=6.117;HaplotypeScore=12.9225;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=1.642;QD=21.99;ReadPosRankSum=2.774;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:4,13:17:99:402,0,106 -chr1 176308 . T A 420.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.556;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-2.302;QD=26.30;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:2,14:16:32:449,0,32 -chr1 176309 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=16;Dels=0.00;FS=6.317;HaplotypeScore=14.9199;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-1.637;QD=5.24;ReadPosRankSum=0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,4:16:99:112,0,330 -chr1 176346 . T A 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.960;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.11;MQ0=0;MQRankSum=-1.920;QD=5.44;ReadPosRankSum=-0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:137,0,516 -chr1 176350 . T C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440;DP=21;Dels=0.00;FS=7.501;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.68;MQ0=0;MQRankSum=0.662;QD=22.85;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:6,15:21:99:508,0,178 -chr1 176364 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.154;DP=30;Dels=0.00;FS=6.914;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-0.110;QD=9.29;ReadPosRankSum=-0.374;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:307,0,694 -chr1 176371 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.936;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=0.363;QD=9.24;ReadPosRankSum=-0.325;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:333,0,777 -chr1 176391 . A G 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.646;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.568;QD=8.05;ReadPosRankSum=-1.273;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:294,0,820 -chr1 176394 . G A 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.255;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.333;QD=8.39;ReadPosRankSum=-0.842;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:305,0,820 -chr1 176397 . C T 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338;DP=32;Dels=0.00;FS=9.755;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=0.427;QD=8.12;ReadPosRankSum=-1.037;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:288,0,782 -chr1 176402 . T A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.647;DP=34;Dels=0.00;FS=11.168;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=0.472;QD=19.23;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,20:34:99:682,0,440 -chr1 176422 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=43;Dels=0.00;FS=10.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.013;QD=10.02;ReadPosRankSum=0.716;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:459,0,874 -chr1 176432 . G T 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=44;Dels=0.00;FS=10.793;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.275;QD=19.24;ReadPosRankSum=-0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:875,0,599 -chr1 176471 . G C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;DP=39;Dels=0.00;FS=2.886;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.520;QD=15.99;ReadPosRankSum=-0.239;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:652,0,620 -chr1 176483 . T G 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.208;DP=46;Dels=0.00;FS=2.660;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.714;QD=16.23;ReadPosRankSum=-0.022;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:775,0,731 -chr1 176494 . G A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.467;DP=44;Dels=0.00;FS=4.658;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.705;QD=17.68;ReadPosRankSum=1.292;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:806,0,667 -chr1 176561 . T C 1205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=45;Dels=0.00;FS=7.565;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=26.79;ReadPosRankSum=-1.424;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,33:45:99:1234,0,358 -chr1 176568 . G C 285.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=44;Dels=0.00;FS=5.029;HaplotypeScore=20.3301;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;QD=6.49;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:314,0,1180 -chr1 176599 . G C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.076;QD=0.94;ReadPosRankSum=-0.227;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,4:37:63:63,0,1130 -chr1 176618 . C T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=49;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.553;QD=14.46;ReadPosRankSum=-2.864;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:737,0,944 -chr1 176635 . C T 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.787;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.075;QD=13.67;ReadPosRankSum=1.784;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:657,0,863 -chr1 176688 . T C 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.618;DP=44;Dels=0.00;FS=5.897;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=1;MQRankSum=-0.962;QD=18.13;ReadPosRankSum=0.110;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:826,0,625 -chr1 176761 . A T 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=1;MQRankSum=1.449;QD=2.15;ReadPosRankSum=-2.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,3:18:67:67,0,485 -chr1 177059 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.067;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.03;MQ0=24;MQRankSum=-1.333;QD=1.47;ReadPosRankSum=2.933;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,11:38:84:84,0,91 -chr1 177070 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=11.58;MQ0=27;MQRankSum=-0.689;QD=1.43;ReadPosRankSum=-2.793;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,9:39:84:84,0,91 -chr1 177252 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.667;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=10.59;MQ0=35;MQRankSum=-1.333;QD=1.14;ReadPosRankSum=-1.867;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,13:49:84:84,0,91 -chr1 177522 . A C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=0;MQRankSum=-1.692;QD=19.39;ReadPosRankSum=-0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,15:25:99:513,0,327 -chr1 177533 . A C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.661;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-1.713;QD=17.07;ReadPosRankSum=-0.415;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:472,0,360 -chr1 177668 . A G 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.893;QD=10.57;ReadPosRankSum=0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:430,0,785 -chr1 177672 . C G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.827;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.730;QD=11.08;ReadPosRankSum=0.438;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:427,0,755 -chr1 177673 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.730;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.990;QD=11.33;ReadPosRankSum=0.406;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:436,0,759 -chr1 177713 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.12;MQ0=0;MQRankSum=4.183;QD=19.34;ReadPosRankSum=0.383;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:705,0,508 -chr1 177736 . T G 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-4.078;QD=12.81;ReadPosRankSum=0.906;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:438,0,601 -chr1 177771 . C T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-4.477;QD=16.37;ReadPosRankSum=0.663;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:683,0,691 -chr1 177789 . A G 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.25;MQ0=0;MQRankSum=4.009;QD=13.47;ReadPosRankSum=1.245;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,20:46:99:648,0,869 -chr1 177795 . G T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.622;DP=44;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-1.983;QD=16.77;ReadPosRankSum=-0.270;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:766,0,709 -chr1 177797 . C T 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-2.636;QD=17.06;ReadPosRankSum=-0.595;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:762,0,706 -chr1 177814 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-2.138;QD=16.18;ReadPosRankSum=-0.047;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:740,0,797 -chr1 177863 . C A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.327;DP=44;Dels=0.00;FS=2.649;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.900;QD=18.79;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:855,0,637 -chr1 177874 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=46;Dels=0.00;FS=2.569;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.816;QD=14.93;ReadPosRankSum=-0.860;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:715,0,849 -chr1 177924 . T G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.175;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.467;QD=14.22;ReadPosRankSum=0.014;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:583,0,741 -chr1 177937 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.402;QD=13.92;ReadPosRankSum=-1.034;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:571,0,787 -chr1 177938 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.869;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.327;QD=14.73;ReadPosRankSum=-1.556;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:632,0,783 -chr1 177940 . C T 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-1.786;QD=17.81;ReadPosRankSum=1.645;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:812,0,687 -chr1 177955 . T C 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.014;QD=20.06;ReadPosRankSum=0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,28:48:99:991,0,659 -chr1 177959 . T G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=49;Dels=0.00;FS=1.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.359;QD=12.16;ReadPosRankSum=0.544;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:624,0,1063 -chr1 177992 . G A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.388;QD=17.00;ReadPosRankSum=0.466;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:878,0,780 -chr1 178064 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.137;QD=14.80;ReadPosRankSum=-0.229;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:576,0,654 -chr1 178089 . G C 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.777;DP=34;Dels=0.00;FS=3.270;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=1;MQRankSum=-0.777;QD=17.73;ReadPosRankSum=0.235;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:631,0,457 -chr1 178121 . C A 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=41;Dels=0.00;FS=1.294;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=-1.035;QD=19.46;ReadPosRankSum=0.676;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:826,0,488 -chr1 178255 . T C 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.918;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.153;QD=11.21;ReadPosRankSum=1.458;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:387,0,613 -chr1 178259 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.469;DP=29;Dels=0.00;FS=1.449;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.329;QD=13.89;ReadPosRankSum=1.206;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:431,0,537 -chr1 178261 . T A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.066;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.460;QD=12.41;ReadPosRankSum=1.250;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:388,0,533 -chr1 178263 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.963;DP=30;Dels=0.00;FS=1.484;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.879;QD=13.29;ReadPosRankSum=1.549;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,13:30:99:427,0,582 -chr1 178287 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.465;QD=12.47;ReadPosRankSum=-0.575;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:340,0,480 -chr1 178289 . G C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.205;QD=11.87;ReadPosRankSum=-0.263;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,481 -chr1 178299 . A T 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=23;Dels=0.00;FS=1.674;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.403;QD=11.42;ReadPosRankSum=-0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:291,0,437 -chr1 178322 . G A 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.414;DP=26;Dels=0.00;FS=5.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.723;QD=14.53;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:406,0,467 -chr1 178360 . A G 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=39;Dels=0.00;FS=9.536;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.169;QD=13.33;ReadPosRankSum=0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:548,0,674 -chr1 178364 . T A 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=42;Dels=0.00;FS=6.822;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.639;QD=13.02;ReadPosRankSum=0.928;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:575,0,786 -chr1 178406 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=3.905;QD=16.45;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:637,0,616 -chr1 178470 . C T 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=34;Dels=0.00;FS=2.928;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-2.467;QD=17.46;ReadPosRankSum=-1.570;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:622,0,545 -chr1 178476 . G T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.884;QD=8.63;ReadPosRankSum=1.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,611 -chr1 178477 . A G 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.269;DP=26;Dels=0.00;FS=1.596;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.910;QD=9.80;ReadPosRankSum=0.701;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:283,0,607 -chr1 178478 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.466;QD=8.11;ReadPosRankSum=1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:231,0,607 -chr1 178481 . A G 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.408;QD=8.63;ReadPosRankSum=1.486;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,606 -chr1 178485 . T C 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.141;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.540;QD=11.53;ReadPosRankSum=0.329;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:351,0,575 -chr1 178493 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-2.900;QD=12.23;ReadPosRankSum=1.207;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,593 -chr1 178499 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.953;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.630;QD=12.23;ReadPosRankSum=1.503;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,603 -chr1 178504 . A G 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=28;Dels=0.00;FS=1.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.019;QD=13.17;ReadPosRankSum=0.998;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:397,0,533 -chr1 178548 . T C 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.026;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.451;QD=11.14;ReadPosRankSum=-0.975;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:318,0,550 -chr1 178628 . A G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.831;DP=38;Dels=0.00;FS=1.378;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-1.015;QD=9.68;ReadPosRankSum=0.708;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:396,0,801 -chr1 178645 . G T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=31;Dels=0.00;FS=1.525;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.35;MQ0=0;MQRankSum=-0.152;QD=7.54;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:262,0,672 -chr1 178740 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.796;DP=26;Dels=0.00;FS=6.166;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.19;MQ0=11;MQRankSum=-1.408;QD=1.41;ReadPosRankSum=-0.674;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,8:26:65:65,0,324 -chr1 178796 . T C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.153;DP=25;Dels=0.00;FS=6.726;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.15;MQ0=9;MQRankSum=0.404;QD=2.11;ReadPosRankSum=2.153;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,10:25:81:81,0,383 -chr1 178979 . T C 232.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.041;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.286;QD=12.25;ReadPosRankSum=-0.041;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,9:19:99:261,0,334 -chr1 179198 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.885;DP=40;Dels=0.00;FS=9.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=3;MQRankSum=4.522;QD=12.94;ReadPosRankSum=2.437;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:546,0,642 -chr1 179320 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=4.336;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-0.475;QD=15.77;ReadPosRankSum=0.578;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:785,0,835 -chr1 179364 . T G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.428;DP=58;Dels=0.00;FS=7.156;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.284;QD=17.29;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1031,0,933 -chr1 179511 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=55;Dels=0.00;FS=1.064;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=1.179;QD=14.23;ReadPosRankSum=1.655;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:811,0,1053 -chr1 179518 . C T 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.855;QD=5.68;ReadPosRankSum=-0.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:318,0,1406 -chr1 179542 . C T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.582;DP=59;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.05;MQ0=0;MQRankSum=2.112;QD=5.64;ReadPosRankSum=-0.814;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:361,0,1612 -chr1 179564 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=67;Dels=0.00;FS=6.477;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.831;QD=16.70;ReadPosRankSum=-0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,34:67:99:1147,0,1135 -chr1 179762 . G A 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=51;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.21;MQ0=0;MQRankSum=-1.618;QD=18.31;ReadPosRankSum=-0.407;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:962,0,770 -chr1 179884 . G C 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=28;Dels=0.00;FS=4.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.47;MQ0=0;MQRankSum=-1.658;QD=11.03;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:337,0,516 -chr1 179951 . C T 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.506;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=61.42;MQ0=0;MQRankSum=-2.488;QD=11.47;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:579,0,987 -chr1 180063 . G T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.238;QD=18.63;ReadPosRankSum=-0.015;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1146,0,891 -chr1 180136 . T A 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.350;QD=16.88;ReadPosRankSum=-0.012;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:754,0,646 -chr1 180164 . C T 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.143;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.075;QD=14.02;ReadPosRankSum=1.546;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:687,0,853 -chr1 180372 . A C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.314;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=-1.285;QD=16.26;ReadPosRankSum=0.671;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:646,0,633 -chr1 180463 . T A 537.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.550;DP=35;Dels=0.00;FS=1.423;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=1;MQRankSum=2.273;QD=15.36;ReadPosRankSum=-0.517;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:566,0,578 -chr1 180470 . G C 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=36;Dels=0.00;FS=1.373;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=3.571;QD=16.24;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,18:36:99:613,0,506 -chr1 180531 . A C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=1;MQRankSum=0.486;QD=16.20;ReadPosRankSum=-0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:579,0,522 -chr1 180708 . G A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=24;Dels=0.00;FS=4.269;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.223;QD=24.12;ReadPosRankSum=0.953;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S43N|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:7,17:24:99:607,0,206 -chr1 180728 . A G 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.774;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.437;QD=9.58;ReadPosRankSum=-0.489;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R50G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:18,9:27:99:287,0,626 -chr1 180758 . C T 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=25;Dels=0.00;FS=13.757;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.027;QD=12.87;ReadPosRankSum=1.068;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L60F|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:14,11:25:99:350,0,458 -chr1 181012 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.249;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.6617;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.626;QD=23.03;ReadPosRankSum=-0.542;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,20:29:99:696,0,216 -chr1 181024 . C A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.742;QD=20.41;ReadPosRankSum=1.506;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:620,0,319 -chr1 181102 . T G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=33;Dels=0.00;FS=3.837;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.862;QD=17.27;ReadPosRankSum=0.560;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:598,0,487 -chr1 181156 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.560;QD=12.49;ReadPosRankSum=-0.429;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,10:22:99:303,0,376 -chr1 181173 . A C 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=15;Dels=0.00;FS=3.256;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.59;MQ0=0;MQRankSum=0.884;QD=11.45;ReadPosRankSum=-0.648;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:200,0,268 -chr1 181194 . A G 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=19;Dels=0.00;FS=2.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=2.149;QD=7.51;ReadPosRankSum=-2.850;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:171,0,426 -chr1 181276 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=-0.905;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,13:36:99:431,0,793 -chr1 181325 . G C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=2.299;HaplotypeScore=1.8279;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=-1.711;QD=9.16;ReadPosRankSum=0.678;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:239,0,509 -chr1 181340 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.025;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=56.31;MQ0=0;MQRankSum=-1.259;QD=11.87;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,471 -chr1 181363 . C T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.002;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.743;QD=9.21;ReadPosRankSum=0.936;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:240,0,515 -chr1 181373 . C G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.033;DP=23;Dels=0.00;FS=3.982;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.033;QD=8.99;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:235,0,521 -chr1 181378 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.646;DP=23;Dels=0.00;FS=4.200;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=3.647;QD=19.64;ReadPosRankSum=-1.130;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:480,0,235 -chr1 181520 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.692;DP=35;Dels=0.00;FS=3.290;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=2;MQRankSum=-3.125;QD=7.62;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:295,0,721 -chr1 181569 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.437;DP=41;Dels=0.00;FS=11.992;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.50;MQ0=0;MQRankSum=-0.807;QD=11.26;ReadPosRankSum=0.463;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:490,0,840 -chr1 181583 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=39;Dels=0.00;FS=8.484;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-1.317;QD=12.25;ReadPosRankSum=1.827;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:506,0,762 -chr1 181595 . G A 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=37;Dels=0.00;FS=9.049;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-1.322;QD=14.13;ReadPosRankSum=0.319;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:551,0,655 -chr1 181678 . C A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.180;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=11.4067;MLEAC=1;MLEAF=0.500;MQ=54.06;MQ0=0;MQRankSum=-0.467;QD=4.27;ReadPosRankSum=2.335;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,3:14:88:88,0,315 -chr1 181932 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.890;DP=42;Dels=0.00;FS=2.883;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=0;MQRankSum=-0.630;QD=20.26;ReadPosRankSum=0.577;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C159R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:15,27:42:99:879,0,440 -chr1 182026 . T G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=1.966;QD=13.51;ReadPosRankSum=0.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L190R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,608 -chr1 182100 . A G 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.141;DP=37;Dels=0.00;FS=16.118;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=2.302;QD=20.29;ReadPosRankSum=-0.955;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R215G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:14,23:37:99:779,0,366 -chr1 182108 . G A 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=39;Dels=0.00;FS=10.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.794;QD=9.92;ReadPosRankSum=0.188;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S217|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:24,15:39:99:415,0,775 -chr1 182198 . G A 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.182;QD=17.62;ReadPosRankSum=0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L247|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:16,19:35:99:645,0,523 -chr1 182199 . A T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.475;QD=17.35;ReadPosRankSum=0.792;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M248L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:17,19:36:99:653,0,531 -chr1 182291 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.930;DP=43;Dels=0.00;FS=26.079;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.032;QD=9.86;ReadPosRankSum=-0.828;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V278|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:28,15:43:99:452,0,940 -chr1 182317 . C T 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=43;Dels=0.00;FS=22.687;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-0.239;QD=11.09;ReadPosRankSum=1.018;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:505,0,912 -chr1 182395 . C T 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.875;DP=36;Dels=0.00;FS=3.014;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.462;QD=13.88;ReadPosRankSum=-2.786;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:528,0,655 -chr1 182404 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=42;Dels=0.00;FS=1.218;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=0.834;QD=17.09;ReadPosRankSum=0.430;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),SPLICE_SITE_ACCEPTOR(HIGH||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:746,0,627 -chr1 182424 . G A 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.760;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.738;QD=17.82;ReadPosRankSum=0.952;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A287|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:21,26:47:99:866,0,703 -chr1 182545 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.911;DP=38;Dels=0.00;FS=1.257;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.986;QD=11.26;ReadPosRankSum=-1.015;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V328I|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:23,15:38:99:456,0,764 -chr1 182610 . A G 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-2.012;QD=10.40;ReadPosRankSum=1.873;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:382,0,506 -chr1 182637 . T C 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.289;DP=36;Dels=0.00;FS=8.730;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=-2.372;QD=17.99;ReadPosRankSum=1.735;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:676,0,448 -chr1 182641 . T C 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=38;Dels=0.00;FS=13.898;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=-2.511;QD=14.86;ReadPosRankSum=2.365;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:593,0,579 -chr1 182648 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.525;DP=35;Dels=0.00;FS=17.460;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.723;QD=15.34;ReadPosRankSum=2.228;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:565,0,436 -chr1 182657 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=46;Dels=0.00;FS=7.638;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.778;QD=18.06;ReadPosRankSum=-1.934;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:859,0,438 -chr1 182668 . T C 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.640;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=5.9516;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.805;QD=14.92;ReadPosRankSum=-0.685;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:774,0,262 -chr1 182674 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=30.8083;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=-4.923;QD=15.46;ReadPosRankSum=-1.147;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,27:47:99:755,0,282 -chr1 182756 . A G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=40;Dels=0.00;FS=6.474;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.783;QD=5.17;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,9:40:99:235,0,1016 -chr1 182758 . G A 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.359;DP=40;Dels=0.00;FS=9.072;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-1.078;QD=5.67;ReadPosRankSum=0.672;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:255,0,986 -chr1 182775 . T G 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=44;Dels=0.00;FS=3.185;HaplotypeScore=2.9961;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.227;QD=11.61;ReadPosRankSum=-2.232;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:539,0,817 -chr1 182800 . A T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=41;Dels=0.00;FS=1.435;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.552;QD=14.73;ReadPosRankSum=0.039;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:632,0,657 -chr1 182818 . G T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.464;QD=16.27;ReadPosRankSum=1.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A353S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:565,0,472 -chr1 182821 . T G 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4440;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.284;QD=15.90;ReadPosRankSum=1.392;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S354A|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:553,0,504 -chr1 182977 . A G 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=61;Dels=0.00;FS=1.012;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.470;QD=13.67;ReadPosRankSum=1.411;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I406V|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:33,28:61:99:862,0,1096 -chr1 183001 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.024;DP=56;Dels=0.00;FS=2.198;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=1.958;QD=15.73;ReadPosRankSum=0.156;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L414|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:28,28:56:99:909,0,927 -chr1 183099 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.462;QD=15.10;ReadPosRankSum=-1.154;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L446|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:723,0,679 -chr1 183112 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-1.631;QD=13.93;ReadPosRankSum=-1.738;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S451C|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:683,0,847 -chr1 183122 . A G 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.754;DP=49;Dels=0.00;FS=6.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.010;QD=14.34;ReadPosRankSum=-1.538;EFF=SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*454|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:731,0,933 -chr1 183180 . A T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=53;Dels=0.00;FS=2.623;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=-0.670;QD=13.92;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:766,0,944 -chr1 183206 . C T 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=47;Dels=0.00;FS=2.919;HaplotypeScore=3.7882;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.613;QD=12.29;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:606,0,947 -chr1 183264 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=38;Dels=0.00;FS=1.237;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-2.646;QD=15.47;ReadPosRankSum=0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:616,0,690 -chr1 183410 . C A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.9453;MLEAC=1;MLEAF=0.500;MQ=55.82;MQ0=0;MQRankSum=-1.739;QD=4.72;ReadPosRankSum=-2.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:184,0,765 -chr1 184039 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=17;Dels=0.00;FS=11.761;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=14.06;MQ0=10;MQRankSum=1.300;QD=3.87;ReadPosRankSum=1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:12,5:17:39:94,0,39 -chr1 184048 . G A 68.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;DP=14;Dels=0.00;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.98;MQ0=8;MQRankSum=0.000;QD=4.91;ReadPosRankSum=1.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,6:14:25:97,0,25 -chr1 184967 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.750;DP=26;Dels=0.00;FS=4.435;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.68;MQ0=0;MQRankSum=-3.139;QD=6.91;ReadPosRankSum=-2.639;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:208,0,643 -chr1 184971 . G C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=27;Dels=0.00;FS=6.965;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.77;MQ0=0;MQRankSum=-3.060;QD=8.84;ReadPosRankSum=-1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,9:27:99:267,0,627 -chr1 184992 . C A 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=30;Dels=0.00;FS=3.779;HaplotypeScore=7.2988;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=0;MQRankSum=-3.443;QD=10.59;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:346,0,566 -chr1 184999 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.172;DP=36;Dels=0.00;FS=2.798;HaplotypeScore=2.3001;MLEAC=1;MLEAF=0.500;MQ=57.43;MQ0=0;MQRankSum=-2.789;QD=16.38;ReadPosRankSum=-2.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:618,0,532 -chr1 185038 . A T 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=37;Dels=0.00;FS=5.015;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-0.820;QD=19.32;ReadPosRankSum=2.088;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:743,0,477 -chr1 185039 . T A 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=39;Dels=0.00;FS=4.649;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.736;QD=11.46;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:475,0,785 -chr1 185068 . A T 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.341;DP=40;Dels=0.00;FS=6.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=1.559;QD=19.29;ReadPosRankSum=0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:800,0,540 -chr1 185070 . C G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.801;QD=18.68;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:794,0,571 -chr1 185084 . C A 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=41;Dels=0.00;FS=6.934;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.781;QD=18.95;ReadPosRankSum=-0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:805,0,519 -chr1 185096 . A G 492.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=37;Dels=0.00;FS=5.209;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.383;QD=13.32;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:521,0,697 -chr1 185129 . C A 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.123;DP=36;Dels=0.00;FS=2.788;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.459;QD=15.88;ReadPosRankSum=0.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:600,0,584 -chr1 185138 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656;DP=37;Dels=0.00;FS=1.289;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=1.595;QD=14.70;ReadPosRankSum=-0.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:572,0,645 -chr1 185141 . G A 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-1.139;QD=15.31;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:564,0,590 -chr1 185145 . G T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.115;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.139;QD=14.36;ReadPosRankSum=0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:502,0,598 -chr1 185186 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.484;DP=37;Dels=0.00;FS=1.280;HaplotypeScore=19.3302;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.960;QD=16.40;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:635,0,578 -chr1 185222 . T A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.397;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.101;QD=16.48;ReadPosRankSum=1.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:770,0,755 -chr1 185241 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.103;QD=15.31;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:763,0,865 -chr1 185245 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.619;QD=15.29;ReadPosRankSum=-0.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:762,0,868 -chr1 185259 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=49;Dels=0.00;FS=2.460;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.136;QD=13.95;ReadPosRankSum=-0.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:712,0,900 -chr1 185264 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.367;DP=52;Dels=0.00;FS=1.072;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-1.606;QD=14.51;ReadPosRankSum=-1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:783,0,962 -chr1 185289 . C T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-1.022;QD=12.65;ReadPosRankSum=-0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:623,0,933 -chr1 185299 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=16.4921;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=-2.184;QD=11.52;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:535,0,917 -chr1 185346 . C T 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=33;Dels=0.00;FS=8.695;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-3.050;QD=9.45;ReadPosRankSum=1.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:340,0,747 -chr1 185347 . A G 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=33;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.826;QD=10.57;ReadPosRankSum=1.890;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:377,0,759 -chr1 185372 . T C 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=29;Dels=0.00;FS=17.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-4.382;QD=8.51;ReadPosRankSum=0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:275,0,692 -chr1 185376 . C G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.478;DP=28;Dels=0.00;FS=21.622;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=5.49;ReadPosRankSum=1.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:182,0,778 -chr1 185383 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=28;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.24;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:147,0,783 -chr1 185387 . A G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.478;DP=28;Dels=0.00;FS=19.859;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.81;ReadPosRankSum=0.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:163,0,736 -chr1 185394 . A C 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=27;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-3.703;QD=4.25;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:143,0,783 -chr1 185401 . T A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.242;DP=29;Dels=0.00;FS=15.529;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-3.742;QD=3.85;ReadPosRankSum=-0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,6:29:99:140,0,846 -chr1 185689 . A C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.167;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.58;MQ0=1;MQRankSum=-2.906;QD=7.24;ReadPosRankSum=-1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,8:24:99:202,0,578 -chr1 185717 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=33;Dels=0.00;FS=3.365;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=1;MQRankSum=-1.880;QD=10.51;ReadPosRankSum=0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:375,0,665 -chr1 185726 . G C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=39;Dels=0.00;FS=4.887;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=-2.190;QD=15.22;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:622,0,634 -chr1 185747 . A T 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-1.881;QD=20.81;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:923,0,453 -chr1 185776 . A G 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.350;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=1;MQRankSum=-1.287;QD=22.38;ReadPosRankSum=2.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,28:39:99:901,0,314 -chr1 185800 . C T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.468;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.9825;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=1;MQRankSum=-0.406;QD=25.35;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,23:28:89:738,0,89 -chr1 185804 . T G 590.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=28;Dels=0.00;FS=8.073;HaplotypeScore=5.6476;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=1;MQRankSum=1.135;QD=21.10;ReadPosRankSum=0.436;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:3,22:28:16:690,0,16 -chr1 185818 . T G 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=24;Dels=0.00;FS=2.570;HaplotypeScore=2.9824;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=1;MQRankSum=1.176;QD=24.03;ReadPosRankSum=-0.852;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:4,20:24:53:605,0,53 -chr1 186043 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=38;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.26;MQ0=5;MQRankSum=-1.963;QD=15.02;ReadPosRankSum=-2.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:599,0,549 -chr1 186081 . A G 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-0.474;QD=15.86;ReadPosRankSum=2.879;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:710,0,742 -chr1 186083 . T A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=2.928;QD=16.48;ReadPosRankSum=-2.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:737,0,714 -chr1 186128 . C G 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=19.8272;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.043;QD=12.22;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,16:39:99:505,0,805 -chr1 186205 . G C 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=52;Dels=0.00;FS=2.716;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=7;MQRankSum=0.198;QD=8.55;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,19:52:99:473,0,903 -chr1 186248 . C T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=39;Dels=0.00;FS=2.991;HaplotypeScore=12.5646;MLEAC=1;MLEAF=0.500;MQ=51.44;MQ0=4;MQRankSum=-0.750;QD=13.92;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:571,0,491 -chr1 186252 . T C 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=38;Dels=0.00;FS=1.412;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=52.11;MQ0=3;MQRankSum=-1.250;QD=14.41;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:576,0,472 -chr1 186263 . T C 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=45;Dels=0.00;FS=1.264;HaplotypeScore=23.4286;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=2.794;QD=10.37;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:495,0,824 -chr1 186273 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=50;Dels=0.00;FS=8.671;HaplotypeScore=22.6968;MLEAC=1;MLEAF=0.500;MQ=55.43;MQ0=1;MQRankSum=3.184;QD=12.62;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:659,0,894 -chr1 186302 . T C 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=49;Dels=0.00;FS=5.993;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.254;QD=19.63;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:990,0,585 -chr1 186305 . G A 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;DP=45;Dels=0.00;FS=2.751;HaplotypeScore=2.8649;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.332;QD=18.73;ReadPosRankSum=-0.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:871,0,521 -chr1 186318 . T C 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=2.087;QD=10.03;ReadPosRankSum=-0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:560,0,1118 -chr1 186396 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.37;MQ0=0;MQRankSum=-1.756;QD=22.10;ReadPosRankSum=-2.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,16:18:34:426,0,34 -chr1 186407 . T C 557.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.691;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.89;MQ0=0;MQRankSum=-1.909;QD=24.25;ReadPosRankSum=-2.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,21:23:20:586,0,20 -chr1 186440 . C A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;DP=31;Dels=0.00;FS=19.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.71;MQ0=0;MQRankSum=3.153;QD=1.48;ReadPosRankSum=-2.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,4:31:74:74,0,835 -chr1 186454 . C T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.649;DP=34;Dels=0.00;FS=22.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-3.817;QD=27.05;ReadPosRankSum=2.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,28:34:99:948,0,144 -chr1 186460 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=32;Dels=0.00;FS=17.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.19;MQ0=0;MQRankSum=-3.790;QD=26.90;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,26:32:99:889,0,146 -chr1 186464 . T C 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=34;Dels=0.00;FS=19.762;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.63;MQ0=0;MQRankSum=-4.046;QD=25.85;ReadPosRankSum=1.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:7,27:34:99:907,0,182 -chr1 186478 . T C 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=-3.990;QD=21.03;ReadPosRankSum=-0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,17:25:99:554,0,243 -chr1 186480 . A C 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=3.932;QD=8.51;ReadPosRankSum=1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:241,0,553 -chr1 186485 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.47;ReadPosRankSum=-1.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:499,0,249 -chr1 186488 . C T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=19.60;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:479,0,255 -chr1 186496 . G T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.613;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.16;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:492,0,235 -chr1 186499 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.12;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:491,0,247 -chr1 186500 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.08;ReadPosRankSum=-0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:490,0,245 -chr1 186522 . A G 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.47;MQ0=0;MQRankSum=3.201;QD=8.57;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:191,0,365 -chr1 186527 . T A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.452;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.08;MQ0=0;MQRankSum=-3.138;QD=14.60;ReadPosRankSum=0.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,12:18:99:291,0,198 -chr1 186562 . C T 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=12;Dels=0.00;FS=6.818;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=0;MQRankSum=2.637;QD=8.15;ReadPosRankSum=0.825;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,4:12:99:126,0,256 -chr1 186590 . T C 44.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=14.93;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26 -chr1 186605 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=28;Dels=0.00;FS=12.091;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=3.575;QD=20.53;ReadPosRankSum=-3.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,17:28:99:603,0,347 -chr1 186611 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.843;QD=11.44;ReadPosRankSum=2.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:360,0,648 -chr1 186614 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.798;QD=11.72;ReadPosRankSum=2.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:368,0,655 -chr1 186624 . C T 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.559;DP=34;Dels=0.00;FS=11.031;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.146;QD=11.32;ReadPosRankSum=2.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:413,0,758 -chr1 186629 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.439;DP=38;Dels=0.00;FS=8.924;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=4.390;QD=20.20;ReadPosRankSum=-0.695;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:796,0,505 -chr1 186658 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=53;Dels=0.00;FS=6.435;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-3.592;QD=11.94;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:661,0,1102 -chr1 186661 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.611;DP=54;Dels=0.00;FS=6.487;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=0;MQRankSum=-3.283;QD=12.29;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:692,0,1121 -chr1 186663 . C T 1074.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=57;Dels=0.00;FS=8.033;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=3.964;QD=18.86;ReadPosRankSum=1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1103,0,821 -chr1 186666 . G A 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=56;Dels=0.00;FS=6.180;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=3.767;QD=19.30;ReadPosRankSum=0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1109,0,798 -chr1 186683 . A C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=53;Dels=0.00;FS=1.158;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-3.312;QD=12.86;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:710,0,1078 -chr1 186695 . C T 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=4.002;QD=16.74;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:765,0,705 -chr1 186696 . C T 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=3.924;QD=17.18;ReadPosRankSum=0.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:767,0,660 -chr1 186702 . C T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.286;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.080;QD=13.35;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:629,0,825 -chr1 186707 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.738;QD=15.75;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:737,0,782 -chr1 186723 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.815;DP=40;Dels=0.00;FS=2.843;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.650;QD=16.19;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:676,0,656 -chr1 186725 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.588;QD=16.65;ReadPosRankSum=-1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:711,0,635 -chr1 186730 . C T 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=6.398;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.477;QD=2.81;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:36,7:43:99:149,0,1300 -chr1 186735 . T C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.621;DP=43;Dels=0.00;FS=4.425;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.278;QD=14.62;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:657,0,661 -chr1 186738 . C T 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.029;DP=43;Dels=0.00;FS=1.242;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.109;QD=14.95;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:671,0,692 -chr1 186800 . T C 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.519;QD=17.51;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:921,0,810 -chr1 186853 . A G 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.007;DP=60;Dels=0.00;FS=1.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.037;QD=13.25;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:823,0,1142 -chr1 186856 . A G 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.735;QD=17.49;ReadPosRankSum=1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1095,0,816 -chr1 186922 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=39;Dels=0.00;FS=10.184;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.363;QD=15.74;ReadPosRankSum=0.576;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:642,0,675 -chr1 186958 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=38;Dels=0.00;FS=9.513;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.015;QD=15.89;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:632,0,693 -chr1 186990 . T A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.733;DP=43;Dels=0.00;FS=1.194;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=1.494;QD=16.67;ReadPosRankSum=-0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:745,0,730 -chr1 186991 . G A 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.624;DP=42;Dels=0.00;FS=1.170;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-2.632;QD=15.64;ReadPosRankSum=0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:685,0,742 -chr1 186992 . C T 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.654;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.503;QD=15.31;ReadPosRankSum=0.980;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:656,0,735 -chr1 187055 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.270;DP=49;Dels=0.00;FS=6.133;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.990;QD=15.77;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:801,0,876 -chr1 187064 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=47;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.075;QD=16.42;ReadPosRankSum=-0.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:800,0,846 -chr1 187065 . G A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=46;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.923;QD=16.71;ReadPosRankSum=-1.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:797,0,815 -chr1 187147 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=1.192;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.400;QD=15.06;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:676,0,759 -chr1 187173 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=1.128;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.970;QD=15.78;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:833,0,844 -chr1 187185 . A T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.328;DP=59;Dels=0.00;FS=1.046;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.148;QD=15.59;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:948,0,1051 -chr1 187200 . T C 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286;DP=70;Dels=0.00;FS=12.081;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=0;MQRankSum=-5.431;QD=3.13;ReadPosRankSum=-3.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:58,12:70:99:247,0,2146 -chr1 187208 . T G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=73;Dels=0.00;FS=9.609;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=-5.455;QD=2.83;ReadPosRankSum=-2.746;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:61,12:73:99:235,0,2122 -chr1 187209 . A C 990.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=73;Dels=0.00;FS=1.959;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=2.896;QD=13.57;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:42,31:73:99:1019,0,1427 -chr1 187247 . G A 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.510;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.33;MQ0=0;MQRankSum=-1.357;QD=19.20;ReadPosRankSum=-1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1084,0,781 -chr1 187248 . G T 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.193;DP=53;Dels=0.00;FS=3.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-1.911;QD=18.18;ReadPosRankSum=-0.763;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:992,0,786 -chr1 187270 . C G 518.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=38;Dels=0.00;FS=2.937;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-5.255;QD=13.65;ReadPosRankSum=3.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:547,0,742 -chr1 187298 . C T 1101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=0;MQRankSum=0.258;QD=21.60;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,36:51:99:1130,0,459 -chr1 187362 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=38;Dels=0.00;FS=1.434;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=4;MQRankSum=-2.189;QD=9.18;ReadPosRankSum=0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:377,0,655 -chr1 187753 . T C 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.068;DP=59;Dels=0.00;FS=1.104;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=0.555;QD=14.44;ReadPosRankSum=-5.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:880,0,1099 -chr1 187793 . T C 1189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=15.7240;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.945;QD=19.83;ReadPosRankSum=3.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1218,0,816 -chr1 187844 . T C 876.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.394;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.259;QD=21.38;ReadPosRankSum=-0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,26:41:99:905,0,488 -chr1 187894 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=46;Dels=0.00;FS=4.031;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.055;QD=15.97;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:763,0,746 -chr1 187903 . C T 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=46;Dels=0.00;FS=6.439;HaplotypeScore=4.0994;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=0.791;QD=16.86;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:804,0,717 -chr1 188013 . T A 834.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.291;QD=16.37;ReadPosRankSum=0.725;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:863,0,808 -chr1 188103 . G A 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073;DP=55;Dels=0.00;FS=4.032;HaplotypeScore=2.6641;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.347;QD=14.07;ReadPosRankSum=0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:30,25:55:99:802,0,993 -chr1 188173 . G A 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=42;Dels=0.00;FS=2.786;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=16.61;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:20,22:42:99:726,0,669 -chr1 188266 . A G 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:28,27:56:99:907,0,965 -chr1 188270 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,27:54:99:879,0,898 -chr1 188311 . T G 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,28:53:99:930,0,831 -chr1 188364 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,770 -chr1 188393 . T C 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:24,18:42:99:544,0,828 -chr1 188395 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:23,18:41:99:572,0,791 -chr1 188416 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,14:39:99:426,0,821 -chr1 188438 . C A 930.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:21,29:50:99:959,0,659 -chr1 188621 . G A 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,22:49:99:733,0,926
--- a/VCFToolFilter/test-data/sample.vcf Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5000 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER=<ID=LowQual,Description="Low quality"> -##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> -##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> -##contig=<ID=chr1,length=38193400> -##contig=<ID=chr10,length=27624748> -##contig=<ID=chr11,length=33540656> -##contig=<ID=chr2,length=54522928> -##contig=<ID=chr3,length=32030951> -##contig=<ID=chr4,length=28191985> -##contig=<ID=chr5,length=29137935> -##contig=<ID=chr6,length=37293965> -##contig=<ID=chr7,length=29833120> -##contig=<ID=chr8,length=31585744> -##contig=<ID=chr9,length=22352177> -##contig=<ID=chr0,length=205603396> -##reference=file:///data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta -##SnpEffVersion="2.0.5d (build 2012-01-19), by Pablo Cingolani" -##SnpEffCmd="SnpEff eff coffea /apps/www/sniplay.cirad.fr/data/Coffee/Argemo_genomic.nonannotated.vcf.2 -i VCF -o VCF -c snpEff.config " -##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' "> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 -chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 -chr1 2232 . A C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;QD=11.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr1 2264 . C T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=5;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=0.358;QD=13.75;ReadPosRankSum=-1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:2,3:5:53:97,0,53 -chr1 2353 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.5027;MLEAC=1;MLEAF=0.500;MQ=31.07;MQ0=3;MQRankSum=0.261;QD=1.18;ReadPosRankSum=-1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:19,7:26:59:59,0,409 -chr1 2482 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.294;DP=19;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=26.95;MQ0=7;MQRankSum=0.370;QD=10.94;ReadPosRankSum=-1.109;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:5,14:19:83:236,0,83 -chr1 2558 . A T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=45;Dels=0.00;FS=4.170;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=28.40;MQ0=13;MQRankSum=0.121;QD=17.55;ReadPosRankSum=-0.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,32:45:99:818,0,101 -chr1 2925 . A T 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.619;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=5.7776;MLEAC=1;MLEAF=0.500;MQ=38.24;MQ0=1;MQRankSum=0.372;QD=17.59;ReadPosRankSum=-1.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:380,0,275 -chr1 2941 . A G 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.63;MQ0=1;MQRankSum=1.524;QD=14.78;ReadPosRankSum=0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:7,8:15:99:250,0,227 -chr1 2985 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.19;MQ0=8;QD=6.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:7,4:11:9:101,9,0 -chr1 3705 . G T 103.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.32;MQ0=0;QD=14.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:131,12,0 -chr1 3745 . A T 180.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.44;MQ0=0;QD=22.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:209,18,0 -chr1 3864 . C T 33.74 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.81;MQ0=4;QD=3.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,9:9:6:61,6,0 -chr1 3887 . G C 131.9 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.03;MQ0=5;QD=6.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,22:22:15:160,15,0 -chr1 3944 . G T 182.84 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.63;MQ0=5;QD=7.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,25:25:18:211,18,0 -chr1 4109 . C T 151.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.59;MQ0=0;QD=21.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:180,15,0 -chr1 4438 . T C 90.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.849;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.69;MQ0=2;MQRankSum=2.700;QD=6.00;ReadPosRankSum=-2.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:10,5:15:12:118,12,0 -chr1 4555 . G A 51.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.51;MQ0=0;QD=17.25;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:79,6,0 -chr1 4733 . C G 135.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.22;MQ0=0;QD=22.51;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:163,12,0 -chr1 4879 . T C 114.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.81;MQ0=0;QD=19.01;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:142,12,0 -chr1 4945 . G A 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=29;Dels=0.00;FS=3.123;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.25;MQ0=1;MQRankSum=3.132;QD=11.10;ReadPosRankSum=3.363;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,15:29:43:350,0,43 -chr1 4947 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.742;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.38;MQ0=1;MQRankSum=3.401;QD=11.64;ReadPosRankSum=3.360;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:16,15:31:40:389,0,40 -chr1 4961 . C T 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.427;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.65;MQ0=1;MQRankSum=-3.749;QD=0.99;ReadPosRankSum=-0.165;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,25:43:71:71,0,437 -chr1 4967 . T C 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.980;DP=41;Dels=0.00;FS=1.219;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=26.25;MQ0=1;MQRankSum=4.072;QD=10.09;ReadPosRankSum=-0.897;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,16:41:70:442,0,70 -chr1 4981 . A C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=6.8693;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=3.500;QD=6.80;ReadPosRankSum=-1.759;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,11:36:88:273,0,88 -chr1 4987 . T G 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.583;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=13.8254;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=-2.450;QD=1.66;ReadPosRankSum=1.983;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,15:36:88:88,0,296 -chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0 -chr1 5110 . A G 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.328;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.75;MQ0=3;MQRankSum=-0.421;QD=4.51;ReadPosRankSum=-1.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:123,0,278 -chr1 5170 . A G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.23;MQ0=2;MQRankSum=0.212;QD=3.65;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,7:15:83:83,0,127 -chr1 5171 . T G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=26.11;MQ0=1;MQRankSum=0.212;QD=3.91;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,6:14:83:83,0,122 -chr1 5284 . A C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.9827;MLEAC=1;MLEAF=0.500;MQ=34.72;MQ0=1;MQRankSum=-0.784;QD=3.49;ReadPosRankSum=-1.445;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:105,0,410 -chr1 5324 . C T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=3;MQRankSum=1.491;QD=10.44;ReadPosRankSum=-0.818;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:10,10:20:99:237,0,166 -chr1 5361 . A G 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=24.40;MQ0=2;MQRankSum=1.412;QD=11.41;ReadPosRankSum=0.688;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,14:24:44:302,0,44 -chr1 5557 . A G 298.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.74;MQ0=5;QD=18.67;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:327,30,0 -chr1 5648 . T C 59.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.66;MQ0=3;QD=6.59;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:1,8:9:9:87,9,0 -chr1 5834 . G T 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.3843;MLEAC=1;MLEAF=0.500;MQ=27.17;MQ0=1;MQRankSum=1.191;QD=0.93;ReadPosRankSum=0.714;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,2:17:44:44,0,279 -chr1 5889 . T G 147.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=21.23;MQ0=4;MQRankSum=-0.248;QD=8.17;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:4,14:18:11:175,0,11 -chr1 5890 . T G 229.78 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=2;MLEAF=1.00;MQ=21.11;MQ0=4;QD=12.09;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,19:19:24:258,24,0 -chr1 5938 . C G 64.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.520;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.73;MQ0=10;MQRankSum=1.034;QD=3.08;ReadPosRankSum=0.597;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,6:21:69:93,0,69 -chr1 5968 . A T 115.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.07;MQ0=8;QD=7.24;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:144,15,0 -chr1 5974 . A G 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.818;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=18.51;MQ0=8;MQRankSum=0.296;QD=1.88;ReadPosRankSum=1.580;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:14,4:18:62:62,0,114 -chr1 6010 . A T 490.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.66;MQ0=2;QD=21.34;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,23:23:45:519,45,0 -chr1 6041 . T A 311.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=28.89;MQ0=0;QD=14.85;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,21:21:33:340,33,0 -chr1 6209 . A G 273.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.61;MQ0=6;QD=13.04;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,20:21:30:302,30,0 -chr1 6350 . T G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=16.20;MQ0=21;MQRankSum=1.670;QD=2.93;ReadPosRankSum=-0.085;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:163,0,206 -chr1 6426 . T C 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=25.78;MQ0=2;MQRankSum=-1.099;QD=5.25;ReadPosRankSum=0.859;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:301,0,677 -chr1 6486 . A G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=16;MQRankSum=-0.330;QD=8.00;ReadPosRankSum=0.268;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:39,25:64:99:540,0,604 -chr1 6532 . C T 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=53;Dels=0.00;FS=4.619;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=17.32;MQ0=28;MQRankSum=0.087;QD=2.22;ReadPosRankSum=-0.379;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:146,0,419 -chr1 6577 . G A 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.35;MQ0=17;MQRankSum=-1.883;QD=6.11;ReadPosRankSum=0.269;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,25:33:28:230,0,28 -chr1 6607 . T C 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=-1.702;QD=2.28;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:117,0,385 -chr1 6609 . G T 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=0.904;QD=2.30;ReadPosRankSum=-0.204;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:32,7:39:99:118,0,377 -chr1 6675 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=52;Dels=0.00;FS=8.076;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.45;MQ0=15;MQRankSum=-1.788;QD=1.13;ReadPosRankSum=-0.973;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,16:52:87:87,0,729 -chr1 6691 . G T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=49;Dels=0.00;FS=8.321;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=17;MQRankSum=-0.467;QD=0.71;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,13:49:63:63,0,703 -chr1 6725 . G A 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=26;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=22.03;MQ0=9;MQRankSum=-0.927;QD=7.45;ReadPosRankSum=-0.146;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,13:26:99:222,0,183 -chr1 6752 . T C 113.9 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.88;MQ0=6;QD=10.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,11:11:15:142,15,0 -chr1 6942 . G C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.400;DP=21;Dels=0.00;FS=13.222;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.08;MQ0=7;MQRankSum=0.267;QD=2.66;ReadPosRankSum=-1.067;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,7:21:84:84,0,137 -chr1 7107 . C T 262.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.283;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.07;MQ0=9;MQRankSum=1.189;QD=10.11;ReadPosRankSum=-1.302;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:7,19:26:6:290,6,0 -chr1 7384 . T G 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.91;MQ0=30;MQRankSum=0.259;QD=1.40;ReadPosRankSum=0.583;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,16:42:87:87,0,93 -chr1 8682 . T G 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.57;MQ0=23;MQRankSum=-1.898;QD=7.02;ReadPosRankSum=0.429;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:8,30:38:99:295,0,141 -chr1 8738 . A G 850.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.36;MQ0=29;QD=15.75;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:72:879,72,0 -chr1 8785 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.453;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.27;MQ0=40;MQRankSum=-2.450;QD=1.48;ReadPosRankSum=1.668;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:102,0,173 -chr1 8936 . C T 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;DP=47;Dels=0.00;FS=11.458;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.37;MQ0=14;MQRankSum=2.448;QD=5.61;ReadPosRankSum=1.430;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,12:47:99:292,0,700 -chr1 8946 . A G 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.028;DP=39;Dels=0.00;FS=15.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=13;MQRankSum=1.417;QD=5.94;ReadPosRankSum=0.472;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:260,0,533 -chr1 9013 . A T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=33;Dels=0.00;FS=3.522;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.84;MQ0=24;MQRankSum=0.729;QD=2.05;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,9:33:96:96,0,100 -chr1 9080 . C T 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.47;MQ0=24;MQRankSum=-1.866;QD=1.82;ReadPosRankSum=0.633;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,13:34:90:90,0,190 -chr1 10305 . A G 786.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.23;MQ0=10;QD=23.84;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:6,27:33:63:815,63,0 -chr1 10540 . G C 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.965;DP=45;Dels=0.00;FS=17.175;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.78;MQ0=1;MQRankSum=-1.779;QD=6.82;ReadPosRankSum=2.279;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:335,0,1095 -chr1 10565 . T C 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.695;DP=49;Dels=0.00;FS=38.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.02;MQ0=2;MQRankSum=0.662;QD=20.57;ReadPosRankSum=-2.211;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,31:49:99:1036,0,420 -chr1 10997 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=59;Dels=0.00;FS=1.096;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=27.99;MQ0=9;MQRankSum=0.204;QD=10.11;ReadPosRankSum=-0.961;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:625,0,593 -chr1 11025 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.654;QD=4.94;ReadPosRankSum=1.721;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:310,0,779 -chr1 11026 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.814;QD=4.84;ReadPosRankSum=1.694;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:304,0,778 -chr1 11155 . G T 882.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.9841;MLEAC=2;MLEAF=1.00;MQ=25.38;MQ0=8;QD=22.07;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:84:911,84,0 -chr1 11199 . G A 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.053;DP=54;Dels=0.00;FS=15.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.97;MQ0=5;MQRankSum=-2.335;QD=4.79;ReadPosRankSum=2.164;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:287,0,1004 -chr1 11255 . A G 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=45;Dels=0.00;FS=8.137;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=44.39;MQ0=0;MQRankSum=-1.761;QD=1.79;ReadPosRankSum=-2.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,10:45:99:109,0,1164 -chr1 11591 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.305;DP=31;Dels=0.00;FS=8.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.119;QD=4.96;ReadPosRankSum=-1.665;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:182,0,762 -chr1 11716 . T C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.463;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-0.962;QD=0.60;ReadPosRankSum=-2.049;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:43:43,0,741 -chr1 11719 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-1.213;QD=0.48;ReadPosRankSum=-2.132;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:40:40,0,773 -chr1 11750 . A T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.197;DP=39;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.68;MQ0=1;MQRankSum=-4.052;QD=2.58;ReadPosRankSum=-2.335;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:129,0,976 -chr1 11773 . T C 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=49;Dels=0.00;FS=8.883;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.29;MQ0=1;MQRankSum=-5.316;QD=5.40;ReadPosRankSum=-0.400;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:293,0,1185 -chr1 11891 . A T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.82;MQ0=0;MQRankSum=-3.709;QD=8.61;ReadPosRankSum=-0.055;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:433,0,1013 -chr1 11902 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.656;DP=42;Dels=0.00;FS=1.270;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.98;MQ0=0;MQRankSum=-3.019;QD=7.21;ReadPosRankSum=-0.525;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:331,0,973 -chr1 11906 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.095;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.51;MQ0=0;MQRankSum=-2.883;QD=7.41;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:332,0,920 -chr1 11911 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=38;Dels=0.00;FS=3.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.65;MQ0=0;MQRankSum=-2.124;QD=4.81;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:211,0,908 -chr1 11921 . A T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.641;DP=38;Dels=0.00;FS=5.870;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-1.608;QD=3.52;ReadPosRankSum=0.348;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,10:38:99:162,0,926 -chr1 11929 . A G 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.970;DP=36;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.95;MQ0=0;MQRankSum=-1.465;QD=3.13;ReadPosRankSum=-0.171;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,8:36:99:141,0,932 -chr1 11994 . G A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.393;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=38.03;MQ0=3;MQRankSum=-1.960;QD=1.98;ReadPosRankSum=0.635;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:127,0,1191 -chr1 12008 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=38.65;MQ0=3;MQRankSum=-3.004;QD=4.01;ReadPosRankSum=0.628;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:265,0,1308 -chr1 12023 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=68;Dels=0.00;FS=3.645;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=41.63;MQ0=3;MQRankSum=-1.795;QD=7.56;ReadPosRankSum=-1.088;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:43,25:68:99:542,0,1441 -chr1 12050 . G C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=68;Dels=0.00;FS=5.033;HaplotypeScore=2.9268;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=3;MQRankSum=-1.538;QD=11.88;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:836,0,1326 -chr1 12090 . A G 888.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=57;Dels=0.00;FS=2.245;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=0;MQRankSum=-4.892;QD=15.59;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:917,0,995 -chr1 12162 . A T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.98;MQ0=2;MQRankSum=-4.602;QD=6.88;ReadPosRankSum=-0.119;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:21,13:34:99:262,0,708 -chr1 12186 . G C 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=38;Dels=0.00;FS=3.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=2;MQRankSum=-3.949;QD=6.10;ReadPosRankSum=-1.854;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:25,13:38:99:260,0,884 -chr1 12195 . C G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.111;DP=39;Dels=0.00;FS=1.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=2;MQRankSum=-3.882;QD=4.64;ReadPosRankSum=-1.898;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:209,0,927 -chr1 12249 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.999;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.19;MQ0=0;MQRankSum=-5.596;QD=11.75;ReadPosRankSum=2.865;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:686,0,1109 -chr1 12250 . C A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.017;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=-5.563;QD=11.66;ReadPosRankSum=2.848;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:33,23:56:99:681,0,1094 -chr1 12252 . T C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.084;DP=55;Dels=0.00;FS=2.426;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.486;QD=12.00;ReadPosRankSum=2.722;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:688,0,1075 -chr1 12271 . A G 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.19;ReadPosRankSum=0.908;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,18:47:99:507,0,1022 -chr1 12273 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.00;ReadPosRankSum=0.711;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:498,0,1029 -chr1 12283 . T G 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=45;Dels=0.00;FS=6.601;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.612;QD=8.97;ReadPosRankSum=-0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,16:45:99:432,0,953 -chr1 12293 . G C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.726;DP=43;Dels=0.00;FS=13.073;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=-4.370;QD=9.81;ReadPosRankSum=-2.000;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:28,15:43:99:450,0,932 -chr1 12432 . C T 860.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.21;MQ0=0;QD=31.88;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:889,72,0 -chr1 12461 . A T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=31;Dels=0.00;FS=6.929;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.06;MQ0=0;MQRankSum=-3.047;QD=3.44;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:135,0,662 -chr1 12610 . A C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=16;Dels=0.00;FS=2.796;HaplotypeScore=10.5708;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=1.371;QD=2.99;ReadPosRankSum=-2.526;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:13,3:16:76:76,0,324 -chr1 12640 . T G 605.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=1;QD=30.29;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:51:634,51,0 -chr1 12680 . A T 555.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.13;MQ0=1;QD=32.69;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,17:17:42:584,42,0 -chr1 12768 . A C 859.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=32.48;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:888,69,0 -chr1 12883 . G A 787.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=29.11;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:816,60,0 -chr1 12886 . G A 784.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=27.81;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:813,60,0 -chr1 12926 . T C 761.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.31;MQ0=0;QD=28.06;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:790,60,0 -chr1 12964 . G C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=38;Dels=0.00;FS=15.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-3.703;QD=1.41;ReadPosRankSum=1.421;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,6:38:82:82,0,1161 -chr1 12993 . G T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=43;Dels=0.00;FS=25.224;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.523;QD=5.20;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:252,0,1151 -chr1 12994 . A T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=43;Dels=0.00;FS=21.598;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.528;QD=4.25;ReadPosRankSum=-1.193;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:211,0,1187 -chr1 13041 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=33;Dels=0.00;FS=12.234;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-3.337;QD=2.66;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,6:33:99:116,0,945 -chr1 13045 . G A 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=32;Dels=0.00;FS=12.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=0;MQRankSum=-3.307;QD=2.77;ReadPosRankSum=2.148;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,6:32:99:117,0,908 -chr1 13074 . C T 821.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.270;DP=27;Dels=0.00;FS=3.388;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;MQRankSum=2.122;QD=30.44;ReadPosRankSum=0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:3,24:27:32:850,32,0 -chr1 13123 . T A 1348.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.40;MQ0=0;QD=34.58;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1377,102,0 -chr1 13136 . C T 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=41;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.46;MQ0=0;MQRankSum=-1.074;QD=4.43;ReadPosRankSum=3.016;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,11:41:99:210,0,1033 -chr1 13137 . C T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=42;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.95;MQ0=0;MQRankSum=0.715;QD=24.21;ReadPosRankSum=-3.118;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:11,31:42:99:1045,0,215 -chr1 13270 . G A 1048.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=3;QD=34.96;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,30:30:81:1077,81,0 -chr1 13273 . A T 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=30;Dels=0.00;FS=2.876;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.55;MQ0=3;MQRankSum=-3.741;QD=9.36;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:309,0,598 -chr1 13280 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.606;DP=28;Dels=0.00;FS=2.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.14;MQ0=2;MQRankSum=-3.610;QD=8.85;ReadPosRankSum=-1.080;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:276,0,564 -chr1 13292 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=29;Dels=0.00;FS=5.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.02;MQ0=2;MQRankSum=-3.138;QD=10.03;ReadPosRankSum=-0.276;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:319,0,601 -chr1 13308 . T G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=29;Dels=0.00;FS=2.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=-3.380;QD=9.68;ReadPosRankSum=3.332;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,644 -chr1 13344 . T C 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=19;Dels=0.00;FS=23.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=1;MQRankSum=-0.592;QD=1.94;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,3:19:65:65,0,546 -chr1 13347 . A T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.846;DP=21;Dels=0.00;FS=37.433;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=1;MQRankSum=1.196;QD=5.47;ReadPosRankSum=-2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:143,0,499 -chr1 13363 . G A 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=17;Dels=0.00;FS=33.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.13;MQ0=0;MQRankSum=0.818;QD=13.87;ReadPosRankSum=0.337;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:264,0,308 -chr1 13378 . C G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=13;Dels=0.00;FS=19.956;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=0.529;QD=15.29;ReadPosRankSum=1.461;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,7:13:99:227,0,159 -chr1 13390 . T C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=13;Dels=0.00;FS=21.553;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.47;MQ0=0;MQRankSum=-0.212;QD=17.52;ReadPosRankSum=2.927;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,8:13:99:256,0,126 -chr1 13403 . G A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-1.580;QD=21.18;ReadPosRankSum=2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,7:10:88:240,0,88 -chr1 13404 . T A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=0.895;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,217 -chr1 13405 . A G 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,244 -chr1 13407 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=19.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.48;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:83:83,0,214 -chr1 13424 . C A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;DP=7;Dels=0.00;FS=15.441;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=54.99;MQ0=0;MQRankSum=-1.754;QD=13.25;ReadPosRankSum=-0.550;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,4:7:90:121,0,90 -chr1 13484 . T A 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=11;Dels=0.00;FS=6.264;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=0;MQRankSum=-2.228;QD=9.07;ReadPosRankSum=-1.398;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,4:11:99:128,0,245 -chr1 13514 . C T 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.67;ReadPosRankSum=1.312;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:128,0,321 -chr1 13526 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.91;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:131,0,293 -chr1 13529 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.700;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,261 -chr1 13533 . A C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,316 -chr1 13543 . G T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=13;Dels=0.00;FS=16.782;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=0.377;QD=13.06;ReadPosRankSum=-2.777;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,6:13:99:198,0,209 -chr1 13601 . C T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.355;DP=33;Dels=0.00;FS=6.893;HaplotypeScore=2.5316;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-0.954;QD=18.30;ReadPosRankSum=1.732;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:12,20:33:99:632,0,392 -chr1 13654 . T G 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;DP=32;Dels=0.00;FS=2.000;HaplotypeScore=17.2143;MLEAC=1;MLEAF=0.500;MQ=44.78;MQ0=0;MQRankSum=-3.367;QD=6.71;ReadPosRankSum=0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:243,0,696 -chr1 13805 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=1.000;QD=13.95;ReadPosRankSum=1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:712,0,955 -chr1 13962 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=56;Dels=0.00;FS=1.048;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.041;QD=15.07;ReadPosRankSum=0.567;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:872,0,1029 -chr1 14025 . A G 1167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=4.5620;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.490;QD=19.14;ReadPosRankSum=0.702;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,36:61:99:1196,0,669 -chr1 14039 . C T 781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.305;DP=61;Dels=0.00;FS=1.002;HaplotypeScore=2.6609;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.839;QD=12.82;ReadPosRankSum=-1.116;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:810,0,1140 -chr1 14053 . A G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.152;DP=61;Dels=0.00;FS=3.495;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.107;QD=16.44;ReadPosRankSum=1.469;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1031,0,874 -chr1 14525 . C T 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=57;Dels=0.00;FS=7.529;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.041;QD=20.52;ReadPosRankSum=0.447;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1198,0,732 -chr1 14531 . A G 1030.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=54;Dels=0.00;FS=7.625;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.153;QD=19.09;ReadPosRankSum=0.045;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,31:54:99:1059,0,726 -chr1 14540 . C T 1109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.716;DP=56;Dels=0.00;FS=9.774;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.899;QD=19.82;ReadPosRankSum=-0.716;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1138,0,754 -chr1 14569 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.646;QD=16.28;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:956,0,955 -chr1 14614 . T G 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.395;QD=17.88;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:958,0,770 -chr1 14674 . G T 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.419;QD=17.11;ReadPosRankSum=1.228;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:952,0,875 -chr1 14720 . C A 2453.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2482,187,0 -chr1 14957 . C T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=43;Dels=0.00;FS=2.756;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=1;MQRankSum=-0.253;QD=16.99;ReadPosRankSum=-0.758;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:759,0,646 -chr1 15110 . T A 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=65;Dels=0.00;FS=0.970;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.569;QD=12.66;ReadPosRankSum=0.261;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:39,26:65:99:851,0,1349 -chr1 15135 . A G 1010.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.364;QD=16.04;ReadPosRankSum=-1.767;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1039,0,1093 -chr1 15338 . C T 1812.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.74;MQ0=1;QD=24.29;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1841,138,0 -chr1 15597 . C A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=47;Dels=0.00;FS=6.639;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.617;QD=9.89;ReadPosRankSum=-0.797;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:493,0,1065 -chr1 15875 . A C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=42;Dels=0.00;FS=1.222;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=1;MQRankSum=-0.066;QD=12.90;ReadPosRankSum=1.064;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:570,0,798 -chr1 15977 . A T 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.672;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=53.37;MQ0=3;MQRankSum=-3.958;QD=12.64;ReadPosRankSum=-1.385;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:736,0,832 -chr1 16014 . C G 2424.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=10.8438;MLEAC=2;MLEAF=1.00;MQ=52.58;MQ0=3;QD=33.68;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,69:72:99:2453,187,0 -chr1 16017 . T G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=72;Dels=0.00;FS=1.018;HaplotypeScore=11.7597;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=3;MQRankSum=-3.104;QD=11.80;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,28:72:99:878,0,1143 -chr1 16621 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=65;Dels=0.00;FS=3.448;HaplotypeScore=2.7337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.323;QD=18.41;ReadPosRankSum=-1.247;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1225,0,946 -chr1 16671 . C T 1029.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=52;Dels=0.00;FS=2.477;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.746;QD=19.80;ReadPosRankSum=0.075;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1058,0,684 -chr1 16700 . C G 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=1.092;QD=18.80;ReadPosRankSum=-0.912;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:893,0,570 -chr1 16782 . C T 1114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9279;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.342;QD=17.69;ReadPosRankSum=-0.791;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1143,0,988 -chr1 16844 . C A 2131.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.55;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2160,160,0 -chr1 16871 . T C 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=59;Dels=0.00;FS=5.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.494;QD=14.76;ReadPosRankSum=-0.373;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:899,0,1075 -chr1 16912 . T A 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.631;DP=51;Dels=0.00;FS=7.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.556;QD=15.86;ReadPosRankSum=-1.724;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:837,0,878 -chr1 16926 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.660;DP=48;Dels=0.00;FS=6.044;HaplotypeScore=2.7745;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=0.042;QD=14.35;ReadPosRankSum=-0.249;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:717,0,884 -chr1 17027 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=65;Dels=0.00;FS=4.856;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.944;QD=14.46;ReadPosRankSum=-0.495;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:968,0,1247 -chr1 17241 . C G 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.811;QD=17.86;ReadPosRankSum=-0.258;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S190C|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_17170_17247),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:975,0,797 -chr1 17324 . T G 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.562;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.432;QD=18.63;ReadPosRankSum=0.875;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,675 -chr1 17567 . C T 1999.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.64;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2028,153,0 -chr1 17672 . A G 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.381;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.326;QD=14.24;ReadPosRankSum=1.143;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:555,0,636 -chr1 17713 . A T 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.481;DP=51;Dels=0.00;FS=2.418;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=15.64;ReadPosRankSum=-0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:826,0,870 -chr1 17738 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=56;Dels=0.00;FS=2.356;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=12.19;ReadPosRankSum=0.820;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:711,0,1047 -chr1 17873 . G C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.910;QD=21.06;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:997,0,530 -chr1 17905 . A G 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=57;Dels=0.00;FS=2.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.659;QD=19.52;ReadPosRankSum=0.773;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1141,0,733 -chr1 18041 . A G 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=57;Dels=0.00;FS=2.316;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.610;QD=18.47;ReadPosRankSum=-0.569;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I221V|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18036_18114) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1081,0,804 -chr1 18164 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.433;QD=11.99;ReadPosRankSum=-0.972;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:568,0,952 -chr1 18166 . T C 1777.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.02;MQ0=0;QD=28.69;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1806,135,0 -chr1 18454 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=45;Dels=0.00;FS=1.130;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=0.329;QD=16.22;ReadPosRankSum=0.102;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T314M|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:22,23:45:99:758,0,703 -chr1 18478 . T C 502.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=1.364;QD=13.59;ReadPosRankSum=1.242;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L322P|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:21,16:37:99:531,0,711 -chr1 18624 . T A 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=47;Dels=0.00;FS=4.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.140;QD=13.06;ReadPosRankSum=1.194;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:642,0,913 -chr1 19081 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.091;QD=22.92;ReadPosRankSum=-0.051;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A390|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:16,35:51:99:1197,0,486 -chr1 19138 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.496;DP=58;Dels=0.00;FS=5.223;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.717;QD=14.88;ReadPosRankSum=-0.655;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y409|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:31,27:58:99:891,0,1083 -chr1 19465 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=16.00;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:924,0,944 -chr1 19863 . T G 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.194;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.2772;MLEAC=1;MLEAF=0.500;MQ=60.50;MQ0=0;MQRankSum=-0.350;QD=8.83;ReadPosRankSum=-0.868;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,14:43:99:408,0,1042 -chr1 20158 . T C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.686;QD=16.39;ReadPosRankSum=-0.668;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:897,0,842 -chr1 20454 . T C 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-1.324;QD=15.62;ReadPosRankSum=0.255;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:700,0,709 -chr1 20566 . G T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=35;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-1.275;QD=14.34;ReadPosRankSum=-2.633;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:530,0,669 -chr1 20614 . T C 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.266;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.223;QD=15.59;ReadPosRankSum=1.394;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:761,0,807 -chr1 20629 . A G 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.400;DP=45;Dels=0.00;FS=1.143;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=15.64;ReadPosRankSum=2.446;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:732,0,822 -chr1 20630 . A C 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.984;QD=16.60;ReadPosRankSum=1.956;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:742,0,712 -chr1 20726 . T G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.220;DP=40;Dels=0.00;FS=1.408;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.190;QD=10.77;ReadPosRankSum=0.512;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:459,0,906 -chr1 20954 . G T 1159.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.566;QD=14.14;ReadPosRankSum=1.500;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1188,0,1568 -chr1 21221 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.356;QD=18.35;ReadPosRankSum=0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L545|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_20985_21233) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1056,0,780 -chr1 21683 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=0.586;QD=14.07;ReadPosRankSum=-0.823;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:802,0,1087 -chr1 21687 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.157;DP=55;Dels=0.00;FS=1.070;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.182;QD=20.14;ReadPosRankSum=-0.026;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1136,0,682 -chr1 21744 . A G 953.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.008;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.188;QD=16.73;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:57:99:982,0,944 -chr1 21947 . T G 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.907;QD=12.46;ReadPosRankSum=-0.326;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:701,0,1131 -chr1 22299 . T C 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=48;Dels=0.00;FS=6.116;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.826;QD=19.77;ReadPosRankSum=0.324;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A649|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:20,28:48:99:977,0,660 -chr1 22327 . T G 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=45;Dels=0.00;FS=4.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.767;QD=21.53;ReadPosRankSum=-0.059;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S659A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:17,28:45:99:997,0,550 -chr1 23334 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=39;Dels=0.00;FS=2.875;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.928;QD=12.87;ReadPosRankSum=-0.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A994|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:23,16:39:99:530,0,737 -chr1 23394 . A T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=52;Dels=0.00;FS=2.388;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.410;QD=16.90;ReadPosRankSum=0.531;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,27:52:99:907,0,841 -chr1 23447 . T A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=47;Dels=0.00;FS=1.119;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.054;QD=16.36;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:797,0,690 -chr1 23455 . T G 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768;DP=47;Dels=0.00;FS=2.552;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.646;QD=18.46;ReadPosRankSum=-0.821;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:896,0,614 -chr1 23515 . G A,T 1409.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.35;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/2:0,23,21:44:99:1623,749,680,874,0,814 -chr1 23725 . G A 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=42;Dels=0.00;FS=6.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.428;QD=16.80;ReadPosRankSum=1.384;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:734,0,720 -chr1 23982 . C T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=55;Dels=0.00;FS=2.640;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-1.005;QD=19.45;ReadPosRankSum=0.885;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,33:55:99:1098,0,682 -chr1 24069 . T A 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.713;DP=48;Dels=0.00;FS=8.862;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=1;MQRankSum=0.330;QD=15.50;ReadPosRankSum=0.713;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:772,0,789 -chr1 24151 . A G 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.694;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.785;QD=17.06;ReadPosRankSum=1.854;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1021|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24104_24302) GT:AD:DP:GQ:PL 0/1:21,25:46:99:813,0,677 -chr1 24389 . C A 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=48;Dels=0.00;FS=6.267;HaplotypeScore=27.9952;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=1;MQRankSum=0.567;QD=17.52;ReadPosRankSum=-0.546;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:869,0,711 -chr1 24436 . T C 934.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.691;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=-1.964;QD=18.33;ReadPosRankSum=-0.577;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1080|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24411_24543) GT:AD:DP:GQ:PL 0/1:23,28:51:99:963,0,687 -chr1 24548 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=46;Dels=0.00;FS=6.474;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.411;QD=21.39;ReadPosRankSum=1.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:1012,0,541 -chr1 24661 . C G 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-1.176;QD=13.44;ReadPosRankSum=1.960;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:687,0,875 -chr1 24708 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=43;Dels=0.00;FS=1.164;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-1.588;QD=11.79;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:535,0,872 -chr1 24751 . C T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=50;Dels=0.00;FS=8.018;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.278;QD=12.94;ReadPosRankSum=-1.022;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:675,0,1009 -chr1 24820 . T A 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.600;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.461;QD=18.66;ReadPosRankSum=1.129;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1148,0,824 -chr1 24862 . T C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.409;DP=51;Dels=0.00;FS=13.641;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.789;QD=13.52;ReadPosRankSum=-0.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:718,0,995 -chr1 24930 . T C 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;DP=52;Dels=0.00;FS=27.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.560;QD=15.23;ReadPosRankSum=0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:820,0,960 -chr1 25113 . T A 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=40;Dels=0.00;FS=16.130;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.639;QD=18.64;ReadPosRankSum=1.998;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:774,0,623 -chr1 25137 . G A 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=0.665;QD=17.66;ReadPosRankSum=-0.317;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:664,0,574 -chr1 25267 . A G 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.616;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.877;QD=18.93;ReadPosRankSum=-2.014;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:861,0,649 -chr1 25375 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.084;QD=16.13;ReadPosRankSum=0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:980,0,985 -chr1 25379 . A G 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.716;QD=17.74;ReadPosRankSum=0.093;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1004,0,818 -chr1 25601 . A G 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.979;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=16.39;ReadPosRankSum=1.281;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:995,0,972 -chr1 25654 . G T 2337.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.57;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2366,175,0 -chr1 25678 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=47;Dels=0.00;FS=2.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.653;QD=11.34;ReadPosRankSum=0.875;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1175|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:30,17:47:99:561,0,1005 -chr1 25747 . G A 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.324;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.246;QD=9.48;ReadPosRankSum=1.361;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1198|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:29,14:43:99:436,0,1051 -chr1 25763 . G C 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.339;DP=44;Dels=0.00;FS=9.359;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.817;QD=10.97;ReadPosRankSum=-1.570;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V1204L|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:27,16:44:99:511,0,956 -chr1 26086 . G T 2202.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=3.4093;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.67;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2231,169,0 -chr1 26087 . A G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=54;Dels=0.00;FS=1.059;HaplotypeScore=2.6207;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.099;QD=17.55;ReadPosRankSum=1.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:976,0,871 -chr1 26119 . G T 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=55;Dels=0.00;FS=2.268;HaplotypeScore=2.9962;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.557;QD=16.52;ReadPosRankSum=-1.540;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:937,0,919 -chr1 26334 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.965;DP=50;Dels=0.00;FS=1.280;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-0.080;QD=6.24;ReadPosRankSum=3.146;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:340,0,1268 -chr1 26660 . T C 1722.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=38.42;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1751,129,0 -chr1 26702 . A T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.942;DP=54;Dels=0.00;FS=10.090;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.192;QD=12.53;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:705,0,1095 -chr1 26910 . T G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.210;DP=49;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.332;QD=17.36;ReadPosRankSum=-0.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S1297A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:23,26:49:99:879,0,760 -chr1 27095 . A T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;DP=41;Dels=0.00;FS=4.926;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.784;QD=21.90;ReadPosRankSum=-0.151;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P1358|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:14,27:41:99:926,0,391 -chr1 27394 . A G 928.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=53;Dels=0.00;FS=5.960;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.100;QD=17.52;ReadPosRankSum=-0.809;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1458S|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:21,32:53:99:957,0,694 -chr1 27940 . G T 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.545;QD=15.06;ReadPosRankSum=-0.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:781,0,874 -chr1 28249 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=41;Dels=0.00;FS=1.216;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.088;QD=19.41;ReadPosRankSum=0.696;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:824,0,613 -chr1 28269 . C T 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.609;QD=18.99;ReadPosRankSum=-1.031;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:845,0,552 -chr1 28430 . T C 718.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.035;QD=14.09;ReadPosRankSum=-0.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:747,0,985 -chr1 28468 . T C 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=55;Dels=0.00;FS=3.953;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=1;MQRankSum=0.650;QD=15.50;ReadPosRankSum=0.419;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:881,0,955 -chr1 28487 . T G 2391.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=1;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2420,178,0 -chr1 28990 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.224;DP=58;Dels=0.00;FS=16.948;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.031;QD=17.39;ReadPosRankSum=0.202;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:1037,0,1003 -chr1 29042 . A C 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=57;Dels=0.00;FS=5.341;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.937;QD=18.98;ReadPosRankSum=1.049;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1110,0,905 -chr1 29090 . G T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.457;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.506;QD=23.46;ReadPosRankSum=-0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,36:52:99:1248,0,498 -chr1 29155 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.513;QD=18.08;ReadPosRankSum=-0.050;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:914,0,699 -chr1 29212 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=59;Dels=0.00;FS=2.209;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.359;QD=15.64;ReadPosRankSum=-2.011;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:951,0,1091 -chr1 29443 . T C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.937;DP=47;Dels=0.00;FS=7.013;HaplotypeScore=2.8089;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.184;QD=8.40;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:423,0,970 -chr1 29543 . G C 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=52;Dels=0.00;FS=2.441;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=2;MQRankSum=-0.700;QD=11.09;ReadPosRankSum=0.260;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:605,0,1005 -chr1 29549 . T A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=50;Dels=0.00;FS=4.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=2;MQRankSum=0.096;QD=11.00;ReadPosRankSum=0.607;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:578,0,972 -chr1 29794 . C G 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.493;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.447;QD=14.07;ReadPosRankSum=-0.865;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:746,0,926 -chr1 30062 . C G 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.890;DP=56;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.330;QD=18.85;ReadPosRankSum=0.725;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1084,0,794 -chr1 30283 . A G 1779.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.20;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1808,135,0 -chr1 30505 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.057;DP=59;Dels=0.00;FS=3.878;HaplotypeScore=2.5980;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.388;QD=14.98;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1668|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:32,27:59:99:912,0,1076 -chr1 30578 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=59;Dels=0.00;FS=5.208;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.220;QD=16.66;ReadPosRankSum=0.523;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S1693G|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1011,0,918 -chr1 30610 . G A 853.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.888;DP=63;Dels=0.00;FS=2.122;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.012;QD=13.55;ReadPosRankSum=0.709;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1703|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:33,30:63:99:882,0,1106 -chr1 30810 . T G 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=52;Dels=0.00;FS=1.095;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.743;QD=12.21;ReadPosRankSum=-0.141;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:663,0,1056 -chr1 30850 . G A 1094.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;DP=56;Dels=0.00;FS=1.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.864;QD=19.55;ReadPosRankSum=1.099;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1123,0,720 -chr1 30887 . A C 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.841;QD=16.93;ReadPosRankSum=0.720;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1027,0,969 -chr1 30927 . C G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.191;DP=49;Dels=0.00;FS=8.536;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.040;QD=18.49;ReadPosRankSum=1.296;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:934,0,707 -chr1 31004 . G T 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.387;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.766;QD=15.64;ReadPosRankSum=1.054;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:951,0,1000 -chr1 31025 . A C 964.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=59;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.371;QD=16.35;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:993,0,950 -chr1 31036 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.950;QD=16.34;ReadPosRankSum=-0.770;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:829,0,810 -chr1 31213 . A G 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=51;Dels=0.00;FS=3.933;HaplotypeScore=24.9899;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.293;QD=17.62;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:927,0,826 -chr1 31497 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.007;DP=35;Dels=0.00;FS=4.982;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.347;QD=16.14;ReadPosRankSum=-0.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:593,0,535 -chr1 31537 . T A 1517.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.76;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1546,114,0 -chr1 31710 . G T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.314;DP=41;Dels=0.00;FS=6.637;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=13.19;ReadPosRankSum=0.876;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:569,0,741 -chr1 31712 . G A 1534.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=32.25;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1563,120,0 -chr1 31714 . A G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.219;DP=40;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.163;QD=15.17;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:635,0,705 -chr1 31754 . A T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=45;Dels=0.00;FS=1.145;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.058;QD=14.73;ReadPosRankSum=0.102;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:691,0,823 -chr1 31917 . G A 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=60;Dels=0.00;FS=3.613;HaplotypeScore=1.9981;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.430;QD=20.53;ReadPosRankSum=0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1260,0,770 -chr1 31921 . G A 1051.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.128;DP=55;Dels=0.00;FS=1.022;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.561;QD=19.12;ReadPosRankSum=0.691;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1080,0,742 -chr1 32111 . A G 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=49;Dels=0.00;FS=2.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.156;QD=18.44;ReadPosRankSum=0.211;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:932,0,729 -chr1 32214 . G A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.166;DP=48;Dels=0.00;FS=6.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=1;MQRankSum=-0.118;QD=14.31;ReadPosRankSum=1.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:715,0,905 -chr1 32230 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.182;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=2;MQRankSum=-0.176;QD=15.49;ReadPosRankSum=-1.233;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:710,0,732 -chr1 32312 . A T 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306;DP=57;Dels=0.00;FS=7.278;HaplotypeScore=0.9159;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.485;QD=16.08;ReadPosRankSum=-0.978;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:945,0,894 -chr1 32410 . A G 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.180;DP=58;Dels=0.00;FS=7.306;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.539;QD=13.43;ReadPosRankSum=-1.008;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:807,0,1109 -chr1 32760 . G T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.396;QD=15.74;ReadPosRankSum=0.648;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:894,0,892 -chr1 32761 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.076;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=1.577;QD=15.01;ReadPosRankSum=1.274;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,925 -chr1 32762 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.506;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.151;QD=14.77;ReadPosRankSum=1.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:811,0,950 -chr1 32810 . T A 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.129;DP=44;Dels=0.00;FS=1.278;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.481;QD=15.63;ReadPosRankSum=0.246;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:716,0,594 -chr1 32950 . A G 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=2.4536;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.302;QD=20.89;ReadPosRankSum=-0.427;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1779|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:1010,0,566 -chr1 33016 . T G 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.707;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=-0.787;QD=2.54;ReadPosRankSum=-1.826;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P1801|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,11:48:99:150,0,1307 -chr1 33031 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=10.1485;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=3;MQRankSum=0.261;QD=2.75;ReadPosRankSum=0.239;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1806|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,13:56:99:182,0,1518 -chr1 33037 . T C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.294;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=22.7136;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=1.518;QD=11.25;ReadPosRankSum=0.008;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1808|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,22:59:99:692,0,1127 -chr1 33046 . T A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.993;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=13.5584;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=-1.164;QD=4.86;ReadPosRankSum=0.237;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1811|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,17:59:99:315,0,1459 -chr1 33129 . A T 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.555;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=2.016;QD=6.77;ReadPosRankSum=-0.990;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K1839I|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,18:65:99:468,0,1588 -chr1 33136 . T A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=61;Dels=0.00;FS=16.845;HaplotypeScore=2.3893;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=2.025;QD=6.85;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1841|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,16:61:99:446,0,1486 -chr1 33139 . G T 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=57;Dels=0.00;FS=11.731;HaplotypeScore=5.2554;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=1.441;QD=6.50;ReadPosRankSum=-1.169;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1842|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:57:99:399,0,1431 -chr1 33146 . A C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.634;DP=65;Dels=0.00;FS=13.675;HaplotypeScore=4.3887;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.261;QD=6.46;ReadPosRankSum=-1.112;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R1845|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:448,0,1646 -chr1 33199 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.004;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.694;QD=8.54;ReadPosRankSum=0.743;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1862|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,21:72:99:643,0,1752 -chr1 33262 . G A 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=78;Dels=0.00;FS=3.343;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-1.196;QD=7.68;ReadPosRankSum=-0.514;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1883|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,24:78:99:627,0,1895 -chr1 33289 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=77;Dels=0.00;FS=6.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.605;QD=8.93;ReadPosRankSum=2.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1892|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:716,0,1845 -chr1 33320 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.494;QD=8.34;ReadPosRankSum=0.778;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,24:75:99:654,0,1810 -chr1 33322 . A G 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.707;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.160;QD=7.88;ReadPosRankSum=0.267;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,23:74:99:611,0,1773 -chr1 33328 . C T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.608;QD=8.90;ReadPosRankSum=-0.662;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1905|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,26:76:99:705,0,1756 -chr1 33511 . T C 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.801;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=28.0954;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.180;QD=7.78;ReadPosRankSum=-0.255;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:63,27:90:99:728,0,2042 -chr1 33518 . T A 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.325;DP=89;Dels=0.00;FS=0.876;HaplotypeScore=29.8838;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.272;QD=8.12;ReadPosRankSum=-1.798;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:751,0,2141 -chr1 33534 . A T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=82;Dels=0.00;FS=1.081;HaplotypeScore=4.6992;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.708;QD=3.67;ReadPosRankSum=0.006;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,16:82:99:329,0,2363 -chr1 33542 . A G 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=84;Dels=0.00;FS=2.421;HaplotypeScore=3.3981;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.159;QD=3.43;ReadPosRankSum=-0.427;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,16:84:99:316,0,2385 -chr1 33544 . T C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.216;DP=85;Dels=0.00;FS=5.901;HaplotypeScore=2.3989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-2.519;QD=2.62;ReadPosRankSum=0.156;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:70,15:85:99:251,0,2424 -chr1 33549 . T C 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.895;DP=85;Dels=0.00;FS=5.608;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.928;QD=3.20;ReadPosRankSum=-0.983;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:300,0,2403 -chr1 33583 . A G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.183;QD=6.04;ReadPosRankSum=-0.048;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,25:100:99:632,0,2624 -chr1 33591 . T G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.576;QD=6.44;ReadPosRankSum=0.766;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,27:102:99:685,0,2559 -chr1 33634 . G T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=92;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.309;QD=10.87;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,33:92:99:1028,0,2053 -chr1 33635 . T A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=93;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.261;QD=10.54;ReadPosRankSum=0.285;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:60,33:93:99:1008,0,2023 -chr1 33648 . T C 1214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.582;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.076;QD=12.40;ReadPosRankSum=-1.008;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,40:98:99:1243,0,1959 -chr1 33649 . T C 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.519;DP=97;Dels=0.00;FS=0.836;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-0.096;QD=8.31;ReadPosRankSum=3.319;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:67,29:97:99:834,0,2354 -chr1 33669 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.973;DP=93;Dels=0.00;FS=2.768;HaplotypeScore=17.9952;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.606;QD=12.58;ReadPosRankSum=0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1198,0,1907 -chr1 33692 . G A 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.680;DP=95;Dels=0.00;FS=8.628;HaplotypeScore=1.7719;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.994;QD=11.82;ReadPosRankSum=1.470;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,38:95:99:1151,0,1994 -chr1 33756 . T A 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.209;DP=101;Dels=0.00;FS=21.595;HaplotypeScore=25.9789;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.917;QD=10.34;ReadPosRankSum=-0.467;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:1073,0,2323 -chr1 33765 . T C 2096.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.987;DP=97;Dels=0.00;FS=2.797;HaplotypeScore=26.9788;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.109;QD=21.62;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,62:97:99:2125,0,1120 -chr1 33783 . C A 3600.77 . AC=2;AF=1.00;AN=2;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,91:91:99:3629,274,0 -chr1 33800 . T C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=84;Dels=0.00;FS=1.935;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-2.651;QD=8.32;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,25:84:99:727,0,2083 -chr1 33805 . A G 2115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;DP=85;Dels=0.00;FS=0.901;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=4.074;QD=24.89;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,60:85:99:2144,0,700 -chr1 33816 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=74;Dels=0.00;FS=2.126;HaplotypeScore=26.8598;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-5.767;QD=8.16;ReadPosRankSum=0.084;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:632,0,1874 -chr1 33817 . C T 1791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.176;DP=75;Dels=0.00;FS=2.086;HaplotypeScore=25.9931;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-1.936;QD=23.89;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,51:75:99:1820,0,743 -chr1 33825 . C G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.639;DP=73;Dels=0.00;FS=2.189;HaplotypeScore=66.4539;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.355;QD=8.34;ReadPosRankSum=-0.152;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:637,0,1756 -chr1 33827 . A G 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.248;DP=73;Dels=0.00;FS=3.559;HaplotypeScore=65.4541;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.574;QD=8.26;ReadPosRankSum=-0.262;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:631,0,1850 -chr1 33850 . G A 967.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=85;Dels=0.00;FS=5.848;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-4.789;QD=11.39;ReadPosRankSum=-1.730;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:996,0,1874 -chr1 33851 . C T 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=85;Dels=0.00;FS=5.930;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-5.199;QD=11.44;ReadPosRankSum=-1.593;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:1001,0,1842 -chr1 33860 . A T 1131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=94;Dels=0.00;FS=0.798;HaplotypeScore=46.8065;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=2.315;QD=12.04;ReadPosRankSum=-0.705;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,38:94:99:1160,0,1948 -chr1 33863 . A G 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.497;DP=93;Dels=0.00;FS=0.897;HaplotypeScore=49.5927;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=2.899;QD=7.59;ReadPosRankSum=-0.568;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,25:93:99:734,0,2127 -chr1 33867 . T C 877.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=88;Dels=0.00;FS=5.938;HaplotypeScore=51.2136;MLEAC=1;MLEAF=0.500;MQ=58.15;MQ0=0;MQRankSum=-2.770;QD=9.97;ReadPosRankSum=1.358;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,29:88:99:906,0,2073 -chr1 33870 . A T 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.369;DP=86;Dels=0.00;FS=6.242;HaplotypeScore=47.2312;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.848;QD=9.56;ReadPosRankSum=2.170;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:850,0,1959 -chr1 33871 . G C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=86;Dels=0.00;FS=7.832;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.203;QD=10.01;ReadPosRankSum=2.382;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:889,0,1966 -chr1 33872 . A T 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=86;Dels=0.00;FS=5.975;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.211;QD=10.02;ReadPosRankSum=2.503;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,29:86:99:890,0,1958 -chr1 33881 . T C 2424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.386;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=26.4025;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-0.490;QD=25.80;ReadPosRankSum=1.236;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,70:94:99:2453,0,686 -chr1 33890 . C T 1338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.822;DP=97;Dels=0.00;FS=16.850;HaplotypeScore=21.9948;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-2.421;QD=13.80;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,41:97:99:1367,0,1887 -chr1 33916 . A T 1213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.196;DP=82;Dels=0.00;FS=19.829;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.075;QD=14.80;ReadPosRankSum=1.230;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1242,0,1531 -chr1 33954 . T A 3289.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.00;MQ=59.22;MQ0=0;QD=34.54;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:3318,250,0 -chr1 33959 . A T 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.821;DP=80;Dels=0.00;FS=8.032;HaplotypeScore=19.9908;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.205;QD=10.91;ReadPosRankSum=-0.277;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,28:80:99:901,0,1837 -chr1 33967 . G T 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=83;Dels=0.00;FS=3.410;HaplotypeScore=22.8560;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.531;QD=6.85;ReadPosRankSum=0.160;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:597,0,2149 -chr1 33970 . T C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.516;DP=83;Dels=0.00;FS=4.648;HaplotypeScore=21.8565;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.792;QD=9.15;ReadPosRankSum=-1.739;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,26:83:99:788,0,1880 -chr1 33978 . T C 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.032;QD=8.11;ReadPosRankSum=-1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,23:81:99:685,0,2028 -chr1 33982 . G T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.029;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-3.048;QD=7.57;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,21:77:99:611,0,1932 -chr1 34048 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=83;Dels=0.00;FS=3.608;HaplotypeScore=36.7760;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=1;MQRankSum=2.374;QD=5.44;ReadPosRankSum=1.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:480,0,2239 -chr1 34056 . A T 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.173;DP=83;Dels=0.00;FS=11.444;HaplotypeScore=20.9499;MLEAC=1;MLEAF=0.500;MQ=55.66;MQ0=1;MQRankSum=-5.405;QD=13.89;ReadPosRankSum=-2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,36:83:99:1181,0,1566 -chr1 34066 . T C 1342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;DP=87;Dels=0.00;FS=8.990;HaplotypeScore=6.9949;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=2;MQRankSum=-5.146;QD=15.43;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1371,0,1526 -chr1 34080 . G A 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=97;Dels=0.00;FS=6.820;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-2.713;QD=2.35;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,13:97:99:256,0,2928 -chr1 34081 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.776;DP=97;Dels=0.00;FS=1.486;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-3.102;QD=0.20;ReadPosRankSum=1.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,8:97:48:48,0,3121 -chr1 34096 . C A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.605;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=1;MQRankSum=0.463;QD=5.36;ReadPosRankSum=3.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,22:104:99:586,0,2872 -chr1 34098 . A G 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-3.070;QD=8.59;ReadPosRankSum=3.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,31:103:99:913,0,2440 -chr1 34099 . T A 3974.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=2;MLEAF=1.00;MQ=56.44;MQ0=1;QD=32.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:4003,298,0 -chr1 34115 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=117;Dels=0.00;FS=2.007;HaplotypeScore=38.4977;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=0.701;QD=4.35;ReadPosRankSum=0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,22:117:99:537,0,3369 -chr1 34126 . A G 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=133;Dels=0.00;FS=3.779;HaplotypeScore=3.5158;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=1;MQRankSum=4.108;QD=6.87;ReadPosRankSum=-0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,34:133:99:942,0,3399 -chr1 34143 . T C 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.256;DP=120;Dels=0.00;FS=6.188;HaplotypeScore=2.5772;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=1.550;QD=10.02;ReadPosRankSum=-0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,40:120:99:1231,0,2753 -chr1 34161 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.244;DP=113;Dels=0.00;FS=0.978;HaplotypeScore=2.7868;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=1;MQRankSum=-0.596;QD=3.30;ReadPosRankSum=1.772;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,18:113:99:401,0,3276 -chr1 34191 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=45;Dels=0.00;FS=9.532;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=0.990;QD=18.35;ReadPosRankSum=1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:854,0,672 -chr1 34210 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.402;DP=49;Dels=0.00;FS=6.502;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.291;QD=18.63;ReadPosRankSum=0.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:941,0,668 -chr1 34256 . A T 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=36;Dels=0.00;FS=2.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.317;QD=15.52;ReadPosRankSum=1.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:587,0,649 -chr1 34258 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.991;QD=16.78;ReadPosRankSum=1.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:582,0,541 -chr1 34267 . C T 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=43;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.832;QD=12.16;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:551,0,893 -chr1 34273 . T C 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;DP=50;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.867;QD=19.76;ReadPosRankSum=0.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1016,0,658 -chr1 34278 . G C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.618;DP=51;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.998;QD=12.47;ReadPosRankSum=-1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:664,0,1003 -chr1 34304 . G A 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=62;Dels=0.00;FS=23.390;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.136;QD=19.01;ReadPosRankSum=0.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1207,0,837 -chr1 34343 . C T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=52;Dels=0.00;FS=19.687;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.695;QD=19.98;ReadPosRankSum=-1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1067,0,693 -chr1 34344 . A G 2050.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2079,154,0 -chr1 34345 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;DP=53;Dels=0.00;FS=19.902;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.803;QD=12.77;ReadPosRankSum=1.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:705,0,1098 -chr1 34354 . G A 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=50;Dels=0.00;FS=11.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-1.241;QD=19.06;ReadPosRankSum=-1.182;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:981,0,660 -chr1 34385 . T G 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.698;DP=63;Dels=0.00;FS=57.702;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-5.740;QD=12.35;ReadPosRankSum=-2.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:806,0,989 -chr1 34399 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=48;Dels=0.00;FS=35.938;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.904;QD=7.72;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:48:99:399,0,977 -chr1 34401 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=47;Dels=0.00;FS=33.249;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.64;MQ0=0;MQRankSum=-4.904;QD=7.87;ReadPosRankSum=3.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:47:99:398,0,951 -chr1 34402 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=48;Dels=0.00;FS=36.487;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.958;QD=7.66;ReadPosRankSum=2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,17:48:99:396,0,1008 -chr1 34406 . A C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=49;Dels=0.00;FS=17.048;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-4.478;QD=1.51;ReadPosRankSum=2.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:102,0,1316 -chr1 34420 . C A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.268;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.57;ReadPosRankSum=4.621;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:279,0,1055 -chr1 34423 . G C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.758;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.55;ReadPosRankSum=4.989;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:278,0,1050 -chr1 34434 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=29;Dels=0.00;FS=1.455;HaplotypeScore=1.6637;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.196;QD=12.99;ReadPosRankSum=0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:405,0,509 -chr1 34498 . G A 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.733;DP=43;Dels=0.00;FS=5.601;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.273;QD=5.44;ReadPosRankSum=-0.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:262,0,1179 -chr1 34554 . A G 1556.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1585,120,0 -chr1 34561 . G A 1507.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=28.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1536,123,0 -chr1 34587 . A G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=1.339;QD=18.49;ReadPosRankSum=-1.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:583,0,433 -chr1 34649 . C T 1118.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.34;MQ0=0;QD=36.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1147,84,0 -chr1 34723 . C T 1680.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.32;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1709,132,0 -chr1 34750 . C T 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=43;Dels=0.00;FS=6.795;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=0.628;QD=19.09;ReadPosRankSum=-1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:849,0,524 -chr1 34774 . C A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=4;MQRankSum=-2.557;QD=0.57;ReadPosRankSum=-2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,5:47:55:55,0,1310 -chr1 34784 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.92;MQ0=4;MQRankSum=-2.318;QD=1.69;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,6:46:99:106,0,1235 -chr1 34787 . C T 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.62;MQ0=4;MQRankSum=-2.195;QD=1.88;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,6:45:99:113,0,1162 -chr1 34789 . C G 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=49;Dels=0.00;FS=1.637;HaplotypeScore=3.7163;MLEAC=1;MLEAF=0.500;MQ=47.34;MQ0=4;MQRankSum=-2.928;QD=2.06;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:129,0,1309 -chr1 34798 . A G 471.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.7158;MLEAC=1;MLEAF=0.500;MQ=43.82;MQ0=4;MQRankSum=-3.693;QD=7.86;ReadPosRankSum=-1.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:500,0,1302 -chr1 34809 . A C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=57;Dels=0.00;FS=2.399;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-4.370;QD=11.56;ReadPosRankSum=-0.063;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:687,0,973 -chr1 34810 . A T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.662;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-3.916;QD=8.31;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:502,0,1179 -chr1 34837 . G A 96.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.873;DP=54;Dels=0.00;FS=3.624;HaplotypeScore=73.4163;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=4;MQRankSum=-0.811;QD=1.79;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:125,0,1456 -chr1 34841 . G A 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.447;DP=52;Dels=0.00;FS=1.656;HaplotypeScore=90.4049;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=4;MQRankSum=-0.555;QD=2.05;ReadPosRankSum=2.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,10:52:99:135,0,1269 -chr1 34842 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.032;DP=49;Dels=0.00;FS=4.664;HaplotypeScore=91.4038;MLEAC=1;MLEAF=0.500;MQ=45.63;MQ0=4;MQRankSum=1.770;QD=0.55;ReadPosRankSum=-3.277;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,6:49:55:55,0,1172 -chr1 34864 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=48;Dels=0.00;FS=9.092;HaplotypeScore=49.3566;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-4.082;QD=7.35;ReadPosRankSum=3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,14:48:99:381,0,1135 -chr1 34865 . A G 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=48;Dels=0.00;FS=19.848;HaplotypeScore=56.3327;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-2.525;QD=1.75;ReadPosRankSum=3.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,7:48:99:112,0,1393 -chr1 34879 . G C 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=71;Dels=0.04;FS=44.625;HaplotypeScore=41.5658;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=4;MQRankSum=-6.053;QD=8.41;ReadPosRankSum=-2.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,27:68:99:625,0,1412 -chr1 34886 . A T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=74;Dels=0.00;FS=13.029;HaplotypeScore=24.3736;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=4;MQRankSum=-3.738;QD=0.75;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:84:84,0,2145 -chr1 34898 . G A 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.605;DP=77;Dels=0.00;FS=42.789;HaplotypeScore=2.7797;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=4;MQRankSum=-5.924;QD=7.45;ReadPosRankSum=0.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,27:77:99:602,0,1708 -chr1 34918 . G A 1463.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.14;MQ0=1;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1492,114,0 -chr1 34936 . A C 1246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.631;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.68;MQ0=0;MQRankSum=-1.529;QD=26.64;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,33:34:78:1275,78,0 -chr1 34944 . G T 1292.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1321,99,0 -chr1 34949 . A T 1277.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1306,99,0 -chr1 34958 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7321;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=0;QD=28.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1146,87,0 -chr1 34980 . A C 287.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.76;MQ0=0;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:316,24,0 -chr1 34983 . A T 363.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.46;MQ0=0;QD=30.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:392,30,0 -chr1 34999 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=46;Dels=0.00;FS=5.844;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=-2.426;QD=3.97;ReadPosRankSum=-3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,9:46:99:211,0,1278 -chr1 35001 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.443;DP=47;Dels=0.00;FS=8.113;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=-2.404;QD=4.29;ReadPosRankSum=-3.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,10:47:99:230,0,1358 -chr1 35012 . C T 3813.77 . AC=2;AF=1.00;AN=2;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=43.12;MQ0=18;QD=31.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:121:99:3842,307,0 -chr1 35021 . C A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.012;DP=128;Dels=0.00;FS=17.106;HaplotypeScore=9.9826;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=18;MQRankSum=-0.515;QD=0.24;ReadPosRankSum=2.376;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:118,10:128:59:59,0,3327 -chr1 35026 . C T 1359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.350;DP=127;Dels=0.00;FS=27.172;HaplotypeScore=10.7166;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=18;MQRankSum=-7.635;QD=10.71;ReadPosRankSum=-3.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,50:127:99:1388,0,1991 -chr1 35045 . T C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=133;Dels=0.00;FS=0.000;HaplotypeScore=40.6483;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=16;MQRankSum=3.328;QD=1.80;ReadPosRankSum=-0.988;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,16:133:99:267,0,3398 -chr1 35046 . A G 1154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.005;DP=127;Dels=0.00;FS=27.280;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=47.31;MQ0=14;MQRankSum=-8.458;QD=9.09;ReadPosRankSum=4.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,44:127:99:1183,0,2391 -chr1 35047 . T C 1481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.640;DP=126;Dels=0.00;FS=10.732;HaplotypeScore=40.9141;MLEAC=1;MLEAF=0.500;MQ=47.97;MQ0=14;MQRankSum=-8.951;QD=11.76;ReadPosRankSum=7.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,51:126:99:1510,0,2115 -chr1 35052 . A T 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=120;Dels=0.00;FS=2.223;HaplotypeScore=77.1059;MLEAC=1;MLEAF=0.500;MQ=49.27;MQ0=9;MQRankSum=2.565;QD=2.49;ReadPosRankSum=-2.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,16:120:99:327,0,3293 -chr1 35056 . C T 4286.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=62.1757;MLEAC=2;MLEAF=1.00;MQ=50.09;MQ0=7;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4315,337,0 -chr1 35058 . C T 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.351;DP=119;Dels=0.00;FS=4.666;HaplotypeScore=52.1779;MLEAC=1;MLEAF=0.500;MQ=50.70;MQ0=5;MQRankSum=-5.373;QD=3.75;ReadPosRankSum=2.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,23:119:99:475,0,3197 -chr1 35060 . G A 79.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.055;DP=117;Dels=0.00;FS=17.881;HaplotypeScore=51.1782;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=4;MQRankSum=-5.477;QD=0.68;ReadPosRankSum=3.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:103,14:117:99:108,0,3463 -chr1 35062 . G A 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.950;DP=113;Dels=0.00;FS=18.470;HaplotypeScore=57.1737;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-8.371;QD=7.89;ReadPosRankSum=5.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,36:113:99:920,0,2624 -chr1 35075 . G C 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.602;DP=107;Dels=0.00;FS=5.257;HaplotypeScore=32.3401;MLEAC=1;MLEAF=0.500;MQ=53.81;MQ0=0;MQRankSum=-8.219;QD=7.81;ReadPosRankSum=1.447;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,33:107:99:864,0,2509 -chr1 35077 . C G 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=33.3400;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=-5.857;QD=2.21;ReadPosRankSum=0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,14:107:99:265,0,2739 -chr1 35087 . C T 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=97;Dels=0.00;FS=2.025;HaplotypeScore=16.1548;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=0;MQRankSum=-7.328;QD=5.34;ReadPosRankSum=-2.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:546,0,2468 -chr1 35095 . C T 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=88;Dels=0.00;FS=1.246;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=0;MQRankSum=-5.345;QD=0.66;ReadPosRankSum=-2.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,11:88:86:86,0,2675 -chr1 35096 . A G 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=88;Dels=0.00;FS=1.393;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-5.134;QD=0.32;ReadPosRankSum=-2.860;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,10:88:56:56,0,2777 -chr1 35164 . T G 3737.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=115.8992;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=26.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,95:95:99:3766,283,0 -chr1 35172 . A C 1478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.986;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=29.8173;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=2;MQRankSum=2.017;QD=14.64;ReadPosRankSum=1.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1507,0,1792 -chr1 35184 . C G 3588.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.10;MQ0=2;QD=33.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3617,277,0 -chr1 35205 . G A 2760.77 . AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=50.07;MQ0=2;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,80:80:99:2789,217,0 -chr1 35248 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.610;DP=59;Dels=0.00;FS=5.425;HaplotypeScore=11.8817;MLEAC=1;MLEAF=0.500;MQ=36.39;MQ0=4;MQRankSum=1.904;QD=4.39;ReadPosRankSum=-1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:287,0,1045 -chr1 35251 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=57;Dels=0.00;FS=6.294;HaplotypeScore=10.9876;MLEAC=1;MLEAF=0.500;MQ=36.08;MQ0=4;MQRankSum=-1.563;QD=8.49;ReadPosRankSum=2.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:512,0,755 -chr1 35260 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=49;Dels=0.00;FS=2.866;HaplotypeScore=5.9548;MLEAC=1;MLEAF=0.500;MQ=32.62;MQ0=4;MQRankSum=-1.252;QD=6.97;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:370,0,613 -chr1 35264 . G A 863.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=29.67;MQ0=4;QD=21.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:892,75,0 -chr1 35265 . C A 872.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=30.23;MQ0=4;QD=20.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:901,75,0 -chr1 35283 . A G 1303.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.9990;MLEAC=2;MLEAF=1.00;MQ=35.84;MQ0=2;QD=24.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:1332,111,0 -chr1 35288 . G T 267.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=6.9868;MLEAC=1;MLEAF=0.500;MQ=37.11;MQ0=2;MQRankSum=-1.073;QD=4.96;ReadPosRankSum=2.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:296,0,926 -chr1 35292 . T C 1507.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.062;DP=60;Dels=0.00;FS=4.130;HaplotypeScore=6.9868;MLEAC=2;MLEAF=1.00;MQ=40.07;MQ0=2;MQRankSum=-0.557;QD=25.13;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,57:60:92:1536,92,0 -chr1 35316 . G A 2080.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=43.24;MQ0=1;QD=31.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2109,165,0 -chr1 35396 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.266;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.6626;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=3.180;QD=22.13;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,29:43:99:980,0,405 -chr1 35403 . C T 1648.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.6634;MLEAC=2;MLEAF=1.00;MQ=54.38;MQ0=0;QD=35.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1677,126,0 -chr1 35406 . T G 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.6632;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=0;MQRankSum=-2.541;QD=9.24;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:398,0,951 -chr1 35445 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.615;DP=32;Dels=0.00;FS=3.211;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=2.394;QD=21.12;ReadPosRankSum=-0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:704,0,324 -chr1 35483 . T A 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.021;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-1.247;QD=7.15;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:250,0,750 -chr1 35491 . G T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.408;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=1;MLEAF=0.500;MQ=48.70;MQ0=0;MQRankSum=1.222;QD=19.59;ReadPosRankSum=1.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:753,0,428 -chr1 35497 . G A 1437.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=2;MLEAF=1.00;MQ=48.93;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1466,111,0 -chr1 35499 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=21.8612;MLEAC=1;MLEAF=0.500;MQ=48.22;MQ0=1;MQRankSum=-1.459;QD=11.77;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:499,0,781 -chr1 35561 . A T 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;QD=35.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0 -chr1 35564 . T A 470.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:499,36,0 -chr1 35576 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.516;DP=32;Dels=0.00;FS=3.734;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.149;QD=7.84;ReadPosRankSum=-4.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:279,0,688 -chr1 35588 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=38;Dels=0.00;FS=5.225;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.261;QD=9.02;ReadPosRankSum=-2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,819 -chr1 35633 . G A 1506.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=53.32;MQ0=1;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1535,117,0 -chr1 35691 . T C 1735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.139;DP=81;Dels=0.00;FS=0.889;HaplotypeScore=1.7319;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.513;QD=21.43;ReadPosRankSum=0.601;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,51:81:99:1764,0,836 -chr1 35707 . C A 3162.77 . AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=32.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,82:82:99:3191,238,0 -chr1 35739 . G A 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=74;Dels=0.00;FS=17.134;HaplotypeScore=1.6483;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-0.689;QD=4.63;ReadPosRankSum=-2.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,16:74:99:371,0,2031 -chr1 35804 . T C 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.427;DP=109;Dels=0.00;FS=5.672;HaplotypeScore=3.9987;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=1;MQRankSum=-6.467;QD=6.13;ReadPosRankSum=0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,28:109:99:696,0,2821 -chr1 35807 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.906;DP=108;Dels=0.00;FS=7.240;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=2;MQRankSum=-6.417;QD=6.27;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,28:108:99:705,0,2709 -chr1 35843 . A T 2756.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=30.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2785,214,0 -chr1 35857 . C A 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=53.9074;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.442;QD=2.19;ReadPosRankSum=-1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,10:68:99:177,0,1820 -chr1 35860 . A C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.173;DP=74;Dels=0.00;FS=3.561;HaplotypeScore=73.8862;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=0;MQRankSum=0.722;QD=6.77;ReadPosRankSum=3.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,20:74:99:529,0,1811 -chr1 35870 . A T 2448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.943;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=27.0091;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=1;MQRankSum=2.228;QD=26.05;ReadPosRankSum=-0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,72:94:99:2477,0,566 -chr1 35900 . T C 3238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355;DP=119;Dels=0.00;FS=8.381;HaplotypeScore=194.4919;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=3;MQRankSum=-1.040;QD=27.22;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,96:119:99:3267,0,489 -chr1 35951 . T A 1015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=2;MQRankSum=-0.149;QD=8.00;ReadPosRankSum=0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,37:127:99:1044,0,2832 -chr1 35968 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=50.3624;MLEAC=2;MLEAF=1.00;MQ=56.18;MQ0=0;QD=29.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2085,162,0 -chr1 35979 . G A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.196;DP=96;Dels=0.00;FS=17.564;HaplotypeScore=12.6997;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=2;MQRankSum=-1.392;QD=0.89;ReadPosRankSum=3.011;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,10:96:99:114,0,2869 -chr1 36004 . G A 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=72;Dels=0.00;FS=9.104;HaplotypeScore=76.6328;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-1.369;QD=0.25;ReadPosRankSum=-1.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,7:72:46:46,0,2207 -chr1 36045 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=132;Dels=0.00;FS=0.896;HaplotypeScore=43.4929;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.565;QD=3.33;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:110,22:132:99:468,0,3861 -chr1 36103 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=141;Dels=0.00;FS=41.173;HaplotypeScore=7.9970;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.254;QD=0.83;ReadPosRankSum=2.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:126,15:141:99:145,0,4391 -chr1 36153 . G C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=89;Dels=0.00;FS=7.730;HaplotypeScore=3.8273;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.014;QD=6.33;ReadPosRankSum=1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,21:89:99:592,0,2434 -chr1 36180 . T A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=100;Dels=0.00;FS=0.858;HaplotypeScore=3.7118;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.137;QD=7.78;ReadPosRankSum=0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,29:100:99:806,0,2559 -chr1 36205 . C T 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.427;DP=124;Dels=0.00;FS=0.755;HaplotypeScore=17.7034;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.466;QD=7.79;ReadPosRankSum=-0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,35:124:99:994,0,3181 -chr1 36213 . T C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.280;DP=132;Dels=0.00;FS=2.347;HaplotypeScore=19.5352;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.237;QD=1.48;ReadPosRankSum=0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,15:132:99:223,0,4265 -chr1 36259 . T C 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.248;DP=134;Dels=0.00;FS=3.770;HaplotypeScore=89.4890;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.222;QD=6.63;ReadPosRankSum=-1.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,33:134:99:916,0,3559 -chr1 36261 . A G 780.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.776;DP=132;Dels=0.00;FS=2.746;HaplotypeScore=86.5740;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.433;QD=5.91;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,32:132:99:809,0,3579 -chr1 36273 . T C 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.181;DP=118;Dels=0.00;FS=1.774;HaplotypeScore=117.6849;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.361;QD=5.75;ReadPosRankSum=-0.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,28:118:99:707,0,3229 -chr1 36286 . A T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=98;Dels=0.00;FS=0.915;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=2.210;QD=5.89;ReadPosRankSum=0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:605,0,2724 -chr1 36287 . A T 2373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.322;DP=96;Dels=0.00;FS=1.851;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=0.853;QD=24.73;ReadPosRankSum=1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,68:96:99:2402,0,835 -chr1 36289 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.239;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=83.8835;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=1;MQRankSum=2.678;QD=5.48;ReadPosRankSum=1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,22:99:99:571,0,2798 -chr1 36290 . A T 2719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=84.8831;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=1;MQRankSum=-1.327;QD=27.20;ReadPosRankSum=-0.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,76:100:99:2748,0,648 -chr1 36320 . T A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=92;Dels=0.00;FS=0.939;HaplotypeScore=45.5348;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-3.017;QD=6.49;ReadPosRankSum=0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,23:92:99:625,0,2459 -chr1 36333 . G A 2428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.737;DP=96;Dels=0.00;FS=12.492;HaplotypeScore=24.9952;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=1;MQRankSum=-3.960;QD=25.30;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,71:96:99:2457,0,747 -chr1 36341 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=100;Dels=0.00;FS=14.157;HaplotypeScore=25.7839;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=1;MQRankSum=-3.263;QD=8.96;ReadPosRankSum=0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,30:100:99:924,0,2374 -chr1 36361 . G A 2302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=91;Dels=0.00;FS=2.218;HaplotypeScore=4.6978;MLEAC=1;MLEAF=0.500;MQ=55.09;MQ0=1;MQRankSum=-4.586;QD=25.31;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,69:91:99:2331,0,612 -chr1 36362 . T G 3325.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=3.9091;MLEAC=2;MLEAF=1.00;MQ=54.92;MQ0=1;QD=32.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3354,250,0 -chr1 36377 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=102;Dels=0.00;FS=10.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-5.406;QD=9.55;ReadPosRankSum=-0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,34:102:99:1002,0,2367 -chr1 36383 . T C 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.211;DP=103;Dels=0.00;FS=9.011;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-6.104;QD=9.69;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,36:103:99:1026,0,2320 -chr1 36393 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.454;DP=108;Dels=0.00;FS=2.766;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-6.108;QD=8.56;ReadPosRankSum=-0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,38:108:99:953,0,2423 -chr1 36408 . C T 2376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=104;Dels=0.00;FS=4.359;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=0;MQRankSum=-0.816;QD=22.85;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,77:104:99:2405,0,763 -chr1 36427 . A T 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.872;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=3.8148;MLEAC=1;MLEAF=0.500;MQ=51.50;MQ0=0;MQRankSum=-6.246;QD=6.56;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,28:94:99:645,0,2385 -chr1 36447 . A T 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.515;DP=107;Dels=0.00;FS=0.770;HaplotypeScore=3.5157;MLEAC=1;MLEAF=0.500;MQ=51.35;MQ0=0;MQRankSum=-6.584;QD=7.45;ReadPosRankSum=-0.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,35:107:99:825,0,2544 -chr1 36455 . A C 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=26.1134;MLEAC=1;MLEAF=0.500;MQ=51.36;MQ0=0;MQRankSum=-6.423;QD=7.65;ReadPosRankSum=-1.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:832,0,2482 -chr1 36464 . A C 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.836;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=48.2350;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-2.154;QD=5.85;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:602,0,2428 -chr1 36466 . C T 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.251;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=27.3765;MLEAC=1;MLEAF=0.500;MQ=51.39;MQ0=0;MQRankSum=-7.882;QD=17.75;ReadPosRankSum=-0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,59:96:99:1732,0,1115 -chr1 36483 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-3.339;QD=5.65;ReadPosRankSum=0.429;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,21:91:99:542,0,2305 -chr1 36503 . T C 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.33;MQ0=0;MQRankSum=-0.635;QD=0.59;ReadPosRankSum=3.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,9:86:79:79,0,2347 -chr1 36504 . T C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.112;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.130;QD=5.11;ReadPosRankSum=5.608;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,19:88:99:478,0,2018 -chr1 36505 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=79.0748;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.029;QD=4.27;ReadPosRankSum=5.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,17:88:99:404,0,2137 -chr1 36518 . A G 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.366;DP=101;Dels=0.00;FS=5.616;HaplotypeScore=12.9006;MLEAC=1;MLEAF=0.500;MQ=47.84;MQ0=0;MQRankSum=-1.467;QD=8.87;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:924,0,1480 -chr1 36532 . C G 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=115;Dels=0.00;FS=1.129;HaplotypeScore=33.9847;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=0;MQRankSum=2.072;QD=2.35;ReadPosRankSum=-1.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,15:115:99:298,0,2777 -chr1 36538 . C T 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=114;Dels=0.00;FS=3.778;HaplotypeScore=31.9878;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-8.542;QD=10.94;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,62:114:99:1275,0,1800 -chr1 36561 . C T 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=91;Dels=0.00;FS=7.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-6.542;QD=10.96;ReadPosRankSum=0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,33:91:99:1026,0,2069 -chr1 36566 . G A 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=95;Dels=0.00;FS=7.431;HaplotypeScore=17.9938;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-6.234;QD=10.17;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,33:95:99:994,0,2189 -chr1 36574 . G A 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=93;Dels=0.00;FS=3.666;HaplotypeScore=36.9659;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=-1.444;QD=4.45;ReadPosRankSum=1.036;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,18:93:99:442,0,2629 -chr1 36578 . G A 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=3.342;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-5.365;QD=8.58;ReadPosRankSum=0.452;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,25:83:99:740,0,2021 -chr1 36581 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=24.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2478,187,0 -chr1 36582 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.643;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.757;QD=7.39;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,17:63:99:494,0,1649 -chr1 36587 . G A 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.268;DP=64;Dels=0.00;FS=1.061;HaplotypeScore=19.9719;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-4.946;QD=8.75;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,20:64:99:588,0,1587 -chr1 36594 . C T 1517.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1546,117,0 -chr1 36595 . A C 1513.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=24.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1542,120,0 -chr1 36601 . T C 1588.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=28.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1617,120,0 -chr1 36605 . C T 1541.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1570,117,0 -chr1 36616 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-5.166;QD=11.34;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,15:38:99:459,0,805 -chr1 36621 . T C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.251;DP=36;Dels=0.00;FS=1.421;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=56.02;MQ0=0;MQRankSum=-4.460;QD=12.77;ReadPosRankSum=-1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,751 -chr1 36626 . C T 362.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=67;Dels=0.00;FS=6.207;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=53.11;MQ0=0;MQRankSum=-2.986;QD=5.41;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,15:67:99:391,0,1838 -chr1 36630 . T C 2560.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=1.9985;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=32.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2589,196,0 -chr1 36644 . A G 2044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.378;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=14.7297;MLEAC=1;MLEAF=0.500;MQ=53.58;MQ0=0;MQRankSum=-4.784;QD=26.56;ReadPosRankSum=-3.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,59:77:99:2073,0,508 -chr1 36651 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.907;DP=75;Dels=0.00;FS=2.457;HaplotypeScore=29.6893;MLEAC=1;MLEAF=0.500;MQ=53.83;MQ0=0;MQRankSum=-2.272;QD=4.60;ReadPosRankSum=-2.563;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:373,0,2131 -chr1 36656 . T C 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.462;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=16.6941;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-3.172;QD=3.11;ReadPosRankSum=2.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:277,0,2375 -chr1 36662 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=33.6895;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-1.103;QD=5.30;ReadPosRankSum=-1.807;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,17:80:99:452,0,2194 -chr1 36667 . A G 1572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.127;DP=88;Dels=0.00;FS=6.014;HaplotypeScore=19.7292;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=-3.331;QD=17.87;ReadPosRankSum=3.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,48:88:99:1601,0,1351 -chr1 36673 . G T 1522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190;DP=87;Dels=0.00;FS=6.027;HaplotypeScore=50.6295;MLEAC=1;MLEAF=0.500;MQ=55.85;MQ0=0;MQRankSum=-3.286;QD=17.50;ReadPosRankSum=4.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,46:87:99:1551,0,1404 -chr1 36679 . G A,C 994.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.028;DP=83;Dels=0.00;FS=6.491;HaplotypeScore=3.6668;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.79;MQ0=0;MQRankSum=-3.906;QD=11.98;ReadPosRankSum=3.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:18,20,45:83:99:1681,965,1561,114,0,635 -chr1 36680 . G T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.401;DP=83;Dels=0.00;FS=1.073;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=0.921;QD=6.54;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:571,0,2139 -chr1 36681 . C A 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.220;DP=83;Dels=0.00;FS=2.291;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.95;MQ0=0;MQRankSum=0.648;QD=6.82;ReadPosRankSum=0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,21:83:99:594,0,2067 -chr1 36692 . C T 2055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.272;DP=84;Dels=0.00;FS=1.085;HaplotypeScore=21.9809;MLEAC=1;MLEAF=0.500;MQ=56.56;MQ0=0;MQRankSum=-2.422;QD=24.47;ReadPosRankSum=2.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,63:83:99:2084,0,534 -chr1 36698 . C A 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=83;Dels=0.00;FS=8.813;HaplotypeScore=18.7747;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=0;MQRankSum=0.221;QD=9.43;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,26:83:99:811,0,1969 -chr1 36713 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;DP=86;Dels=0.00;FS=1.174;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-5.106;QD=3.24;ReadPosRankSum=1.351;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:307,0,2592 -chr1 36714 . G A 1263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=86;Dels=0.00;FS=13.988;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-2.103;QD=14.69;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,39:86:99:1292,0,1579 -chr1 36726 . G A 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=93;Dels=0.00;FS=12.102;HaplotypeScore=22.7149;MLEAC=1;MLEAF=0.500;MQ=57.37;MQ0=0;MQRankSum=2.213;QD=7.48;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,26:93:99:724,0,2287 -chr1 36731 . A G 2521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.037;DP=95;Dels=0.00;FS=2.183;HaplotypeScore=22.5037;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-1.447;QD=26.54;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,76:95:99:2550,0,452 -chr1 36745 . C G 1591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.959;DP=97;Dels=0.00;FS=21.761;HaplotypeScore=2.1877;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=0;MQRankSum=-3.929;QD=16.41;ReadPosRankSum=1.490;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,49:97:99:1620,0,1518 -chr1 36764 . T C 1128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.112;DP=75;Dels=0.00;FS=17.360;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-2.794;QD=15.05;ReadPosRankSum=4.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,34:75:99:1157,0,1382 -chr1 36765 . T G 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.179;DP=75;Dels=0.00;FS=14.729;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-2.439;QD=14.36;ReadPosRankSum=4.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,33:75:99:1105,0,1430 -chr1 36767 . T C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.723;DP=76;Dels=0.00;FS=14.305;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.429;QD=15.77;ReadPosRankSum=3.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,36:76:99:1227,0,1335 -chr1 36796 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.162;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.8300;MLEAC=1;MLEAF=0.500;MQ=55.32;MQ0=0;MQRankSum=-6.512;QD=3.92;ReadPosRankSum=0.721;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:420,0,2683 -chr1 36817 . A G 1277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149;DP=101;Dels=0.00;FS=1.617;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-2.941;QD=12.65;ReadPosRankSum=0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,45:101:99:1306,0,1931 -chr1 36850 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=113;Dels=0.00;FS=1.797;HaplotypeScore=42.9345;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=2.503;QD=6.50;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,28:113:99:763,0,2839 -chr1 36857 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=112;Dels=0.00;FS=6.385;HaplotypeScore=44.9514;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=-0.969;QD=4.13;ReadPosRankSum=-0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,21:112:99:491,0,3074 -chr1 36860 . T A 1910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.351;DP=112;Dels=0.00;FS=10.516;HaplotypeScore=64.8364;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=0.143;QD=17.06;ReadPosRankSum=-0.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,60:112:99:1939,0,1715 -chr1 36867 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=115;Dels=0.00;FS=2.674;HaplotypeScore=43.9466;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.637;QD=7.66;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:115:99:909,0,2706 -chr1 36869 . A G 1776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;DP=112;Dels=0.00;FS=8.872;HaplotypeScore=21.9682;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=1;MQRankSum=0.192;QD=15.86;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,55:112:99:1805,0,1829 -chr1 36898 . T G 3694.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=58.61;MQ0=1;QD=33.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3723,283,0 -chr1 36921 . G A 1095.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.776;DP=105;Dels=0.00;FS=1.642;HaplotypeScore=58.3901;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=0.967;QD=10.44;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,37:105:99:1124,0,2298 -chr1 36924 . T C 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=104;Dels=0.01;FS=11.095;HaplotypeScore=64.0672;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=1;MQRankSum=-0.152;QD=6.57;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,27:103:99:711,0,2625 -chr1 36928 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.431;DP=101;Dels=0.01;FS=13.977;HaplotypeScore=62.9043;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=1;MQRankSum=-0.447;QD=6.57;ReadPosRankSum=0.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,26:100:99:692,0,2509 -chr1 36933 . A G 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.768;DP=98;Dels=0.00;FS=1.634;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=3.401;QD=17.77;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,53:98:99:1770,0,1349 -chr1 36937 . C T 1282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=96;Dels=0.00;FS=1.678;HaplotypeScore=21.5624;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-2.005;QD=13.36;ReadPosRankSum=-0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,42:96:99:1311,0,1753 -chr1 36951 . A G 3101.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.536;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=4.9494;MLEAC=2;MLEAF=1.00;MQ=54.16;MQ0=2;MQRankSum=1.691;QD=31.53;ReadPosRankSum=-1.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,85:86:99:3130,247,0 -chr1 36957 . A G 3098.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.648;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=3.2851;MLEAC=2;MLEAF=1.00;MQ=53.34;MQ0=2;MQRankSum=1.690;QD=28.09;ReadPosRankSum=-1.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,83:84:99:3127,241,0 -chr1 36980 . G C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=87;Dels=0.00;FS=5.532;HaplotypeScore=19.2784;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=1;MQRankSum=-2.668;QD=4.49;ReadPosRankSum=1.236;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,17:87:99:419,0,2324 -chr1 36986 . G A,T 2608.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.692;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=1.6385;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.63;MQ0=1;MQRankSum=-0.418;QD=29.64;ReadPosRankSum=-1.015;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:1,37,50:88:99:2946,1693,1587,1253,0,1106 -chr1 36990 . C T 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=88;Dels=0.00;FS=11.050;HaplotypeScore=16.5790;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=-2.013;QD=12.11;ReadPosRankSum=-0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:50,38:88:99:1094,0,1532 -chr1 37033 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=97;Dels=0.00;FS=29.507;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.66;MQ0=1;MQRankSum=1.751;QD=5.93;ReadPosRankSum=-1.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:74,23:97:99:603,0,2295 -chr1 37035 . G A 1683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=95;Dels=0.00;FS=32.836;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.62;MQ0=1;MQRankSum=-1.237;QD=17.72;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:39,56:95:99:1712,0,1110 -chr1 37086 . T C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=83;Dels=0.00;FS=8.748;HaplotypeScore=15.4050;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=1;MQRankSum=0.495;QD=6.67;ReadPosRankSum=-0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:60,23:83:99:582,0,1632 -chr1 37098 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.373;DP=78;Dels=0.00;FS=22.975;HaplotypeScore=17.1337;MLEAC=1;MLEAF=0.500;MQ=38.80;MQ0=1;MQRankSum=2.695;QD=3.33;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,15:78:99:288,0,1577 -chr1 37106 . A C 1959.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.633;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=9.8922;MLEAC=2;MLEAF=1.00;MQ=38.34;MQ0=1;MQRankSum=-0.247;QD=27.60;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:1,70:71:99:1988,143,0 -chr1 37110 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=70;Dels=0.00;FS=20.054;HaplotypeScore=6.6058;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=1;MQRankSum=2.417;QD=3.65;ReadPosRankSum=-0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:57,13:70:99:284,0,1351 -chr1 37144 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.027;DP=75;Dels=0.01;FS=19.781;HaplotypeScore=21.1656;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=0.880;QD=7.64;ReadPosRankSum=0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:49,25:74:99:601,0,1238 -chr1 37145 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=74;Dels=0.00;FS=1.342;HaplotypeScore=17.3626;MLEAC=1;MLEAF=0.500;MQ=33.28;MQ0=5;MQRankSum=-1.467;QD=1.58;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,11:74:99:145,0,1687 -chr1 37146 . T C 1981.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.057;DP=73;Dels=0.00;FS=1.906;HaplotypeScore=17.3626;MLEAC=2;MLEAF=1.00;MQ=33.50;MQ0=5;MQRankSum=0.070;QD=27.15;ReadPosRankSum=-0.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:8,65:73:96:2010,96,0 -chr1 37167 . A G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.120;DP=75;Dels=0.00;FS=11.212;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=30.73;MQ0=5;MQRankSum=-0.123;QD=11.62;ReadPosRankSum=0.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:37,38:75:99:900,0,875 -chr1 37195 . A C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.498;DP=63;Dels=0.00;FS=34.326;HaplotypeScore=4.2993;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=6;MQRankSum=0.788;QD=4.57;ReadPosRankSum=1.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T7|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,16:63:99:316,0,1127 -chr1 37208 . A C 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=59;Dels=0.00;FS=17.669;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=6;MQRankSum=0.988;QD=3.18;ReadPosRankSum=-1.371;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R12|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,12:59:99:216,0,1075 -chr1 37234 . A G 585.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.20;MQ0=5;QD=18.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P20|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,31:31:66:614,66,0 -chr1 37263 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=28.54;MQ0=4;MQRankSum=-0.748;QD=15.24;ReadPosRankSum=-0.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R30L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:10,26:36:99:577,0,117 -chr1 37277 . G A 105.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=37;Dels=0.00;FS=1.773;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=34.79;MQ0=3;MQRankSum=-0.596;QD=2.86;ReadPosRankSum=0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D35N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:27,10:37:99:134,0,662 -chr1 37288 . G T 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7802;MLEAC=1;MLEAF=0.500;MQ=39.98;MQ0=2;MQRankSum=-1.717;QD=2.72;ReadPosRankSum=0.610;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E38D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:36,11:47:99:156,0,970 -chr1 37303 . G A,T 1674.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.9926;MLEAC=1,1;MLEAF=0.500,0.500;MQ=46.60;MQ0=1;QD=26.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q43H|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q43|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:0,54,10:64:99:1936,347,200,1589,0,1559 -chr1 37305 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.346;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=23.7316;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-3.229;QD=1.45;ReadPosRankSum=2.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V44A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:58,11:69:99:128,0,1781 -chr1 37314 . T C 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.448;DP=80;Dels=0.00;FS=1.179;HaplotypeScore=13.7857;MLEAC=1;MLEAF=0.500;MQ=48.12;MQ0=1;MQRankSum=1.805;QD=2.56;ReadPosRankSum=-1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I47T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:67,13:80:99:233,0,1973 -chr1 37336 . T C 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=2.6540;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=2.094;QD=8.05;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D54|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:68,31:99:99:825,0,2213 -chr1 37361 . C A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.201;DP=104;Dels=0.00;FS=2.268;HaplotypeScore=5.3893;MLEAC=1;MLEAF=0.500;MQ=47.39;MQ0=6;MQRankSum=-1.098;QD=2.63;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P63T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:85,19:104:99:302,0,2484 -chr1 37404 . C T 1818.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=7;QD=27.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S77F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1847,159,0 -chr1 37414 . C A 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=53;Dels=0.00;FS=5.282;HaplotypeScore=6.9624;MLEAC=1;MLEAF=0.500;MQ=36.19;MQ0=7;MQRankSum=0.103;QD=3.94;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P80|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:40,13:53:99:237,0,933 -chr1 37420 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.384;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=5.8162;MLEAC=1;MLEAF=0.500;MQ=30.80;MQ0=7;MQRankSum=-0.141;QD=2.92;ReadPosRankSum=-0.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A82|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:30,10:40:99:145,0,591 -chr1 37458 . C T 161.8 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.06;MQ0=0;QD=12.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A95V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,13:13:21:190,21,0 -chr1 37459 . A G 199.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.74;MQ0=0;QD=14.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A95|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,14:14:24:228,24,0 -chr1 37480 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=6.5977;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=1;MQRankSum=-3.019;QD=0.74;ReadPosRankSum=-1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V102|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:24,11:35:54:54,0,540 -chr1 37528 . A T 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.145;DP=99;Dels=0.00;FS=1.426;HaplotypeScore=2.0463;MLEAC=1;MLEAF=0.500;MQ=31.63;MQ0=3;MQRankSum=-2.642;QD=0.76;ReadPosRankSum=1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E118D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:80,19:99:99:103,0,1690 -chr1 37553 . C T 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.618;DP=101;Dels=0.00;FS=0.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=32.94;MQ0=5;MQRankSum=-4.815;QD=2.51;ReadPosRankSum=1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L127|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:66,35:101:99:282,0,1683 -chr1 37602 . C G 2282.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=37.45;MQ0=5;QD=30.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S143C|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2311,186,0 -chr1 37607 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=74;Dels=0.00;FS=8.462;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=38.66;MQ0=5;MQRankSum=0.654;QD=9.08;ReadPosRankSum=1.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Gta|L145V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:43,31:74:99:700,0,1242 -chr1 37632 . T A 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.285;DP=70;Dels=0.00;FS=1.067;HaplotypeScore=165.3085;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=2;MQRankSum=-0.738;QD=5.55;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:417,0,1466 -chr1 37654 . T C 334.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.313;DP=79;Dels=0.00;FS=1.038;HaplotypeScore=60.4783;MLEAC=1;MLEAF=0.500;MQ=40.53;MQ0=0;MQRankSum=-1.554;QD=4.24;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,19:79:99:363,0,1794 -chr1 37679 . T C 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=69;Dels=0.01;FS=3.415;HaplotypeScore=131.3512;MLEAC=1;MLEAF=0.500;MQ=36.89;MQ0=2;MQRankSum=0.051;QD=0.20;ReadPosRankSum=-0.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,7:68:42:42,0,1556 -chr1 37687 . A G 1378.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=69.8232;MLEAC=2;MLEAF=1.00;MQ=34.79;MQ0=2;QD=20.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,65:66:99:1407,129,0 -chr1 37807 . C T 3962.77 . AC=2;AF=1.00;AN=2;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.64;MQ0=1;QD=33.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,105:105:99:3991,313,0 -chr1 37815 . A C 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;DP=107;Dels=0.00;FS=2.466;HaplotypeScore=2.4531;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=2.701;QD=2.40;ReadPosRankSum=1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,15:107:99:285,0,3245 -chr1 37819 . A G 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=106;Dels=0.00;FS=2.428;HaplotypeScore=49.4245;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=2;MQRankSum=3.086;QD=2.82;ReadPosRankSum=0.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:327,0,3127 -chr1 37827 . T C 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.964;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=281.8552;MLEAC=1;MLEAF=0.500;MQ=52.18;MQ0=2;MQRankSum=-1.196;QD=9.12;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:986,0,2427 -chr1 37829 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.186;DP=103;Dels=0.00;FS=1.099;HaplotypeScore=280.8554;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=2;MQRankSum=-5.390;QD=2.67;ReadPosRankSum=-1.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,16:103:99:303,0,3052 -chr1 37845 . C G 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=105;Dels=0.00;FS=1.721;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=2;MQRankSum=-0.287;QD=12.40;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,43:105:99:1330,0,2039 -chr1 37852 . A T 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=114;Dels=0.00;FS=7.406;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=2;MQRankSum=1.342;QD=6.74;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,29:114:99:797,0,2971 -chr1 37858 . G T 4069.77 . AC=2;AF=1.00;AN=2;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=23.1962;MLEAC=2;MLEAF=1.00;MQ=55.35;MQ0=2;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,106:106:99:4098,313,0 -chr1 37891 . A G 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=105;Dels=0.00;FS=3.911;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=1;MQRankSum=1.160;QD=3.39;ReadPosRankSum=-1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,17:105:99:384,0,3122 -chr1 37931 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.853;DP=94;Dels=0.00;FS=6.552;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=3.443;QD=5.77;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,22:94:99:571,0,2560 -chr1 37938 . T G 3392.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3421,259,0 -chr1 37969 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=52;Dels=0.00;FS=4.310;HaplotypeScore=2.3113;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-4.200;QD=11.26;ReadPosRankSum=1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:614,0,1176 -chr1 37972 . A G 2052.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.3111;MLEAC=2;MLEAF=1.00;MQ=57.23;MQ0=0;QD=26.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:2081,154,0 -chr1 37991 . G C 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,153,0 -chr1 37996 . T C 1956.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=28.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1985,147,0 -chr1 37999 . A T 1924.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=43.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1953,144,0 -chr1 38000 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=50;Dels=0.00;FS=9.868;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=-4.276;QD=8.80;ReadPosRankSum=-0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:468,0,1240 -chr1 38009 . A C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=62;Dels=0.00;FS=21.281;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.304;QD=13.03;ReadPosRankSum=-3.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:836,0,1230 -chr1 38043 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=22.795;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.05;MQ0=0;MQRankSum=1.867;QD=15.45;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1048,0,1191 -chr1 38145 . C A 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.426;DP=22;Dels=0.00;FS=4.506;HaplotypeScore=20.3295;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=1.195;QD=18.67;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,13:22:99:439,0,169 -chr1 38190 . A C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=20;Dels=0.00;FS=37.992;HaplotypeScore=15.6751;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-3.279;QD=16.94;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:8,12:20:99:367,0,253 -chr1 38209 . G T 1079.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=11.5981;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1108,84,0 -chr1 38232 . G A 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.397;DP=26;Dels=0.00;FS=45.405;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-4.243;QD=19.84;ReadPosRankSum=-2.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:544,0,277 -chr1 38259 . T A 394.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.43;MQ0=0;QD=32.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:33:423,33,0 -chr1 38267 . C T 397.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=23.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:426,33,0 -chr1 38269 . G C 393.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=28.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:422,33,0 -chr1 38272 . G A 407.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=24.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:436,33,0 -chr1 38282 . G A 562.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:591,45,0 -chr1 38290 . T G 1662.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.33;MQ0=0;QD=30.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1691,132,0 -chr1 38305 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.174;DP=54;Dels=0.00;FS=1.164;HaplotypeScore=26.0834;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-0.232;QD=7.13;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:413,0,1363 -chr1 38320 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.621;DP=61;Dels=0.00;FS=5.712;HaplotypeScore=186.2137;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=2.727;QD=8.73;ReadPosRankSum=0.530;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:561,0,1414 -chr1 38327 . A G 2319.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=146.9227;MLEAC=2;MLEAF=1.00;MQ=53.56;MQ0=0;QD=29.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,61:63:99:2348,184,0 -chr1 38332 . G C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.367;DP=64;Dels=0.00;FS=1.052;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=3.453;QD=7.42;ReadPosRankSum=-2.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,19:64:99:503,0,1580 -chr1 38333 . G A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.193;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=-3.324;QD=11.43;ReadPosRankSum=2.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:771,0,1350 -chr1 38335 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.608;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=19.8719;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-3.117;QD=12.89;ReadPosRankSum=1.435;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,27:66:99:879,0,1194 -chr1 38344 . C T 2874.77 . AC=2;AF=1.00;AN=2;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=36.8803;MLEAC=2;MLEAF=1.00;MQ=54.82;MQ0=0;QD=32.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,220,0 -chr1 38350 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=2.904;QD=7.78;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,26:91:99:736,0,2251 -chr1 38352 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.858;DP=91;Dels=0.00;FS=0.951;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=3.445;QD=5.45;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:91:99:524,0,2399 -chr1 38354 . A G 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=92;Dels=0.00;FS=1.151;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=0.796;QD=1.80;ReadPosRankSum=-3.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,13:92:99:194,0,2761 -chr1 38356 . C T 3570.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.7339;MLEAC=2;MLEAF=1.00;MQ=55.21;MQ0=0;QD=30.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3599,268,0 -chr1 38380 . G C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=103;Dels=0.00;FS=1.016;HaplotypeScore=5.5532;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=0.452;QD=3.40;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,18:103:99:378,0,2986 -chr1 38386 . A G 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.945;DP=101;Dels=0.00;FS=2.163;HaplotypeScore=5.8191;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=1.265;QD=4.05;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,18:101:99:437,0,2897 -chr1 38406 . A G 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.994;DP=110;Dels=0.00;FS=0.886;HaplotypeScore=38.9762;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.927;QD=5.29;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,24:110:99:610,0,2961 -chr1 38410 . G C 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=107;Dels=0.00;FS=5.387;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=1.092;QD=8.61;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,32:107:99:949,0,2628 -chr1 38412 . A G 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=107;Dels=0.00;FS=1.876;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.410;QD=5.99;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,26:107:99:669,0,2864 -chr1 38514 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=93;Dels=0.00;FS=5.348;HaplotypeScore=43.8521;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-1.505;QD=3.79;ReadPosRankSum=1.100;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I168V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:73,19:93:99:381,0,2418 -chr1 38516 . T G 3066.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.284;DP=85;Dels=0.00;FS=3.166;HaplotypeScore=43.8875;MLEAC=2;MLEAF=1.00;MQ=49.63;MQ0=0;MQRankSum=-0.509;QD=31.58;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I168M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:1,84:85:99:3095,218,0 -chr1 38519 . A C 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.706;DP=83;Dels=0.00;FS=18.028;HaplotypeScore=44.8742;MLEAC=1;MLEAF=0.500;MQ=49.02;MQ0=0;MQRankSum=-2.301;QD=15.17;ReadPosRankSum=1.618;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A169|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:40,43:83:99:1287,0,1261 -chr1 38524 . G T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=87;Dels=0.00;FS=8.398;HaplotypeScore=47.8556;MLEAC=1;MLEAF=0.500;MQ=48.63;MQ0=0;MQRankSum=0.082;QD=6.37;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G171V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:64,23:87:99:582,0,2000 -chr1 38580 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.789;DP=83;Dels=0.00;FS=10.079;HaplotypeScore=4.2557;MLEAC=1;MLEAF=0.500;MQ=42.00;MQ0=0;MQRankSum=1.229;QD=9.35;ReadPosRankSum=-1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A190T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:49,33:83:99:804,0,1512 -chr1 38614 . G T 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=88;Dels=0.00;FS=8.617;HaplotypeScore=41.5773;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=-1.852;QD=7.99;ReadPosRankSum=-1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R201L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:62,26:88:99:731,0,1964 -chr1 38616 . C T 1299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.710;DP=88;Dels=0.00;FS=3.034;HaplotypeScore=74.9440;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=2.195;QD=14.77;ReadPosRankSum=0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L202|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:45,43:88:99:1328,0,1423 -chr1 38621 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=92;Dels=0.00;FS=8.548;HaplotypeScore=74.6108;MLEAC=1;MLEAF=0.500;MQ=45.88;MQ0=0;MQRankSum=-2.005;QD=6.60;ReadPosRankSum=-1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N203|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:68,24:92:99:635,0,2194 -chr1 38624 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=92;Dels=0.00;FS=18.358;HaplotypeScore=71.5984;MLEAC=1;MLEAF=0.500;MQ=45.57;MQ0=0;MQRankSum=-0.682;QD=4.52;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A204|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:70,22:92:99:444,0,2305 -chr1 38633 . G A 1358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.729;DP=93;Dels=0.00;FS=4.284;HaplotypeScore=20.6300;MLEAC=1;MLEAF=0.500;MQ=46.35;MQ0=0;MQRankSum=1.841;QD=14.61;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P207|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,51:93:99:1387,0,1217 -chr1 38643 . A G 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.552;DP=96;Dels=0.00;FS=1.832;HaplotypeScore=4.1979;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=1.806;QD=17.82;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T211A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,54:96:99:1739,0,1020 -chr1 38657 . C T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.378;DP=85;Dels=0.00;FS=2.540;HaplotypeScore=14.1583;MLEAC=1;MLEAF=0.500;MQ=45.85;MQ0=1;MQRankSum=1.974;QD=26.04;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H215|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,70:85:99:2242,0,177 -chr1 38659 . A C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.241;DP=83;Dels=0.00;FS=9.582;HaplotypeScore=13.1589;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=1.020;QD=5.08;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E216A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:63,20:83:99:450,0,1930 -chr1 38708 . T C 1093.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.976;DP=42;Dels=0.00;FS=2.564;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=2;MQRankSum=1.592;QD=26.04;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D232|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:3,39:42:29:1122,29,0 -chr1 38723 . C T 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=4.5678;MLEAC=1;MLEAF=0.500;MQ=34.19;MQ0=2;MQRankSum=1.958;QD=16.83;ReadPosRankSum=-0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S237|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,22:30:76:533,0,76 -chr1 38732 . C T 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;DP=25;Dels=0.00;FS=2.077;HaplotypeScore=8.5290;MLEAC=1;MLEAF=0.500;MQ=28.41;MQ0=2;MQRankSum=1.921;QD=7.63;ReadPosRankSum=-1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F240|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,9:25:99:219,0,204 -chr1 38739 . A G 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.986;DP=21;Dels=0.00;FS=14.564;HaplotypeScore=7.2577;MLEAC=1;MLEAF=0.500;MQ=26.73;MQ0=2;MQRankSum=1.056;QD=11.42;ReadPosRankSum=-1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T243A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:7,14:21:61:268,0,61 -chr1 38754 . C T 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;DP=27;Dels=0.00;FS=23.314;HaplotypeScore=3.4383;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=1;MQRankSum=1.291;QD=6.03;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L248|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:17,10:27:99:191,0,164 -chr1 38813 . G A 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=45;Dels=0.00;FS=10.745;HaplotypeScore=6.7165;MLEAC=1;MLEAF=0.500;MQ=23.36;MQ0=6;MQRankSum=0.418;QD=3.44;ReadPosRankSum=-0.933;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T267|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,14:45:99:183,0,334 -chr1 38818 . G A 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.899;DP=44;Dels=0.00;FS=36.491;HaplotypeScore=10.4483;MLEAC=1;MLEAF=0.500;MQ=23.61;MQ0=6;MQRankSum=2.543;QD=5.45;ReadPosRankSum=-1.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C269Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,12:44:99:268,0,339 -chr1 38827 . G T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.662;DP=48;Dels=0.00;FS=16.528;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.16;MQ0=7;MQRankSum=0.544;QD=3.04;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R272L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,14:48:99:174,0,437 -chr1 38828 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.199;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.63;MQ0=7;MQRankSum=1.593;QD=10.36;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R272|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,33:49:99:536,0,103 -chr1 38834 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.131;DP=50;Dels=0.00;FS=1.394;HaplotypeScore=10.1537;MLEAC=1;MLEAF=0.500;MQ=24.71;MQ0=8;MQRankSum=0.472;QD=5.02;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R274|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,18:50:99:279,0,381 -chr1 38874 . G A 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.215;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=9.5155;MLEAC=1;MLEAF=0.500;MQ=24.48;MQ0=8;MQRankSum=-0.446;QD=6.30;ReadPosRankSum=0.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V288M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:22,21:43:99:299,0,317 -chr1 38881 . G A 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=41;Dels=0.00;FS=18.266;HaplotypeScore=21.0278;MLEAC=1;MLEAF=0.500;MQ=26.69;MQ0=6;MQRankSum=0.334;QD=1.80;ReadPosRankSum=-1.159;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C290Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,11:41:99:102,0,593 -chr1 38886 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=42;Dels=0.00;FS=1.336;HaplotypeScore=14.7997;MLEAC=1;MLEAF=0.500;MQ=27.24;MQ0=6;MQRankSum=0.652;QD=4.83;ReadPosRankSum=2.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V292I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:31,11:42:99:231,0,490 -chr1 38927 . G A 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.113;DP=30;Dels=0.00;FS=1.455;HaplotypeScore=5.5545;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=1;MQRankSum=-0.895;QD=9.99;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G305|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,15:30:99:328,0,330 -chr1 38933 . C T 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.620;DP=28;Dels=0.00;FS=4.494;HaplotypeScore=6.2885;MLEAC=1;MLEAF=0.500;MQ=33.72;MQ0=0;MQRankSum=-1.020;QD=1.35;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y307|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:23,5:28:66:66,0,561 -chr1 38942 . G C 697.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=10.5944;MLEAC=2;MLEAF=1.00;MQ=34.49;MQ0=0;QD=26.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G310|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,26:26:63:726,63,0 -chr1 38949 . T C 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.480;DP=23;Dels=0.00;FS=6.415;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=34.90;MQ0=0;MQRankSum=1.291;QD=14.51;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,14:23:99:362,0,165 -chr1 38951 . T G 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=21;Dels=0.00;FS=2.884;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=36.04;MQ0=0;MQRankSum=0.151;QD=1.18;ReadPosRankSum=-2.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,3:21:53:53,0,465 -chr1 38954 . A G 534.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=2;MLEAF=1.00;MQ=36.30;MQ0=0;QD=28.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P314|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,19:19:48:563,48,0 -chr1 38996 . T G 345.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=32.02;MQ0=1;QD=19.21;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L328|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,13:18:30:374,30,0 -chr1 38998 . G A 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=22;Dels=0.00;FS=3.358;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=30.79;MQ0=1;MQRankSum=2.426;QD=14.94;ReadPosRankSum=2.499;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G329E|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,13:22:30:357,0,30 -chr1 39012 . C T 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.081;DP=31;Dels=0.00;FS=6.864;HaplotypeScore=3.8698;MLEAC=1;MLEAF=0.500;MQ=29.64;MQ0=2;MQRankSum=0.242;QD=0.99;ReadPosRankSum=1.534;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L334|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:25,6:31:59:59,0,466 -chr1 39047 . T C 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.226;DP=43;Dels=0.00;FS=8.463;HaplotypeScore=12.3919;MLEAC=1;MLEAF=0.500;MQ=26.75;MQ0=5;MQRankSum=0.113;QD=2.27;ReadPosRankSum=-0.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D345|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:36,7:43:99:126,0,608 -chr1 39056 . A T 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.448;DP=51;Dels=0.00;FS=13.801;HaplotypeScore=11.9705;MLEAC=1;MLEAF=0.500;MQ=26.54;MQ0=6;MQRankSum=1.911;QD=6.82;ReadPosRankSum=-0.405;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K348N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,19:51:99:376,0,461 -chr1 39103 . C T 1400.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=3.9611;MLEAC=2;MLEAF=1.00;MQ=29.47;MQ0=10;QD=21.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A364V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,66:66:99:1429,129,0 -chr1 39113 . C T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.057;DP=67;Dels=0.00;FS=2.370;HaplotypeScore=12.4314;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=9;MQRankSum=-3.266;QD=8.16;ReadPosRankSum=1.680;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T367|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,41:67:99:575,0,677 -chr1 39116 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.93;MQ0=9;MQRankSum=3.100;QD=8.41;ReadPosRankSum=-0.858;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y368|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,24:67:99:592,0,634 -chr1 39117 . G C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.149;DP=67;Dels=0.00;FS=1.309;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.61;MQ0=9;MQRankSum=1.678;QD=16.32;ReadPosRankSum=-0.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V369L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,49:67:99:1122,0,102 -chr1 39150 . G A 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.147;DP=74;Dels=0.00;FS=5.772;HaplotypeScore=13.8080;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=6;MQRankSum=2.238;QD=5.12;ReadPosRankSum=1.855;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E380K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:57,17:74:99:407,0,823 -chr1 39172 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;DP=58;Dels=0.00;FS=4.464;HaplotypeScore=6.4651;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=1;MQRankSum=2.790;QD=5.15;ReadPosRankSum=0.121;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R387K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:44,14:58:99:327,0,622 -chr1 39178 . A C 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.108;DP=53;Dels=0.00;FS=7.365;HaplotypeScore=8.0329;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=0;MQRankSum=2.138;QD=3.96;ReadPosRankSum=0.384;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E389A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,11:53:99:238,0,621 -chr1 39240 . C A 821.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.94;MQ0=0;QD=21.07;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P410T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:78:850,78,0 -chr1 39253 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.96;MQ0=2;QD=20.64;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R414K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:75:833,75,0 -chr1 39271 . G T 806.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.780;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=5.3949;MLEAC=2;MLEAF=1.00;MQ=26.69;MQ0=8;MQRankSum=2.441;QD=18.34;ReadPosRankSum=1.535;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R420I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:9,35:44:50:835,50,0 -chr1 39276 . G T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.189;DP=48;Dels=0.00;FS=2.414;HaplotypeScore=5.3949;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=9;MQRankSum=0.777;QD=1.14;ReadPosRankSum=-0.609;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V422F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,5:48:83:83,0,754 -chr1 39306 . G A 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.9525;MLEAC=1;MLEAF=0.500;MQ=26.06;MQ0=10;MQRankSum=0.296;QD=2.81;ReadPosRankSum=1.235;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D432N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:41,8:49:99:166,0,570 -chr1 39324 . C T 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=8.4793;MLEAC=1;MLEAF=0.500;MQ=22.99;MQ0=11;MQRankSum=0.420;QD=3.08;ReadPosRankSum=-0.128;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L438|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,12:46:99:170,0,488 -chr1 39353 . C T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=9;MQRankSum=-0.726;QD=3.15;ReadPosRankSum=-0.286;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H447|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,13:39:99:151,0,416 -chr1 39356 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=24.07;MQ0=9;MQRankSum=-0.636;QD=1.55;ReadPosRankSum=0.194;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S448|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:27,9:36:84:84,0,463 -chr1 39366 . C G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.6622;MLEAC=1;MLEAF=0.500;MQ=24.65;MQ0=7;MQRankSum=1.387;QD=13.05;ReadPosRankSum=0.000;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R452G|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,25:33:68:459,0,68 -chr1 39388 . T C 309.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V459A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:338,36,0 -chr1 39389 . T C 316.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.80;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V459|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:345,36,0 -chr1 39403 . T C 290.98 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.255;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.86;MQ0=2;MQRankSum=1.104;QD=17.12;ReadPosRankSum=-0.255;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:3,14:17:13:319,13,0 -chr1 39422 . T C 231.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.16;MQ0=1;QD=19.32;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:260,24,0 -chr1 39447 . T C 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.212;DP=26;Dels=0.00;FS=9.558;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=4;MQRankSum=2.899;QD=4.53;ReadPosRankSum=-0.862;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,5:26:99:146,0,489 -chr1 39484 . T C 611.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8320;MLEAC=2;MLEAF=1.00;MQ=30.77;MQ0=3;QD=26.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:640,51,0 -chr1 39510 . G A 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=20;Dels=0.00;FS=2.963;HaplotypeScore=7.6395;MLEAC=1;MLEAF=0.500;MQ=30.59;MQ0=3;MQRankSum=2.583;QD=6.49;ReadPosRankSum=-0.053;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:158,0,271 -chr1 39526 . A G 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=28.66;MQ0=3;MQRankSum=-1.408;QD=6.20;ReadPosRankSum=1.749;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,8:14:99:115,0,155 -chr1 39567 . G C 371.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.10;MQ0=1;QD=15.49;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:42:400,42,0 -chr1 39584 . T C 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.136;DP=38;Dels=0.03;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.96;MQ0=1;MQRankSum=0.330;QD=14.99;ReadPosRankSum=0.330;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:74:598,0,74 -chr1 39587 . T C 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=40;Dels=0.03;FS=7.160;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.64;MQ0=1;MQRankSum=-0.714;QD=1.07;ReadPosRankSum=-0.165;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,7:39:71:71,0,649 -chr1 39596 . A T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=52;Dels=0.00;FS=9.385;HaplotypeScore=3.4616;MLEAC=1;MLEAF=0.500;MQ=33.54;MQ0=1;MQRankSum=-1.360;QD=0.76;ReadPosRankSum=0.065;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,8:52:68:68,0,1009 -chr1 39631 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=77;Dels=0.00;FS=1.669;HaplotypeScore=7.9697;MLEAC=1;MLEAF=0.500;MQ=33.50;MQ0=1;MQRankSum=-0.513;QD=0.63;ReadPosRankSum=1.240;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:77:77:77,0,1546 -chr1 39643 . C A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.541;QD=1.37;ReadPosRankSum=-1.004;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:116,0,1373 -chr1 39644 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.657;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.599;QD=1.54;ReadPosRankSum=-0.966;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:127,0,1357 -chr1 39648 . G C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=58.2273;MLEAC=1;MLEAF=0.500;MQ=35.15;MQ0=0;MQRankSum=3.645;QD=21.79;ReadPosRankSum=-1.153;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,48:62:58:1379,0,58 -chr1 39651 . C G 1622.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=56.2590;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=0;QD=27.98;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:1651,138,0 -chr1 39652 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=58;Dels=0.00;FS=1.714;HaplotypeScore=66.4027;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-1.217;QD=0.34;ReadPosRankSum=0.263;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,7:58:48:48,0,1327 -chr1 39656 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=58;Dels=0.00;FS=17.787;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-3.172;QD=6.93;ReadPosRankSum=1.492;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:430,0,880 -chr1 39657 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=57;Dels=0.00;FS=10.567;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.40;MQ0=0;MQRankSum=-2.652;QD=3.77;ReadPosRankSum=1.846;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:243,0,1124 -chr1 39659 . C T 63.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=56;Dels=0.00;FS=3.377;HaplotypeScore=37.1251;MLEAC=1;MLEAF=0.500;MQ=36.35;MQ0=0;MQRankSum=0.246;QD=1.14;ReadPosRankSum=0.199;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,8:56:92:92,0,1236 -chr1 39662 . A G 1224.79 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=54.7091;MLEAC=1;MLEAF=0.500;MQ=36.36;MQ0=0;QD=22.68;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:54:99:1385,118,0 -chr1 39664 . A C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.270;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=53.7676;MLEAC=1;MLEAF=0.500;MQ=36.29;MQ0=0;MQRankSum=-3.301;QD=0.21;ReadPosRankSum=1.393;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,11:53:39:39,0,1193 -chr1 39669 . G A 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.015;DP=50;Dels=0.00;FS=1.659;HaplotypeScore=69.6890;MLEAC=1;MLEAF=0.500;MQ=35.68;MQ0=0;MQRankSum=-0.075;QD=0.30;ReadPosRankSum=1.955;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,6:50:43:43,0,1137 -chr1 39670 . C T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=44;Dels=0.00;FS=2.860;HaplotypeScore=65.0263;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=1.698;QD=6.43;ReadPosRankSum=0.000;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:311,0,662 -chr1 39671 . C A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=69.6870;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=-2.765;QD=0.86;ReadPosRankSum=-0.217;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,11:44:66:66,0,915 -chr1 39673 . C A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.953;DP=42;Dels=0.00;FS=4.360;HaplotypeScore=59.5432;MLEAC=1;MLEAF=0.500;MQ=33.27;MQ0=0;MQRankSum=1.563;QD=9.57;ReadPosRankSum=0.902;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:430,0,510 -chr1 39676 . G A 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=41;Dels=0.00;FS=5.757;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=-0.931;QD=13.90;ReadPosRankSum=-0.215;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,29:41:99:598,0,311 -chr1 39678 . G A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=41;Dels=0.00;FS=6.236;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=1.091;QD=2.77;ReadPosRankSum=1.923;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,7:41:99:142,0,757 -chr1 39681 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=40;Dels=0.00;FS=1.360;HaplotypeScore=29.6132;MLEAC=1;MLEAF=0.500;MQ=33.13;MQ0=0;MQRankSum=1.431;QD=6.37;ReadPosRankSum=-0.635;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:283,0,590 -chr1 39685 . T C 820.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=10.9898;MLEAC=2;MLEAF=1.00;MQ=34.61;MQ0=0;QD=24.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:75:849,75,0 -chr1 39710 . A G 29.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.30;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.736;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:1,2:3:29:58,0,29 -chr1 39718 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr1 39719 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr1 39722 . C A 37.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=18.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr1 39725 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.42;MQ0=0;QD=13.25;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:67,6,0 -chr1 39728 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.26;MQ0=0;QD=9.94;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,4:4:6:67,6,0 -chr1 39736 . C T 237.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.78;MQ0=0;QD=19.82;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:266,24,0 -chr1 39751 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.930;QD=14.14;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:212,0,40 -chr1 39756 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.761;QD=14.60;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:218,0,40 -chr1 39758 . A G 241.78 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=30.63;MQ0=0;QD=18.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:13:24:270,24,0 -chr1 39777 . T A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=21.2570;MLEAC=1;MLEAF=0.500;MQ=36.27;MQ0=0;MQRankSum=1.668;QD=22.67;ReadPosRankSum=-0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,21:25:29:595,0,29 -chr1 39810 . T C 2246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.769;DP=69;Dels=0.00;FS=2.663;HaplotypeScore=6.9006;MLEAC=2;MLEAF=1.00;MQ=41.37;MQ0=0;MQRankSum=1.949;QD=32.56;ReadPosRankSum=0.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,67:69:99:2275,144,0 -chr1 39820 . T G 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=75;Dels=0.00;FS=0.967;HaplotypeScore=5.9128;MLEAC=1;MLEAF=0.500;MQ=40.90;MQ0=0;MQRankSum=2.599;QD=10.33;ReadPosRankSum=1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:803,0,1331 -chr1 39826 . A C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.234;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=2.9758;MLEAC=1;MLEAF=0.500;MQ=40.59;MQ0=0;MQRankSum=2.470;QD=10.80;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:892,0,1425 -chr1 39866 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.071;DP=50;Dels=0.04;FS=1.930;HaplotypeScore=58.2750;MLEAC=1;MLEAF=0.500;MQ=43.17;MQ0=0;MQRankSum=0.945;QD=0.48;ReadPosRankSum=-3.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,5:48:52:52,0,1435 -chr1 39890 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.405;DP=34;Dels=0.00;FS=6.017;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.76;MQ0=0;MQRankSum=-2.459;QD=5.43;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:213,0,772 -chr1 39891 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=43;Dels=0.00;FS=1.596;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.93;MQ0=1;MQRankSum=-2.575;QD=3.44;ReadPosRankSum=2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:176,0,1067 -chr1 39914 . A T 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=23.4102;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=4;MQRankSum=0.588;QD=15.15;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:710,0,508 -chr1 39960 . C A,T 1177.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=42.42;MQ0=3;QD=25.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,22,25:47:99:1385,655,589,730,0,673 -chr1 39961 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=47;Dels=0.00;FS=1.512;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=42.42;MQ0=3;MQRankSum=1.537;QD=14.12;ReadPosRankSum=-0.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:692,0,570 -chr1 39965 . A G 1518.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.4258;MLEAC=2;MLEAF=1.00;MQ=42.93;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:47:99:1547,126,0 -chr1 39976 . A G 1421.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.63;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1450,117,0 -chr1 39993 . A G 1637.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.2512;MLEAC=2;MLEAF=1.00;MQ=43.23;MQ0=0;QD=34.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1666,135,0 -chr1 40003 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.65;MQ0=0;MQRankSum=-3.665;QD=10.36;ReadPosRankSum=-2.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:453,0,706 -chr1 40005 . G A 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=42;Dels=0.00;FS=12.410;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=0.221;QD=5.64;ReadPosRankSum=-2.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:265,0,940 -chr1 40007 . T A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=42;Dels=0.00;FS=4.327;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=3.748;QD=16.04;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:702,0,465 -chr1 40020 . C T 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=42;Dels=0.00;FS=15.124;HaplotypeScore=19.7971;MLEAC=1;MLEAF=0.500;MQ=41.55;MQ0=0;MQRankSum=1.991;QD=3.33;ReadPosRankSum=-2.632;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:99:168,0,1045 -chr1 40026 . A G 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.995;DP=44;Dels=0.00;FS=1.981;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1169 -chr1 40027 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.961;DP=44;Dels=0.00;FS=4.177;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.37;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1200 -chr1 40029 . T C 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=38;Dels=0.00;FS=1.939;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=1.977;QD=25.73;ReadPosRankSum=0.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:5,32:38:68:1006,0,68 -chr1 40032 . T C 1048.85 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=0;MQRankSum=4.052;QD=28.35;ReadPosRankSum=-2.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:17:1077,0,17 -chr1 40037 . G T 1253.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=0;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1282,108,0 -chr1 40050 . T C 1369.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.02;MQ0=0;QD=33.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1398,117,0 -chr1 40053 . C G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=5.5950;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=0;MQRankSum=1.442;QD=5.73;ReadPosRankSum=-0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,11:46:99:292,0,1057 -chr1 40084 . T A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=0.136;QD=13.27;ReadPosRankSum=-0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:665,0,943 -chr1 40096 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=0.374;QD=13.50;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:676,0,875 -chr1 40115 . G A 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.138;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=21.9178;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.379;QD=19.83;ReadPosRankSum=-1.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:980,0,633 -chr1 40186 . A G 2354.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=55.52;MQ0=0;QD=25.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2383,181,0 -chr1 40187 . T C 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=65;Dels=0.00;FS=14.460;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-3.656;QD=0.92;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,9:65:88:88,0,1926 -chr1 40200 . A G 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=16.7520;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.152;QD=1.71;ReadPosRankSum=-1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:153,0,2048 -chr1 40205 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=74;Dels=0.00;FS=1.321;HaplotypeScore=20.7504;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.008;QD=0.46;ReadPosRankSum=2.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:62:62,0,1934 -chr1 40212 . G A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=73;Dels=0.00;FS=1.331;HaplotypeScore=32.7378;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-0.609;QD=2.30;ReadPosRankSum=1.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,11:73:99:196,0,1961 -chr1 40216 . C T 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=77;Dels=0.00;FS=3.483;HaplotypeScore=23.9149;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=2.932;QD=7.82;ReadPosRankSum=-1.909;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:630,0,1637 -chr1 40235 . A G 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.661;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=35.5558;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-0.751;QD=9.86;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,29:80:99:817,0,1701 -chr1 40238 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.173;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=31.6873;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-3.462;QD=5.38;ReadPosRankSum=-2.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:475,0,2185 -chr1 40257 . G A 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=89;Dels=0.00;FS=1.765;HaplotypeScore=39.6559;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-4.194;QD=14.62;ReadPosRankSum=-0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,40:89:99:1329,0,1466 -chr1 40262 . T C 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;DP=90;Dels=0.00;FS=12.546;HaplotypeScore=41.5222;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.449;QD=14.11;ReadPosRankSum=-0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,40:90:99:1298,0,1623 -chr1 40276 . G A 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;DP=99;Dels=0.00;FS=2.892;HaplotypeScore=39.6083;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=4.526;QD=8.99;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,30:99:99:918,0,2233 -chr1 40279 . A C,G 2850.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.6138;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.31;MQ0=0;QD=28.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,73,17:100:99:3203,624,407,2579,0,2528 -chr1 40299 . T C 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=94;Dels=0.00;FS=4.739;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.77;MQ0=0;MQRankSum=1.944;QD=0.97;ReadPosRankSum=1.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,10:94:99:119,0,2786 -chr1 40300 . A G 1244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=96;Dels=0.00;FS=2.677;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.317;QD=12.97;ReadPosRankSum=1.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,43:96:99:1273,0,1762 -chr1 40316 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=100;Dels=0.00;FS=6.354;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.47;MQ0=0;MQRankSum=-6.856;QD=4.66;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:494,0,2754 -chr1 40317 . G A 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;DP=98;Dels=0.00;FS=6.790;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=0.824;QD=4.58;ReadPosRankSum=-0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:477,0,2577 -chr1 40321 . T A 3751.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=68.1412;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3780,292,0 -chr1 40326 . T C 1103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=102;Dels=0.00;FS=8.509;HaplotypeScore=104.4492;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=5.492;QD=10.82;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,37:102:99:1132,0,2119 -chr1 40331 . C T 611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=42.7177;MLEAC=1;MLEAF=0.500;MQ=54.62;MQ0=0;MQRankSum=3.620;QD=6.58;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:640,0,2316 -chr1 40336 . C T 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;DP=89;Dels=0.00;FS=7.137;HaplotypeScore=40.7185;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=4.995;QD=12.21;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,34:89:99:1115,0,1717 -chr1 40340 . T C 1638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=87;Dels=0.00;FS=8.927;HaplotypeScore=60.7684;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.839;QD=18.84;ReadPosRankSum=-0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,52:87:99:1667,0,1091 -chr1 40350 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.570;DP=100;Dels=0.00;FS=2.227;HaplotypeScore=42.2843;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=0;MQRankSum=-3.916;QD=2.79;ReadPosRankSum=-0.327;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:307,0,2907 -chr1 40357 . A G 1180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=101;Dels=0.00;FS=8.331;HaplotypeScore=60.4654;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-3.892;QD=11.69;ReadPosRankSum=-1.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,40:100:99:1209,0,1863 -chr1 40359 . T C 3820.77 . AC=2;AF=1.00;AN=2;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=60.4654;MLEAC=2;MLEAF=1.00;MQ=56.15;MQ0=0;QD=29.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:101:99:3849,295,0 -chr1 40367 . G A 1455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.630;DP=100;Dels=0.00;FS=2.623;HaplotypeScore=40.4721;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=3.679;QD=14.56;ReadPosRankSum=-0.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,45:100:99:1484,0,1789 -chr1 40385 . A T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.211;DP=99;Dels=0.00;FS=2.269;HaplotypeScore=13.6606;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=0;MQRankSum=-2.742;QD=3.11;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,17:99:99:336,0,2801 -chr1 40386 . T C 3699.77 . AC=2;AF=1.00;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=13.6606;MLEAC=2;MLEAF=1.00;MQ=57.21;MQ0=0;QD=26.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:100:99:3728,298,0 -chr1 40390 . C A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=102;Dels=0.00;FS=10.470;HaplotypeScore=47.4671;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=0;MQRankSum=-0.627;QD=2.08;ReadPosRankSum=-1.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,14:102:99:240,0,3128 -chr1 40397 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=99;Dels=0.00;FS=2.447;HaplotypeScore=91.1211;MLEAC=1;MLEAF=0.500;MQ=57.63;MQ0=0;MQRankSum=-2.184;QD=2.04;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:230,0,3009 -chr1 40398 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=98;Dels=0.00;FS=0.959;HaplotypeScore=91.9098;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-0.904;QD=4.41;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:460,0,2711 -chr1 40401 . C A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.162;DP=96;Dels=0.00;FS=2.289;HaplotypeScore=54.1136;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-1.696;QD=3.29;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,16:96:99:344,0,2884 -chr1 40405 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.881;DP=97;Dels=0.00;FS=4.295;HaplotypeScore=68.8441;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=1.976;QD=7.68;ReadPosRankSum=-0.753;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,27:97:99:773,0,2466 -chr1 40415 . A G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.202;DP=95;Dels=0.00;FS=4.129;HaplotypeScore=16.3079;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.121;QD=2.67;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:282,0,2906 -chr1 40423 . G A 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=14.9944;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-0.719;QD=7.61;ReadPosRankSum=-0.969;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,27:94:99:744,0,2306 -chr1 40444 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=25.1958;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=1.888;QD=4.66;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,18:91:99:452,0,2590 -chr1 40450 . C T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=86;Dels=0.00;FS=10.543;HaplotypeScore=36.1917;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=-0.407;QD=1.33;ReadPosRankSum=0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,10:86:99:143,0,2614 -chr1 40451 . C T 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.552;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=37.1784;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=2.698;QD=1.68;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,12:86:99:173,0,2633 -chr1 40454 . T C 3335.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=37.1746;MLEAC=2;MLEAF=1.00;MQ=54.30;MQ0=0;QD=34.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:88:99:3364,259,0 -chr1 40455 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=89;Dels=0.00;FS=5.908;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=0.165;QD=8.65;ReadPosRankSum=0.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:798,0,2174 -chr1 40458 . G A 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.752;DP=90;Dels=0.00;FS=1.024;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=1.062;QD=3.88;ReadPosRankSum=0.175;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,17:90:99:377,0,2596 -chr1 40468 . C T 3532.77 . AC=2;AF=1.00;AN=2;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=32.9796;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:94:99:3561,277,0 -chr1 40469 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.779;DP=94;Dels=0.00;FS=5.381;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-1.186;QD=0.15;ReadPosRankSum=2.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,8:94:42:42,0,3030 -chr1 40480 . C A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=106;Dels=0.00;FS=4.744;HaplotypeScore=40.7109;MLEAC=1;MLEAF=0.500;MQ=53.17;MQ0=0;MQRankSum=-0.111;QD=4.04;ReadPosRankSum=0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,21:106:99:456,0,3043 -chr1 40490 . T C 2948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=107;Dels=0.00;FS=9.034;HaplotypeScore=71.4806;MLEAC=1;MLEAF=0.500;MQ=52.29;MQ0=0;MQRankSum=1.008;QD=27.56;ReadPosRankSum=2.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,85:107:99:2977,0,405 -chr1 40495 . C G 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.391;DP=114;Dels=0.00;FS=1.985;HaplotypeScore=71.4457;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-0.918;QD=5.58;ReadPosRankSum=1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,23:114:99:664,0,2502 -chr1 40497 . G C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=69.4473;MLEAC=1;MLEAF=0.500;MQ=51.94;MQ0=0;MQRankSum=-0.543;QD=2.38;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,17:112:99:295,0,3323 -chr1 40511 . A G 3183.76 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=39.7486;MLEAC=1;MLEAF=0.500;MQ=52.34;MQ0=0;MQRankSum=0.371;QD=27.45;ReadPosRankSum=0.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,92:116:99:3212,0,569 -chr1 40524 . G A 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.064;DP=123;Dels=0.00;FS=2.035;HaplotypeScore=26.4109;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=0;MQRankSum=-2.672;QD=2.92;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,21:123:99:387,0,3524 -chr1 40526 . G A 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=123;Dels=0.00;FS=2.894;HaplotypeScore=26.2780;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-0.204;QD=5.13;ReadPosRankSum=1.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:123:99:659,0,3056 -chr1 40541 . G T 4628.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=54.46;MQ0=0;QD=34.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4657,346,0 -chr1 40559 . T A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.703;DP=122;Dels=0.00;FS=1.745;HaplotypeScore=75.4361;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=3.818;QD=5.47;ReadPosRankSum=1.838;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:122:99:695,0,3342 -chr1 40562 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=119;Dels=0.00;FS=6.618;HaplotypeScore=120.3506;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-3.315;QD=3.02;ReadPosRankSum=-1.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,20:119:99:388,0,3464 -chr1 40565 . G A 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=115;Dels=0.00;FS=3.367;HaplotypeScore=128.0268;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-0.666;QD=3.55;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,19:115:99:437,0,3355 -chr1 40570 . T A 2544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=116.1873;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.456;QD=20.86;ReadPosRankSum=-3.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,76:122:99:2573,0,1468 -chr1 40572 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050;DP=126;Dels=0.00;FS=16.724;HaplotypeScore=113.1887;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-3.211;QD=2.10;ReadPosRankSum=-0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,19:126:99:293,0,3847 -chr1 40574 . G A 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.747;DP=128;Dels=0.00;FS=3.770;HaplotypeScore=81.5684;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=1.064;QD=1.61;ReadPosRankSum=1.108;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,16:128:99:234,0,3817 -chr1 40587 . A G 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=153;Dels=0.00;FS=0.744;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=2.151;QD=5.55;ReadPosRankSum=0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,34:153:99:877,0,4088 -chr1 40598 . A T 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.298;DP=145;Dels=0.00;FS=0.898;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=1;MQRankSum=-3.872;QD=2.10;ReadPosRankSum=2.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:124,21:145:99:333,0,4371 -chr1 40601 . T C 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.858;DP=141;Dels=0.00;FS=0.951;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=55.65;MQ0=1;MQRankSum=-4.326;QD=2.24;ReadPosRankSum=3.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:122,19:141:99:344,0,4357 -chr1 40604 . A G 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=140;Dels=0.00;FS=0.952;HaplotypeScore=3.7881;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=-4.123;QD=2.30;ReadPosRankSum=3.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:121,19:140:99:350,0,4326 -chr1 40607 . A T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=138;Dels=0.00;FS=2.058;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=1;MQRankSum=-3.796;QD=2.44;ReadPosRankSum=2.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,19:138:99:365,0,4122 -chr1 40613 . T C 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=138;Dels=0.00;FS=0.884;HaplotypeScore=34.9737;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=1;MQRankSum=-4.247;QD=2.75;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:408,0,4053 -chr1 40618 . A G 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=140;Dels=0.00;FS=8.579;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.14;MQ0=1;MQRankSum=1.916;QD=0.23;ReadPosRankSum=3.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:128,12:140:60:60,0,4583 -chr1 40619 . T G 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.123;DP=141;Dels=0.00;FS=6.410;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.05;MQ0=1;MQRankSum=-2.776;QD=2.23;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:120,20:141:99:342,0,4240 -chr1 40629 . A T 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.928;DP=134;Dels=0.00;FS=0.868;HaplotypeScore=126.7357;MLEAC=1;MLEAF=0.500;MQ=53.57;MQ0=1;MQRankSum=-4.720;QD=3.33;ReadPosRankSum=-1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,22:134:99:474,0,3749 -chr1 40630 . C T 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.225;DP=133;Dels=0.00;FS=2.109;HaplotypeScore=106.7571;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=1;MQRankSum=-3.232;QD=2.08;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:113,19:133:99:305,0,3912 -chr1 40631 . C T 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.935;DP=134;Dels=0.00;FS=0.896;HaplotypeScore=109.5452;MLEAC=1;MLEAF=0.500;MQ=53.51;MQ0=1;MQRankSum=-4.705;QD=3.01;ReadPosRankSum=-1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,21:134:99:432,0,3926 -chr1 40635 . C A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.206;DP=136;Dels=0.00;FS=10.739;HaplotypeScore=148.7017;MLEAC=1;MLEAF=0.500;MQ=53.34;MQ0=1;MQRankSum=5.098;QD=5.45;ReadPosRankSum=-0.010;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,29:136:99:770,0,3047 -chr1 40637 . G T 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.363;DP=138;Dels=0.00;FS=1.925;HaplotypeScore=146.7025;MLEAC=1;MLEAF=0.500;MQ=53.22;MQ0=1;MQRankSum=-4.406;QD=3.06;ReadPosRankSum=-1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:450,0,4023 -chr1 40643 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=137;Dels=0.00;FS=0.905;HaplotypeScore=80.3353;MLEAC=1;MLEAF=0.500;MQ=53.30;MQ0=1;MQRankSum=-4.704;QD=2.56;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,20:137:99:379,0,4082 -chr1 40644 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=136;Dels=0.00;FS=0.917;HaplotypeScore=81.3352;MLEAC=1;MLEAF=0.500;MQ=53.25;MQ0=1;MQRankSum=-4.475;QD=2.54;ReadPosRankSum=-0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,20:136:99:373,0,4107 -chr1 40647 . G A 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=143;Dels=0.00;FS=7.049;HaplotypeScore=90.1298;MLEAC=1;MLEAF=0.500;MQ=52.42;MQ0=1;MQRankSum=6.086;QD=4.35;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:115,28:143:99:650,0,3953 -chr1 40653 . C T 5160.77 . AC=2;AF=1.00;AN=2;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=104.2700;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=1;QD=24.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,138:138:99:5189,397,0 -chr1 40656 . C A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=136;Dels=0.00;FS=2.901;HaplotypeScore=65.3188;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=1;MQRankSum=3.870;QD=4.26;ReadPosRankSum=2.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:109,27:136:99:607,0,3691 -chr1 40663 . C T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;DP=131;Dels=0.00;FS=1.470;HaplotypeScore=51.1808;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=2;MQRankSum=0.022;QD=9.31;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,44:131:99:1248,0,2916 -chr1 40665 . G A 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.989;DP=129;Dels=0.00;FS=4.193;HaplotypeScore=50.1809;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=2;MQRankSum=3.905;QD=4.50;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:101,28:129:99:609,0,3457 -chr1 40667 . C A 4617.77 . AC=2;AF=1.00;AN=2;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=25.5251;MLEAC=2;MLEAF=1.00;MQ=50.53;MQ0=2;QD=27.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,125:125:99:4646,352,0 -chr1 40679 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=116;Dels=0.00;FS=3.025;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=-6.403;QD=4.21;ReadPosRankSum=0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:517,0,3113 -chr1 40680 . C A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=116;Dels=0.00;FS=5.789;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=3.479;QD=5.26;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,27:116:99:638,0,3045 -chr1 40695 . G A 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=109;Dels=0.00;FS=4.432;HaplotypeScore=15.8769;MLEAC=1;MLEAF=0.500;MQ=48.67;MQ0=1;MQRankSum=4.736;QD=1.38;ReadPosRankSum=0.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,12:109:99:179,0,3292 -chr1 40702 . G A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.179;DP=118;Dels=0.00;FS=1.878;HaplotypeScore=12.9449;MLEAC=1;MLEAF=0.500;MQ=49.34;MQ0=1;MQRankSum=3.135;QD=5.11;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,24:118:99:631,0,3094 -chr1 40724 . C T 2276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.371;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=76.4647;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=1;MQRankSum=-4.544;QD=18.51;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,73:123:99:2305,0,1587 -chr1 40726 . A G 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=121;Dels=0.00;FS=0.855;HaplotypeScore=78.4642;MLEAC=1;MLEAF=0.500;MQ=50.50;MQ0=1;MQRankSum=3.987;QD=5.24;ReadPosRankSum=-0.827;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,25:121:99:662,0,3213 -chr1 40730 . T C 2668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.318;DP=119;Dels=0.00;FS=0.742;HaplotypeScore=131.5265;MLEAC=1;MLEAF=0.500;MQ=50.60;MQ0=1;MQRankSum=-1.336;QD=22.43;ReadPosRankSum=1.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,83:119:99:2697,0,1090 -chr1 40731 . T C 163.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=129.2953;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-0.479;QD=1.38;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,14:119:99:192,0,3588 -chr1 40742 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=108;Dels=0.00;FS=0.859;HaplotypeScore=18.6626;MLEAC=1;MLEAF=0.500;MQ=51.05;MQ0=1;MQRankSum=-5.117;QD=4.95;ReadPosRankSum=-1.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,26:108:99:563,0,2912 -chr1 40757 . C T 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=119;Dels=0.00;FS=2.628;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=-5.477;QD=9.18;ReadPosRankSum=-1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:119:99:1121,0,2615 -chr1 40760 . C T 4275.77 . AC=2;AF=1.00;AN=2;DP=117;Dels=0.00;FS=0.000;HaplotypeScore=23.5723;MLEAC=2;MLEAF=1.00;MQ=50.52;MQ0=1;QD=31.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,117:117:99:4304,331,0 -chr1 40769 . C T 3289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=123;Dels=0.00;FS=0.861;HaplotypeScore=41.4575;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=1;MQRankSum=-4.495;QD=26.75;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,99:123:99:3318,0,576 -chr1 40773 . G A 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=126;Dels=0.00;FS=2.716;HaplotypeScore=43.4570;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=-2.084;QD=6.91;ReadPosRankSum=2.684;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,32:126:99:899,0,2993 -chr1 40788 . A C 1705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=118;Dels=0.00;FS=2.394;HaplotypeScore=117.6775;MLEAC=1;MLEAF=0.500;MQ=49.33;MQ0=1;MQRankSum=-6.557;QD=14.46;ReadPosRankSum=2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,62:118:99:1734,0,1876 -chr1 40789 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=123;Dels=0.00;FS=11.420;HaplotypeScore=119.6765;MLEAC=1;MLEAF=0.500;MQ=49.20;MQ0=1;MQRankSum=3.191;QD=5.27;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,25:123:99:677,0,3103 -chr1 40791 . A G 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.823;DP=121;Dels=0.00;FS=1.004;HaplotypeScore=70.2853;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=1;MQRankSum=-4.589;QD=2.12;ReadPosRankSum=1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,24:121:99:285,0,3412 -chr1 40795 . A T 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=72.2808;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=1;MQRankSum=-2.514;QD=1.04;ReadPosRankSum=2.201;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:108,17:125:99:158,0,3699 -chr1 40803 . C T 2015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.782;DP=118;Dels=0.00;FS=2.491;HaplotypeScore=47.3955;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=1;MQRankSum=-6.205;QD=17.08;ReadPosRankSum=-0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,71:118:99:2044,0,1478 -chr1 40809 . C T 2959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.887;DP=111;Dels=0.00;FS=0.920;HaplotypeScore=68.1753;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=1;MQRankSum=0.903;QD=26.66;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,91:111:99:2988,0,335 -chr1 40816 . G A 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.969;DP=113;Dels=0.00;FS=9.418;HaplotypeScore=31.1266;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=1;MQRankSum=-1.806;QD=4.02;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,20:113:99:483,0,2777 -chr1 40819 . T C 4137.77 . AC=2;AF=1.00;AN=2;DP=115;Dels=0.00;FS=0.000;HaplotypeScore=28.2112;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=1;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,115:115:99:4166,316,0 -chr1 40830 . G C 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=19.6261;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=1;MQRankSum=-2.358;QD=0.59;ReadPosRankSum=1.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,15:120:99:99,0,3552 -chr1 40833 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.298;DP=124;Dels=0.00;FS=3.723;HaplotypeScore=34.4038;MLEAC=1;MLEAF=0.500;MQ=46.84;MQ0=1;MQRankSum=-1.292;QD=2.15;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,20:124:99:295,0,3416 -chr1 40839 . T C 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.184;DP=119;Dels=0.00;FS=8.132;HaplotypeScore=32.8812;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=1;MQRankSum=-0.467;QD=1.86;ReadPosRankSum=0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,17:119:99:249,0,3382 -chr1 40841 . T A,C 2.14748372629E9 . AC=1,1;AF=0.500,0.500;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=19.0976;MLEAC=1,1;MLEAF=0.500,0.500;MQ=47.51;MQ0=1;QD=27.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,17,105:122:99:4117,3653,3614,465,0,164 -chr1 40851 . C G 787.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.730;DP=129;Dels=0.00;FS=22.816;HaplotypeScore=16.7771;MLEAC=1;MLEAF=0.500;MQ=48.66;MQ0=1;MQRankSum=2.703;QD=6.11;ReadPosRankSum=-0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,30:129:99:816,0,3155 -chr1 40863 . T C 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.921;DP=118;Dels=0.00;FS=4.700;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.335;QD=12.98;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,57:118:99:1560,0,2100 -chr1 40865 . A G 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.140;DP=120;Dels=0.00;FS=2.661;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=50.52;MQ0=0;MQRankSum=-2.918;QD=7.64;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,36:120:99:945,0,2823 -chr1 40881 . T C 1883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.649;DP=113;Dels=0.00;FS=6.057;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=52.96;MQ0=0;MQRankSum=-3.511;QD=16.67;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,61:113:99:1912,0,1701 -chr1 40884 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.416;DP=112;Dels=0.00;FS=4.487;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=0.616;QD=0.92;ReadPosRankSum=1.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,12:112:99:131,0,3505 -chr1 40890 . T C 4000.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.376;DP=108;Dels=0.00;FS=3.638;HaplotypeScore=17.6640;MLEAC=2;MLEAF=1.00;MQ=53.47;MQ0=0;MQRankSum=-1.570;QD=32.92;ReadPosRankSum=-0.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,106:108:99:4029,271,0 -chr1 40908 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=-4.713;QD=3.49;ReadPosRankSum=-0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:444,0,3404 -chr1 40913 . A T 4662.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=7.8494;MLEAC=2;MLEAF=1.00;MQ=54.87;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,119:120:99:4691,355,0 -chr1 40932 . T C 4651.77 . AC=2;AF=1.00;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=29.4883;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:122:99:4680,358,0 -chr1 40939 . C T 1562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=122;Dels=0.00;FS=5.633;HaplotypeScore=53.6940;MLEAC=1;MLEAF=0.500;MQ=53.55;MQ0=0;MQRankSum=-6.420;QD=12.81;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,53:122:99:1591,0,2373 -chr1 40942 . G C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=117;Dels=0.00;FS=3.010;HaplotypeScore=52.6941;MLEAC=1;MLEAF=0.500;MQ=53.19;MQ0=0;MQRankSum=2.832;QD=5.14;ReadPosRankSum=2.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,24:117:99:630,0,3142 -chr1 40949 . A T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.841;DP=116;Dels=0.00;FS=1.882;HaplotypeScore=91.2099;MLEAC=1;MLEAF=0.500;MQ=51.71;MQ0=1;MQRankSum=2.660;QD=5.38;ReadPosRankSum=3.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:652,0,3037 -chr1 40953 . G T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=114;Dels=0.00;FS=4.536;HaplotypeScore=90.5131;MLEAC=1;MLEAF=0.500;MQ=51.22;MQ0=1;MQRankSum=-6.362;QD=4.05;ReadPosRankSum=-0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,25:114:99:490,0,2704 -chr1 40963 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.072;DP=115;Dels=0.00;FS=2.488;HaplotypeScore=45.8271;MLEAC=1;MLEAF=0.500;MQ=50.61;MQ0=1;MQRankSum=-6.812;QD=9.88;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,45:115:99:1164,0,2427 -chr1 40965 . A C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=111;Dels=0.00;FS=1.995;HaplotypeScore=24.4867;MLEAC=1;MLEAF=0.500;MQ=50.29;MQ0=1;MQRankSum=-5.421;QD=2.79;ReadPosRankSum=1.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,22:111:99:338,0,3112 -chr1 40977 . A G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.248;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=7.5174;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=1;MQRankSum=3.438;QD=5.38;ReadPosRankSum=0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,25:106:99:598,0,2425 -chr1 40988 . C T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=97;Dels=0.00;FS=7.020;HaplotypeScore=26.1924;MLEAC=1;MLEAF=0.500;MQ=46.91;MQ0=1;MQRankSum=1.225;QD=3.47;ReadPosRankSum=-0.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,18:97:99:365,0,2417 -chr1 40989 . T C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.909;DP=94;Dels=0.00;FS=7.233;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=1;MQRankSum=1.405;QD=3.77;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,18:94:99:383,0,2284 -chr1 40990 . C T 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=1;MQRankSum=-4.177;QD=1.04;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,15:92:99:124,0,2472 -chr1 40992 . A T 2915.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=105.3192;MLEAC=2;MLEAF=1.00;MQ=45.42;MQ0=1;QD=33.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:2944,235,0 -chr1 41013 . C T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.016;DP=84;Dels=0.00;FS=15.260;HaplotypeScore=153.8354;MLEAC=1;MLEAF=0.500;MQ=39.77;MQ0=1;MQRankSum=0.325;QD=5.07;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:454,0,1750 -chr1 41015 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=85;Dels=0.00;FS=1.324;HaplotypeScore=57.0601;MLEAC=1;MLEAF=0.500;MQ=39.97;MQ0=1;MQRankSum=-2.501;QD=0.41;ReadPosRankSum=0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:85:63:63,0,2037 -chr1 41017 . T C 2590.77 . AC=2;AF=1.00;AN=2;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=57.5017;MLEAC=2;MLEAF=1.00;MQ=39.87;MQ0=1;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:87:99:2619,217,0 -chr1 41026 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.073;DP=97;Dels=0.00;FS=3.387;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=40.65;MQ0=1;MQRankSum=1.677;QD=0.36;ReadPosRankSum=-2.910;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,9:97:63:63,0,2499 -chr1 41043 . C T 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.8776;MLEAC=1;MLEAF=0.500;MQ=42.40;MQ0=1;MQRankSum=0.065;QD=1.44;ReadPosRankSum=0.698;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,12:92:99:161,0,2256 -chr1 41046 . G A 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.146;DP=89;Dels=0.00;FS=6.728;HaplotypeScore=67.8534;MLEAC=1;MLEAF=0.500;MQ=42.77;MQ0=1;MQRankSum=-2.122;QD=0.77;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:97:97,0,2293 -chr1 41049 . T C 2779.77 . AC=2;AF=1.00;AN=2;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=92.5392;MLEAC=2;MLEAF=1.00;MQ=43.08;MQ0=1;QD=32.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,85:86:99:2808,226,0 -chr1 41054 . G A 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.137;DP=87;Dels=0.00;FS=2.873;HaplotypeScore=97.5277;MLEAC=1;MLEAF=0.500;MQ=43.55;MQ0=0;MQRankSum=-1.875;QD=1.18;ReadPosRankSum=1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,13:87:99:131,0,2231 -chr1 41056 . G T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.880;DP=86;Dels=0.00;FS=12.658;HaplotypeScore=70.2196;MLEAC=1;MLEAF=0.500;MQ=43.45;MQ0=0;MQRankSum=0.504;QD=8.25;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,31:86:99:738,0,1637 -chr1 41059 . A T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=85;Dels=0.00;FS=1.923;HaplotypeScore=62.5392;MLEAC=1;MLEAF=0.500;MQ=43.72;MQ0=0;MQRankSum=-1.385;QD=7.07;ReadPosRankSum=2.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,28:85:99:629,0,1583 -chr1 41064 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=88;Dels=0.00;FS=1.164;HaplotypeScore=86.8690;MLEAC=1;MLEAF=0.500;MQ=44.00;MQ0=0;MQRankSum=-1.609;QD=1.93;ReadPosRankSum=1.221;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,15:88:99:198,0,2343 -chr1 41084 . T C 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=106;Dels=0.00;FS=1.092;HaplotypeScore=17.4304;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=-1.180;QD=1.68;ReadPosRankSum=-2.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,14:106:99:206,0,3074 -chr1 41100 . C A 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.112;DP=116;Dels=0.00;FS=0.765;HaplotypeScore=58.6282;MLEAC=1;MLEAF=0.500;MQ=48.59;MQ0=0;MQRankSum=0.652;QD=7.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,34:116:99:915,0,2691 -chr1 41103 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.020;DP=114;Dels=0.00;FS=7.549;HaplotypeScore=60.6270;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=0.692;QD=5.02;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,25:114:99:601,0,2970 -chr1 41108 . G A 2256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=104;Dels=0.00;FS=1.668;HaplotypeScore=55.9666;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-3.973;QD=21.70;ReadPosRankSum=0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,68:104:99:2285,0,1135 -chr1 41121 . C T 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=106;Dels=0.00;FS=8.022;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=0;MQRankSum=-4.307;QD=11.10;ReadPosRankSum=1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,39:106:99:1205,0,2309 -chr1 41142 . C A 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.819;DP=93;Dels=0.00;FS=4.344;HaplotypeScore=109.3818;MLEAC=1;MLEAF=0.500;MQ=50.67;MQ0=0;MQRankSum=-3.272;QD=1.78;ReadPosRankSum=-0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,12:93:99:194,0,2886 -chr1 41167 . T A 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.059;DP=80;Dels=0.00;FS=2.024;HaplotypeScore=81.4181;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-5.890;QD=8.08;ReadPosRankSum=2.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,24:80:99:675,0,1872 -chr1 41168 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=85;Dels=0.00;FS=1.308;HaplotypeScore=70.7865;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-3.430;QD=1.28;ReadPosRankSum=1.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,10:85:99:137,0,2676 -chr1 41170 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.253;DP=86;Dels=0.00;FS=2.556;HaplotypeScore=38.2377;MLEAC=1;MLEAF=0.500;MQ=51.83;MQ0=0;MQRankSum=-4.581;QD=2.28;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,13:86:99:224,0,2606 -chr1 41179 . T C 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.172;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=18.4473;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-4.595;QD=7.31;ReadPosRankSum=-2.191;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,23:85:99:650,0,2189 -chr1 41195 . C G 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=99;Dels=0.00;FS=3.526;HaplotypeScore=25.2904;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=3.710;QD=4.40;ReadPosRankSum=1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,19:99:99:464,0,2786 -chr1 41199 . C T 552.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=96;Dels=0.00;FS=4.808;HaplotypeScore=40.2922;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=2.060;QD=5.76;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,22:96:99:581,0,2606 -chr1 41208 . T C 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.073;DP=95;Dels=0.00;FS=3.709;HaplotypeScore=57.4526;MLEAC=1;MLEAF=0.500;MQ=52.97;MQ0=0;MQRankSum=3.607;QD=4.12;ReadPosRankSum=2.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,17:95:99:420,0,2797 -chr1 41212 . A C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=95;Dels=0.00;FS=0.946;HaplotypeScore=22.4583;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-3.985;QD=5.00;ReadPosRankSum=-1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,20:95:99:503,0,2582 -chr1 41218 . T A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=96;Dels=0.00;FS=2.139;HaplotypeScore=56.9737;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=4.681;QD=4.80;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,19:96:99:489,0,2728 -chr1 41224 . C T 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=92;Dels=0.00;FS=8.582;HaplotypeScore=46.8527;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=-6.262;QD=11.77;ReadPosRankSum=0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,36:92:99:1111,0,1880 -chr1 41227 . A C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=95;Dels=0.00;FS=1.160;HaplotypeScore=73.8186;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.984;QD=2.05;ReadPosRankSum=1.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:223,0,2919 -chr1 41234 . A T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.452;DP=100;Dels=0.00;FS=2.117;HaplotypeScore=65.6546;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=2.503;QD=4.66;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,20:100:99:494,0,2851 -chr1 41236 . T C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.280;DP=101;Dels=0.00;FS=3.152;HaplotypeScore=35.6864;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.963;QD=0.23;ReadPosRankSum=0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,9:101:51:51,0,3322 -chr1 41244 . C G 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.262;DP=106;Dels=0.00;FS=4.109;HaplotypeScore=48.8041;MLEAC=1;MLEAF=0.500;MQ=54.46;MQ0=0;MQRankSum=-2.340;QD=1.59;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,13:106:99:197,0,3333 -chr1 41248 . T C 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=109;Dels=0.00;FS=1.115;HaplotypeScore=41.7628;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-3.636;QD=1.78;ReadPosRankSum=0.974;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,14:109:99:222,0,3400 -chr1 41253 . T A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.602;DP=119;Dels=0.00;FS=6.215;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=1;MQRankSum=0.176;QD=4.21;ReadPosRankSum=1.441;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:529,0,3111 -chr1 41254 . A T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.018;DP=120;Dels=0.00;FS=15.351;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=1;MQRankSum=-4.673;QD=0.63;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,13:120:99:104,0,3713 -chr1 41267 . T A 1376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=124;Dels=0.00;FS=10.609;HaplotypeScore=25.9401;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-7.080;QD=11.10;ReadPosRankSum=0.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,47:124:99:1405,0,2587 -chr1 41268 . T C 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=124;Dels=0.00;FS=4.257;HaplotypeScore=82.8206;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-0.901;QD=0.91;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,13:124:99:141,0,3898 -chr1 41278 . G A 2734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.082;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=36.6252;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=1;MQRankSum=1.173;QD=22.98;ReadPosRankSum=0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,80:119:99:2763,0,670 -chr1 41290 . C T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=114;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=51.25;MQ0=1;MQRankSum=-4.504;QD=5.81;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,27:114:99:691,0,2884 -chr1 41305 . C T 1582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.376;DP=107;Dels=0.00;FS=1.558;HaplotypeScore=63.7217;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=1;MQRankSum=-7.979;QD=14.79;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,55:107:99:1611,0,1766 -chr1 41308 . T C 1593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=-8.201;QD=14.90;ReadPosRankSum=0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,56:107:99:1622,0,1675 -chr1 41310 . C G 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.320;DP=105;Dels=0.00;FS=0.974;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=1;MQRankSum=-2.583;QD=3.70;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,21:105:99:417,0,2941 -chr1 41313 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.319;DP=103;Dels=0.00;FS=0.870;HaplotypeScore=103.1863;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=4.857;QD=7.01;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,26:103:99:750,0,2499 -chr1 41314 . G A,T 1081.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.513;DP=103;Dels=0.00;FS=0.976;HaplotypeScore=42.1919;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.10;MQ0=1;MQRankSum=-4.684;QD=10.50;ReadPosRankSum=-0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:21,25,57:103:99:1879,1019,1719,147,0,769 -chr1 41322 . G A 1422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=107;Dels=0.00;FS=1.576;HaplotypeScore=70.4344;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=1;MQRankSum=1.616;QD=13.30;ReadPosRankSum=0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,49:107:99:1451,0,1855 -chr1 41331 . C T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=103;Dels=0.00;FS=4.657;HaplotypeScore=99.4972;MLEAC=1;MLEAF=0.500;MQ=48.40;MQ0=1;MQRankSum=4.235;QD=5.51;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,22:103:99:596,0,2616 -chr1 41334 . A C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;DP=101;Dels=0.00;FS=2.142;HaplotypeScore=117.9442;MLEAC=1;MLEAF=0.500;MQ=48.38;MQ0=1;MQRankSum=-2.696;QD=3.51;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,19:101:99:383,0,2677 -chr1 41335 . C A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.870;DP=98;Dels=0.00;FS=0.996;HaplotypeScore=118.9429;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=1;MQRankSum=-3.055;QD=4.25;ReadPosRankSum=-0.712;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:98:99:445,0,2383 -chr1 41337 . G A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=99;Dels=0.00;FS=3.218;HaplotypeScore=122.9204;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=1;MQRankSum=2.970;QD=6.55;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,24:99:99:677,0,2337 -chr1 41343 . G A 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=74.5936;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=1;MQRankSum=-3.683;QD=5.19;ReadPosRankSum=1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:537,0,2493 -chr1 41365 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=86;Dels=0.00;FS=2.433;HaplotypeScore=14.9634;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=0;MQRankSum=1.753;QD=3.47;ReadPosRankSum=1.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,15:86:99:327,0,2341 -chr1 41375 . T C 2374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=87;Dels=0.00;FS=1.026;HaplotypeScore=33.9683;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.561;QD=27.30;ReadPosRankSum=-1.912;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,71:87:99:2403,0,364 -chr1 41376 . T G 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.803;DP=87;Dels=0.00;FS=4.036;HaplotypeScore=34.9615;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=0;MQRankSum=-0.455;QD=3.19;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:306,0,2524 -chr1 41377 . T C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.157;DP=88;Dels=0.00;FS=0.884;HaplotypeScore=39.7608;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-0.490;QD=7.20;ReadPosRankSum=3.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,25:88:99:662,0,2148 -chr1 41395 . A G 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.677;DP=84;Dels=0.00;FS=1.101;HaplotypeScore=112.5646;MLEAC=1;MLEAF=0.500;MQ=48.92;MQ0=0;MQRankSum=2.499;QD=3.81;ReadPosRankSum=0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:348,0,2361 -chr1 41396 . A T 1616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.249;DP=79;Dels=0.00;FS=3.137;HaplotypeScore=87.3597;MLEAC=1;MLEAF=0.500;MQ=48.75;MQ0=0;MQRankSum=-0.300;QD=20.47;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,50:79:99:1645,0,823 -chr1 41398 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.022;DP=81;Dels=0.00;FS=3.484;HaplotypeScore=80.5740;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-1.669;QD=8.63;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,24:81:99:727,0,1467 -chr1 41404 . T C 2294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=97;Dels=0.00;FS=0.832;HaplotypeScore=104.9252;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=4.062;QD=23.66;ReadPosRankSum=2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,68:97:99:2323,0,710 -chr1 41409 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.386;DP=105;Dels=0.00;FS=11.861;HaplotypeScore=51.0534;MLEAC=1;MLEAF=0.500;MQ=48.48;MQ0=0;MQRankSum=-4.669;QD=0.65;ReadPosRankSum=-2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,13:105:96:96,0,3129 -chr1 41415 . G A 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=107;Dels=0.00;FS=11.635;HaplotypeScore=15.7947;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=1.795;QD=3.14;ReadPosRankSum=-0.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,18:107:99:364,0,2936 -chr1 41433 . A G 1679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=111;Dels=0.00;FS=3.563;HaplotypeScore=105.5605;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-5.707;QD=15.13;ReadPosRankSum=1.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,57:111:99:1708,0,1780 -chr1 41435 . A G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=109;Dels=0.00;FS=17.321;HaplotypeScore=102.6178;MLEAC=1;MLEAF=0.500;MQ=49.30;MQ0=0;MQRankSum=-4.352;QD=0.94;ReadPosRankSum=2.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,13:109:99:131,0,3341 -chr1 41438 . T G 3087.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.252;DP=111;Dels=0.00;FS=11.712;HaplotypeScore=118.7379;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=0.604;QD=27.82;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,93:111:99:3116,0,375 -chr1 41441 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=115;Dels=0.00;FS=6.121;HaplotypeScore=118.1844;MLEAC=1;MLEAF=0.500;MQ=49.65;MQ0=0;MQRankSum=5.083;QD=5.02;ReadPosRankSum=-0.127;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,24:115:99:605,0,2982 -chr1 41447 . C T 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=113;Dels=0.00;FS=2.061;HaplotypeScore=55.8367;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-4.171;QD=3.53;ReadPosRankSum=-0.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,22:113:99:427,0,3162 -chr1 41451 . T C 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.403;DP=114;Dels=0.00;FS=25.914;HaplotypeScore=63.6216;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=0;MQRankSum=-4.658;QD=1.12;ReadPosRankSum=3.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,14:114:99:156,0,3508 -chr1 41458 . T G 2070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.880;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=14.9365;MLEAC=1;MLEAF=0.500;MQ=50.88;MQ0=0;MQRankSum=-8.252;QD=17.55;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,67:118:99:2099,0,1630 -chr1 41472 . G A 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=118;Dels=0.00;FS=4.281;HaplotypeScore=23.8857;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=4.715;QD=5.35;ReadPosRankSum=1.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,25:118:99:660,0,3092 -chr1 41477 . C T 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=116;Dels=0.00;FS=24.979;HaplotypeScore=26.4514;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-4.819;QD=2.26;ReadPosRankSum=-1.044;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,17:116:99:290,0,3370 -chr1 41490 . C T 1347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=120;Dels=0.00;FS=7.377;HaplotypeScore=103.2713;MLEAC=1;MLEAF=0.500;MQ=51.74;MQ0=0;MQRankSum=-4.581;QD=11.23;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,43:120:99:1376,0,2560 -chr1 41492 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.358;DP=122;Dels=0.00;FS=4.136;HaplotypeScore=109.9755;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-5.075;QD=4.19;ReadPosRankSum=0.670;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,27:122:99:540,0,3167 -chr1 41495 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=120;Dels=0.00;FS=6.076;HaplotypeScore=130.0290;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-4.101;QD=10.63;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:120:99:1304,0,2562 -chr1 41499 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=121;Dels=0.00;FS=8.830;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=4.822;QD=5.84;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,27:121:99:735,0,3300 -chr1 41500 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=123;Dels=0.00;FS=4.152;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.46;MQ0=0;MQRankSum=-4.922;QD=4.27;ReadPosRankSum=2.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,26:123:99:554,0,3500 -chr1 41503 . T C 2252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=119;Dels=0.00;FS=4.440;HaplotypeScore=73.1398;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-7.475;QD=18.93;ReadPosRankSum=0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,69:119:99:2281,0,1652 -chr1 41543 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=1.422;QD=1.67;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,12:94:99:185,0,2657 -chr1 41544 . C A 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=94;Dels=0.00;FS=5.349;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=0.591;QD=4.56;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:94:99:457,0,2138 -chr1 41546 . A G 3381.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=27.5019;MLEAC=2;MLEAF=1.00;MQ=45.55;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:95:99:3410,268,0 -chr1 41562 . G A 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=90;Dels=0.00;FS=3.007;HaplotypeScore=34.8266;MLEAC=1;MLEAF=0.500;MQ=42.64;MQ0=0;MQRankSum=-0.632;QD=6.88;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,28:90:99:647,0,1945 -chr1 41564 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=55.5562;MLEAC=1;MLEAF=0.500;MQ=41.85;MQ0=0;MQRankSum=1.630;QD=1.23;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:99:130,0,2184 -chr1 41566 . C A 2583.77 . AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=62.4145;MLEAC=2;MLEAF=1.00;MQ=41.29;MQ0=0;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,77:77:99:2612,211,0 -chr1 41569 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.046;DP=76;Dels=0.00;FS=3.973;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.71;MQ0=0;MQRankSum=1.851;QD=5.79;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,18:76:99:468,0,1633 -chr1 41572 . T C 2032.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;DP=75;Dels=0.00;FS=1.682;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.70;MQ0=0;MQRankSum=-0.869;QD=27.11;ReadPosRankSum=-0.537;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,69:75:15:2061,0,15 -chr1 41574 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.327;DP=76;Dels=0.00;FS=3.699;HaplotypeScore=53.4650;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=0;MQRankSum=0.032;QD=9.00;ReadPosRankSum=3.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,25:76:99:712,0,1145 -chr1 41576 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=83;Dels=0.00;FS=1.310;HaplotypeScore=45.4818;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=-1.812;QD=0.39;ReadPosRankSum=-0.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:61:61,0,2187 -chr1 41587 . C T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=59.1819;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=0;MQRankSum=2.270;QD=10.01;ReadPosRankSum=1.892;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:969,0,1542 -chr1 41588 . T A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.902;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=56.1832;MLEAC=1;MLEAF=0.500;MQ=38.88;MQ0=0;MQRankSum=-1.330;QD=3.74;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,21:92:99:372,0,2076 -chr1 41593 . A G 2833.77 . AC=2;AF=1.00;AN=2;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=51.2291;MLEAC=2;MLEAF=1.00;MQ=39.22;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,89:89:99:2862,241,0 -chr1 41597 . T A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=93;Dels=0.00;FS=1.013;HaplotypeScore=58.9239;MLEAC=1;MLEAF=0.500;MQ=39.40;MQ0=0;MQRankSum=-1.253;QD=3.26;ReadPosRankSum=-0.777;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,19:93:99:331,0,2049 -chr1 41612 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=94;Dels=0.00;FS=3.843;HaplotypeScore=30.0447;MLEAC=1;MLEAF=0.500;MQ=39.90;MQ0=0;MQRankSum=-1.714;QD=1.66;ReadPosRankSum=-0.857;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,15:94:99:184,0,2308 -chr1 41623 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=95;Dels=0.00;FS=1.274;HaplotypeScore=34.4885;MLEAC=1;MLEAF=0.500;MQ=41.23;MQ0=0;MQRankSum=-1.146;QD=0.23;ReadPosRankSum=-2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,10:95:50:50,0,2553 -chr1 41633 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=97;Dels=0.00;FS=0.962;HaplotypeScore=42.7026;MLEAC=1;MLEAF=0.500;MQ=41.75;MQ0=0;MQRankSum=-1.768;QD=4.76;ReadPosRankSum=1.633;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,23:97:99:490,0,2247 -chr1 41638 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.578;DP=99;Dels=0.00;FS=11.653;HaplotypeScore=45.8263;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=1.485;QD=4.36;ReadPosRankSum=-0.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,21:99:99:460,0,2342 -chr1 41640 . A T 3476.77 . AC=2;AF=1.00;AN=2;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=43.8379;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=34.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,102:102:99:3505,280,0 -chr1 41642 . C T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=102;Dels=0.00;FS=4.287;HaplotypeScore=43.8379;MLEAC=1;MLEAF=0.500;MQ=42.97;MQ0=0;MQRankSum=-1.538;QD=0.99;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,12:102:99:129,0,2667 -chr1 41645 . G A 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=106;Dels=0.00;FS=2.304;HaplotypeScore=28.8553;MLEAC=1;MLEAF=0.500;MQ=42.92;MQ0=0;MQRankSum=-1.566;QD=1.82;ReadPosRankSum=-1.328;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:221,0,2816 -chr1 41657 . T C 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.271;DP=113;Dels=0.00;FS=4.518;HaplotypeScore=64.9583;MLEAC=1;MLEAF=0.500;MQ=44.13;MQ0=0;MQRankSum=-2.414;QD=4.06;ReadPosRankSum=1.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,23:113:99:487,0,2786 -chr1 41663 . A T 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.503;DP=114;Dels=0.00;FS=3.858;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=-1.442;QD=1.36;ReadPosRankSum=1.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,15:114:99:183,0,3367 -chr1 41665 . T A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=113;Dels=0.00;FS=3.826;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.28;MQ0=0;MQRankSum=-1.612;QD=1.48;ReadPosRankSum=1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,15:113:99:196,0,3343 -chr1 41669 . A G 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.192;DP=119;Dels=0.00;FS=4.933;HaplotypeScore=68.0952;MLEAC=1;MLEAF=0.500;MQ=45.13;MQ0=0;MQRankSum=-1.839;QD=2.10;ReadPosRankSum=0.185;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,19:119:99:278,0,3198 -chr1 41678 . T C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.051;DP=115;Dels=0.00;FS=6.885;HaplotypeScore=79.4081;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=0;MQRankSum=-3.479;QD=3.11;ReadPosRankSum=3.870;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,20:115:99:386,0,3047 -chr1 41679 . G A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.748;DP=111;Dels=0.00;FS=3.602;HaplotypeScore=78.4123;MLEAC=1;MLEAF=0.500;MQ=46.33;MQ0=0;MQRankSum=-3.517;QD=2.09;ReadPosRankSum=-0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,17:111:99:260,0,3158 -chr1 41680 . A C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=108;Dels=0.00;FS=1.071;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-3.109;QD=1.71;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,15:108:99:213,0,3172 -chr1 41687 . G C 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.837;DP=112;Dels=0.00;FS=2.333;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=0;MQRankSum=-2.828;QD=1.31;ReadPosRankSum=-0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,15:112:99:175,0,3221 -chr1 41717 . G C 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.104;DP=101;Dels=0.00;FS=10.379;HaplotypeScore=39.1666;MLEAC=1;MLEAF=0.500;MQ=42.12;MQ0=0;MQRankSum=-0.222;QD=1.90;ReadPosRankSum=2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,15:101:99:220,0,2653 -chr1 41723 . C T 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.845;DP=104;Dels=0.00;FS=7.631;HaplotypeScore=57.0647;MLEAC=1;MLEAF=0.500;MQ=41.47;MQ0=0;MQRankSum=0.585;QD=7.04;ReadPosRankSum=0.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,30:104:99:760,0,2081 -chr1 41727 . T C 1110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=103;Dels=0.00;FS=25.678;HaplotypeScore=89.0081;MLEAC=1;MLEAF=0.500;MQ=41.42;MQ0=0;MQRankSum=-2.718;QD=10.78;ReadPosRankSum=-0.518;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,43:103:99:1139,0,1804 -chr1 41733 . C T 126.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=101;Dels=0.00;FS=8.661;HaplotypeScore=68.3374;MLEAC=1;MLEAF=0.500;MQ=40.86;MQ0=0;MQRankSum=0.319;QD=1.26;ReadPosRankSum=0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,13:101:99:155,0,2688 -chr1 41737 . G A 28.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.067;DP=98;Dels=0.00;FS=1.384;HaplotypeScore=41.8358;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=0;MQRankSum=-0.972;QD=0.29;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,9:98:57:57,0,2778 -chr1 41760 . C T 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=84;Dels=0.00;FS=4.638;HaplotypeScore=16.6682;MLEAC=1;MLEAF=0.500;MQ=38.94;MQ0=0;MQRankSum=2.250;QD=7.74;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,26:84:99:678,0,1606 -chr1 41790 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.449;DP=72;Dels=0.00;FS=0.904;HaplotypeScore=22.5923;MLEAC=1;MLEAF=0.500;MQ=41.27;MQ0=0;MQRankSum=1.292;QD=12.39;ReadPosRankSum=1.235;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,34:72:99:920,0,1016 -chr1 41797 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=56;Dels=0.00;FS=17.110;HaplotypeScore=26.2547;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=0.349;QD=4.44;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:277,0,1304 -chr1 41816 . T C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.517;DP=70;Dels=0.00;FS=19.980;HaplotypeScore=12.2986;MLEAC=1;MLEAF=0.500;MQ=44.44;MQ0=0;MQRankSum=1.485;QD=5.95;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:445,0,1433 -chr1 41832 . A G 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.295;DP=72;Dels=0.00;FS=47.755;HaplotypeScore=25.8822;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=-5.914;QD=4.62;ReadPosRankSum=0.334;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,25:72:99:361,0,1584 -chr1 41839 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104;DP=75;Dels=0.00;FS=46.700;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=1;MQRankSum=-6.222;QD=5.20;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:418,0,1578 -chr1 41841 . A G 1684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=73;Dels=0.00;FS=17.617;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.38;MQ0=1;MQRankSum=3.993;QD=23.08;ReadPosRankSum=2.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,57:73:99:1713,0,219 -chr1 41855 . A G 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=75;Dels=0.00;FS=34.596;HaplotypeScore=5.5757;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=4;MQRankSum=-4.879;QD=2.30;ReadPosRankSum=2.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,17:75:99:201,0,1834 -chr1 41867 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=76;Dels=0.00;FS=7.041;HaplotypeScore=8.7104;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=4;MQRankSum=4.354;QD=8.84;ReadPosRankSum=-1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,24:76:99:700,0,1282 -chr1 41874 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=75;Dels=0.00;FS=14.535;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.20;MQ0=4;MQRankSum=-3.082;QD=0.37;ReadPosRankSum=2.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:75:56:56,0,1930 -chr1 41875 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.568;DP=73;Dels=0.00;FS=5.210;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.03;MQ0=4;MQRankSum=3.339;QD=10.49;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,25:73:99:794,0,1121 -chr1 41887 . T C 2160.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=18.1629;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=4;QD=30.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2189,175,0 -chr1 41891 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=76.6927;MLEAC=1;MLEAF=0.500;MQ=45.05;MQ0=4;MQRankSum=1.412;QD=10.65;ReadPosRankSum=0.443;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,24:69:99:763,0,786 -chr1 41899 . T A 1216.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.812;DP=52;Dels=0.02;FS=6.283;HaplotypeScore=36.3869;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.157;QD=23.40;ReadPosRankSum=-0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,42:51:14:1245,14,0 -chr1 41900 . T C 1523.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.417;DP=52;Dels=0.00;FS=5.909;HaplotypeScore=45.3219;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.172;QD=29.30;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,43:52:29:1552,29,0 -chr1 41931 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=48.90;MQ0=3;MQRankSum=0.304;QD=11.97;ReadPosRankSum=1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:806,0,1148 -chr1 41944 . C G 2024.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=51.55;MQ0=0;QD=32.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2053,156,0 -chr1 41946 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.696;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=51.55;MQ0=0;MQRankSum=-0.278;QD=14.11;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:776,0,935 -chr1 41952 . T C 1861.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.38;MQ0=0;QD=36.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1890,144,0 -chr1 41954 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.11;MQ0=0;MQRankSum=-0.942;QD=15.68;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:812,0,822 -chr1 41991 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=56;Dels=0.00;FS=7.656;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=1.035;QD=12.37;ReadPosRankSum=0.654;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:721,0,1091 -chr1 42007 . G A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.444;DP=51;Dels=0.00;FS=10.314;HaplotypeScore=2.4441;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=1.161;QD=13.51;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:717,0,897 -chr1 42036 . A G 1816.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.7826;MLEAC=2;MLEAF=1.00;MQ=49.42;MQ0=1;QD=29.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1845,144,0 -chr1 42038 . G T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.265;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=5.5713;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=2.868;QD=10.28;ReadPosRankSum=0.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:532,0,906 -chr1 42046 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=52;Dels=0.00;FS=2.418;HaplotypeScore=4.5717;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=1;MQRankSum=-3.243;QD=17.82;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:955,0,706 -chr1 42061 . C T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.775;DP=49;Dels=0.00;FS=5.764;HaplotypeScore=4.9754;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=1;MQRankSum=3.673;QD=14.79;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:753,0,792 -chr1 42071 . C T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.982;DP=45;Dels=0.00;FS=4.388;HaplotypeScore=4.7774;MLEAC=1;MLEAF=0.500;MQ=49.26;MQ0=1;MQRankSum=-4.302;QD=15.22;ReadPosRankSum=-0.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:713,0,676 -chr1 42082 . T C 1927.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=49.55;MQ0=1;QD=25.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1956,150,0 -chr1 42083 . G T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.128;DP=49;Dels=0.00;FS=4.144;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=1;MQRankSum=-4.087;QD=13.97;ReadPosRankSum=1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:713,0,858 -chr1 42106 . A G 1999.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.98;MQ0=2;QD=36.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2028,156,0 -chr1 42149 . T C 1779.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.012;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4982;MLEAC=2;MLEAF=1.00;MQ=39.34;MQ0=6;MQRankSum=2.932;QD=26.56;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,58:67:99:1808,122,0 -chr1 42196 . C T 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=73;Dels=0.00;FS=15.517;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=35.03;MQ0=7;MQRankSum=3.313;QD=10.94;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,28:73:99:827,0,820 -chr1 42202 . T C 1564.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.114;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=23.7489;MLEAC=2;MLEAF=1.00;MQ=32.75;MQ0=6;MQRankSum=3.687;QD=24.84;ReadPosRankSum=-0.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:8,55:63:99:1593,107,0 -chr1 42204 . C T 644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.569;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.649;QD=10.40;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:673,0,666 -chr1 42208 . C T 643.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=19.1747;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.599;QD=10.38;ReadPosRankSum=2.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:672,0,666 -chr1 42212 . T A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=60;Dels=0.00;FS=12.104;HaplotypeScore=19.4395;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=6;MQRankSum=3.512;QD=10.15;ReadPosRankSum=2.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:637,0,656 -chr1 42218 . A G 1530.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.638;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.9344;MLEAC=2;MLEAF=1.00;MQ=32.94;MQ0=6;MQRankSum=-0.881;QD=24.30;ReadPosRankSum=-1.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,62:63:93:1559,93,0 -chr1 42221 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=65;Dels=0.00;FS=5.554;HaplotypeScore=8.9344;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=6;MQRankSum=-1.189;QD=9.63;ReadPosRankSum=0.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,30:65:99:654,0,793 -chr1 42234 . A G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=52;Dels=0.00;FS=7.954;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=36.56;MQ0=1;MQRankSum=-1.940;QD=11.46;ReadPosRankSum=0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:624,0,788 -chr1 42260 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;DP=42;Dels=0.00;FS=4.638;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=36.16;MQ0=0;MQRankSum=-1.412;QD=8.95;ReadPosRankSum=0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:404,0,716 -chr1 42263 . G A 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=37;Dels=0.00;FS=4.803;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=0.904;QD=14.56;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:567,0,421 -chr1 42280 . G A 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=36.50;MQ0=2;MQRankSum=0.805;QD=9.84;ReadPosRankSum=2.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:412,0,542 -chr1 42294 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.243;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=36.41;MQ0=2;MQRankSum=-0.883;QD=11.65;ReadPosRankSum=-0.558;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:436,0,494 -chr1 42305 . C T 1338.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.50;MQ0=2;QD=33.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1367,111,0 -chr1 42316 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=38.47;MQ0=2;MQRankSum=-1.556;QD=10.46;ReadPosRankSum=-0.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:457,0,721 -chr1 42344 . C T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7128;MLEAC=1;MLEAF=0.500;MQ=39.55;MQ0=2;MQRankSum=1.059;QD=16.22;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:823,0,592 -chr1 42360 . A G 1733.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.46;MQ0=1;QD=34.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1762,141,0 -chr1 42373 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.78;MQ0=0;MQRankSum=-1.866;QD=13.38;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:657,0,768 -chr1 42400 . A C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=4.7967;MLEAC=1;MLEAF=0.500;MQ=44.88;MQ0=0;MQRankSum=-2.723;QD=12.16;ReadPosRankSum=1.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:612,0,919 -chr1 42416 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.7990;MLEAC=1;MLEAF=0.500;MQ=44.11;MQ0=0;MQRankSum=2.735;QD=16.06;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:735,0,601 -chr1 42478 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.823;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.32;MQ0=1;MQRankSum=-2.431;QD=5.99;ReadPosRankSum=1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,10:21:99:154,0,359 -chr1 42479 . A G 606.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=1;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,22:22:54:635,54,0 -chr1 42486 . A G 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.373;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.44;MQ0=2;MQRankSum=-2.500;QD=6.25;ReadPosRankSum=0.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:172,0,350 -chr1 42503 . T A 579.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=2;QD=25.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:608,51,0 -chr1 42535 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.226;QD=12.17;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,18:33:99:430,0,463 -chr1 42539 . G A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.544;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.381;QD=13.42;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,19:33:99:471,0,422 -chr1 42553 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=39.64;MQ0=2;MQRankSum=0.155;QD=15.72;ReadPosRankSum=-1.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:594,0,398 -chr1 42568 . A G 1099.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=40.82;MQ0=1;QD=33.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1128,87,0 -chr1 42617 . A T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=1;MQRankSum=0.049;QD=7.30;ReadPosRankSum=-1.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:240,0,633 -chr1 42618 . A G 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.87;MQ0=1;MQRankSum=-0.029;QD=7.03;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:211,0,532 -chr1 42641 . A G 782.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.44;MQ0=2;MQRankSum=1.595;QD=28.99;ReadPosRankSum=1.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,25:27:63:811,63,0 -chr1 42646 . G A 734.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.828;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.88;MQ0=1;MQRankSum=1.306;QD=29.39;ReadPosRankSum=1.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,23:25:60:763,60,0 -chr1 42650 . A G 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=22;Dels=0.00;FS=1.719;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=37.75;MQ0=1;MQRankSum=-2.354;QD=6.58;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,9:22:99:173,0,443 -chr1 42661 . T C 766.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.02;MQ0=1;QD=31.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:63:795,63,0 -chr1 42680 . G T 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.405;DP=23;Dels=0.00;FS=1.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.36;MQ0=1;MQRankSum=-0.922;QD=17.95;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,17:23:99:441,0,171 -chr1 42698 . A G 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.880;DP=34;Dels=0.00;FS=3.589;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=48.79;MQ0=1;MQRankSum=-0.707;QD=22.93;ReadPosRankSum=1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,25:34:99:808,0,202 -chr1 42700 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.444;DP=35;Dels=0.00;FS=3.712;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=0.156;QD=5.31;ReadPosRankSum=-1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,9:35:99:214,0,848 -chr1 42716 . C A 1242.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=51.83;MQ0=0;QD=25.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1271,96,0 -chr1 42723 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.200;DP=39;Dels=0.00;FS=3.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=1.358;QD=5.20;ReadPosRankSum=-2.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:231,0,953 -chr1 42738 . G A 1423.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=54.09;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1452,108,0 -chr1 42747 . C T 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=-1.468;QD=21.23;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:835,0,401 -chr1 42749 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.407;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=2.557;QD=9.02;ReadPosRankSum=-1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,833 -chr1 42815 . T C 1223.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=1;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,37:37:96:1252,96,0 -chr1 42840 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.801;DP=40;Dels=0.00;FS=1.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=1;MQRankSum=0.745;QD=14.59;ReadPosRankSum=1.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:612,0,601 -chr1 42845 . A G 575.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=39;Dels=0.00;FS=1.210;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=0.482;QD=14.76;ReadPosRankSum=1.710;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:604,0,571 -chr1 42846 . G A 1308.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.65;MQ0=1;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1337,102,0 -chr1 42848 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.965;DP=41;Dels=0.00;FS=1.189;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=1;MQRankSum=0.720;QD=14.29;ReadPosRankSum=1.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:614,0,573 -chr1 42865 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=50;Dels=0.00;FS=4.589;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.645;QD=6.80;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,14:50:99:368,0,1156 -chr1 42867 . G A 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=50;Dels=0.00;FS=2.949;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.500;QD=5.86;ReadPosRankSum=1.965;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,13:50:99:321,0,1202 -chr1 42868 . T C 1723.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1752,135,0 -chr1 42872 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=49;Dels=0.00;FS=2.969;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=1;MQRankSum=0.821;QD=23.85;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,36:49:99:1197,0,340 -chr1 42885 . T C 1721.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.922;DP=50;Dels=0.00;FS=3.297;HaplotypeScore=2.9991;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=2;MQRankSum=-0.479;QD=34.44;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,48:50:99:1750,100,0 -chr1 42886 . C T 1072.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.810;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=2;MQRankSum=1.039;QD=21.46;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1101,0,484 -chr1 42890 . G T 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.510;DP=56;Dels=0.00;FS=1.156;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=2;MQRankSum=-0.672;QD=7.39;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,18:56:99:442,0,1293 -chr1 42926 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.287;DP=58;Dels=0.00;FS=7.798;HaplotypeScore=2.7439;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=-0.975;QD=20.50;ReadPosRankSum=0.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1217,0,729 -chr1 42931 . T C 2121.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7439;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=1;QD=32.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2150,163,0 -chr1 42980 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.991;QD=18.08;ReadPosRankSum=1.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:878,0,734 -chr1 43004 . A G 1350.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.45;MQ0=0;QD=34.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1379,105,0 -chr1 43009 . G A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=2.090;QD=14.47;ReadPosRankSum=0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:578,0,652 -chr1 43016 . A G 1291.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1320,99,0 -chr1 43030 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=40;Dels=0.00;FS=1.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-2.465;QD=14.89;ReadPosRankSum=-0.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:624,0,708 -chr1 43039 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.020;DP=38;Dels=0.00;FS=2.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.44;MQ0=0;MQRankSum=-1.493;QD=12.99;ReadPosRankSum=0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:522,0,755 -chr1 43040 . G A 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=40;Dels=0.00;FS=4.756;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.155;QD=13.87;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:583,0,758 -chr1 43050 . T C 1807.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=26.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1836,141,0 -chr1 43061 . T A 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.626;DP=49;Dels=0.00;FS=4.322;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=0;MQRankSum=1.606;QD=17.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:893,0,625 -chr1 43067 . C T 855.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=4.058;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-0.462;QD=16.78;ReadPosRankSum=2.101;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:884,0,760 -chr1 43068 . G T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=2.286;QD=16.58;ReadPosRankSum=2.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:907,0,821 -chr1 43083 . G C 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.92;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,169,0 -chr1 43097 . T C 2191.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.07;MQ0=0;QD=28.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:57:99:2220,166,0 -chr1 43150 . T A 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=54;Dels=0.00;FS=2.461;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=1.401;QD=18.50;ReadPosRankSum=-1.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1027,0,700 -chr1 43153 . G A 1106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=58;Dels=0.00;FS=3.788;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=1.366;QD=19.08;ReadPosRankSum=-1.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1135,0,730 -chr1 43183 . T C 1947.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.34;MQ0=0;QD=33.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1976,147,0 -chr1 43187 . G A 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.656;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-0.333;QD=14.13;ReadPosRankSum=0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:749,0,974 -chr1 43195 . A G 2077.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.472;DP=56;Dels=0.00;FS=5.362;HaplotypeScore=4.9656;MLEAC=2;MLEAF=1.00;MQ=50.45;MQ0=0;MQRankSum=0.283;QD=34.04;ReadPosRankSum=1.669;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,54:56:99:2106,123,0 -chr1 43197 . G A 1062.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=58;Dels=0.00;FS=1.101;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=0.868;QD=18.32;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1091,0,879 -chr1 43231 . C A 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.226;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=0;MQRankSum=-0.040;QD=12.06;ReadPosRankSum=0.473;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,22:58:99:728,0,1277 -chr1 43246 . T C 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=72;Dels=0.00;FS=7.335;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=53.67;MQ0=0;MQRankSum=-3.808;QD=0.61;ReadPosRankSum=-2.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,8:72:72:72,0,2204 -chr1 43265 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=75;Dels=0.00;FS=7.472;HaplotypeScore=3.7546;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-3.233;QD=0.44;ReadPosRankSum=-2.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,7:75:61:61,0,2183 -chr1 43276 . G A 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.432;DP=69;Dels=0.00;FS=3.775;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-3.715;QD=1.13;ReadPosRankSum=1.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,9:69:99:106,0,2099 -chr1 43278 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.807;DP=70;Dels=0.00;FS=18.468;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-6.081;QD=5.05;ReadPosRankSum=2.009;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:382,0,1868 -chr1 43282 . A G 2155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.741;DP=72;Dels=0.00;FS=5.810;HaplotypeScore=18.7776;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=3.314;QD=29.94;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,62:72:99:2184,0,134 -chr1 43285 . G A 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.628;DP=73;Dels=0.00;FS=5.951;HaplotypeScore=50.5662;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-3.088;QD=1.42;ReadPosRankSum=2.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:132,0,2235 -chr1 43291 . C G 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=74;Dels=0.00;FS=19.101;HaplotypeScore=33.7389;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-3.986;QD=2.73;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:230,0,2102 -chr1 43293 . A T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.021;DP=71;Dels=0.00;FS=10.885;HaplotypeScore=23.8257;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=1;MQRankSum=-3.987;QD=2.73;ReadPosRankSum=2.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:222,0,1937 -chr1 43298 . C T 2572.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=13.9125;MLEAC=2;MLEAF=1.00;MQ=49.91;MQ0=1;QD=27.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2601,199,0 -chr1 43315 . A C 2446.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=1;QD=24.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2475,196,0 -chr1 43326 . A T 2504.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=25.9658;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=1;QD=28.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2533,196,0 -chr1 43328 . C G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.840;DP=70;Dels=0.00;FS=18.175;HaplotypeScore=28.9637;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=1;MQRankSum=-1.433;QD=4.03;ReadPosRankSum=-2.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,16:70:99:310,0,1933 -chr1 43332 . G C 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;DP=68;Dels=0.00;FS=31.387;HaplotypeScore=27.9641;MLEAC=1;MLEAF=0.500;MQ=48.56;MQ0=2;MQRankSum=3.076;QD=5.57;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:407,0,1696 -chr1 43333 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.715;DP=63;Dels=0.00;FS=24.273;HaplotypeScore=25.9652;MLEAC=1;MLEAF=0.500;MQ=48.61;MQ0=2;MQRankSum=-3.220;QD=4.08;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:285,0,1646 -chr1 43371 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=73;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.66;MQ0=2;MQRankSum=2.809;QD=6.64;ReadPosRankSum=-0.324;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,18:73:99:513,0,1764 -chr1 43372 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=74;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.31;MQ0=3;MQRankSum=2.584;QD=6.60;ReadPosRankSum=-0.403;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,18:74:99:517,0,1762 -chr1 43392 . C T 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.597;DP=82;Dels=0.00;FS=11.173;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=2;MQRankSum=3.354;QD=9.66;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,27:82:99:820,0,1545 -chr1 43419 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.314;DP=85;Dels=0.00;FS=4.704;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.922;QD=0.80;ReadPosRankSum=-1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,15:85:96:96,0,2450 -chr1 43420 . T C 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=85;Dels=0.00;FS=8.730;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.994;QD=1.48;ReadPosRankSum=-1.438;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:154,0,2361 -chr1 43424 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=86;Dels=0.00;FS=5.028;HaplotypeScore=83.0946;MLEAC=1;MLEAF=0.500;MQ=52.08;MQ0=2;MQRankSum=2.883;QD=9.25;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,27:86:99:824,0,1702 -chr1 43442 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=81;Dels=0.00;FS=4.587;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=51.64;MQ0=1;MQRankSum=-5.183;QD=2.57;ReadPosRankSum=1.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,18:81:99:236,0,2162 -chr1 43464 . T C 1004.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=83;Dels=0.00;FS=6.657;HaplotypeScore=7.8783;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-7.377;QD=12.11;ReadPosRankSum=-0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,40:83:99:1033,0,1434 -chr1 43478 . C T 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=78;Dels=0.00;FS=2.728;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=1;MQRankSum=-1.601;QD=4.14;ReadPosRankSum=-1.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,15:78:99:351,0,2012 -chr1 43479 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=78;Dels=0.00;FS=7.130;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-1.781;QD=0.23;ReadPosRankSum=0.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,8:78:46:46,0,2305 -chr1 43500 . C G 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=75;Dels=0.00;FS=9.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=1;MQRankSum=3.454;QD=2.78;ReadPosRankSum=-0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,12:75:99:237,0,2108 -chr1 43510 . A G 135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=78;Dels=0.00;FS=13.593;HaplotypeScore=39.7676;MLEAC=1;MLEAF=0.500;MQ=48.31;MQ0=1;MQRankSum=3.326;QD=1.74;ReadPosRankSum=-1.053;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:78:99:164,0,2251 -chr1 43512 . T C 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=79;Dels=0.00;FS=5.766;HaplotypeScore=29.7717;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=1;MQRankSum=-2.674;QD=5.09;ReadPosRankSum=-1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:430,0,1984 -chr1 43517 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=74;Dels=0.00;FS=7.633;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=47.06;MQ0=1;MQRankSum=-2.543;QD=0.98;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:101,0,2153 -chr1 43520 . C A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=74;Dels=0.00;FS=3.451;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.123;QD=0.54;ReadPosRankSum=0.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:68:68,0,2205 -chr1 43523 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=77;Dels=0.00;FS=9.238;HaplotypeScore=43.3257;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=1;MQRankSum=2.335;QD=0.44;ReadPosRankSum=-0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,7:77:62:62,0,2240 -chr1 43525 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=75;Dels=0.00;FS=2.429;HaplotypeScore=41.3363;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=1;MQRankSum=2.219;QD=4.41;ReadPosRankSum=0.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:359,0,1931 -chr1 43532 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=73;Dels=0.00;FS=11.099;HaplotypeScore=23.1272;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=2;MQRankSum=1.051;QD=8.75;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:667,0,1489 -chr1 43535 . C G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=71;Dels=0.00;FS=13.340;HaplotypeScore=30.0213;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=2;MQRankSum=1.228;QD=8.70;ReadPosRankSum=-0.541;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,24:71:99:646,0,1479 -chr1 43544 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=67;Dels=0.00;FS=8.590;HaplotypeScore=21.3628;MLEAC=1;MLEAF=0.500;MQ=43.73;MQ0=2;MQRankSum=-0.099;QD=12.70;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,30:67:99:879,0,1032 -chr1 43548 . T C 2142.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=18.0294;MLEAC=2;MLEAF=1.00;MQ=43.48;MQ0=1;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2171,171,0 -chr1 43554 . A G 1643.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=19.3162;MLEAC=2;MLEAF=1.00;MQ=40.15;MQ0=1;QD=32.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1672,135,0 -chr1 43556 . A T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=50;Dels=0.00;FS=20.048;HaplotypeScore=10.4239;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=1;MQRankSum=1.405;QD=6.36;ReadPosRankSum=-0.232;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,981 -chr1 43562 . A C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.681;DP=50;Dels=0.00;FS=14.927;HaplotypeScore=31.3082;MLEAC=1;MLEAF=0.500;MQ=40.43;MQ0=1;MQRankSum=1.421;QD=7.74;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:415,0,1027 -chr1 43569 . T C 1156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.578;DP=43;Dels=0.00;FS=13.268;HaplotypeScore=30.7711;MLEAC=1;MLEAF=0.500;MQ=39.33;MQ0=1;MQRankSum=-1.864;QD=26.90;ReadPosRankSum=1.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,39:43:35:1185,0,35 -chr1 43571 . A G 1091.86 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=1;QD=25.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:43:99:1234,99,0 -chr1 43572 . A G 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=45;Dels=0.00;FS=3.225;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=2;MQRankSum=-0.039;QD=6.37;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:315,0,750 -chr1 43594 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.410;DP=44;Dels=0.00;FS=5.674;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.55;MQ0=2;MQRankSum=0.307;QD=3.77;ReadPosRankSum=0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,10:44:99:194,0,793 -chr1 43610 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=33;Dels=0.00;FS=6.419;HaplotypeScore=4.5214;MLEAC=1;MLEAF=0.500;MQ=33.96;MQ0=2;MQRankSum=-0.609;QD=3.30;ReadPosRankSum=-0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:137,0,510 -chr1 43619 . T C 412.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=5.3349;MLEAC=2;MLEAF=1.00;MQ=30.87;MQ0=2;QD=17.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:36:441,36,0 -chr1 43627 . T G 140.9 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.23;MQ0=1;QD=9.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:15:169,15,0 -chr1 43635 . C T 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.559;DP=28;Dels=0.00;FS=10.098;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-0.717;QD=0.64;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,4:28:46:46,0,498 -chr1 43639 . C T 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=28;Dels=0.00;FS=3.565;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-1.029;QD=4.46;ReadPosRankSum=0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:153,0,405 -chr1 43643 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=13.8923;MLEAC=1;MLEAF=0.500;MQ=36.79;MQ0=1;MQRankSum=0.952;QD=1.16;ReadPosRankSum=-1.543;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,5:29:62:62,0,530 -chr1 43651 . G A 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=33;Dels=0.00;FS=1.393;HaplotypeScore=3.9569;MLEAC=1;MLEAF=0.500;MQ=39.46;MQ0=1;MQRankSum=1.499;QD=7.78;ReadPosRankSum=1.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:285,0,426 -chr1 43662 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.298;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=0;MQRankSum=0.474;QD=3.35;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,6:37:99:152,0,768 -chr1 43664 . A G 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=36;Dels=0.00;FS=5.877;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=45.71;MQ0=0;MQRankSum=-2.505;QD=4.72;ReadPosRankSum=-0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,11:36:99:198,0,750 -chr1 43668 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=39;Dels=0.00;FS=8.049;HaplotypeScore=10.2065;MLEAC=1;MLEAF=0.500;MQ=45.43;MQ0=0;MQRankSum=-2.825;QD=7.71;ReadPosRankSum=-0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:329,0,752 -chr1 43678 . T A 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=52;Dels=0.00;FS=11.972;HaplotypeScore=19.6024;MLEAC=1;MLEAF=0.500;MQ=44.28;MQ0=0;MQRankSum=-1.814;QD=3.86;ReadPosRankSum=1.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,12:52:99:229,0,1169 -chr1 43686 . T C 1665.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=13.0300;MLEAC=2;MLEAF=1.00;MQ=44.10;MQ0=0;QD=29.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:1694,138,0 -chr1 43688 . C T 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=30.3912;MLEAC=1;MLEAF=0.500;MQ=43.92;MQ0=0;MQRankSum=4.253;QD=8.54;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,17:55:99:498,0,1002 -chr1 43698 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;DP=67;Dels=0.00;FS=8.840;HaplotypeScore=47.7369;MLEAC=1;MLEAF=0.500;MQ=45.08;MQ0=0;MQRankSum=-4.239;QD=8.07;ReadPosRankSum=-0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,26:67:99:569,0,1255 -chr1 43705 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=69;Dels=0.00;FS=3.045;HaplotypeScore=32.6622;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=-0.571;QD=2.33;ReadPosRankSum=0.145;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,10:69:99:189,0,1720 -chr1 43713 . A C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.553;DP=77;Dels=0.00;FS=11.201;HaplotypeScore=42.6440;MLEAC=1;MLEAF=0.500;MQ=45.67;MQ0=0;MQRankSum=-5.163;QD=8.23;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,32:77:99:662,0,1440 -chr1 43719 . A T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=81;Dels=0.00;FS=4.781;HaplotypeScore=21.7031;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=-0.691;QD=1.52;ReadPosRankSum=-0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,10:81:99:151,0,2102 -chr1 43742 . A T 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.288;DP=82;Dels=0.00;FS=35.671;HaplotypeScore=38.7529;MLEAC=1;MLEAF=0.500;MQ=46.28;MQ0=0;MQRankSum=1.619;QD=4.07;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,15:82:99:362,0,1988 -chr1 43754 . G A 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.834;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.306;QD=4.89;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:424,0,1874 -chr1 43755 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.189;QD=4.47;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:390,0,1864 -chr1 43771 . C T 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=17.4268;MLEAC=1;MLEAF=0.500;MQ=48.68;MQ0=0;MQRankSum=-0.578;QD=0.63;ReadPosRankSum=-0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,9:84:81:81,0,2479 -chr1 43781 . A C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=27.2915;MLEAC=1;MLEAF=0.500;MQ=50.47;MQ0=0;MQRankSum=-1.448;QD=1.76;ReadPosRankSum=-0.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:99:185,0,2613 -chr1 43786 . G A 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=84;Dels=0.00;FS=1.288;HaplotypeScore=17.3780;MLEAC=1;MLEAF=0.500;MQ=51.33;MQ0=0;MQRankSum=-1.617;QD=1.74;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:174,0,2552 -chr1 43806 . T C 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=35.5387;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-6.251;QD=15.98;ReadPosRankSum=0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,41:82:99:1339,0,1390 -chr1 43810 . C T 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=79;Dels=0.00;FS=10.312;HaplotypeScore=35.5390;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=0;MQRankSum=-2.175;QD=1.48;ReadPosRankSum=1.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:79:99:145,0,2427 -chr1 43816 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=76;Dels=0.00;FS=1.622;HaplotypeScore=86.3319;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-2.822;QD=2.44;ReadPosRankSum=1.394;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,11:76:99:214,0,1931 -chr1 43818 . A G 2850.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=49.3811;MLEAC=2;MLEAF=1.00;MQ=52.68;MQ0=0;QD=33.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,74:75:99:2879,223,0 -chr1 43821 . G A 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.751;DP=80;Dels=0.00;FS=3.003;HaplotypeScore=41.4503;MLEAC=1;MLEAF=0.500;MQ=52.13;MQ0=2;MQRankSum=-3.694;QD=4.70;ReadPosRankSum=0.476;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,16:80:99:404,0,2083 -chr1 43823 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=47.4468;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=3.459;QD=8.60;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,24:81:99:725,0,1844 -chr1 43834 . A C 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.959;DP=87;Dels=0.00;FS=5.047;HaplotypeScore=27.3319;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=2;MQRankSum=-6.863;QD=11.49;ReadPosRankSum=1.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1028,0,1538 -chr1 43840 . C T 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.139;DP=85;Dels=0.00;FS=1.532;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=2;MQRankSum=-0.945;QD=1.09;ReadPosRankSum=-1.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,11:85:99:121,0,2480 -chr1 43841 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=88;Dels=0.00;FS=8.668;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=2;MQRankSum=-6.447;QD=6.87;ReadPosRankSum=1.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:633,0,2003 -chr1 43851 . A G 3242.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=1.7273;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=3;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3271,253,0 -chr1 43863 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.312;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.86;MQ0=3;MQRankSum=-4.540;QD=0.20;ReadPosRankSum=0.738;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,14:97:48:48,0,2773 -chr1 43864 . G A 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.505;DP=94;Dels=0.00;FS=1.845;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.56;MQ0=3;MQRankSum=3.253;QD=11.17;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:1078,0,1669 -chr1 43866 . G C 1601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.813;DP=89;Dels=0.00;FS=2.991;HaplotypeScore=55.7192;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=3;MQRankSum=6.796;QD=18.00;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,49:89:99:1630,0,963 -chr1 43877 . T G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.373;DP=82;Dels=0.00;FS=4.511;HaplotypeScore=22.6567;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=3;MQRankSum=-6.816;QD=8.86;ReadPosRankSum=-0.734;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,34:82:99:755,0,1613 -chr1 43880 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=81;Dels=0.00;FS=3.784;HaplotypeScore=34.1328;MLEAC=1;MLEAF=0.500;MQ=47.59;MQ0=3;MQRankSum=4.821;QD=5.75;ReadPosRankSum=0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,19:81:99:494,0,1845 -chr1 43886 . A G 2779.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=36.7766;MLEAC=2;MLEAF=1.00;MQ=47.06;MQ0=3;QD=33.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:2808,223,0 -chr1 43895 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.900;DP=84;Dels=0.00;FS=3.557;HaplotypeScore=5.7833;MLEAC=1;MLEAF=0.500;MQ=47.29;MQ0=3;MQRankSum=3.874;QD=6.95;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:612,0,1874 -chr1 43919 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.966;DP=90;Dels=0.00;FS=10.596;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=48.00;MQ0=3;MQRankSum=-3.047;QD=1.38;ReadPosRankSum=2.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:90:99:152,0,2472 -chr1 43921 . C T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;DP=89;Dels=0.00;FS=11.456;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=3;MQRankSum=-0.291;QD=12.58;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,38:89:99:1148,0,1412 -chr1 43929 . G C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.254;DP=96;Dels=0.00;FS=0.861;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.78;MQ0=4;MQRankSum=4.123;QD=8.49;ReadPosRankSum=0.847;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,31:96:99:843,0,1928 -chr1 43954 . G A 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=98;Dels=0.00;FS=3.403;HaplotypeScore=31.4020;MLEAC=1;MLEAF=0.500;MQ=48.81;MQ0=3;MQRankSum=-1.940;QD=5.12;ReadPosRankSum=-1.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:530,0,2436 -chr1 43958 . T C 1162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=98;Dels=0.00;FS=0.772;HaplotypeScore=41.3969;MLEAC=1;MLEAF=0.500;MQ=49.49;MQ0=3;MQRankSum=-3.408;QD=11.86;ReadPosRankSum=0.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,42:98:99:1191,0,1753 -chr1 43959 . T C 3463.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=41.4115;MLEAC=2;MLEAF=1.00;MQ=49.49;MQ0=3;QD=29.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3492,268,0 -chr1 43966 . G T 228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.214;DP=107;Dels=0.00;FS=4.094;HaplotypeScore=60.8308;MLEAC=1;MLEAF=0.500;MQ=49.53;MQ0=3;MQRankSum=-0.729;QD=2.14;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,14:107:99:257,0,2992 -chr1 43969 . G A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=107;Dels=0.00;FS=1.978;HaplotypeScore=35.1970;MLEAC=1;MLEAF=0.500;MQ=49.50;MQ0=3;MQRankSum=-2.173;QD=5.55;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,27:107:99:622,0,2650 -chr1 43976 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.740;DP=112;Dels=0.00;FS=3.944;HaplotypeScore=55.4395;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=4;MQRankSum=-1.018;QD=2.50;ReadPosRankSum=-0.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,15:112:99:308,0,3072 -chr1 43984 . G A 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=118;Dels=0.00;FS=2.892;HaplotypeScore=75.9412;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=4;MQRankSum=0.547;QD=6.90;ReadPosRankSum=-0.638;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,29:118:99:842,0,2830 -chr1 43988 . A C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=116;Dels=0.00;FS=5.433;HaplotypeScore=43.4214;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=4;MQRankSum=4.795;QD=7.25;ReadPosRankSum=-1.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:116:99:869,0,2451 -chr1 44002 . A G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=116;Dels=0.00;FS=0.958;HaplotypeScore=39.4904;MLEAC=1;MLEAF=0.500;MQ=51.56;MQ0=3;MQRankSum=-2.313;QD=3.79;ReadPosRankSum=1.726;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,20:116:99:468,0,2935 -chr1 44007 . T A 1436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.367;DP=111;Dels=0.00;FS=6.411;HaplotypeScore=43.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=3;MQRankSum=-6.177;QD=12.94;ReadPosRankSum=0.970;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,51:111:99:1465,0,1937 -chr1 44026 . T C 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.135;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=6.8459;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=-3.383;QD=0.29;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,12:110:60:60,0,3255 -chr1 44060 . T C 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=84;Dels=0.00;FS=2.470;HaplotypeScore=22.4896;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=4.395;QD=5.53;ReadPosRankSum=0.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,20:84:99:493,0,2021 -chr1 44069 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.048;DP=73;Dels=0.00;FS=3.136;HaplotypeScore=49.4176;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-5.204;QD=3.39;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,13:73:99:276,0,1726 -chr1 44072 . T A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=71;Dels=0.00;FS=1.293;HaplotypeScore=23.4451;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.737;QD=3.56;ReadPosRankSum=-1.197;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:281,0,1830 -chr1 44082 . C T 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=69;Dels=0.00;FS=10.437;HaplotypeScore=20.4044;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.783;QD=3.49;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,13:69:99:269,0,1813 -chr1 44096 . C T 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=19.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=0;MQRankSum=4.352;QD=10.13;ReadPosRankSum=1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,20:60:99:636,0,1132 -chr1 44099 . T G 1703.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=15.7767;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1732,132,0 -chr1 44100 . A T 1683.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=13.9885;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1712,129,0 -chr1 44102 . A C 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.658;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.00;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:122,0,1452 -chr1 44103 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.14;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:129,0,1433 -chr1 44111 . T A 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=55;Dels=0.00;FS=2.927;HaplotypeScore=2.1550;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.824;QD=3.38;ReadPosRankSum=-0.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,13:55:99:214,0,1474 -chr1 44117 . C T 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=61;Dels=0.00;FS=5.158;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-3.964;QD=2.88;ReadPosRankSum=0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,12:61:99:204,0,1632 -chr1 44120 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=63;Dels=0.00;FS=5.124;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-4.000;QD=2.69;ReadPosRankSum=1.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:198,0,1749 -chr1 44126 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.677;DP=63;Dels=0.00;FS=8.122;HaplotypeScore=17.4822;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=-4.789;QD=6.36;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,21:63:99:429,0,1420 -chr1 44133 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=64;Dels=0.00;FS=3.868;HaplotypeScore=13.3538;MLEAC=1;MLEAF=0.500;MQ=51.28;MQ0=0;MQRankSum=-2.947;QD=0.39;ReadPosRankSum=-2.323;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,7:64:53:53,0,1875 -chr1 44145 . T A 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.048;DP=72;Dels=0.00;FS=14.645;HaplotypeScore=3.9967;MLEAC=1;MLEAF=0.500;MQ=50.27;MQ0=0;MQRankSum=-4.480;QD=6.77;ReadPosRankSum=2.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:516,0,1706 -chr1 44157 . T C 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.780;DP=70;Dels=0.00;FS=5.275;HaplotypeScore=5.7502;MLEAC=1;MLEAF=0.500;MQ=49.89;MQ0=0;MQRankSum=-1.502;QD=1.11;ReadPosRankSum=2.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,10:70:99:106,0,2013 -chr1 44177 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;DP=73;Dels=0.00;FS=7.693;HaplotypeScore=14.5600;MLEAC=1;MLEAF=0.500;MQ=49.07;MQ0=0;MQRankSum=0.080;QD=7.48;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,20:73:99:574,0,1711 -chr1 44183 . T C 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=73;Dels=0.00;FS=3.202;HaplotypeScore=50.8308;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=0;MQRankSum=-1.131;QD=1.08;ReadPosRankSum=-0.425;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:107,0,2164 -chr1 44188 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=74;Dels=0.00;FS=14.435;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=0;MQRankSum=-4.140;QD=6.90;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,24:74:99:539,0,1696 -chr1 44191 . C G 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=78;Dels=0.00;FS=1.989;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=0;MQRankSum=3.081;QD=11.29;ReadPosRankSum=1.210;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,29:78:99:909,0,1490 -chr1 44202 . T C 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=70;Dels=0.00;FS=18.949;HaplotypeScore=45.1512;MLEAC=1;MLEAF=0.500;MQ=50.32;MQ0=0;MQRankSum=-3.780;QD=4.45;ReadPosRankSum=-1.041;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,17:70:99:340,0,1880 -chr1 44205 . T G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.786;DP=71;Dels=0.00;FS=2.009;HaplotypeScore=52.8564;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=2.066;QD=13.29;ReadPosRankSum=0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,30:71:99:972,0,1251 -chr1 44214 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=65;Dels=0.00;FS=6.471;HaplotypeScore=49.1081;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-3.604;QD=0.55;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,8:65:64:64,0,1916 -chr1 44224 . C T 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=65;Dels=0.00;FS=11.066;HaplotypeScore=41.7947;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=3.011;QD=10.97;ReadPosRankSum=-1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:741,0,1311 -chr1 44226 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.161;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=0.468;QD=10.58;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:663,0,1231 -chr1 44227 . T C 1771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=60;Dels=0.00;FS=3.739;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=3.270;QD=29.53;ReadPosRankSum=-1.934;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,52:60:43:1800,0,43 -chr1 44239 . C T 1746.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1775,138,0 -chr1 44240 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=2.627;HaplotypeScore=23.3747;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=2.800;QD=10.58;ReadPosRankSum=1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:536,0,932 -chr1 44241 . T C 1696.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1725,135,0 -chr1 44248 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=9.054;HaplotypeScore=23.3746;MLEAC=1;MLEAF=0.500;MQ=50.11;MQ0=0;MQRankSum=-4.405;QD=3.08;ReadPosRankSum=2.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,10:48:99:176,0,1356 -chr1 44249 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.419;DP=49;Dels=0.00;FS=8.239;HaplotypeScore=24.3740;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.565;QD=3.65;ReadPosRankSum=1.809;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:207,0,1354 -chr1 44258 . T A 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.562;DP=54;Dels=0.00;FS=4.366;HaplotypeScore=24.1638;MLEAC=1;MLEAF=0.500;MQ=48.73;MQ0=0;MQRankSum=4.329;QD=10.64;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:603,0,1025 -chr1 44278 . A G 1907.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=6.7023;MLEAC=2;MLEAF=1.00;MQ=46.93;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:1936,153,0 -chr1 44282 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=57;Dels=0.00;FS=1.055;HaplotypeScore=8.1141;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=0;MQRankSum=4.194;QD=11.70;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,24:57:99:695,0,881 -chr1 44295 . A T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.344;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=9.3874;MLEAC=1;MLEAF=0.500;MQ=43.43;MQ0=2;MQRankSum=-2.337;QD=0.18;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,7:63:39:39,0,1747 -chr1 44304 . T C 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=23.9832;MLEAC=1;MLEAF=0.500;MQ=43.23;MQ0=2;MQRankSum=4.033;QD=11.74;ReadPosRankSum=0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,25:62:99:756,0,963 -chr1 44307 . C G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.815;DP=60;Dels=0.00;FS=6.252;HaplotypeScore=26.1832;MLEAC=1;MLEAF=0.500;MQ=43.38;MQ0=2;MQRankSum=-0.025;QD=7.33;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:468,0,1201 -chr1 44311 . A G 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.265;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=30.9134;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=2;MQRankSum=-2.338;QD=10.90;ReadPosRankSum=-0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,29:60:99:682,0,949 -chr1 44317 . T A 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.835;DP=59;Dels=0.00;FS=4.227;HaplotypeScore=16.7737;MLEAC=1;MLEAF=0.500;MQ=42.80;MQ0=2;MQRankSum=0.606;QD=6.47;ReadPosRankSum=-2.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:410,0,1154 -chr1 44335 . T A 1721.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=18.1882;MLEAC=2;MLEAF=1.00;MQ=40.95;MQ0=2;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:1750,144,0 -chr1 44342 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=61;Dels=0.00;FS=4.324;HaplotypeScore=34.0871;MLEAC=1;MLEAF=0.500;MQ=42.11;MQ0=2;MQRankSum=-1.601;QD=6.18;ReadPosRankSum=0.691;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,16:61:99:405,0,1260 -chr1 44367 . C T 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=9.9194;MLEAC=1;MLEAF=0.500;MQ=42.27;MQ0=2;MQRankSum=2.251;QD=15.05;ReadPosRankSum=0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:886,0,731 -chr1 44402 . T C 1512.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=45.06;MQ0=0;QD=27.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1541,117,0 -chr1 44414 . C T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.135;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=14.3006;MLEAC=1;MLEAF=0.500;MQ=44.91;MQ0=0;MQRankSum=0.590;QD=12.70;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:714,0,919 -chr1 44417 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.333;DP=59;Dels=0.00;FS=7.276;HaplotypeScore=15.3006;MLEAC=1;MLEAF=0.500;MQ=45.19;MQ0=0;MQRankSum=-3.435;QD=2.13;ReadPosRankSum=-2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:154,0,1624 -chr1 44447 . T C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.70;MQ0=0;MQRankSum=-0.207;QD=1.35;ReadPosRankSum=-0.960;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,7:57:99:105,0,1613 -chr1 44452 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=58;Dels=0.00;FS=3.537;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.96;MQ0=0;MQRankSum=-0.530;QD=2.01;ReadPosRankSum=-0.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,8:58:99:145,0,1592 -chr1 44473 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=69;Dels=0.00;FS=9.852;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=-4.187;QD=0.71;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,12:69:77:77,0,2026 -chr1 44477 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.028;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=0;MQRankSum=-0.984;QD=1.30;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:118,0,1985 -chr1 44478 . G C 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.175;DP=70;Dels=0.00;FS=1.536;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.34;MQ0=0;MQRankSum=-0.858;QD=1.21;ReadPosRankSum=2.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,8:70:99:113,0,2020 -chr1 44484 . A G 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=36.7273;MLEAC=1;MLEAF=0.500;MQ=45.51;MQ0=0;MQRankSum=-1.246;QD=1.13;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:106,0,1981 -chr1 44498 . A C 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=59;Dels=0.03;FS=1.285;HaplotypeScore=66.6807;MLEAC=1;MLEAF=0.500;MQ=46.25;MQ0=0;MQRankSum=1.067;QD=5.03;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,12:57:99:325,0,1534 -chr1 44501 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.558;DP=54;Dels=0.00;FS=2.868;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=0.142;QD=6.25;ReadPosRankSum=-0.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,13:54:99:366,0,1280 -chr1 44503 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=55;Dels=0.00;FS=2.476;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=-0.130;QD=18.18;ReadPosRankSum=1.776;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1028,0,672 -chr1 44505 . T C 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.716;DP=56;Dels=0.00;FS=1.565;HaplotypeScore=46.3941;MLEAC=1;MLEAF=0.500;MQ=46.01;MQ0=0;MQRankSum=-0.697;QD=1.69;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:56:99:123,0,1510 -chr1 44517 . G A 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=8.8138;MLEAC=1;MLEAF=0.500;MQ=44.77;MQ0=0;MQRankSum=-3.350;QD=2.42;ReadPosRankSum=2.577;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,11:54:99:159,0,1479 -chr1 44560 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=43;Dels=0.00;FS=9.300;HaplotypeScore=4.7566;MLEAC=1;MLEAF=0.500;MQ=41.88;MQ0=0;MQRankSum=0.807;QD=9.95;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:456,0,729 -chr1 44572 . C A 1243.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.646;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=41.69;MQ0=0;MQRankSum=0.866;QD=31.09;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,39:40:99:1272,105,0 -chr1 44587 . T C 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.665;DP=38;Dels=0.00;FS=13.265;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=40.46;MQ0=0;MQRankSum=-1.286;QD=9.10;ReadPosRankSum=-0.547;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:374,0,691 -chr1 44614 . C G 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.420;DP=43;Dels=0.00;FS=1.868;HaplotypeScore=14.4733;MLEAC=1;MLEAF=0.500;MQ=42.93;MQ0=0;MQRankSum=0.020;QD=1.11;ReadPosRankSum=0.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,6:43:76:76,0,1119 -chr1 44624 . G A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.102;DP=51;Dels=0.00;FS=12.856;HaplotypeScore=21.4215;MLEAC=1;MLEAF=0.500;MQ=42.84;MQ0=0;MQRankSum=-2.880;QD=0.20;ReadPosRankSum=1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,6:51:38:38,0,1509 -chr1 44632 . A T 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=54;Dels=0.00;FS=2.363;HaplotypeScore=21.5373;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=1.153;QD=12.81;ReadPosRankSum=-0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:720,0,934 -chr1 44637 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=22.5160;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=-0.673;QD=1.44;ReadPosRankSum=0.812;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,9:54:99:106,0,1529 -chr1 44642 . C T 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=52;Dels=0.00;FS=20.166;HaplotypeScore=24.5152;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=0;MQRankSum=-3.351;QD=0.36;ReadPosRankSum=-0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:52:47:47,0,1525 -chr1 44646 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=50;Dels=0.00;FS=21.581;HaplotypeScore=15.6098;MLEAC=1;MLEAF=0.500;MQ=43.77;MQ0=0;MQRankSum=-3.383;QD=0.52;ReadPosRankSum=-0.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,7:50:54:54,0,1474 -chr1 44657 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=58;Dels=0.00;FS=2.599;HaplotypeScore=22.8584;MLEAC=1;MLEAF=0.500;MQ=44.43;MQ0=0;MQRankSum=2.619;QD=7.03;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:58:99:436,0,1315 -chr1 44662 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=55;Dels=0.00;FS=16.338;HaplotypeScore=20.8592;MLEAC=1;MLEAF=0.500;MQ=44.81;MQ0=0;MQRankSum=-3.253;QD=0.34;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,6:55:47:47,0,1653 -chr1 44666 . T C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=4.523;HaplotypeScore=18.8632;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=0;MQRankSum=-3.198;QD=5.00;ReadPosRankSum=0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,14:51:99:283,0,1321 -chr1 44682 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=48;Dels=0.00;FS=1.217;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=44.53;MQ0=0;MQRankSum=-2.438;QD=21.25;ReadPosRankSum=-0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,34:48:99:1048,0,416 -chr1 44699 . G A 1395.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=43.18;MQ0=0;QD=33.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1424,117,0 -chr1 44721 . A T 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=38;Dels=0.00;FS=2.913;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=0;MQRankSum=1.227;QD=11.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:471,0,475 -chr1 44722 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=40;Dels=0.00;FS=1.222;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.48;MQ0=0;MQRankSum=0.137;QD=8.77;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:379,0,602 -chr1 44747 . A G 853.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.64;MQ0=2;QD=23.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:36:75:882,75,0 -chr1 44750 . T C 772.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.71;MQ0=2;QD=22.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:69:801,69,0 -chr1 44764 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.890;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.22;MQ0=2;MQRankSum=-0.925;QD=0.33;ReadPosRankSum=0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:42:42,0,799 -chr1 44766 . G A 933.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.92;MQ0=2;QD=23.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:81:962,81,0 -chr1 44844 . C T 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.998;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=13.6215;MLEAC=1;MLEAF=0.500;MQ=39.32;MQ0=0;MQRankSum=0.233;QD=13.06;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,25:50:99:681,0,649 -chr1 44846 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=13.5548;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=32.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1552,123,0 -chr1 44848 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=50;Dels=0.00;FS=1.565;HaplotypeScore=12.7662;MLEAC=1;MLEAF=0.500;MQ=40.79;MQ0=0;MQRankSum=-2.924;QD=0.54;ReadPosRankSum=1.522;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,8:50:55:55,0,1346 -chr1 44875 . C T 224.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=6.7552;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=0;MQRankSum=-1.397;QD=3.57;ReadPosRankSum=-1.910;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,14:63:99:253,0,1577 -chr1 44905 . C G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.316;DP=72;Dels=0.00;FS=2.379;HaplotypeScore=14.6636;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=1;MQRankSum=0.928;QD=8.39;ReadPosRankSum=-1.284;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,23:72:99:632,0,1456 -chr1 44912 . A G 1743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677;DP=68;Dels=0.00;FS=1.336;HaplotypeScore=30.8580;MLEAC=1;MLEAF=0.500;MQ=43.96;MQ0=2;MQRankSum=-0.403;QD=25.64;ReadPosRankSum=-1.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,53:68:99:1772,0,267 -chr1 44920 . T C 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.714;DP=73;Dels=0.00;FS=7.931;HaplotypeScore=5.9984;MLEAC=1;MLEAF=0.500;MQ=42.33;MQ0=4;MQRankSum=-0.128;QD=5.48;ReadPosRankSum=1.793;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,21:73:99:428,0,1524 -chr1 44950 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=38.40;MQ0=5;MQRankSum=0.127;QD=7.52;ReadPosRankSum=1.502;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,23:72:99:570,0,1227 -chr1 44968 . A G 1512.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=2;MLEAF=1.00;MQ=35.93;MQ0=5;QD=25.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,60:60:99:1541,132,0 -chr1 44980 . T G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=53;Dels=0.00;FS=1.794;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=32.25;MQ0=6;MQRankSum=0.207;QD=17.41;ReadPosRankSum=-1.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,47:53:53:951,0,53 -chr1 44999 . A G 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=6;MQRankSum=-2.111;QD=4.22;ReadPosRankSum=-0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:231,0,671 -chr1 45005 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=44;Dels=0.00;FS=5.608;HaplotypeScore=21.5580;MLEAC=1;MLEAF=0.500;MQ=30.42;MQ0=4;MQRankSum=1.637;QD=10.11;ReadPosRankSum=1.096;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:473,0,341 -chr1 45011 . A G 805.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.6852;MLEAC=2;MLEAF=1.00;MQ=30.05;MQ0=2;QD=21.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:38:78:834,78,0 -chr1 45027 . C T 849.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.9559;MLEAC=2;MLEAF=1.00;MQ=31.41;MQ0=4;QD=20.23;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:78:878,78,0 -chr1 45055 . C T 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.634;DP=71;Dels=0.00;FS=12.767;HaplotypeScore=11.6629;MLEAC=1;MLEAF=0.500;MQ=43.94;MQ0=9;MQRankSum=-0.438;QD=0.94;ReadPosRankSum=-0.182;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:53,15:71:95:95,0,1604 -chr1 45090 . C T 1075.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=87;Dels=0.00;FS=4.246;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=3.081;QD=12.37;ReadPosRankSum=-0.758;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,34:87:99:1104,0,1445 -chr1 45092 . C T 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=86;Dels=0.00;FS=18.933;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=1;MQRankSum=-0.050;QD=0.57;ReadPosRankSum=-0.221;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:77,9:86:77:77,0,2524 -chr1 45093 . A C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=84;Dels=0.04;FS=4.282;HaplotypeScore=44.0211;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=1;MQRankSum=-2.754;QD=0.47;ReadPosRankSum=0.306;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,16:81:68:68,0,2273 -chr1 45100 . A T 1063.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=91;Dels=0.00;FS=1.785;HaplotypeScore=46.2820;MLEAC=1;MLEAF=0.500;MQ=50.63;MQ0=1;MQRankSum=0.114;QD=11.69;ReadPosRankSum=1.119;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,34:91:99:1092,0,1575 -chr1 45104 . C T 1245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.511;DP=93;Dels=0.00;FS=5.290;HaplotypeScore=20.4240;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=1;MQRankSum=1.122;QD=13.40;ReadPosRankSum=-0.845;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1274,0,1627 -chr1 45135 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.219;DP=93;Dels=0.00;FS=0.788;HaplotypeScore=3.1233;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=0.496;QD=15.87;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,46:93:99:1504,0,1552 -chr1 45155 . C T 3133.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.690;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=145.5703;MLEAC=2;MLEAF=1.00;MQ=50.31;MQ0=0;MQRankSum=1.436;QD=30.69;ReadPosRankSum=-0.338;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,81:82:99:3162,241,0 -chr1 45200 . A T 2113.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=1;QD=32.38;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2142,169,0 -chr1 45254 . G A 2049.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=47.40;MQ0=0;QD=29.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2078,156,0 -chr1 45271 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.331;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=0.761;QD=14.36;ReadPosRankSum=-0.072;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,26:58:99:861,0,1025 -chr1 45272 . C A 2207.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=33.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2236,169,0 -chr1 45286 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7329;MLEAC=1;MLEAF=0.500;MQ=49.43;MQ0=0;MQRankSum=0.497;QD=16.06;ReadPosRankSum=0.752;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,31:64:99:1056,0,1087 -chr1 45290 . T A 1146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;DP=65;Dels=0.00;FS=2.073;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=49.75;MQ0=0;MQRankSum=-0.151;QD=17.64;ReadPosRankSum=0.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1175,0,1019 -chr1 45343 . T A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.611;DP=74;Dels=0.00;FS=3.119;HaplotypeScore=3.9919;MLEAC=1;MLEAF=0.500;MQ=51.54;MQ0=0;MQRankSum=1.189;QD=16.85;ReadPosRankSum=0.605;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,37:74:99:1275,0,1131 -chr1 45344 . G A 2859.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=2.9920;MLEAC=2;MLEAF=1.00;MQ=51.54;MQ0=0;QD=33.68;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2888,220,0 -chr1 45355 . T C 2778.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.98;MQ0=0;QD=24.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2807,211,0 -chr1 45366 . A C 2847.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.43;MQ0=0;QD=31.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2876,220,0 -chr1 45377 . C T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=72;Dels=0.00;FS=27.679;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-2.895;QD=0.71;ReadPosRankSum=-1.328;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,9:72:79:79,0,2293 -chr1 45382 . A G 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.364;DP=74;Dels=0.00;FS=24.375;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.91;MQ0=0;MQRankSum=-3.126;QD=0.20;ReadPosRankSum=0.050;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,9:74:43:43,0,2344 -chr1 45385 . T A 2874.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=27.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2903,220,0 -chr1 45401 . T G 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=75;Dels=0.00;FS=42.438;HaplotypeScore=1.8656;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-2.624;QD=2.74;ReadPosRankSum=2.484;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,13:75:99:234,0,2260 -chr1 45425 . T C 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=62;Dels=0.00;FS=32.888;HaplotypeScore=11.8192;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.715;QD=3.33;ReadPosRankSum=2.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,12:62:99:235,0,1811 -chr1 45428 . C A 2117.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=21.6418;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;QD=27.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2146,163,0 -chr1 45430 . C A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.713;DP=50;Dels=0.00;FS=4.121;HaplotypeScore=21.6418;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=0.980;QD=12.74;ReadPosRankSum=0.446;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,20:50:99:665,0,987 -chr1 45435 . T C 1851.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.4494;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=26.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1880,141,0 -chr1 45436 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.196;DP=48;Dels=0.00;FS=17.629;HaplotypeScore=19.6275;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-3.668;QD=3.45;ReadPosRankSum=0.470;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:38,10:48:99:194,0,1412 -chr1 45442 . G A 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.766;DP=53;Dels=0.00;FS=20.851;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-3.761;QD=3.49;ReadPosRankSum=-0.055;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,11:53:99:213,0,1458 -chr1 45445 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=54;Dels=0.00;FS=3.890;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=0.857;QD=15.44;ReadPosRankSum=-0.441;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,26:54:99:862,0,877 -chr1 45455 . C T 1668.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=21.9167;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1697,132,0 -chr1 45456 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=47;Dels=0.00;FS=15.317;HaplotypeScore=22.9164;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-2.324;QD=20.91;ReadPosRankSum=-1.560;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,31:47:99:1011,0,399 -chr1 45458 . C A 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.943;DP=49;Dels=0.00;FS=1.157;HaplotypeScore=24.9247;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=0.389;QD=9.83;ReadPosRankSum=0.305;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,17:49:99:510,0,1061 -chr1 45460 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.945;DP=51;Dels=0.00;FS=20.268;HaplotypeScore=33.8333;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-2.966;QD=2.00;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,8:51:99:130,0,1482 -chr1 45468 . T C 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.974;DP=54;Dels=0.00;FS=11.572;HaplotypeScore=42.6787;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=3.688;QD=9.07;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,17:54:99:518,0,1120 -chr1 45469 . C G 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=54;Dels=0.00;FS=25.872;HaplotypeScore=26.8594;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-2.910;QD=1.38;ReadPosRankSum=-0.791;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,8:54:99:103,0,1615 -chr1 45473 . G A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.252;DP=57;Dels=0.00;FS=27.090;HaplotypeScore=18.7370;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=0;MQRankSum=-3.140;QD=1.47;ReadPosRankSum=-0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,9:57:99:112,0,1689 -chr1 45486 . T G 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=59;Dels=0.00;FS=26.386;HaplotypeScore=19.2723;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.044;QD=0.72;ReadPosRankSum=-0.122;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:51,8:59:71:71,0,1772 -chr1 45491 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.621;DP=56;Dels=0.00;FS=11.681;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=2.678;QD=7.98;ReadPosRankSum=-0.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:39,16:56:99:475,0,1141 -chr1 45492 . A C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=56;Dels=0.00;FS=36.390;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-3.873;QD=1.34;ReadPosRankSum=-0.513;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,10:56:99:103,0,1545 -chr1 45515 . A C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=55;Dels=0.00;FS=18.588;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.91;MQ0=0;MQRankSum=1.483;QD=4.54;ReadPosRankSum=1.105;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,11:55:99:278,0,1358 -chr1 45516 . T C 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=55;Dels=0.00;FS=32.991;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.72;MQ0=0;MQRankSum=-5.064;QD=1.89;ReadPosRankSum=0.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,12:55:99:132,0,1550 -chr1 45518 . C T 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102;DP=57;Dels=0.00;FS=26.291;HaplotypeScore=37.5622;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-5.240;QD=2.29;ReadPosRankSum=-0.162;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,13:57:99:159,0,1581 -chr1 45530 . G A 1057.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=61;Dels=0.00;FS=1.071;HaplotypeScore=2.8319;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=4.182;QD=17.34;ReadPosRankSum=-0.133;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,32:61:99:1086,0,615 -chr1 45538 . T C 2219.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.8319;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=1;QD=33.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2248,175,0 -chr1 45549 . G A 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.457;DP=67;Dels=0.00;FS=21.346;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=45.62;MQ0=1;MQRankSum=1.140;QD=2.58;ReadPosRankSum=0.504;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:58,9:67:99:201,0,1627 -chr1 45550 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.636;DP=67;Dels=0.00;FS=0.940;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=46.27;MQ0=1;MQRankSum=-4.933;QD=9.31;ReadPosRankSum=0.982;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,33:67:99:652,0,1160 -chr1 45576 . A T 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=86;Dels=0.00;FS=0.996;HaplotypeScore=31.9081;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.062;QD=5.30;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,26:86:99:484,0,1787 -chr1 45578 . A G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.189;DP=84;Dels=0.00;FS=6.011;HaplotypeScore=57.3640;MLEAC=1;MLEAF=0.500;MQ=44.80;MQ0=1;MQRankSum=-6.448;QD=10.99;ReadPosRankSum=-1.326;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,44:84:99:951,0,1314 -chr1 45586 . T C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=80;Dels=0.00;FS=1.341;HaplotypeScore=88.2105;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.105;QD=0.92;ReadPosRankSum=-0.165;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:102,0,2084 -chr1 45587 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=80;Dels=0.00;FS=1.232;HaplotypeScore=75.5755;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.092;QD=1.20;ReadPosRankSum=-0.086;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:124,0,2088 -chr1 45588 . A G 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=81;Dels=0.00;FS=1.248;HaplotypeScore=76.3642;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=1;MQRankSum=-4.082;QD=1.15;ReadPosRankSum=0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:67,14:81:99:121,0,2109 -chr1 45600 . G A 1328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=109;Dels=0.00;FS=1.699;HaplotypeScore=36.6790;MLEAC=1;MLEAF=0.500;MQ=42.25;MQ0=2;MQRankSum=-6.013;QD=12.19;ReadPosRankSum=0.815;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,63:109:99:1357,0,1334 -chr1 45609 . A C 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=114;Dels=0.00;FS=0.838;HaplotypeScore=28.9230;MLEAC=1;MLEAF=0.500;MQ=42.08;MQ0=2;MQRankSum=-1.161;QD=6.55;ReadPosRankSum=1.490;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,34:114:99:775,0,2078 -chr1 45619 . C T 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=119;Dels=0.00;FS=2.580;HaplotypeScore=3.6750;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=2;MQRankSum=-0.216;QD=7.02;ReadPosRankSum=1.214;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:83,36:119:99:864,0,1946 -chr1 45632 . G T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=119;Dels=0.00;FS=0.893;HaplotypeScore=6.6304;MLEAC=1;MLEAF=0.500;MQ=40.17;MQ0=2;MQRankSum=-5.708;QD=2.94;ReadPosRankSum=1.745;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,37:119:99:378,0,2346 -chr1 45659 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.317;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=71.6402;MLEAC=1;MLEAF=0.500;MQ=41.20;MQ0=3;MQRankSum=-6.632;QD=3.24;ReadPosRankSum=0.893;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,39:120:99:417,0,2397 -chr1 45660 . A G 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.966;DP=117;Dels=0.00;FS=2.575;HaplotypeScore=63.3294;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=3;MQRankSum=-1.543;QD=0.31;ReadPosRankSum=1.048;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:117:64:64,0,2593 -chr1 45663 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.724;DP=116;Dels=0.00;FS=2.578;HaplotypeScore=119.3449;MLEAC=1;MLEAF=0.500;MQ=41.26;MQ0=3;MQRankSum=-1.489;QD=0.24;ReadPosRankSum=1.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:116:56:56,0,2716 -chr1 45672 . T G 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=105;Dels=0.00;FS=0.751;HaplotypeScore=110.4878;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=2;MQRankSum=-5.196;QD=8.45;ReadPosRankSum=0.761;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,45:105:99:915,0,1759 -chr1 45673 . G A 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=105;Dels=0.00;FS=0.897;HaplotypeScore=111.2217;MLEAC=1;MLEAF=0.500;MQ=43.63;MQ0=2;MQRankSum=-5.747;QD=1.35;ReadPosRankSum=1.937;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,24:105:99:170,0,2516 -chr1 45679 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.082;DP=116;Dels=0.00;FS=2.067;HaplotypeScore=85.5662;MLEAC=1;MLEAF=0.500;MQ=43.87;MQ0=2;MQRankSum=-0.621;QD=3.21;ReadPosRankSum=-0.794;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,23:116:99:401,0,2219 -chr1 45694 . A G 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=125;Dels=0.00;FS=4.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.00;MQ0=2;MQRankSum=-5.132;QD=1.74;ReadPosRankSum=-0.229;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,25:125:99:246,0,3244 -chr1 45707 . T C 2311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=121;Dels=0.00;FS=6.874;HaplotypeScore=39.0259;MLEAC=1;MLEAF=0.500;MQ=45.33;MQ0=2;MQRankSum=-7.286;QD=19.11;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,87:121:99:2340,0,940 -chr1 45717 . G A 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.975;DP=109;Dels=0.00;FS=1.591;HaplotypeScore=73.3895;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=2;MQRankSum=-1.982;QD=6.89;ReadPosRankSum=2.664;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,43:109:99:779,0,1809 -chr1 45724 . C G 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=100;Dels=0.00;FS=0.957;HaplotypeScore=83.7585;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=2;MQRankSum=-1.008;QD=5.78;ReadPosRankSum=1.509;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,25:100:99:606,0,1819 -chr1 45725 . C T 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=98;Dels=0.00;FS=0.966;HaplotypeScore=96.3231;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=5.039;QD=4.35;ReadPosRankSum=-2.841;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,19:98:99:455,0,2414 -chr1 45727 . A G 3406.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=131.4140;MLEAC=2;MLEAF=1.00;MQ=46.96;MQ0=2;QD=34.41;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3435,274,0 -chr1 45728 . T C 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;DP=100;Dels=0.00;FS=12.270;HaplotypeScore=130.4542;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=-0.733;QD=1.80;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,13:100:99:208,0,2628 -chr1 45729 . A G 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.199;DP=98;Dels=0.00;FS=7.239;HaplotypeScore=143.0188;MLEAC=1;MLEAF=0.500;MQ=47.26;MQ0=2;MQRankSum=-2.286;QD=9.53;ReadPosRankSum=1.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,35:98:99:962,0,1812 -chr1 45733 . C T 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.767;DP=103;Dels=0.00;FS=11.158;HaplotypeScore=175.1243;MLEAC=1;MLEAF=0.500;MQ=45.48;MQ0=2;MQRankSum=-0.096;QD=2.07;ReadPosRankSum=2.500;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:90,13:103:99:241,0,2768 -chr1 45744 . A T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=97;Dels=0.00;FS=3.403;HaplotypeScore=141.3914;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=6;MQRankSum=-2.164;QD=0.15;ReadPosRankSum=0.983;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,11:97:43:43,0,2548 -chr1 45746 . C G 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.871;DP=98;Dels=0.00;FS=5.658;HaplotypeScore=144.7874;MLEAC=1;MLEAF=0.500;MQ=43.28;MQ0=6;MQRankSum=-2.422;QD=11.04;ReadPosRankSum=-1.217;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,41:98:99:1110,0,1505 -chr1 45749 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.332;DP=105;Dels=0.00;FS=20.438;HaplotypeScore=99.1311;MLEAC=1;MLEAF=0.500;MQ=42.61;MQ0=6;MQRankSum=-1.228;QD=0.58;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:93,12:105:89:89,0,2686 -chr1 45752 . C A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.973;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=60.4379;MLEAC=1;MLEAF=0.500;MQ=42.32;MQ0=7;MQRankSum=3.784;QD=2.22;ReadPosRankSum=3.512;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:91,16:107:99:266,0,2493 -chr1 45756 . T C 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=54.1966;MLEAC=1;MLEAF=0.500;MQ=41.83;MQ0=7;MQRankSum=3.711;QD=3.90;ReadPosRankSum=2.139;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,19:105:99:438,0,2316 -chr1 45774 . G A 2856.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=1.8661;MLEAC=2;MLEAF=1.00;MQ=40.57;MQ0=8;QD=29.15;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,98:98:99:2885,247,0 -chr1 45792 . A T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=73;Dels=0.00;FS=9.059;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.74;MQ0=7;MQRankSum=-2.340;QD=8.15;ReadPosRankSum=-0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,26:73:99:623,0,946 -chr1 45793 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=74;Dels=0.00;FS=6.479;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=-1.025;QD=10.97;ReadPosRankSum=-1.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,32:74:99:840,0,770 -chr1 45796 . T A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=73;Dels=0.03;FS=11.097;HaplotypeScore=57.0004;MLEAC=1;MLEAF=0.500;MQ=32.88;MQ0=7;MQRankSum=-0.761;QD=2.38;ReadPosRankSum=3.011;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,16:71:99:202,0,1418 -chr1 45803 . C T 2095.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=66.1329;MLEAC=2;MLEAF=1.00;MQ=33.59;MQ0=6;QD=27.58;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2124,183,0 -chr1 45826 . A T 1113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=78;Dels=0.01;FS=3.363;HaplotypeScore=5.1586;MLEAC=1;MLEAF=0.500;MQ=36.05;MQ0=3;MQRankSum=-3.121;QD=14.28;ReadPosRankSum=2.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,46:77:99:1142,0,798 -chr1 45844 . T A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.235;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=38.54;MQ0=3;MQRankSum=-3.089;QD=4.97;ReadPosRankSum=0.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,25:96:99:505,0,2123 -chr1 45863 . A T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.601;DP=97;Dels=0.00;FS=0.931;HaplotypeScore=2.8214;MLEAC=1;MLEAF=0.500;MQ=39.70;MQ0=1;MQRankSum=3.322;QD=5.27;ReadPosRankSum=-0.737;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,22:97:99:539,0,2180 -chr1 45895 . C T 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;DP=86;Dels=0.00;FS=3.221;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=40.11;MQ0=2;MQRankSum=2.945;QD=7.57;ReadPosRankSum=1.653;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:61,25:86:99:679,0,1779 -chr1 45899 . T G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=84;Dels=0.00;FS=5.870;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=39.85;MQ0=3;MQRankSum=-2.045;QD=4.13;ReadPosRankSum=-0.184;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,20:84:99:375,0,1957 -chr1 45911 . C T 1407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=77;Dels=0.00;FS=0.933;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.22;MQ0=3;MQRankSum=-3.291;QD=18.28;ReadPosRankSum=1.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,51:77:99:1436,0,660 -chr1 45928 . G A 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364;DP=63;Dels=0.00;FS=1.202;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-2.063;QD=3.84;ReadPosRankSum=-0.054;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,13:63:99:270,0,1333 -chr1 45929 . C G 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=63;Dels=0.00;FS=1.173;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-1.844;QD=3.39;ReadPosRankSum=0.603;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,15:63:99:242,0,1410 -chr1 45934 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=10.8117;MLEAC=1;MLEAF=0.500;MQ=38.27;MQ0=3;MQRankSum=-1.596;QD=3.36;ReadPosRankSum=0.489;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,14:55:99:213,0,1231 -chr1 45957 . T C 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=26;Dels=0.00;FS=2.754;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=3;MQRankSum=-0.385;QD=3.11;ReadPosRankSum=0.385;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,7:26:99:109,0,455 -chr1 45965 . T C 275.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.61;MQ0=2;QD=19.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,14:14:27:304,27,0 -chr1 45991 . T C 138.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.85;MQ0=1;QD=19.84;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:15:167,15,0 -chr1 46015 . T A 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.89;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:83:83,0,581 -chr1 46016 . G T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.96;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:85:85,0,588 -chr1 46017 . A G 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.40;MQ0=7;MQRankSum=-1.457;QD=0.72;ReadPosRankSum=1.386;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,4:33:52:52,0,712 -chr1 46033 . A C 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.857;DP=62;Dels=0.00;FS=17.444;HaplotypeScore=12.6635;MLEAC=1;MLEAF=0.500;MQ=30.48;MQ0=9;MQRankSum=0.683;QD=2.08;ReadPosRankSum=0.683;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,8:62:99:157,0,1251 -chr1 46036 . C T 1669.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=12.6635;MLEAC=2;MLEAF=1.00;MQ=29.79;MQ0=10;QD=25.69;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1698,141,0 -chr1 46051 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=90;Dels=0.00;FS=6.369;HaplotypeScore=23.7978;MLEAC=1;MLEAF=0.500;MQ=30.89;MQ0=10;MQRankSum=-1.053;QD=5.56;ReadPosRankSum=1.556;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,26:90:99:529,0,1416 -chr1 46062 . T A 1644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.702;DP=97;Dels=0.00;FS=0.875;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.34;MQ0=10;MQRankSum=2.289;QD=16.96;ReadPosRankSum=2.106;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,62:97:99:1673,0,454 -chr1 46064 . T C 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=99;Dels=0.00;FS=7.151;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=10;MQRankSum=-1.046;QD=0.26;ReadPosRankSum=-0.955;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:54:54,0,2051 -chr1 46073 . A T 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=18.4418;MLEAC=1;MLEAF=0.500;MQ=30.65;MQ0=10;MQRankSum=3.059;QD=15.41;ReadPosRankSum=3.428;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,64:111:99:1739,0,618 -chr1 46082 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=119;Dels=0.00;FS=2.762;HaplotypeScore=10.8856;MLEAC=1;MLEAF=0.500;MQ=30.51;MQ0=11;MQRankSum=-0.591;QD=0.29;ReadPosRankSum=1.598;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:105,14:119:63:63,0,2389 -chr1 46123 . T A 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=118;Dels=0.00;FS=2.620;HaplotypeScore=14.0204;MLEAC=1;MLEAF=0.500;MQ=29.74;MQ0=16;MQRankSum=0.492;QD=1.49;ReadPosRankSum=-1.118;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:204,0,2132 -chr1 46130 . G C 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.815;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=12.9254;MLEAC=1;MLEAF=0.500;MQ=28.94;MQ0=18;MQRankSum=2.438;QD=9.95;ReadPosRankSum=0.465;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:59,54:113:99:1153,0,946 -chr1 46134 . A C 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=28.45;MQ0=19;MQRankSum=3.071;QD=10.54;ReadPosRankSum=0.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,52:106:99:1146,0,745 -chr1 46151 . A C 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=29.0289;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=23;MQRankSum=2.003;QD=2.89;ReadPosRankSum=2.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,22:96:99:306,0,1339 -chr1 46158 . G C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=96;Dels=0.00;FS=1.341;HaplotypeScore=39.0149;MLEAC=1;MLEAF=0.500;MQ=26.29;MQ0=24;MQRankSum=1.288;QD=2.65;ReadPosRankSum=2.514;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,22:96:99:283,0,1187 -chr1 46169 . C A 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=33.7549;MLEAC=1;MLEAF=0.500;MQ=29.68;MQ0=25;MQRankSum=0.853;QD=1.55;ReadPosRankSum=-0.449;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,14:105:99:191,0,1752 -chr1 46178 . A G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=40.5352;MLEAC=1;MLEAF=0.500;MQ=29.80;MQ0=26;MQRankSum=1.065;QD=5.13;ReadPosRankSum=-0.715;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,32:106:99:572,0,1382 -chr1 46199 . T G 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.172;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=146.8097;MLEAC=1;MLEAF=0.500;MQ=35.49;MQ0=8;MQRankSum=0.538;QD=3.53;ReadPosRankSum=-0.275;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,17:90:99:346,0,1892 -chr1 46203 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=95;Dels=0.00;FS=4.713;HaplotypeScore=115.8313;MLEAC=1;MLEAF=0.500;MQ=36.73;MQ0=7;MQRankSum=2.951;QD=8.13;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,30:95:99:801,0,1544 -chr1 46204 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=99;Dels=0.00;FS=1.263;HaplotypeScore=104.3565;MLEAC=1;MLEAF=0.500;MQ=36.99;MQ0=7;MQRankSum=-3.158;QD=1.27;ReadPosRankSum=2.038;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,14:99:99:154,0,2379 -chr1 46209 . G C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=105;Dels=0.00;FS=2.148;HaplotypeScore=73.4158;MLEAC=1;MLEAF=0.500;MQ=37.74;MQ0=6;MQRankSum=-0.435;QD=4.08;ReadPosRankSum=1.073;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,22:105:99:457,0,2172 -chr1 46217 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=107;Dels=0.00;FS=7.349;HaplotypeScore=36.8004;MLEAC=1;MLEAF=0.500;MQ=38.39;MQ0=6;MQRankSum=2.982;QD=7.89;ReadPosRankSum=-0.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,33:107:99:872,0,1991 -chr1 46223 . A T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=110;Dels=0.00;FS=16.066;HaplotypeScore=84.6532;MLEAC=1;MLEAF=0.500;MQ=39.41;MQ0=4;MQRankSum=3.566;QD=7.08;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,30:110:99:807,0,2258 -chr1 46259 . A C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.583;DP=125;Dels=0.00;FS=8.544;HaplotypeScore=18.7174;MLEAC=1;MLEAF=0.500;MQ=39.29;MQ0=5;MQRankSum=-2.002;QD=5.90;ReadPosRankSum=0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:68,35:125:99:766,0,2032 -chr1 46279 . G T 1314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.148;DP=126;Dels=0.00;FS=16.583;HaplotypeScore=16.7188;MLEAC=1;MLEAF=0.500;MQ=36.95;MQ0=11;MQRankSum=-2.173;QD=10.43;ReadPosRankSum=1.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,64:126:99:1343,0,1687 -chr1 46288 . A T 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=25.9225;MLEAC=1;MLEAF=0.500;MQ=35.56;MQ0=13;MQRankSum=-0.037;QD=2.17;ReadPosRankSum=0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:103,21:124:99:297,0,2552 -chr1 46293 . T A 3320.77 . AC=2;AF=1.00;AN=2;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=27.7337;MLEAC=2;MLEAF=1.00;MQ=34.88;MQ0=13;QD=26.78;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,124:124:99:3349,268,0 -chr1 46297 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=123;Dels=0.00;FS=1.177;HaplotypeScore=28.4676;MLEAC=1;MLEAF=0.500;MQ=34.77;MQ0=13;MQRankSum=-1.404;QD=1.19;ReadPosRankSum=0.112;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,15:123:99:174,0,2572 -chr1 46303 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=113;Dels=0.00;FS=5.395;HaplotypeScore=31.8222;MLEAC=1;MLEAF=0.500;MQ=33.25;MQ0=13;MQRankSum=-0.279;QD=4.00;ReadPosRankSum=0.573;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,31:113:99:480,0,1952 -chr1 46311 . T C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=106;Dels=0.00;FS=4.629;HaplotypeScore=71.9889;MLEAC=1;MLEAF=0.500;MQ=31.67;MQ0=13;MQRankSum=-1.015;QD=2.43;ReadPosRankSum=1.472;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,25:106:99:286,0,1902 -chr1 46313 . T A 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=108;Dels=0.00;FS=12.679;HaplotypeScore=73.9836;MLEAC=1;MLEAF=0.500;MQ=31.59;MQ0=13;MQRankSum=-1.299;QD=2.52;ReadPosRankSum=0.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,23:108:99:300,0,1934 -chr1 46345 . G T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;DP=118;Dels=0.00;FS=1.369;HaplotypeScore=15.7222;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=12;MQRankSum=0.291;QD=2.25;ReadPosRankSum=1.341;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:95,23:118:99:294,0,1983 -chr1 46349 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;DP=129;Dels=0.00;FS=0.000;HaplotypeScore=20.2580;MLEAC=1;MLEAF=0.500;MQ=32.38;MQ0=11;MQRankSum=4.078;QD=2.87;ReadPosRankSum=-1.669;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:107,22:129:99:399,0,2225 -chr1 46360 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.738;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=144.3890;MLEAC=1;MLEAF=0.500;MQ=34.17;MQ0=10;MQRankSum=-0.032;QD=2.73;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:96,25:121:99:359,0,2284 -chr1 46365 . G T 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=86.2004;MLEAC=1;MLEAF=0.500;MQ=34.29;MQ0=10;MQRankSum=-0.261;QD=1.43;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:197,0,2403 -chr1 46370 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=121;Dels=0.00;FS=0.988;HaplotypeScore=85.2005;MLEAC=1;MLEAF=0.500;MQ=35.94;MQ0=9;MQRankSum=3.941;QD=2.91;ReadPosRankSum=0.376;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,21:121:99:380,0,2395 -chr1 46385 . A T 1987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=41.86;MQ0=1;MQRankSum=-4.706;QD=15.06;ReadPosRankSum=0.577;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,78:132:99:2016,0,1639 -chr1 46409 . G A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.697;DP=147;Dels=0.00;FS=5.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.328;QD=4.48;ReadPosRankSum=2.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:119,28:147:99:687,0,3761 -chr1 46413 . G A 5462.77 . AC=2;AF=1.00;AN=2;DP=150;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=1;QD=31.52;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,150:150:99:5491,421,0 -chr1 46441 . G A 5317.77 . AC=2;AF=1.00;AN=2;DP=134;Dels=0.00;FS=0.000;HaplotypeScore=24.9609;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=1;QD=30.22;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,134:134:99:5346,400,0 -chr1 46442 . A T 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=132;Dels=0.00;FS=6.626;HaplotypeScore=24.9609;MLEAC=1;MLEAF=0.500;MQ=46.74;MQ0=1;MQRankSum=0.945;QD=6.40;ReadPosRankSum=2.434;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,31:132:99:873,0,3591 -chr1 46448 . T C 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.670;DP=120;Dels=0.00;FS=1.884;HaplotypeScore=45.9537;MLEAC=1;MLEAF=0.500;MQ=46.81;MQ0=1;MQRankSum=-1.356;QD=4.39;ReadPosRankSum=0.293;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,23:120:99:555,0,3478 -chr1 46453 . T A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=109;Dels=0.00;FS=3.408;HaplotypeScore=1.9892;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=1;MQRankSum=-1.198;QD=4.26;ReadPosRankSum=1.024;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,20:109:99:493,0,3241 -chr1 46466 . T A 1384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.022;DP=98;Dels=0.00;FS=1.650;HaplotypeScore=38.9441;MLEAC=1;MLEAF=0.500;MQ=46.96;MQ0=1;MQRankSum=0.510;QD=14.13;ReadPosRankSum=0.930;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,46:98:99:1413,0,1799 -chr1 46486 . T A 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=62;Dels=0.00;FS=0.975;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=43.40;MQ0=1;MQRankSum=-0.195;QD=14.11;ReadPosRankSum=-0.137;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,29:62:99:903,0,1128 -chr1 46489 . A G 2225.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=42.98;MQ0=1;QD=30.18;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2254,175,0 -chr1 46505 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=39.03;MQ0=0;MQRankSum=1.388;QD=8.99;ReadPosRankSum=-1.130;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,8:24:99:244,0,502 -chr1 46511 . G C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=13;Dels=0.00;FS=2.920;HaplotypeScore=1.9890;MLEAC=1;MLEAF=0.500;MQ=36.55;MQ0=0;MQRankSum=0.592;QD=4.06;ReadPosRankSum=-1.099;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,3:13:81:81,0,328 -chr1 46521 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=33.95;MQ0=0;MQRankSum=-0.198;QD=2.13;ReadPosRankSum=0.198;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:5,2:7:43:43,0,159 -chr1 46524 . A C 63.23 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=2.9781;MLEAC=1;MLEAF=0.500;MQ=32.80;MQ0=0;QD=12.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:5:9:107,9,0 -chr1 46567 . T C 942.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.84;MQ0=0;QD=28.57;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:81:971,81,0 -chr1 46579 . T C 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.651;DP=54;Dels=0.00;FS=2.600;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=0;MQRankSum=-0.248;QD=8.00;ReadPosRankSum=-0.266;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,18:54:99:460,0,1017 -chr1 46608 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=97;Dels=0.00;FS=7.798;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=45.77;MQ0=1;MQRankSum=0.169;QD=6.28;ReadPosRankSum=0.458;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,27:97:99:637,0,2291 -chr1 46649 . C G 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=128;Dels=0.00;FS=5.797;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=1;MQRankSum=0.828;QD=4.14;ReadPosRankSum=-0.170;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,26:128:99:558,0,3425 -chr1 46661 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=1.8874;MLEAC=1;MLEAF=0.500;MQ=52.82;MQ0=1;MQRankSum=-1.890;QD=4.49;ReadPosRankSum=-0.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:98,25:123:99:580,0,3412 -chr1 46669 . T C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=71.8527;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=2;MQRankSum=-1.040;QD=2.79;ReadPosRankSum=0.046;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:94,17:111:99:338,0,3242 -chr1 46672 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.735;DP=101;Dels=0.00;FS=1.153;HaplotypeScore=51.8777;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=2;MQRankSum=0.285;QD=2.14;ReadPosRankSum=1.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,13:101:99:244,0,3052 -chr1 46675 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=49.8785;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=2;MQRankSum=0.732;QD=1.80;ReadPosRankSum=2.032;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,12:100:99:208,0,3050 -chr1 46676 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=65.8754;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=2;MQRankSum=0.553;QD=1.87;ReadPosRankSum=1.978;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:99:213,0,3001 -chr1 46677 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=103;Dels=0.00;FS=3.208;HaplotypeScore=64.9814;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=2;MQRankSum=-2.102;QD=4.91;ReadPosRankSum=0.977;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,24:103:99:534,0,2803 -chr1 46680 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=105;Dels=0.00;FS=3.142;HaplotypeScore=55.7727;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=2;MQRankSum=-1.393;QD=4.65;ReadPosRankSum=1.009;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,23:105:99:516,0,2857 -chr1 46706 . T A 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.654;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=2.7898;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=2;MQRankSum=0.757;QD=2.05;ReadPosRankSum=-0.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,17:91:99:215,0,2448 -chr1 46718 . A C 1001.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.273;DP=81;Dels=0.00;FS=1.893;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.582;QD=12.37;ReadPosRankSum=1.963;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,34:81:99:1030,0,1456 -chr1 46719 . A C 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.250;QD=3.16;ReadPosRankSum=-0.404;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,15:81:99:284,0,2191 -chr1 46726 . T C 2626.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=11.9384;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=2;QD=34.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:76:99:2655,202,0 -chr1 46731 . T C 2453.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=48.88;MQ0=2;QD=34.08;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2482,193,0 -chr1 46759 . C A 1490.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=9.8664;MLEAC=2;MLEAF=1.00;MQ=36.57;MQ0=2;QD=28.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1519,129,0 -chr1 46779 . T A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=47;Dels=0.00;FS=2.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=8;MQRankSum=-1.409;QD=0.34;ReadPosRankSum=-0.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,14:47:44:44,0,779 -chr1 46829 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=28.31;MQ0=9;MQRankSum=-1.417;QD=3.18;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:165,0,685 -chr1 46863 . T A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6918;MLEAC=1;MLEAF=0.500;MQ=34.16;MQ0=4;MQRankSum=1.021;QD=3.19;ReadPosRankSum=-0.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,10:31:99:127,0,637 -chr1 46875 . C T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=0.391;QD=7.75;ReadPosRankSum=0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:222,0,386 -chr1 46877 . A G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.036;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=-0.391;QD=7.71;ReadPosRankSum=0.675;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:221,0,382 -chr1 46911 . T C 225.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.295;QD=11.88;ReadPosRankSum=1.120;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,13:19:99:254,0,170 -chr1 46912 . T C 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.059;QD=7.36;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:168,0,256 -chr1 46921 . A T 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=1.120;QD=6.94;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:160,0,232 -chr1 46929 . T C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=2.9987;MLEAC=1;MLEAF=0.500;MQ=30.25;MQ0=4;MQRankSum=1.826;QD=1.36;ReadPosRankSum=-1.396;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,2:16:50:50,0,263 -chr1 46930 . T C 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.382;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=0.382;QD=2.05;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,3:15:59:59,0,224 -chr1 46932 . T G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=-0.278;QD=10.05;ReadPosRankSum=0.597;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,11:15:99:179,0,100 -chr1 47124 . A G 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.189;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=2.616;QD=3.49;ReadPosRankSum=-0.713;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,5:30:99:133,0,417 -chr1 47130 . C A 109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=-0.972;QD=3.54;ReadPosRankSum=-0.417;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,8:31:99:138,0,432 -chr1 47133 . A T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.968;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=15.5825;MLEAC=1;MLEAF=0.500;MQ=29.36;MQ0=5;MQRankSum=2.905;QD=5.37;ReadPosRankSum=-1.743;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,7:32:99:200,0,418 -chr1 47143 . G A 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.890;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.6961;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.890;QD=0.78;ReadPosRankSum=1.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,3:33:54:54,0,575 -chr1 47144 . A G 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.060;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.9886;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.440;QD=17.39;ReadPosRankSum=-0.420;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,26:33:45:602,0,45 -chr1 47176 . T C 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.24;MQ0=6;MQRankSum=-3.114;QD=8.56;ReadPosRankSum=-0.467;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,20:32:99:302,0,299 -chr1 47177 . G A 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=6;MQRankSum=0.027;QD=6.93;ReadPosRankSum=0.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,11:31:99:243,0,342 -chr1 47200 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.35;MQ0=1;MQRankSum=0.312;QD=7.13;ReadPosRankSum=1.954;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,7:14:99:128,0,187 -chr1 47230 . T A 178.8 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=19.08;MQ0=3;QD=9.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:21:207,21,0 -chr1 47234 . T C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.58;MQ0=3;MQRankSum=-1.721;QD=2.61;ReadPosRankSum=1.721;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,13:21:83:83,0,132 -chr1 47250 . G A 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.640;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=5.7510;MLEAC=1;MLEAF=0.500;MQ=21.76;MQ0=5;MQRankSum=-1.456;QD=2.27;ReadPosRankSum=0.646;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,22:66:99:178,0,749 -chr1 47261 . A G 1410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=6.7299;MLEAC=1;MLEAF=0.500;MQ=24.69;MQ0=5;MQRankSum=-5.094;QD=13.44;ReadPosRankSum=1.015;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,92:105:99:1439,0,288 -chr1 47285 . A T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.781;DP=169;Dels=0.00;FS=25.466;HaplotypeScore=47.9098;MLEAC=1;MLEAF=0.500;MQ=25.11;MQ0=7;MQRankSum=-4.336;QD=4.42;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,68:169:99:776,0,2136 -chr1 47298 . G A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=190;Dels=0.00;FS=15.234;HaplotypeScore=62.4649;MLEAC=1;MLEAF=0.500;MQ=25.20;MQ0=9;MQRankSum=0.954;QD=0.07;ReadPosRankSum=-0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:171,18:190:41:41,0,3305 -chr1 47310 . A T 485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.824;DP=205;Dels=0.00;FS=0.000;HaplotypeScore=49.7328;MLEAC=1;MLEAF=0.500;MQ=25.09;MQ0=7;MQRankSum=4.634;QD=2.37;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:176,29:205:99:514,0,2996 -chr1 47323 . G A 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.212;DP=211;Dels=0.00;FS=17.070;HaplotypeScore=51.7365;MLEAC=1;MLEAF=0.500;MQ=25.41;MQ0=8;MQRankSum=-0.372;QD=4.96;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:139,72:211:99:1074,0,2488 -chr1 47338 . C T 938.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.180;DP=186;Dels=0.02;FS=12.473;HaplotypeScore=79.8806;MLEAC=1;MLEAF=0.500;MQ=25.59;MQ0=8;MQRankSum=-2.645;QD=5.05;ReadPosRankSum=-1.238;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:110,73:183:99:967,0,2144 -chr1 47343 . A C 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.678;DP=175;Dels=0.00;FS=24.414;HaplotypeScore=63.4079;MLEAC=1;MLEAF=0.500;MQ=25.75;MQ0=8;MQRankSum=-4.741;QD=1.42;ReadPosRankSum=-2.918;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:123,52:175:99:276,0,2689 -chr1 47371 . T C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=89;Dels=0.00;FS=1.351;HaplotypeScore=13.6568;MLEAC=1;MLEAF=0.500;MQ=24.59;MQ0=7;MQRankSum=-0.275;QD=11.91;ReadPosRankSum=-0.593;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,70:89:99:1088,0,261 -chr1 47393 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=52;Dels=0.00;FS=11.083;HaplotypeScore=2.6277;MLEAC=1;MLEAF=0.500;MQ=22.57;MQ0=6;MQRankSum=-1.494;QD=0.31;ReadPosRankSum=1.210;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,11:52:44:44,0,511 -chr1 47428 . T C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.940;DP=69;Dels=0.00;FS=2.933;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=23.55;MQ0=5;MQRankSum=3.350;QD=4.91;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,22:69:99:367,0,707 -chr1 47434 . T C 785.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.090;DP=72;Dels=0.00;FS=5.763;HaplotypeScore=21.1457;MLEAC=1;MLEAF=0.500;MQ=23.17;MQ0=5;MQRankSum=-4.249;QD=10.91;ReadPosRankSum=1.041;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,57:72:99:814,0,307 -chr1 47443 . G A 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=18.3434;MLEAC=1;MLEAF=0.500;MQ=20.97;MQ0=15;MQRankSum=-0.420;QD=0.53;ReadPosRankSum=1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,18:99:81:81,0,1206 -chr1 47486 . T C 1453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;DP=155;Dels=0.00;FS=0.000;HaplotypeScore=12.8061;MLEAC=1;MLEAF=0.500;MQ=22.09;MQ0=28;MQRankSum=-5.676;QD=9.38;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,119:155:99:1482,0,780 -chr1 47491 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=17.2378;MLEAC=1;MLEAF=0.500;MQ=22.27;MQ0=26;MQRankSum=5.308;QD=3.06;ReadPosRankSum=-1.409;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:133,23:156:99:506,0,1813 -chr1 47535 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=93;Dels=0.02;FS=0.000;HaplotypeScore=38.1338;MLEAC=1;MLEAF=0.500;MQ=21.13;MQ0=22;MQRankSum=2.066;QD=3.23;ReadPosRankSum=1.772;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,16:91:99:329,0,900 -chr1 47567 . G A 567.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.580;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=4.7649;MLEAC=2;MLEAF=1.00;MQ=23.23;MQ0=4;MQRankSum=0.223;QD=17.74;ReadPosRankSum=-1.561;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:6,26:32:31:596,31,0 -chr1 47584 . T C 27.75 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.33;MQ0=4;QD=4.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,2:6:6:55,6,0 -chr1 47788 . G A 57.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.406;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.71;MQ0=14;MQRankSum=1.537;QD=2.86;ReadPosRankSum=0.406;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:17,3:20:9:85,9,0 -chr1 47807 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.86;MQ0=12;MQRankSum=-1.709;QD=0.70;ReadPosRankSum=-2.534;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,18:27:47:47,0,128 -chr1 47841 . C A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=15.69;MQ0=10;MQRankSum=0.024;QD=2.26;ReadPosRankSum=0.315;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:38:99:114,0,159 -chr1 47868 . A G 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=14.6837;MLEAC=1;MLEAF=0.500;MQ=16.29;MQ0=5;MQRankSum=0.408;QD=1.05;ReadPosRankSum=0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,10:33:63:63,0,165 -chr1 47905 . T C 76.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.123;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=14.10;MQ0=0;MQRankSum=-0.919;QD=4.47;ReadPosRankSum=1.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,16:17:12:104,12,0 -chr1 47908 . G C 76.03 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.35;MQ0=0;QD=5.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,15:15:12:104,12,0 -chr1 48010 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.5644;MLEAC=1;MLEAF=0.500;MQ=17.06;MQ0=4;MQRankSum=1.490;QD=1.24;ReadPosRankSum=1.149;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,5:32:68:68,0,115 -chr1 48044 . T C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.952;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=15.75;MQ0=6;MQRankSum=0.905;QD=2.20;ReadPosRankSum=1.323;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,12:34:99:103,0,101 -chr1 48062 . T C 149.84 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.286;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=16.25;MQ0=3;MQRankSum=1.884;QD=5.99;ReadPosRankSum=0.171;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,21:25:18:178,18,0 -chr1 48067 . T C 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.033;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=16.25;MQ0=3;MQRankSum=-0.560;QD=0.99;ReadPosRankSum=-0.033;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,11:25:53:53,0,86 -chr1 48077 . G A 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=11.66;MQ0=2;MQRankSum=0.000;QD=0.65;ReadPosRankSum=1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,5:16:15:38,0,15 -chr1 48103 . C T 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.365;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=13.51;MQ0=0;MQRankSum=0.000;QD=1.03;ReadPosRankSum=1.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,4:10:15:38,0,15 -chr1 69651 . C A 54.28 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.77;MQ0=1;QD=6.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:9:82,9,0 -chr1 69661 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0 -chr1 69674 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0 -chr1 69693 . C G 54.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.747;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.15;MQ0=2;MQRankSum=0.747;QD=5.43;ReadPosRankSum=0.747;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,9:10:9:82,9,0 -chr1 69699 . C T 41.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.03;MQ0=2;MQRankSum=-0.762;QD=3.81;ReadPosRankSum=1.666;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,9:11:15:70,0,15 -chr1 69764 . A G 449.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=37;Dels=0.00;FS=9.031;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=23.29;MQ0=17;MQRankSum=2.126;QD=12.15;ReadPosRankSum=0.047;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:7:477,0,7 -chr1 69840 . G A 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.6917;MLEAC=1;MLEAF=0.500;MQ=29.33;MQ0=7;MQRankSum=-2.507;QD=16.16;ReadPosRankSum=0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,31:36:55:610,0,55 -chr1 69869 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.277;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.44;MQ0=9;MQRankSum=-2.380;QD=0.76;ReadPosRankSum=1.273;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,11:46:63:63,0,767 -chr1 69912 . A G 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.049;DP=89;Dels=0.00;FS=2.410;HaplotypeScore=43.2151;MLEAC=1;MLEAF=0.500;MQ=28.97;MQ0=20;MQRankSum=-2.202;QD=0.85;ReadPosRankSum=-1.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,18:89:99:104,0,1176 -chr1 69914 . T A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=89;Dels=0.00;FS=2.466;HaplotypeScore=31.1187;MLEAC=1;MLEAF=0.500;MQ=28.72;MQ0=20;MQRankSum=-2.123;QD=0.55;ReadPosRankSum=-0.877;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,15:89:77:77,0,1075 -chr1 69917 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.757;DP=93;Dels=0.00;FS=4.107;HaplotypeScore=21.6983;MLEAC=1;MLEAF=0.500;MQ=28.07;MQ0=21;MQRankSum=6.024;QD=8.30;ReadPosRankSum=3.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,33:93:99:800,0,323 -chr1 69936 . T C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.032;DP=99;Dels=0.00;FS=7.704;HaplotypeScore=13.1641;MLEAC=1;MLEAF=0.500;MQ=29.72;MQ0=22;MQRankSum=-2.828;QD=0.58;ReadPosRankSum=-0.226;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,24:99:86:86,0,1391 -chr1 69952 . G A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=98;Dels=0.00;FS=10.410;HaplotypeScore=7.2476;MLEAC=1;MLEAF=0.500;MQ=31.15;MQ0=22;MQRankSum=-3.094;QD=1.13;ReadPosRankSum=1.550;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,23:98:99:139,0,1447 -chr1 70044 . T C 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.831;DP=64;Dels=0.00;FS=17.302;HaplotypeScore=1.4972;MLEAC=1;MLEAF=0.500;MQ=39.43;MQ0=5;MQRankSum=-6.056;QD=6.00;ReadPosRankSum=-3.773;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,29:64:99:412,0,1246 -chr1 70061 . A T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=133;Dels=0.00;FS=7.265;HaplotypeScore=20.7708;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=7;MQRankSum=-0.379;QD=2.95;ReadPosRankSum=-1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,25:133:99:420,0,2776 -chr1 70083 . T A 2582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=229;Dels=0.00;FS=16.594;HaplotypeScore=75.2516;MLEAC=1;MLEAF=0.500;MQ=35.83;MQ0=10;MQRankSum=-6.665;QD=11.28;ReadPosRankSum=-0.109;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,97:229:99:2611,0,1502 -chr1 70125 . G T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=250;Dels=0.00;FS=22.446;HaplotypeScore=27.9709;MLEAC=1;MLEAF=0.500;MQ=34.24;MQ0=12;MQRankSum=6.009;QD=2.97;ReadPosRankSum=-1.398;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:216,34:250:99:771,0,5278 -chr1 70150 . A T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=239;Dels=0.00;FS=21.127;HaplotypeScore=368.1172;MLEAC=1;MLEAF=0.500;MQ=33.77;MQ0=11;MQRankSum=1.765;QD=9.26;ReadPosRankSum=0.325;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:156,83:239:99:2242,0,3406 -chr1 70216 . A C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=108;Dels=0.00;FS=9.502;HaplotypeScore=1.7297;MLEAC=1;MLEAF=0.500;MQ=29.27;MQ0=14;MQRankSum=-0.174;QD=5.67;ReadPosRankSum=-0.831;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,38:108:99:641,0,1179 -chr1 70250 . G A 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.529;DP=135;Dels=0.00;FS=13.533;HaplotypeScore=55.9122;MLEAC=1;MLEAF=0.500;MQ=30.56;MQ0=13;MQRankSum=-4.770;QD=12.90;ReadPosRankSum=-1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,110:135:99:1770,0,694 -chr1 70260 . T A 1494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=159;Dels=0.00;FS=11.693;HaplotypeScore=60.0297;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=12;MQRankSum=3.229;QD=9.40;ReadPosRankSum=-1.725;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,62:159:99:1523,0,1679 -chr1 70302 . G C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.849;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=38.7004;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=27;MQRankSum=2.779;QD=0.09;ReadPosRankSum=-0.062;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:234,14:250:51:51,0,4942 -chr1 70324 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.298;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=36;MQRankSum=-1.206;QD=1.62;ReadPosRankSum=-0.310;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:212,38:250:99:433,0,4781 -chr1 70330 . T C 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;DP=247;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=29.87;MQ0=39;MQRankSum=4.681;QD=4.35;ReadPosRankSum=0.440;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:201,45:247:99:1102,0,3835 -chr1 70352 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.133;DP=231;Dels=0.00;FS=0.000;HaplotypeScore=38.6164;MLEAC=1;MLEAF=0.500;MQ=29.11;MQ0=43;MQRankSum=-0.256;QD=4.09;ReadPosRankSum=1.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:164,67:231:99:973,0,3380 -chr1 70354 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=228;Dels=0.00;FS=0.000;HaplotypeScore=36.7869;MLEAC=1;MLEAF=0.500;MQ=28.93;MQ0=43;MQRankSum=0.019;QD=2.38;ReadPosRankSum=1.450;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:181,47:228:99:571,0,3676 -chr1 70360 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;DP=214;Dels=0.00;FS=0.000;HaplotypeScore=31.5616;MLEAC=1;MLEAF=0.500;MQ=28.34;MQ0=42;MQRankSum=0.615;QD=3.26;ReadPosRankSum=0.618;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:163,51:214:99:725,0,3164 -chr1 70400 . A G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.22;MQ0=0;MQRankSum=-1.795;QD=15.51;ReadPosRankSum=0.535;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,14:23:99:385,0,241 -chr1 70409 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=-2.381;QD=13.95;ReadPosRankSum=0.958;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,14:25:99:377,0,326 -chr1 70454 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=38;Dels=0.00;FS=4.521;HaplotypeScore=2.5142;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=-4.169;QD=10.55;ReadPosRankSum=0.264;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,17:38:99:429,0,678 -chr1 70455 . G C 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=4.198;QD=16.99;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,21:38:99:674,0,427 -chr1 70467 . G A 1182.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.7803;MLEAC=2;MLEAF=1.00;MQ=47.26;MQ0=0;QD=33.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1211,99,0 -chr1 70476 . C T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=28;Dels=0.00;FS=1.583;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=-4.339;QD=6.71;ReadPosRankSum=-2.613;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,10:28:99:216,0,597 -chr1 70481 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.212;DP=29;Dels=0.00;FS=3.696;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.39;MQ0=0;MQRankSum=-4.266;QD=5.23;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:180,0,720 -chr1 70487 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=31;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=0;MQRankSum=-3.992;QD=3.25;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,7:31:99:129,0,866 -chr1 70488 . G C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.493;DP=30;Dels=0.00;FS=12.454;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=-3.759;QD=3.33;ReadPosRankSum=-0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,6:30:99:128,0,824 -chr1 70508 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=31;Dels=0.00;FS=8.915;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.10;MQ0=0;MQRankSum=3.902;QD=21.83;ReadPosRankSum=2.250;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,20:31:99:705,0,304 -chr1 70513 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.673;DP=29;Dels=0.00;FS=6.306;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=0;MQRankSum=-3.512;QD=7.10;ReadPosRankSum=-0.966;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:234,0,716 -chr1 70534 . A T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.500;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=0;MQRankSum=4.082;QD=15.43;ReadPosRankSum=1.082;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:661,0,570 -chr1 70544 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.74;MQ0=0;MQRankSum=-3.969;QD=13.14;ReadPosRankSum=0.202;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,24:47:99:646,0,706 -chr1 70546 . C G 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-3.859;QD=14.29;ReadPosRankSum=0.413;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,25:48:99:714,0,704 -chr1 70565 . A G 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.21;MQ0=0;MQRankSum=-2.949;QD=14.94;ReadPosRankSum=2.436;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:805,0,789 -chr1 70576 . T C 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.260;DP=58;Dels=0.00;FS=5.843;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.49;MQ0=0;MQRankSum=-3.297;QD=14.46;ReadPosRankSum=2.442;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,29:58:99:867,0,930 -chr1 70628 . T G 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.810;DP=62;Dels=0.00;FS=3.540;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-0.331;QD=16.09;ReadPosRankSum=0.416;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,32:62:99:1026,0,961 -chr1 70637 . G A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=57;Dels=0.00;FS=1.010;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=53.93;MQ0=0;MQRankSum=0.813;QD=17.19;ReadPosRankSum=-0.748;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,30:57:99:1008,0,828 -chr1 70655 . A G 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=53;Dels=0.00;FS=1.090;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-0.769;QD=16.79;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:53:99:918,0,834 -chr1 70662 . T G 2101.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=56.72;MQ0=0;QD=34.63;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2130,160,0 -chr1 70684 . C T 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=57;Dels=0.00;FS=3.772;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=1;MQRankSum=1.273;QD=17.59;ReadPosRankSum=-0.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1031,0,872 -chr1 70716 . A G 976.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.361;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=1;MQRankSum=-0.680;QD=16.01;ReadPosRankSum=-0.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1005,0,945 -chr1 70722 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=64;Dels=0.00;FS=0.968;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=1;MQRankSum=-0.310;QD=14.48;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,30:64:99:955,0,1044 -chr1 70732 . T G 1039.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=0.419;QD=16.25;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1068,0,1033 -chr1 70757 . A G 1003.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=57;Dels=0.00;FS=2.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=2;MQRankSum=0.704;QD=17.61;ReadPosRankSum=-0.908;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1032,0,802 -chr1 70801 . T C 1321.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.33;MQ0=1;QD=31.86;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1350,102,0 -chr1 70805 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.701;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=-0.638;QD=11.39;ReadPosRankSum=3.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:427,0,704 -chr1 70806 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=3.192;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,14:36:99:431,0,755 -chr1 70808 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=1;MQRankSum=-0.461;QD=11.99;ReadPosRankSum=2.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,14:34:99:436,0,682 -chr1 70814 . A T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=1;MQRankSum=-0.281;QD=14.22;ReadPosRankSum=1.333;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,779 -chr1 70860 . G C 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.732;QD=15.72;ReadPosRankSum=-0.025;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,28:55:99:893,0,931 -chr1 70872 . A T 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.806;QD=14.49;ReadPosRankSum=-0.247;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,28:57:99:854,0,1019 -chr1 70927 . T A 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.885;QD=15.03;ReadPosRankSum=0.833;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:840,0,984 -chr1 70928 . C T 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.173;QD=14.92;ReadPosRankSum=0.642;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:834,0,975 -chr1 70958 . G A 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=57;Dels=0.00;FS=1.019;HaplotypeScore=3.9961;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.008;QD=15.52;ReadPosRankSum=-0.855;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,27:57:99:913,0,1033 -chr1 70978 . A C 1879.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.75;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1908,144,0 -chr1 71024 . T A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;QD=10.97;ReadPosRankSum=0.418;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,15:38:99:445,0,742 -chr1 71043 . A G 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=38;Dels=0.00;FS=1.271;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.530;QD=10.86;ReadPosRankSum=-0.257;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,14:38:99:441,0,841 -chr1 71062 . G A 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=39;Dels=0.00;FS=9.774;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.61;MQ0=0;MQRankSum=-1.775;QD=10.92;ReadPosRankSum=-1.342;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,15:39:99:454,0,819 -chr1 71078 . A G 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=46;Dels=0.00;FS=9.879;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-2.684;QD=7.15;ReadPosRankSum=1.952;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,13:46:99:357,0,1152 -chr1 71081 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=45;Dels=0.00;FS=9.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-2.992;QD=7.59;ReadPosRankSum=1.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,13:45:99:370,0,1120 -chr1 71151 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=48;Dels=0.00;FS=6.211;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.755;QD=14.79;ReadPosRankSum=0.962;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:738,0,906 -chr1 71164 . T G 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=52;Dels=0.00;FS=5.816;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.829;QD=13.75;ReadPosRankSum=2.635;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,23:52:99:743,0,987 -chr1 71175 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.190;DP=49;Dels=0.00;FS=8.135;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.410;QD=15.79;ReadPosRankSum=2.570;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,24:49:99:802,0,806 -chr1 71183 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=50;Dels=0.00;FS=5.868;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=-0.740;QD=13.42;ReadPosRankSum=3.290;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:699,0,927 -chr1 71188 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=50;Dels=0.00;FS=4.061;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=-1.246;QD=13.50;ReadPosRankSum=2.647;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:703,0,954 -chr1 71222 . A C 1672.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.6203;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1701,129,0 -chr1 71229 . C T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.588;QD=9.33;ReadPosRankSum=-2.495;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,14:42:99:420,0,1008 -chr1 71244 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.527;QD=4.99;ReadPosRankSum=-1.716;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,8:37:99:213,0,1037 -chr1 71245 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-3.757;QD=4.10;ReadPosRankSum=-1.239;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,7:36:99:176,0,1059 -chr1 71254 . G T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-3.568;QD=1.91;ReadPosRankSum=-0.412;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,5:36:97:97,0,1070 -chr1 71258 . C T 1176.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=34.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1205,99,0 -chr1 71280 . T C 924.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:75:953,75,0 -chr1 71284 . T C 956.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:985,78,0 -chr1 71319 . G A 770.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:799,63,0 -chr1 71344 . G C 750.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:779,60,0 -chr1 71359 . G T 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=32;Dels=0.00;FS=18.730;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=8.59;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:303,0,699 -chr1 71365 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=15.204;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.18;MQ0=0;MQRankSum=-4.593;QD=9.83;ReadPosRankSum=-1.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:323,0,626 -chr1 71371 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=34;Dels=0.00;FS=14.526;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.775;QD=8.11;ReadPosRankSum=0.414;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:304,0,729 -chr1 71381 . C T 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=32;Dels=0.00;FS=11.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=9.18;ReadPosRankSum=2.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:322,0,668 -chr1 71388 . T C 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=35;Dels=0.00;FS=18.303;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-4.813;QD=8.08;ReadPosRankSum=3.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:311,0,784 -chr1 71570 . G A 897.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.40;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:926,69,0 -chr1 71608 . A G 632.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.26;MQ0=0;QD=28.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:661,51,0 -chr1 71631 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.385;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.055;QD=11.37;ReadPosRankSum=-2.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:301,0,519 -chr1 71646 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=21;Dels=0.00;FS=9.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-3.873;QD=13.42;ReadPosRankSum=-0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:310,0,392 -chr1 71649 . C T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=20;Dels=0.00;FS=10.263;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-3.799;QD=14.19;ReadPosRankSum=-0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,9:20:99:312,0,385 -chr1 71668 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.732;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.94;ReadPosRankSum=2.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:181,0,541 -chr1 71670 . C T 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.518;DP=21;Dels=0.00;FS=12.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-3.542;QD=7.42;ReadPosRankSum=2.997;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:184,0,526 -chr1 71673 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.72;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:176,0,563 -chr1 71675 . T C 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.63;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:174,0,568 -chr1 71676 . A G 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.455;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-3.606;QD=5.99;ReadPosRankSum=3.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:166,0,592 -chr1 71693 . T G 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.595;DP=27;Dels=0.00;FS=8.671;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-3.703;QD=4.03;ReadPosRankSum=1.895;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:137,0,745 -chr1 71715 . A T 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=27.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0 -chr1 71716 . A T 611.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=32.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:640,48,0 -chr1 71717 . A T 625.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=35.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:654,48,0 -chr1 71718 . A T 704.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=28.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:733,54,0 -chr1 71734 . G A 950.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.031;DP=49;Dels=0.00;FS=6.300;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=2.206;QD=19.40;ReadPosRankSum=2.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:979,0,585 -chr1 71751 . T C 1954.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.88;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1983,147,0 -chr1 71752 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.360;DP=52;Dels=0.00;FS=8.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=1;MQRankSum=-0.751;QD=11.90;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:647,0,1034 -chr1 71768 . T G 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210;DP=50;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=0.630;QD=13.48;ReadPosRankSum=1.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:702,0,834 -chr1 71769 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=6.329;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-0.010;QD=13.47;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,24:48:99:675,0,839 -chr1 71772 . C T 1772.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=58.12;MQ0=0;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1801,135,0 -chr1 71809 . A C 2024.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=1;QD=30.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2053,153,0 -chr1 71829 . C A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=56;Dels=0.00;FS=2.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=1;MQRankSum=0.563;QD=19.05;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1095,0,684 -chr1 71834 . T C 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=51;Dels=0.00;FS=2.568;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=1;MQRankSum=0.212;QD=20.49;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,33:51:99:1073,0,570 -chr1 71853 . T C 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=55.00;MQ0=1;MQRankSum=-0.422;QD=19.24;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:971,0,612 -chr1 71859 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=49;Dels=0.00;FS=1.079;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=1;MQRankSum=-1.148;QD=16.89;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:856,0,696 -chr1 71860 . A T 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.606;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=1;MQRankSum=-0.374;QD=17.77;ReadPosRankSum=1.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:881,0,668 -chr1 71878 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.614;DP=44;Dels=0.00;FS=2.696;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=1;MQRankSum=-1.741;QD=16.99;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:776,0,611 -chr1 71879 . G T 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.817;DP=45;Dels=0.00;FS=2.750;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.60;MQ0=1;MQRankSum=-1.880;QD=16.79;ReadPosRankSum=1.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:784,0,584 -chr1 71900 . G A 544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=26.2859;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=0.829;QD=13.97;ReadPosRankSum=-0.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:573,0,657 -chr1 71921 . G C 513.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.24;MQ0=0;QD=27.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:542,42,0 -chr1 71950 . T A 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=28;Dels=0.00;FS=21.924;HaplotypeScore=4.3987;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=2;MQRankSum=-0.462;QD=3.24;ReadPosRankSum=-1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:119,0,331 -chr1 71973 . C A 115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=5.0534;MLEAC=1;MLEAF=0.500;MQ=13.29;MQ0=15;MQRankSum=2.752;QD=1.90;ReadPosRankSum=3.058;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:54,7:61:75:144,0,75 -chr1 71995 . C T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.495;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=22.9908;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=18;MQRankSum=2.453;QD=1.44;ReadPosRankSum=3.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:66,8:74:99:135,0,173 -chr1 72037 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.0800;MLEAC=1;MLEAF=0.500;MQ=11.16;MQ0=17;MQRankSum=2.289;QD=0.63;ReadPosRankSum=2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:61,2:63:68:68,0,74 -chr1 72059 . T C 106.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.241;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.7351;MLEAC=2;MLEAF=1.00;MQ=11.90;MQ0=9;MQRankSum=1.061;QD=2.65;ReadPosRankSum=-2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:9,31:40:12:134,12,0 -chr1 72137 . C T 135.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.983;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=6;MQRankSum=3.138;QD=5.63;ReadPosRankSum=0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:16,7:24:12:163,12,0 -chr1 72198 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.408;DP=34;Dels=0.03;FS=0.000;HaplotypeScore=32.2822;MLEAC=1;MLEAF=0.500;MQ=18.40;MQ0=8;MQRankSum=0.642;QD=0.79;ReadPosRankSum=-0.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,3:33:55:55,0,194 -chr1 72220 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.1644;MLEAC=1;MLEAF=0.500;MQ=16.77;MQ0=8;MQRankSum=2.009;QD=1.02;ReadPosRankSum=2.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,3:33:62:62,0,141 -chr1 72245 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=1.052;QD=0.99;ReadPosRankSum=-1.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,3:30:58:58,0,156 -chr1 72246 . G T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.144;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=2.261;QD=0.99;ReadPosRankSum=-0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,2:30:58:58,0,154 -chr1 72269 . T C 18.83 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=23;Dels=0.00;FS=4.771;HaplotypeScore=5.5051;MLEAC=1;MLEAF=0.500;MQ=11.28;MQ0=6;MQRankSum=-0.537;QD=0.82;ReadPosRankSum=2.293;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,7:23:39:47,0,39 -chr1 72271 . T C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=22;Dels=0.00;FS=4.771;HaplotypeScore=4.7711;MLEAC=1;MLEAF=0.500;MQ=11.53;MQ0=6;MQRankSum=1.799;QD=0.51;ReadPosRankSum=-1.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,10:22:39:39,0,47 -chr1 72309 . T G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=9.6153;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=2.041;QD=2.45;ReadPosRankSum=-0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:65:65,0,114 -chr1 72313 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.788;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=12.8714;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=-1.000;QD=4.38;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:6,9:15:86:94,0,86 -chr1 72362 . A G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.15;MQ0=4;MQRankSum=0.000;QD=3.98;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,6:14:61:84,0,61 -chr1 72457 . T G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.362;DP=19;Dels=0.00;FS=3.979;HaplotypeScore=10.4309;MLEAC=1;MLEAF=0.500;MQ=16.41;MQ0=1;MQRankSum=-0.453;QD=0.68;ReadPosRankSum=2.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,8:19:41:41,0,92 -chr1 72490 . A G 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=17.81;MQ0=2;MQRankSum=2.538;QD=5.57;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,11:24:54:162,0,54 -chr1 72511 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.336;DP=23;Dels=0.00;FS=3.424;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=21.05;MQ0=2;MQRankSum=2.216;QD=0.61;ReadPosRankSum=-2.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,2:23:42:42,0,231 -chr1 72546 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=18;Dels=0.00;FS=3.010;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=22.48;MQ0=2;MQRankSum=2.143;QD=0.77;ReadPosRankSum=0.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:18:42:42,0,183 -chr1 72554 . C T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=24.02;MQ0=2;MQRankSum=2.073;QD=1.59;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:52:52,0,163 -chr1 72558 . C T 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4964;MLEAC=1;MLEAF=0.500;MQ=22.45;MQ0=2;MQRankSum=0.289;QD=1.91;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,4:14:55:55,0,130 -chr1 72562 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=12;Dels=0.00;FS=8.751;HaplotypeScore=4.2846;MLEAC=1;MLEAF=0.500;MQ=22.65;MQ0=2;MQRankSum=1.271;QD=2.23;ReadPosRankSum=1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,2:12:55:55,0,77 -chr1 72602 . G A 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=19;Dels=0.00;FS=10.000;HaplotypeScore=6.4109;MLEAC=1;MLEAF=0.500;MQ=20.13;MQ0=4;MQRankSum=1.734;QD=1.88;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:19:64:64,0,89 -chr1 72626 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.482;DP=23;Dels=0.00;FS=3.332;HaplotypeScore=8.3126;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=5;MQRankSum=0.796;QD=2.34;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:82:82,0,124 -chr1 72630 . G A 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=5;MQRankSum=0.787;QD=1.32;ReadPosRankSum=-1.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:60:60,0,147 -chr1 72631 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.646;DP=25;Dels=0.00;FS=2.680;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.06;MQ0=5;MQRankSum=1.905;QD=2.15;ReadPosRankSum=0.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,3:25:82:82,0,124 -chr1 72638 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=22.7383;MLEAC=1;MLEAF=0.500;MQ=17.66;MQ0=5;MQRankSum=-0.417;QD=3.96;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,17:29:95:143,0,95 -chr1 72646 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.219;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=1.020;QD=0.60;ReadPosRankSum=1.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,9:33:48:48,0,249 -chr1 72647 . A T 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.883;DP=33;Dels=0.00;FS=2.141;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=-1.102;QD=2.24;ReadPosRankSum=-1.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,12:33:99:102,0,158 -chr1 72688 . A C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.2417;MLEAC=1;MLEAF=0.500;MQ=17.84;MQ0=5;MQRankSum=0.604;QD=0.76;ReadPosRankSum=-0.986;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,9:30:51:51,0,209 -chr1 72693 . A G,T 93.3 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.315;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=3.4300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=17.69;MQ0=3;MQRankSum=0.315;QD=4.06;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:3,13,7:23:82:195,82,86,97,0,107 -chr1 72717 . T C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.369;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=16.28;MQ0=1;MQRankSum=0.555;QD=3.41;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:7,7:14:32:76,0,32 -chr1 72825 . G C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.350;QD=1.40;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,4:39:83:83,0,118 -chr1 72829 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.750;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.050;QD=1.40;ReadPosRankSum=1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:35,4:39:83:83,0,121 -chr1 72855 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.464;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=16.6819;MLEAC=1;MLEAF=0.500;MQ=16.39;MQ0=10;MQRankSum=-0.705;QD=0.45;ReadPosRankSum=-1.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,14:27:40:40,0,130 -chr1 72858 . G A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=11.8688;MLEAC=1;MLEAF=0.500;MQ=16.70;MQ0=9;MQRankSum=1.415;QD=2.30;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,4:26:82:88,0,82 -chr1 72865 . G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.456;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=9.3724;MLEAC=1;MLEAF=0.500;MQ=17.99;MQ0=8;MQRankSum=1.004;QD=0.55;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,3:22:40:40,0,130 -chr1 72880 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.386;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.39;MQ0=5;MQRankSum=-0.546;QD=0.99;ReadPosRankSum=-1.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,7:15:43:43,0,103 -chr1 72889 . T A 11.83 LowQual AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.37;MQ0=0;QD=2.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:3:38,3,0 -chr1 73036 . T A 208.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.62;MQ0=0;QD=34.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:237,18,0 -chr1 73048 . A G 266.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=33.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:295,24,0 -chr1 73057 . T C 276.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=34.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:305,24,0 -chr1 73065 . G A 343.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=34.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:372,30,0 -chr1 73081 . G A 317.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.59;MQ0=1;QD=28.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:346,27,0 -chr1 73149 . G C 249.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.69;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:278,21,0 -chr1 73163 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=26.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 73175 . G C 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=27.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 73190 . T C 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-0.021;QD=8.71;ReadPosRankSum=4.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:307,0,753 -chr1 73232 . T G 932.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.025;QD=21.20;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:961,0,450 -chr1 73255 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.483;DP=47;Dels=0.00;FS=6.570;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-2.077;QD=9.48;ReadPosRankSum=-0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:474,0,1089 -chr1 73261 . C A 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.379;DP=44;Dels=0.00;FS=4.722;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.183;QD=21.88;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:991,0,472 -chr1 73263 . C G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=44;Dels=0.00;FS=2.932;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.964;QD=21.31;ReadPosRankSum=1.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:966,0,458 -chr1 73275 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.486;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.535;QD=22.72;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:1028,0,450 -chr1 73316 . C T 2034.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2063,157,0 -chr1 73353 . T C 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.342;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.881;QD=11.40;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:587,0,1121 -chr1 73399 . A G 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.278;DP=55;Dels=0.00;FS=1.104;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.735;QD=9.60;ReadPosRankSum=2.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,18:55:99:556,0,1319 -chr1 73405 . A T 1043.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.503;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.482;QD=21.30;ReadPosRankSum=-0.975;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1072,0,626 -chr1 73409 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=50;Dels=0.00;FS=1.111;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-1.396;QD=19.28;ReadPosRankSum=-0.295;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:992,0,686 -chr1 73415 . A C 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.654;DP=46;Dels=0.00;FS=2.689;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-0.221;QD=17.91;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,629 -chr1 73486 . T A 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.8288;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.472;QD=15.77;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:864,0,913 -chr1 73498 . T G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=60;Dels=0.00;FS=7.060;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.598;QD=16.43;ReadPosRankSum=-1.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1014,0,976 -chr1 73526 . G C 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.141;DP=55;Dels=0.00;FS=5.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.947;QD=18.87;ReadPosRankSum=-1.408;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1066,0,776 -chr1 73533 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.024;DP=53;Dels=0.00;FS=1.107;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.014;QD=17.51;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:956,0,715 -chr1 73553 . C T 2145.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=31.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2174,160,0 -chr1 73559 . G C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.050;QD=12.94;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:753,0,1151 -chr1 73601 . T C 1170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.426;DP=64;Dels=0.00;FS=0.969;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.995;QD=18.29;ReadPosRankSum=-0.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1199,0,892 -chr1 73621 . C T 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=67;Dels=0.00;FS=0.922;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.292;QD=18.98;ReadPosRankSum=-0.019;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,37:67:99:1300,0,965 -chr1 73648 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.955;DP=69;Dels=0.00;FS=2.001;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.776;QD=13.56;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,32:69:99:964,0,1308 -chr1 73726 . T A 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.512;QD=18.38;ReadPosRankSum=1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:800,0,577 -chr1 73823 . G C 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.311;QD=16.01;ReadPosRankSum=1.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:877,0,914 -chr1 73849 . G A 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;DP=62;Dels=0.00;FS=1.017;HaplotypeScore=3.9989;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.015;QD=21.00;ReadPosRankSum=-0.146;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,39:62:99:1330,0,730 -chr1 73870 . G A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=62;Dels=0.00;FS=3.539;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.230;QD=20.11;ReadPosRankSum=0.861;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1275,0,847 -chr1 73877 . A G 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=64;Dels=0.00;FS=3.431;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-0.836;QD=17.84;ReadPosRankSum=1.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1170,0,987 -chr1 73917 . A G 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=2.047;HaplotypeScore=1.9912;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.905;QD=16.80;ReadPosRankSum=-0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1137,0,1083 -chr1 73927 . T C 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.691;DP=59;Dels=0.00;FS=3.614;HaplotypeScore=2.6984;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.812;QD=17.32;ReadPosRankSum=-1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:1050,0,941 -chr1 73941 . C G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6987;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=0.313;QD=14.74;ReadPosRankSum=0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:839,0,1011 -chr1 73956 . A C 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.468;QD=13.53;ReadPosRankSum=0.514;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:637,0,849 -chr1 74024 . G C 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=3;MQRankSum=-2.569;QD=14.19;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:681,0,673 -chr1 74047 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=52;Dels=0.00;FS=6.153;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.43;MQ0=4;MQRankSum=-3.097;QD=12.90;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:699,0,647 -chr1 74080 . G A 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=58;Dels=0.00;FS=2.389;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=48.01;MQ0=4;MQRankSum=-5.098;QD=10.86;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:658,0,902 -chr1 74086 . A T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.43;MQ0=1;MQRankSum=-6.245;QD=9.29;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:530,0,995 -chr1 74089 . T G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-6.297;QD=9.30;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:540,0,1006 -chr1 74105 . G A 433.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=50.74;MQ0=1;MQRankSum=-6.154;QD=8.18;ReadPosRankSum=-0.700;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:462,0,1044 -chr1 74115 . A G 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=1;MQRankSum=-5.772;QD=6.19;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:319,0,952 -chr1 74119 . A G 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.277;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=1;MQRankSum=-5.551;QD=7.02;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:337,0,895 -chr1 74274 . A T 879.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.47;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:908,69,0 -chr1 74343 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.338;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.918;QD=17.18;ReadPosRankSum=3.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:973,0,882 -chr1 74475 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.652;DP=61;Dels=0.00;FS=12.530;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.79;MQ0=0;MQRankSum=-6.052;QD=16.83;ReadPosRankSum=2.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1055,0,1074 -chr1 74477 . T C 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.511;DP=59;Dels=0.00;FS=10.241;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-5.936;QD=17.84;ReadPosRankSum=2.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1081,0,1017 -chr1 74481 . G A 1104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.304;DP=60;Dels=0.00;FS=7.540;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-5.682;QD=18.41;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,32:60:99:1133,0,933 -chr1 74490 . A G 836.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.635;DP=62;Dels=0.00;FS=5.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=5.728;QD=13.50;ReadPosRankSum=1.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:865,0,1275 -chr1 74532 . C T 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.207;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.874;QD=18.60;ReadPosRankSum=-1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1163,0,974 -chr1 74539 . T A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-2.447;QD=15.63;ReadPosRankSum=0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:935,0,1102 -chr1 74540 . A T 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.639;QD=15.55;ReadPosRankSum=0.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:930,0,1112 -chr1 74544 . T C 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=1.937;QD=16.08;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,30:63:99:1041,0,1120 -chr1 74554 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=62;Dels=0.00;FS=0.939;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.760;QD=15.63;ReadPosRankSum=1.056;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:997,0,1066 -chr1 74559 . A G 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.648;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.806;QD=16.03;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,30:60:99:990,0,1042 -chr1 74590 . G A 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=0.903;QD=14.71;ReadPosRankSum=2.690;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:808,0,980 -chr1 74638 . C T 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=1.355;QD=14.74;ReadPosRankSum=-1.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:839,0,868 -chr1 74648 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=53;Dels=0.00;FS=3.775;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=1.331;QD=14.88;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:817,0,917 -chr1 74652 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.459;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=1.026;QD=14.20;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:738,0,887 -chr1 74691 . C T 1222.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1251,96,0 -chr1 74732 . C A 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.435;DP=42;Dels=0.00;FS=18.002;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.102;QD=12.26;ReadPosRankSum=-0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:543,0,832 -chr1 74805 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=32;Dels=0.00;FS=11.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.183;QD=8.59;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:303,0,769 -chr1 74809 . A G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.788;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.297;QD=7.10;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:227,0,624 -chr1 74810 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.348;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.687;QD=7.67;ReadPosRankSum=0.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:243,0,706 -chr1 74816 . A T 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.472;DP=30;Dels=0.00;FS=8.475;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=2.064;QD=5.89;ReadPosRankSum=-0.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,7:30:99:205,0,702 -chr1 74826 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9448;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.122;QD=28.38;ReadPosRankSum=2.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:4,19:23:88:681,0,88 -chr1 74830 . A T 738.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.315;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=17.9789;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;MQRankSum=1.419;QD=33.58;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,21:22:25:767,25,0 -chr1 74836 . A T 949.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=18.7128;MLEAC=2;MLEAF=1.00;MQ=59.12;MQ0=0;QD=28.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:978,75,0 -chr1 74877 . C T 1344.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1373,105,0 -chr1 74921 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-0.573;QD=6.31;ReadPosRankSum=1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:249,0,790 -chr1 75391 . G T 704.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.040;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=3.7544;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-0.901;QD=28.19;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:25:733,25,0 -chr1 75393 . T C 692.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.069;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.9658;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-1.040;QD=27.71;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:24:721,24,0 -chr1 75399 . C A 731.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.96;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,24:24:60:760,60,0 -chr1 75407 . G A 466.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:495,39,0 -chr1 75408 . T C 474.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:503,39,0 -chr1 75441 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0 -chr1 75443 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0 -chr1 75447 . C T 75.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 -chr1 75675 . G T 46.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr1 75678 . G T 88.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0 -chr1 75695 . T C 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=34;Dels=0.00;FS=1.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.62;MQ0=1;MQRankSum=-0.738;QD=15.23;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:546,0,545 -chr1 75719 . C T 1840.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=1;QD=26.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1869,138,0 -chr1 75727 . A G 2171.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.64;MQ0=0;QD=34.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2200,163,0 -chr1 75762 . C T 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=56;Dels=0.00;FS=11.912;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.737;QD=13.66;ReadPosRankSum=-0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:793,0,1062 -chr1 75763 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.486;QD=13.21;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:755,0,1074 -chr1 75764 . A G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.339;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.930;QD=13.14;ReadPosRankSum=-0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:751,0,1072 -chr1 75807 . A C 597.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;DP=47;Dels=0.00;FS=1.116;HaplotypeScore=3.2018;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-0.075;QD=12.72;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:626,0,814 -chr1 75832 . A G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.198;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=13.9498;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-3.243;QD=6.99;ReadPosRankSum=3.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,7:22:99:182,0,490 -chr1 75838 . A C,T 525.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=11.9502;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.83;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:0,7,12:19:99:664,409,388,255,0,222 -chr1 75850 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-1.228;QD=19.73;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:9,14:23:99:482,0,253 -chr1 75905 . T G 911.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.627;DP=45;Dels=0.00;FS=4.849;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=1;MQRankSum=-0.699;QD=20.26;ReadPosRankSum=-0.337;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:940,0,570 -chr1 75930 . T C 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=54;Dels=0.00;FS=8.156;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=1;MQRankSum=-2.270;QD=12.68;ReadPosRankSum=-0.996;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:713,0,1060 -chr1 75970 . C G 1604.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.17;MQ0=1;QD=31.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1633,120,0 -chr1 76013 . T G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.758;DP=38;Dels=0.00;FS=1.402;HaplotypeScore=1.9956;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=1;MQRankSum=0.479;QD=12.73;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,658 -chr1 76032 . A T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.051;DP=43;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=1;MQRankSum=1.973;QD=12.72;ReadPosRankSum=-0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:575,0,722 -chr1 76087 . C A 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=51;Dels=0.00;FS=11.471;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=1.732;QD=14.84;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:785,0,818 -chr1 76168 . T C 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=43;Dels=0.00;FS=2.727;HaplotypeScore=5.8324;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=1;MQRankSum=-0.743;QD=19.58;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:870,0,570 -chr1 76236 . C A 728.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=13.5311;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:757,57,0 -chr1 76283 . C A 1892.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=28.55;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1921,147,0 -chr1 76328 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=51;Dels=0.00;FS=4.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.205;QD=10.86;ReadPosRankSum=-2.893;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:582,0,977 -chr1 76334 . A G 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.425;DP=45;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=2.653;QD=12.17;ReadPosRankSum=-1.587;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:576,0,815 -chr1 76427 . A C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.347;DP=54;Dels=0.00;FS=12.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=-0.169;QD=14.07;ReadPosRankSum=0.508;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:788,0,919 -chr1 76443 . T C 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.715;DP=59;Dels=0.00;FS=11.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=1;MQRankSum=0.451;QD=14.91;ReadPosRankSum=-0.513;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:908,0,963 -chr1 76465 . C T 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.671;DP=50;Dels=0.00;FS=19.919;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=-1.733;QD=16.46;ReadPosRankSum=-0.711;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:851,0,769 -chr1 76478 . G T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=48;Dels=0.00;FS=13.782;HaplotypeScore=145.9761;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=-2.207;QD=15.77;ReadPosRankSum=0.565;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:785,0,657 -chr1 76500 . G T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.996;DP=35;Dels=0.00;FS=1.972;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=0.959;QD=0.57;ReadPosRankSum=-3.137;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,4:35:48:48,0,1103 -chr1 76506 . T G 1303.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=30.53;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1332,99,0 -chr1 76543 . A C,T 956.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.625;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.9300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.99;MQ0=0;MQRankSum=0.542;QD=29.88;ReadPosRankSum=0.650;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:1,12,19:32:99:1134,701,665,433,0,376 -chr1 76552 . C A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.464;DP=33;Dels=0.00;FS=1.376;HaplotypeScore=16.6986;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-3.019;QD=17.72;ReadPosRankSum=0.524;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:613,0,416 -chr1 76554 . A T 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=14.9106;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.480;QD=15.93;ReadPosRankSum=0.827;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:570,0,574 -chr1 76667 . C A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=50;Dels=0.00;FS=2.539;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.616;QD=22.38;ReadPosRankSum=2.961;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1147,0,573 -chr1 76736 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.2657;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.771;QD=21.09;ReadPosRankSum=-0.603;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:956,0,527 -chr1 76758 . A G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.695;DP=38;Dels=0.00;FS=1.289;HaplotypeScore=16.4637;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.370;QD=19.39;ReadPosRankSum=0.103;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:765,0,537 -chr1 76765 . A T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=38;Dels=0.00;FS=1.281;HaplotypeScore=62.8561;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.219;QD=17.55;ReadPosRankSum=1.535;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:695,0,601 -chr1 76784 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.258;QD=14.59;ReadPosRankSum=-1.433;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:670,0,738 -chr1 76813 . G T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.627;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.777;QD=19.61;ReadPosRankSum=-1.476;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,32:52:99:1048,0,649 -chr1 76827 . C T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.020;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-1.020;QD=19.94;ReadPosRankSum=-1.218;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1025,0,663 -chr1 76831 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-0.124;QD=19.94;ReadPosRankSum=-1.136;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1105,0,628 -chr1 76885 . G C 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.785;DP=51;Dels=0.00;FS=8.452;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.280;QD=21.15;ReadPosRankSum=0.878;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1107,0,632 -chr1 76963 . A G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;QD=19.62;ReadPosRankSum=0.589;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V46A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:715,0,396 -chr1 76964 . C A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.364;QD=19.68;ReadPosRankSum=0.791;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V46L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:717,0,439 -chr1 76995 . T C 912.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=34.12;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A35|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,24:24:72:941,72,0 -chr1 77019 . T G 807.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=28.76;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G27|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,22:22:66:836,66,0 -chr1 77028 . G T 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.083;QD=11.11;ReadPosRankSum=-0.305;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S24R|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:15,10:25:99:306,0,525 -chr1 77030 . T C 1001.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=33.45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S24G|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1030,78,0 -chr1 77036 . C G 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=2.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.482;QD=9.75;ReadPosRankSum=1.399;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V22L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,10:29:99:311,0,667 -chr1 77040 . A C 1106.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I20M|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,31:31:87:1135,87,0 -chr1 77066 . C T 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.686;QD=15.94;ReadPosRankSum=2.051;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A12T|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:18,19:38:99:634,0,588 -chr1 77068 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.131;QD=16.28;ReadPosRankSum=2.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V11A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:647,0,593 -chr1 77072 . G C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.606;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.518;QD=15.65;ReadPosRankSum=2.628;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L10V|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:623,0,636 -chr1 77092 . C G 1448.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.9948;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.69;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G3A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1477,111,0 -chr1 77096 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=45;Dels=0.00;FS=6.823;HaplotypeScore=2.9948;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.215;QD=17.06;ReadPosRankSum=0.534;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2K|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:22,23:45:99:796,0,679 -chr1 77106 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.035;QD=17.26;ReadPosRankSum=-1.240;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,24:45:99:805,0,662 -chr1 77122 . A G 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.595;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-1.700;QD=14.32;ReadPosRankSum=-0.728;EFF=START_GAINED(LOW||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,15:34:99:515,0,632 -chr1 77126 . A T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=37;Dels=0.00;FS=7.143;HaplotypeScore=3.7335;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-1.844;QD=14.97;ReadPosRankSum=-0.808;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:20,17:37:99:582,0,647 -chr1 77144 . A C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;DP=41;Dels=0.00;FS=4.506;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-1.265;QD=15.85;ReadPosRankSum=0.170;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,20:41:99:678,0,682 -chr1 77180 . C A 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.879;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=4.1179;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.179;QD=17.54;ReadPosRankSum=-0.594;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:16,24:40:99:730,0,535 -chr1 77221 . C G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=43;Dels=0.00;FS=14.813;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.319;QD=20.88;ReadPosRankSum=-0.163;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,27:43:99:926,0,502 -chr1 77244 . G C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=39;Dels=0.00;FS=5.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.512;QD=21.81;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:14,25:39:99:879,0,425 -chr1 77298 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.048;DP=35;Dels=0.00;FS=5.506;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.901;QD=23.14;ReadPosRankSum=1.190;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:838,0,318 -chr1 77325 . T A 1222.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=55.78;MQ0=0;QD=37.76;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1251,96,0 -chr1 77332 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=32;Dels=0.00;FS=3.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-0.516;QD=22.34;ReadPosRankSum=0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,21:32:99:743,0,352 -chr1 77376 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.170;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=83.6545;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.434;QD=15.40;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:783,0,747 -chr1 77378 . A C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=124.2479;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.053;QD=15.32;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:779,0,892 -chr1 77438 . C T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.363;DP=53;Dels=0.00;FS=15.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.633;QD=16.94;ReadPosRankSum=-2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:926,0,869 -chr1 77442 . T G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=51;Dels=0.00;FS=15.703;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.218;QD=15.02;ReadPosRankSum=3.474;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,934 -chr1 77449 . T C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=48;Dels=0.00;FS=11.196;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.972;QD=13.39;ReadPosRankSum=2.206;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:671,0,945 -chr1 77450 . A G 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.917;DP=46;Dels=0.00;FS=11.459;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.853;QD=14.34;ReadPosRankSum=1.673;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:688,0,862 -chr1 77458 . A T 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=51;Dels=0.00;FS=16.807;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=1;MQRankSum=2.301;QD=15.23;ReadPosRankSum=0.146;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:805,0,791 -chr1 77464 . G A 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=49;Dels=0.00;FS=17.115;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=-0.908;QD=16.95;ReadPosRankSum=-1.610;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:859,0,697 -chr1 77489 . G A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.648;DP=46;Dels=0.00;FS=12.506;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=2;MQRankSum=-0.625;QD=14.45;ReadPosRankSum=2.345;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:693,0,690 -chr1 77491 . A G 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=45;Dels=0.00;FS=15.152;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.71;MQ0=2;MQRankSum=2.203;QD=12.71;ReadPosRankSum=-1.489;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:600,0,730 -chr1 77495 . A G 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.505;DP=41;Dels=0.00;FS=16.483;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=2;MQRankSum=2.237;QD=11.36;ReadPosRankSum=-0.476;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:494,0,766 -chr1 77531 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=49;Dels=0.00;FS=11.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=3;MQRankSum=4.899;QD=15.53;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:789,0,677 -chr1 77535 . C T 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=49;Dels=0.00;FS=13.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=3;MQRankSum=-5.229;QD=14.63;ReadPosRankSum=-2.065;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:745,0,801 -chr1 77544 . C T 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.557;DP=48;Dels=0.00;FS=11.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=3;MQRankSum=-5.517;QD=13.20;ReadPosRankSum=-0.330;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:662,0,770 -chr1 77549 . C G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.738;DP=50;Dels=0.00;FS=10.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=3;MQRankSum=-5.596;QD=12.14;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:635,0,869 -chr1 77557 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.869;DP=45;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=3;MQRankSum=-5.553;QD=14.15;ReadPosRankSum=0.416;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:665,0,732 -chr1 77577 . T G 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=3;MQRankSum=-3.998;QD=6.89;ReadPosRankSum=2.292;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:290,0,880 -chr1 77581 . T G 1321.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.74;MQ0=2;QD=31.22;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1350,99,0 -chr1 77582 . A G 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.61;MQ0=2;QD=29.89;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,99,0 -chr1 77589 . C T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=42;Dels=0.00;FS=4.743;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=2;MQRankSum=-2.271;QD=11.95;ReadPosRankSum=-0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:530,0,807 -chr1 77592 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=2.439;QD=16.46;ReadPosRankSum=0.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:736,0,657 -chr1 77593 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-1.969;QD=15.04;ReadPosRankSum=-0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:675,0,722 -chr1 77615 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.765;DP=43;Dels=0.00;FS=2.820;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=2;MQRankSum=-0.327;QD=16.53;ReadPosRankSum=-0.327;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:739,0,655 -chr1 77617 . C T 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.975;DP=42;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=2;MQRankSum=0.488;QD=16.40;ReadPosRankSum=0.027;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,22:42:99:717,0,653 -chr1 77620 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.342;DP=43;Dels=0.00;FS=2.687;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=2;MQRankSum=0.013;QD=12.79;ReadPosRankSum=0.781;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:43:99:578,0,822 -chr1 77633 . G A 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=1.015;QD=11.33;ReadPosRankSum=-0.555;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:504,0,850 -chr1 77648 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.970;DP=44;Dels=0.00;FS=1.269;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=1;MQRankSum=0.304;QD=8.81;ReadPosRankSum=-0.569;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:416,0,909 -chr1 77650 . T C 1540.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=1;QD=31.92;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1569,120,0 -chr1 77695 . A G 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.171;DP=48;Dels=0.00;FS=11.450;HaplotypeScore=1.9984;MLEAC=1;MLEAF=0.500;MQ=56.59;MQ0=1;MQRankSum=-1.215;QD=11.39;ReadPosRankSum=-2.156;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:575,0,980 -chr1 77770 . C T 2115.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=2;QD=26.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2144,163,0 -chr1 77798 . A G 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.110;DP=51;Dels=0.00;FS=4.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-0.292;QD=13.56;ReadPosRankSum=-0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:720,0,928 -chr1 77814 . G T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.710;DP=51;Dels=0.00;FS=4.322;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=54.03;MQ0=1;MQRankSum=-1.124;QD=18.72;ReadPosRankSum=0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:983,0,686 -chr1 77873 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=1.065;QD=20.19;ReadPosRankSum=-2.142;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:937,0,508 -chr1 77951 . C A 2019.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2048,159,0 -chr1 77986 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=56;Dels=0.00;FS=5.494;HaplotypeScore=1.9774;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-1.712;QD=14.80;ReadPosRankSum=0.778;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:857,0,933 -chr1 78007 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.299;DP=43;Dels=0.00;FS=1.315;HaplotypeScore=19.9836;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.842;QD=11.18;ReadPosRankSum=0.565;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:509,0,882 -chr1 78009 . C T 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.704;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.014;QD=19.65;ReadPosRankSum=-0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:893,0,579 -chr1 78012 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.563;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.037;QD=18.65;ReadPosRankSum=-0.185;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:830,0,589 -chr1 78019 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=44;Dels=0.00;FS=3.112;HaplotypeScore=24.9845;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.446;QD=10.13;ReadPosRankSum=2.105;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,15:44:99:474,0,1015 -chr1 78027 . T C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=44;Dels=0.00;FS=12.758;HaplotypeScore=6.9973;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.701;QD=1.72;ReadPosRankSum=-1.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:38,6:44:99:104,0,1372 -chr1 78118 . T A 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.504;DP=54;Dels=0.00;FS=1.040;HaplotypeScore=35.7719;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.892;QD=19.46;ReadPosRankSum=1.994;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1079,0,770 -chr1 78134 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;DP=54;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=0.099;QD=11.72;ReadPosRankSum=-0.958;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:34,20:54:99:661,0,1176 -chr1 78240 . T C 1102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=57;Dels=0.00;FS=3.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.234;QD=19.35;ReadPosRankSum=0.444;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1131,0,782 -chr1 78243 . T A 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=58;Dels=0.00;FS=5.380;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=0.361;QD=19.34;ReadPosRankSum=0.848;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1150,0,823 -chr1 78259 . A G 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=58;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.330;QD=17.05;ReadPosRankSum=0.319;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1017,0,977 -chr1 78296 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=35;Dels=0.00;FS=5.073;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.286;QD=20.34;ReadPosRankSum=1.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:740,0,458 -chr1 78417 . A G 2257.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=1;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2286,172,0 -chr1 78420 . T C 2412.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=1;QD=32.78;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2441,184,0 -chr1 78459 . A G 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=56;Dels=0.00;FS=1.071;HaplotypeScore=2.7605;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=4;MQRankSum=1.156;QD=18.75;ReadPosRankSum=1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1078,0,681 -chr1 78480 . G T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=4;MQRankSum=-1.866;QD=7.95;ReadPosRankSum=-1.529;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:418,0,1082 -chr1 78503 . A C 1406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.844;DP=60;Dels=0.00;FS=2.699;HaplotypeScore=42.4334;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=3;MQRankSum=1.437;QD=23.45;ReadPosRankSum=2.809;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,45:60:99:1435,0,403 -chr1 78548 . T A 2170.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=24.73;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2199,166,0 -chr1 78601 . G A 1151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.289;DP=48;Dels=0.00;FS=5.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=0;MQRankSum=-0.133;QD=24.00;ReadPosRankSum=-0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,33:48:99:1180,0,463 -chr1 78639 . C A 1912.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1941,147,0 -chr1 78753 . G T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=65;Dels=0.00;FS=0.960;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.007;QD=12.77;ReadPosRankSum=-0.353;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:38,27:65:99:858,0,1336 -chr1 78787 . G A 1365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.554;DP=61;Dels=0.00;FS=1.030;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.660;QD=22.39;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,40:61:99:1394,0,614 -chr1 78815 . A G 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.008;DP=57;Dels=0.00;FS=3.773;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;QD=20.50;ReadPosRankSum=1.320;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,35:57:99:1197,0,695 -chr1 78892 . C T 925.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=15.69;ReadPosRankSum=0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:954,0,1057 -chr1 78931 . G A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.869;DP=63;Dels=0.00;FS=11.290;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.796;QD=16.93;ReadPosRankSum=-1.025;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1095,0,1023 -chr1 78981 . T C 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.954;DP=27;Dels=0.00;FS=12.207;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.904;QD=4.88;ReadPosRankSum=2.537;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:160,0,693 -chr1 78994 . T A 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.138;DP=38;Dels=0.00;FS=22.047;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=2.492;QD=20.10;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,25:38:99:792,0,376 -chr1 79011 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.991;DP=42;Dels=0.00;FS=18.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.654;QD=7.21;ReadPosRankSum=1.573;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:331,0,1024 -chr1 79031 . C A 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=45;Dels=0.00;FS=23.835;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=2.704;QD=20.24;ReadPosRankSum=0.386;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:939,0,503 -chr1 79032 . T C 1667.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.02;FS=0.000;HaplotypeScore=16.9978;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.21;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1696,126,0 -chr1 79035 . C G 1664.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.115;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;MQRankSum=1.578;QD=32.37;ReadPosRankSum=0.654;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,44:45:92:1693,92,0 -chr1 79092 . A C 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=56;Dels=0.00;FS=20.015;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-1.258;QD=7.25;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:41,15:56:99:434,0,1487 -chr1 79155 . A G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.851;DP=43;Dels=0.00;FS=24.229;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.433;QD=4.20;ReadPosRankSum=1.776;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:209,0,1210 -chr1 79179 . A G 1612.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=29.41;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1641,126,0 -chr1 79211 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=44;Dels=0.00;FS=24.701;HaplotypeScore=3.9990;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-4.230;QD=6.36;ReadPosRankSum=2.095;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,12:44:99:308,0,1153 -chr1 79215 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=46;Dels=0.00;FS=28.108;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-3.940;QD=5.84;ReadPosRankSum=2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,12:46:99:297,0,1207 -chr1 79219 . C T 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=48;Dels=0.00;FS=32.959;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.417;QD=5.62;ReadPosRankSum=2.464;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:298,0,1293 -chr1 79223 . A C 1751.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1780,135,0 -chr1 79242 . C T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.484;DP=54;Dels=0.00;FS=36.287;HaplotypeScore=13.9681;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-5.699;QD=8.00;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:460,0,1314 -chr1 79253 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.069;DP=49;Dels=0.00;FS=18.054;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=5.556;QD=23.30;ReadPosRankSum=2.594;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,32:49:99:1170,0,488 -chr1 79258 . C T 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=50;Dels=0.00;FS=15.207;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.996;QD=7.74;ReadPosRankSum=-1.397;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:415,0,1279 -chr1 79284 . A T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-4.938;QD=8.83;ReadPosRankSum=1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:452,0,1222 -chr1 79288 . G C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=25.1292;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-5.205;QD=8.68;ReadPosRankSum=1.690;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:445,0,1219 -chr1 79300 . T A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-4.876;QD=8.74;ReadPosRankSum=1.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,14:44:99:413,0,1090 -chr1 79321 . G C 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.836;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-4.816;QD=15.72;ReadPosRankSum=-0.137;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:610,0,654 -chr1 79322 . C A 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.35;MQ0=0;QD=35.79;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0 -chr1 79337 . G A 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-4.610;QD=14.14;ReadPosRankSum=1.392;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:495,0,617 -chr1 79397 . C A 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.587;DP=32;Dels=0.00;FS=32.017;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-4.602;QD=9.12;ReadPosRankSum=-2.420;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,11:32:99:320,0,754 -chr1 79404 . T A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;DP=40;Dels=0.00;FS=20.081;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.252;QD=10.74;ReadPosRankSum=-1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:458,0,853 -chr1 79408 . T A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.460;DP=42;Dels=0.00;FS=18.695;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=0;MQRankSum=-4.894;QD=11.90;ReadPosRankSum=-1.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:528,0,853 -chr1 79425 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.446;DP=44;Dels=0.00;FS=12.871;HaplotypeScore=3.5215;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=-3.990;QD=9.90;ReadPosRankSum=1.522;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,15:44:99:464,0,918 -chr1 79451 . G A 406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.625;DP=45;Dels=0.00;FS=2.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.017;QD=9.04;ReadPosRankSum=1.361;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:435,0,1059 -chr1 79452 . A T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.469;DP=46;Dels=0.00;FS=2.785;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.218;QD=9.36;ReadPosRankSum=1.148;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:459,0,1031 -chr1 79468 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.623;QD=14.00;ReadPosRankSum=-0.748;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:700,0,913 -chr1 79478 . G C 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=1.6648;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.471;QD=16.94;ReadPosRankSum=-1.753;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:926,0,881 -chr1 79598 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.841;DP=38;Dels=0.00;FS=9.653;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-3.061;QD=4.23;ReadPosRankSum=-0.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,8:38:99:189,0,1018 -chr1 79615 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=23.6444;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.17;ReadPosRankSum=0.428;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:475,0,803 -chr1 79617 . T A 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=40;Dels=0.00;FS=9.975;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-4.200;QD=4.77;ReadPosRankSum=0.762;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,8:40:99:219,0,844 -chr1 79618 . G A 138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-3.364;QD=3.47;ReadPosRankSum=0.254;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,8:40:99:167,0,1124 -chr1 79619 . C T 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.201;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.09;ReadPosRankSum=1.256;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:472,0,808 -chr1 79624 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=37;Dels=0.00;FS=12.746;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.605;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,974 -chr1 79626 . G A 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.125;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.83;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:207,0,1010 -chr1 79627 . A G 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.900;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,1015 -chr1 79640 . C T 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=51;Dels=0.00;FS=14.590;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-1.369;QD=9.39;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,17:51:99:507,0,1160 -chr1 79641 . G A 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=51;Dels=0.00;FS=3.858;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-3.463;QD=1.92;ReadPosRankSum=3.189;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:44,7:51:99:126,0,1543 -chr1 79670 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=-3.131;QD=14.97;ReadPosRankSum=1.235;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:717,0,801 -chr1 79675 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=2.704;HaplotypeScore=18.9737;MLEAC=1;MLEAF=0.500;MQ=55.22;MQ0=0;MQRankSum=-2.223;QD=15.51;ReadPosRankSum=0.765;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:695,0,699 -chr1 79697 . C A 978.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=24.70;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1007,78,0 -chr1 79745 . C G 1250.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=25.03;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1279,93,0 -chr1 79753 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.941;DP=37;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.411;QD=13.21;ReadPosRankSum=0.290;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:517,0,675 -chr1 79807 . C T 1019.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7317;MLEAC=2;MLEAF=1.00;MQ=56.83;MQ0=0;QD=31.02;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1048,81,0 -chr1 79827 . C T 1289.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.78;MQ0=0;QD=35.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1318,99,0 -chr1 79840 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.767;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.127;QD=12.11;ReadPosRankSum=0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:428,0,660 -chr1 79842 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.492;QD=20.75;ReadPosRankSum=-0.608;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:713,0,391 -chr1 79860 . G A 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.431;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.839;QD=14.44;ReadPosRankSum=0.000;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:577,0,643 -chr1 80003 . A T 1616.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=28.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1645,123,0 -chr1 80017 . T A 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.877;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.458;QD=12.63;ReadPosRankSum=0.340;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:508,0,721 -chr1 80041 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.861;DP=37;Dels=0.00;FS=2.846;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.611;QD=11.24;ReadPosRankSum=-1.174;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:444,0,776 -chr1 80045 . G C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.955;DP=36;Dels=0.00;FS=1.366;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.811;QD=21.47;ReadPosRankSum=1.548;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,23:36:99:801,0,403 -chr1 80079 . G C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.802;DP=36;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.481;QD=12.77;ReadPosRankSum=-2.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,737 -chr1 80117 . C T 1871.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1900,141,0 -chr1 80171 . A G 1589.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=19.9948;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=31.59;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1618,120,0 -chr1 80184 . G A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.084;QD=20.44;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:846,0,495 -chr1 80244 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=32;Dels=0.00;FS=7.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.62;MQ0=0;MQRankSum=-3.927;QD=16.96;ReadPosRankSum=1.888;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,17:32:99:571,0,493 -chr1 80416 . C A 796.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.16;MQ0=0;QD=33.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:825,63,0 -chr1 80710 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.494;DP=36;Dels=0.00;FS=5.334;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-1.350;QD=10.69;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:413,0,777 -chr1 80861 . C T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=39;Dels=0.00;FS=2.826;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.328;QD=19.05;ReadPosRankSum=1.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:771,0,477 -chr1 80867 . T C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.071;DP=39;Dels=0.00;FS=2.869;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.827;QD=16.40;ReadPosRankSum=1.374;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,22:39:99:668,0,541 -chr1 80925 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=44;Dels=0.00;FS=22.159;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.041;QD=7.20;ReadPosRankSum=0.203;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:345,0,1053 -chr1 80926 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.372;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-0.744;QD=6.37;ReadPosRankSum=0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:302,0,1088 -chr1 80927 . G A 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.057;QD=6.27;ReadPosRankSum=0.372;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:298,0,1101 -chr1 80933 . T G 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=45;Dels=0.00;FS=23.434;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-1.225;QD=7.17;ReadPosRankSum=0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:351,0,1105 -chr1 80959 . T A 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398;DP=45;Dels=0.00;FS=5.002;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=1;MQRankSum=0.940;QD=10.44;ReadPosRankSum=-0.121;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:498,0,944 -chr1 80967 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=44;Dels=0.00;FS=5.002;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=1;MQRankSum=0.490;QD=11.29;ReadPosRankSum=0.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,17:44:99:525,0,924 -chr1 81012 . C G 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=40;Dels=0.00;FS=4.442;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.019;QD=17.52;ReadPosRankSum=1.672;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:729,0,588 -chr1 81069 . C A 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.275;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.919;QD=12.97;ReadPosRankSum=0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:599,0,905 -chr1 81071 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.373;QD=12.54;ReadPosRankSum=0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:580,0,911 -chr1 81072 . C G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.097;DP=45;Dels=0.00;FS=20.102;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.286;QD=12.66;ReadPosRankSum=-0.081;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:598,0,942 -chr1 81095 . C G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.970;DP=57;Dels=0.00;FS=23.054;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.781;QD=8.77;ReadPosRankSum=-1.073;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:528,0,1396 -chr1 81130 . T G 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.726;QD=8.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:440,0,1117 -chr1 81131 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-1.523;QD=8.78;ReadPosRankSum=0.422;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:432,0,1127 -chr1 81133 . T C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;DP=45;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.951;QD=9.33;ReadPosRankSum=0.349;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,15:45:99:448,0,1081 -chr1 81169 . A G 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.374;DP=49;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.172;QD=13.10;ReadPosRankSum=2.091;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:670,0,987 -chr1 81178 . C A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=50;Dels=0.00;FS=8.297;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-3.555;QD=11.28;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:592,0,991 -chr1 81185 . G A 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.606;DP=41;Dels=0.00;FS=12.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=-3.568;QD=11.26;ReadPosRankSum=1.403;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:490,0,818 -chr1 81268 . T C 1503.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1532,114,0 -chr1 81303 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.18;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1707,126,0 -chr1 81317 . C T 1738.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=59.35;MQ0=0;QD=33.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1767,132,0 -chr1 81331 . A C 1662.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.3989;MLEAC=2;MLEAF=1.00;MQ=59.33;MQ0=0;QD=37.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1691,129,0 -chr1 81371 . G A 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.908;DP=48;Dels=0.00;FS=4.645;HaplotypeScore=1.9957;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.473;QD=6.60;ReadPosRankSum=-2.001;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,16:48:99:345,0,1127 -chr1 81408 . A G 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=53;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=0;MQRankSum=-4.943;QD=8.94;ReadPosRankSum=2.754;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:502,0,1182 -chr1 81418 . C T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.718;DP=50;Dels=0.00;FS=21.604;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=0;MQRankSum=-4.962;QD=9.28;ReadPosRankSum=2.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:492,0,1136 -chr1 81422 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.035;DP=48;Dels=0.00;FS=21.618;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=0;MQRankSum=5.281;QD=21.62;ReadPosRankSum=-2.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1066,0,457 -chr1 81453 . C A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-4.476;QD=8.15;ReadPosRankSum=0.442;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:403,0,1150 -chr1 81455 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.808;QD=8.04;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:398,0,1139 -chr1 81456 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.245;DP=47;Dels=0.00;FS=15.915;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-4.013;QD=8.02;ReadPosRankSum=0.384;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,14:47:99:405,0,1154 -chr1 81457 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.062;DP=46;Dels=0.00;FS=15.915;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=-3.617;QD=8.36;ReadPosRankSum=0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:413,0,1151 -chr1 81482 . G T 1236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.464;DP=50;Dels=0.00;FS=4.620;HaplotypeScore=1.7206;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=2.035;QD=24.74;ReadPosRankSum=0.265;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1265,0,325 -chr1 81533 . A G 1828.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.609;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;MQRankSum=2.352;QD=28.88;ReadPosRankSum=-0.619;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:2,48:50:99:1857,123,0 -chr1 81544 . A G 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8400;MLEAC=1;MLEAF=0.500;MQ=56.30;MQ0=0;MQRankSum=2.542;QD=8.41;ReadPosRankSum=-0.370;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:415,0,1040 -chr1 81580 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=43;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=1.644;QD=14.60;ReadPosRankSum=-2.471;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:656,0,776 -chr1 81581 . G A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=4.524;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=0.767;QD=15.18;ReadPosRankSum=-2.496;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:681,0,762 -chr1 81594 . G A 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.680;DP=41;Dels=0.00;FS=1.230;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-0.251;QD=19.53;ReadPosRankSum=1.919;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:829,0,565 -chr1 81600 . T G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-2.660;QD=16.65;ReadPosRankSum=2.588;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:744,0,706 -chr1 81603 . C G,T 1331.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.491;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.66;MQ0=0;MQRankSum=-0.443;QD=30.96;ReadPosRankSum=1.249;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/2:1,19,23:43:99:1506,809,783,668,0,633 -chr1 81634 . A G 2035.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.31;MQ0=0;QD=30.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2064,154,0 -chr1 81638 . C T 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=0;MQRankSum=-2.108;QD=15.37;ReadPosRankSum=-1.219;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:843,0,879 -chr1 81650 . C T 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=59;Dels=0.00;FS=0.989;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=1.677;QD=16.42;ReadPosRankSum=0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:997,0,893 -chr1 81655 . A T 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=50.82;MQ0=1;MQRankSum=-1.189;QD=14.60;ReadPosRankSum=-0.497;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:846,0,959 -chr1 81660 . C G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.26;MQ0=1;MQRankSum=-1.272;QD=14.65;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:834,0,917 -chr1 81676 . T A 1209.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.535;DP=37;Dels=0.03;FS=3.136;HaplotypeScore=2.9325;MLEAC=2;MLEAF=1.00;MQ=45.14;MQ0=1;MQRankSum=-1.733;QD=32.70;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:65:1238,65,0 -chr1 81684 . T C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.407;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.850;QD=11.40;ReadPosRankSum=1.572;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:450,0,653 -chr1 81688 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.947;QD=10.94;ReadPosRankSum=2.054;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:433,0,686 -chr1 81689 . T C 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=36;Dels=0.00;FS=2.958;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=1;MQRankSum=-3.750;QD=10.77;ReadPosRankSum=1.950;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:416,0,612 -chr1 81693 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=38;Dels=0.00;FS=4.815;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.42;MQ0=1;MQRankSum=-3.581;QD=12.68;ReadPosRankSum=1.143;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:510,0,642 -chr1 81698 . T C 1307.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.87;MQ0=1;QD=30.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1336,105,0 -chr1 81707 . T C 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=47;Dels=0.00;FS=1.176;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.19;MQ0=1;MQRankSum=3.636;QD=11.87;ReadPosRankSum=-0.268;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:586,0,810 -chr1 81724 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.003;DP=44;Dels=0.00;FS=1.986;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=-0.378;QD=1.27;ReadPosRankSum=0.609;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,8:44:84:84,0,1258 -chr1 81739 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.983;QD=19.66;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,28:42:99:854,0,419 -chr1 81751 . G A 1532.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;QD=26.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1561,114,0 -chr1 81778 . A G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.868;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=3;MQRankSum=0.964;QD=8.94;ReadPosRankSum=2.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:493,0,1122 -chr1 81794 . A C 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.402;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=3;MQRankSum=0.029;QD=18.77;ReadPosRankSum=-0.488;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1042,0,496 -chr1 81819 . A G 1360.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=45.13;MQ0=3;QD=31.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1389,105,0 -chr1 81854 . T C 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=0;QD=30.67;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0 -chr1 81866 . G C 932.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.99;MQ0=0;QD=30.61;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:961,72,0 -chr1 81879 . A G 1084.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=46.18;MQ0=0;QD=34.99;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,30:31:84:1113,84,0 -chr1 81881 . G A 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=46.68;MQ0=0;MQRankSum=-0.097;QD=21.21;ReadPosRankSum=2.511;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:707,0,302 -chr1 81889 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.311;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=49.01;MQ0=0;MQRankSum=-0.851;QD=9.17;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:340,0,730 -chr1 81914 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.672;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=0;MQRankSum=0.503;QD=17.79;ReadPosRankSum=-3.004;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:740,0,520 -chr1 81927 . C T 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.72;MQ0=0;QD=28.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,123,0 -chr1 81935 . A T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.440;DP=43;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-0.335;QD=12.44;ReadPosRankSum=1.279;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:563,0,831 -chr1 81947 . T A 1397.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.54;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1426,108,0 -chr1 81948 . G C 1380.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=31.38;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1409,105,0 -chr1 81951 . T C 1385.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;QD=25.32;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:38:99:1414,105,0 -chr1 81995 . G A 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.114;QD=12.73;ReadPosRankSum=0.458;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,740 -chr1 82003 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.877;QD=9.37;ReadPosRankSum=3.261;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:375,0,858 -chr1 82004 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.910;QD=9.51;ReadPosRankSum=3.326;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:380,0,857 -chr1 82005 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.190;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.358;QD=9.53;ReadPosRankSum=3.293;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:381,0,863 -chr1 82009 . T C 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.836;DP=36;Dels=0.00;FS=3.018;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-3.574;QD=10.05;ReadPosRankSum=2.970;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:390,0,731 -chr1 82011 . G C 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.763;DP=35;Dels=0.00;FS=1.421;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-3.736;QD=10.42;ReadPosRankSum=2.763;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:393,0,756 -chr1 82025 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.275;DP=40;Dels=0.00;FS=4.364;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.59;MQ0=0;MQRankSum=-4.604;QD=16.92;ReadPosRankSum=0.244;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:705,0,617 -chr1 82036 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.13;MQ0=0;MQRankSum=-4.538;QD=19.31;ReadPosRankSum=-0.103;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:762,0,463 -chr1 82050 . C T 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.144;DP=35;Dels=0.00;FS=10.665;HaplotypeScore=49.2919;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-4.080;QD=21.25;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,22:35:99:772,0,401 -chr1 82064 . T C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.141;DP=31;Dels=0.00;FS=8.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.343;QD=19.41;ReadPosRankSum=1.501;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,18:31:99:630,0,427 -chr1 82080 . C T 1151.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1180,87,0 -chr1 82081 . C T 1143.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1172,87,0 -chr1 82082 . A G 1146.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=28.52;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1175,87,0 -chr1 82096 . T A 1128.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.09;MQ0=0;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1157,93,0 -chr1 82126 . G A 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.199;DP=37;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-1.977;QD=16.02;ReadPosRankSum=-0.169;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:621,0,501 -chr1 82156 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.862;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-0.011;QD=14.34;ReadPosRankSum=0.990;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:702,0,724 -chr1 82158 . T A 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=0.352;QD=13.81;ReadPosRankSum=1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:705,0,824 -chr1 82161 . C G 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.131;QD=16.63;ReadPosRankSum=-1.578;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:843,0,731 -chr1 82181 . T C 1791.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.84;MQ0=0;QD=33.17;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:51:99:1820,138,0 -chr1 82212 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.113;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.113;QD=17.12;ReadPosRankSum=0.788;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:970,0,654 -chr1 82270 . A C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=48;Dels=0.00;FS=7.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=-0.969;QD=11.54;ReadPosRankSum=0.224;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:582,0,945 -chr1 82315 . C T 1935.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.36;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1964,150,0 -chr1 82352 . G C 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.780;QD=14.59;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:787,0,872 -chr1 82367 . G A 907.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.433;DP=60;Dels=0.00;FS=0.988;HaplotypeScore=2.7001;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.509;QD=15.13;ReadPosRankSum=-0.630;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:60:99:936,0,959 -chr1 82385 . G T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.579;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=81.3181;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.230;QD=0.21;ReadPosRankSum=-3.378;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:55,6:62:41:41,0,1896 -chr1 82434 . T C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-1.087;QD=14.15;ReadPosRankSum=1.842;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:764,0,957 -chr1 82440 . G C 859.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=49;Dels=0.00;FS=1.092;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=0.955;QD=17.55;ReadPosRankSum=-1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:888,0,719 -chr1 82482 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=1.064;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=-1.757;QD=14.52;ReadPosRankSum=-1.194;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,24:51:99:769,0,899 -chr1 82487 . T A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=1;MQRankSum=-0.850;QD=15.32;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:794,0,848 -chr1 82613 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-1.183;QD=12.44;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,964 -chr1 82614 . A G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-0.539;QD=12.44;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,934 -chr1 82616 . G C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=1;MQRankSum=-2.266;QD=11.86;ReadPosRankSum=0.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:657,0,973 -chr1 82648 . A G 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=45;Dels=0.00;FS=5.254;HaplotypeScore=6.9393;MLEAC=1;MLEAF=0.500;MQ=52.78;MQ0=3;MQRankSum=-4.177;QD=3.93;ReadPosRankSum=-0.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,12:45:99:205,0,1095 -chr1 82650 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=43;Dels=0.00;FS=5.772;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=3;MQRankSum=-4.146;QD=2.51;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:136,0,1090 -chr1 82656 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=3;MQRankSum=4.699;QD=22.29;ReadPosRankSum=0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,27:41:99:942,0,189 -chr1 82658 . T G 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=42;Dels=0.00;FS=3.333;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=3;MQRankSum=-4.050;QD=2.66;ReadPosRankSum=-1.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:140,0,1017 -chr1 82668 . A C 1112.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.88;MQ0=3;QD=30.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:90:1141,90,0 -chr1 82690 . G T 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=40;Dels=0.00;FS=5.301;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=1;MQRankSum=-2.041;QD=8.64;ReadPosRankSum=-2.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:374,0,898 -chr1 82792 . T A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.636;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=0.289;QD=19.32;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:743,0,494 -chr1 82795 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.114;QD=11.86;ReadPosRankSum=1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:467,0,769 -chr1 82814 . G A 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.079;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.958;QD=8.48;ReadPosRankSum=0.707;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:359,0,871 -chr1 82877 . T C 1238.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.481;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.5775;MLEAC=2;MLEAF=1.00;MQ=59.05;MQ0=0;MQRankSum=0.385;QD=34.41;ReadPosRankSum=1.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:67:1267,67,0 -chr1 82878 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=36;Dels=0.00;FS=2.928;HaplotypeScore=2.5775;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.111;QD=15.72;ReadPosRankSum=-2.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:594,0,499 -chr1 82887 . T C 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.631;DP=36;Dels=0.00;FS=1.344;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.257;QD=11.41;ReadPosRankSum=2.246;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:439,0,686 -chr1 82936 . A T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=28;Dels=0.00;FS=10.544;HaplotypeScore=8.7318;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.839;QD=7.03;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:225,0,697 -chr1 82937 . G A 1059.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=7.7653;MLEAC=2;MLEAF=1.00;MQ=58.58;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1088,84,0 -chr1 82946 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.977;DP=34;Dels=0.00;FS=20.808;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.942;QD=14.52;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:522,0,487 -chr1 82981 . A C 1508.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=33.7746;MLEAC=2;MLEAF=1.00;MQ=57.89;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1537,117,0 -chr1 83013 . A T 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=48;Dels=0.00;FS=46.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.792;QD=11.70;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:590,0,915 -chr1 83024 . A G 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=42.658;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=1;MQRankSum=-2.045;QD=10.57;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:472,0,804 -chr1 83033 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;DP=39;Dels=0.00;FS=31.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=1;MQRankSum=-3.862;QD=6.79;ReadPosRankSum=2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:293,0,843 -chr1 83044 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.349;DP=37;Dels=0.00;FS=27.416;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=1;MQRankSum=-4.362;QD=6.40;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,11:37:99:265,0,839 -chr1 83083 . T C 872.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=27.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,23:23:66:901,66,0 -chr1 83091 . A G 855.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=28.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:884,66,0 -chr1 83162 . C T 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9867;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:682,51,0 -chr1 83337 . A C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.588;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=1;MQRankSum=-2.646;QD=10.34;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:9,8:17:99:204,0,330 -chr1 83398 . G T 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.192;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=0.778;QD=6.32;ReadPosRankSum=2.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:11,4:15:99:123,0,311 -chr1 83404 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=45.65;MQ0=1;MQRankSum=-1.157;QD=4.34;ReadPosRankSum=-1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:9,5:14:89:89,0,317 -chr1 83532 . G T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.264;DP=30;Dels=0.00;FS=5.946;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.56;MQ0=2;MQRankSum=-3.188;QD=6.56;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83509_83569) GT:AD:DP:GQ:PL 0/1:18,12:30:99:225,0,597 -chr1 83605 . A G 62.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=24;Dels=0.00;FS=7.799;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.85;MQ0=0;MQRankSum=-2.167;QD=2.62;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,6:24:91:91,0,606 -chr1 83629 . T G 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=19;Dels=0.00;FS=4.713;HaplotypeScore=1.7880;MLEAC=1;MLEAF=0.500;MQ=41.28;MQ0=0;MQRankSum=-2.268;QD=2.04;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,5:19:67:67,0,465 -chr1 83691 . T G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=35;Dels=0.00;FS=8.175;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=42.05;MQ0=0;MQRankSum=-0.020;QD=5.51;ReadPosRankSum=-1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,8:35:99:221,0,947 -chr1 83704 . C T 1319.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.35;MQ0=1;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1348,102,0 -chr1 83837 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.636;DP=30;Dels=0.00;FS=14.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.28;MQ0=2;MQRankSum=-3.738;QD=5.23;ReadPosRankSum=-0.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83730_84064) GT:AD:DP:GQ:PL 0/1:20,10:30:99:185,0,667 -chr1 84090 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.235;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.8663;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.440;QD=13.44;ReadPosRankSum=-0.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:539,0,732 -chr1 84156 . C T 1240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=56;Dels=0.00;FS=6.157;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-1.818;QD=22.16;ReadPosRankSum=0.463;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,39:56:99:1269,0,542 -chr1 84243 . G A 1544.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1573,120,0 -chr1 84266 . A C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.232;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.392;QD=11.12;ReadPosRankSum=-0.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:484,0,881 -chr1 84467 . C A 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.341;DP=48;Dels=0.00;FS=5.874;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.321;QD=14.87;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,877 -chr1 84548 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=61;Dels=0.00;FS=3.670;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=2.402;QD=16.54;ReadPosRankSum=1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1037,0,988 -chr1 84596 . C T 2308.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.50;MQ0=0;QD=26.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2337,178,0 -chr1 84601 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.270;DP=65;Dels=0.00;FS=2.135;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.172;QD=19.63;ReadPosRankSum=-0.797;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,39:65:99:1304,0,773 -chr1 84805 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.168;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.505;QD=19.46;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S113|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1001,0,641 -chr1 84858 . A C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.541;DP=42;Dels=0.00;FS=8.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.322;QD=16.95;ReadPosRankSum=1.876;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K131T|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,22:42:99:740,0,673 -chr1 84868 . C T 1590.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V134|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1619,123,0 -chr1 84880 . G A 1477.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L138|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1506,114,0 -chr1 84886 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.437;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.521;QD=14.58;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V140|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:21,18:39:99:597,0,712 -chr1 85016 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.347;QD=17.45;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:988,0,847 -chr1 85055 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.450;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.599;QD=16.34;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:992,0,999 -chr1 85064 . T C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=54;Dels=0.00;FS=3.998;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.488;QD=14.61;ReadPosRankSum=0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:817,0,887 -chr1 85114 . A G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.117;DP=47;Dels=0.00;FS=2.488;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=-1.011;QD=16.40;ReadPosRankSum=-0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:799,0,742 -chr1 85206 . A G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=-0.412;QD=14.65;ReadPosRankSum=-1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:834,0,932 -chr1 85257 . C T 2136.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=60.19;MQ0=0;QD=25.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2165,163,0 -chr1 85259 . T C 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.311;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=26.7919;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.070;QD=17.50;ReadPosRankSum=0.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,924 -chr1 85307 . G T 2188.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=23.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2217,166,0 -chr1 85388 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=56;Dels=0.00;FS=2.338;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.972;QD=17.91;ReadPosRankSum=2.060;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1031,0,826 -chr1 85403 . A G 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.803;DP=53;Dels=0.00;FS=3.822;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.045;QD=20.00;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1088,0,713 -chr1 85446 . T G 2073.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2102,157,0 -chr1 85454 . C A 1996.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2025,150,0 -chr1 85460 . A C 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=4.180;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=17.87;ReadPosRankSum=-2.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:886,0,741 -chr1 85552 . A C 1841.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.742;QD=31.35;ReadPosRankSum=-0.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,48:49:99:1870,141,0 -chr1 85658 . T A 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.2566;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.933;QD=12.97;ReadPosRankSum=2.850;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:560,0,680 -chr1 85709 . T A 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=30;Dels=0.00;FS=3.431;HaplotypeScore=15.9845;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.209;QD=17.76;ReadPosRankSum=1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:561,0,349 -chr1 85779 . A G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.928;DP=32;Dels=0.00;FS=10.207;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.042;QD=6.27;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,9:32:99:229,0,795 -chr1 85837 . A T 1322.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1351,102,0 -chr1 85866 . G A 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=15.4975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.788;QD=15.93;ReadPosRankSum=-1.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:506,0,472 -chr1 85928 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=31;Dels=0.00;FS=1.566;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.021;QD=22.54;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,21:31:99:727,0,300 -chr1 85964 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=32;Dels=0.00;FS=3.848;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.936;QD=26.59;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,24:32:99:879,0,222 -chr1 85983 . T C 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;QD=24.67;ReadPosRankSum=-0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:793,0,280 -chr1 85984 . A T 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.413;QD=24.19;ReadPosRankSum=-0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:778,0,283 -chr1 86057 . T A 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.117;QD=16.34;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:796,0,802 -chr1 86096 . T C 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.383;DP=47;Dels=0.00;FS=6.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.171;QD=18.42;ReadPosRankSum=0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:894,0,583 -chr1 86197 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.775;QD=15.83;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:614,0,592 -chr1 86283 . T G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=81;Dels=0.00;FS=11.183;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-1.581;QD=7.98;ReadPosRankSum=-5.926;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:45,36:81:99:675,0,1045 -chr1 86295 . G A 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-0.694;QD=2.69;ReadPosRankSum=-1.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,17:79:99:241,0,1690 -chr1 86334 . C T 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=-1.600;QD=18.65;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:942,0,629 -chr1 86368 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.010;QD=17.87;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:904,0,769 -chr1 86487 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.006;DP=60;Dels=0.00;FS=3.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-2.588;QD=18.93;ReadPosRankSum=1.410;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1164,0,811 -chr1 86494 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.597;DP=62;Dels=0.00;FS=1.012;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.077;QD=11.83;ReadPosRankSum=-0.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:762,0,1311 -chr1 86710 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.161;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=15.58;ReadPosRankSum=-1.135;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:667,0,725 -chr1 86780 . T C 1962.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1991,150,0 -chr1 86783 . T C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.254;DP=51;Dels=0.00;FS=1.083;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.98;ReadPosRankSum=0.141;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:843,0,891 -chr1 86812 . C G 2201.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=28.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2230,172,0 -chr1 86874 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.055;DP=46;Dels=0.00;FS=2.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.587;QD=18.63;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,605 -chr1 86928 . A T 1814.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=28.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1843,138,0 -chr1 86945 . C T 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.551;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.651;QD=15.59;ReadPosRankSum=-1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:792,0,917 -chr1 87016 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.274;DP=53;Dels=0.00;FS=2.380;HaplotypeScore=46.7458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.134;QD=15.01;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,910 -chr1 87161 . A G 1557.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=15.2776;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1586,117,0 -chr1 87182 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=65.7226;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.562;QD=16.77;ReadPosRankSum=-1.948;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:716,0,647 -chr1 87257 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.809;DP=42;Dels=0.00;FS=2.756;HaplotypeScore=3.9986;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.202;QD=14.71;ReadPosRankSum=-0.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:646,0,809 -chr1 87282 . C T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=11.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;QD=17.97;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:783,0,641 -chr1 87399 . T A 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.840;DP=43;Dels=0.00;FS=4.388;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.426;QD=15.41;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:691,0,818 -chr1 87964 . T C 1652.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=31.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R2079|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_87910_88146) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1681,126,0 -chr1 88214 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.856;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4710;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.316;QD=17.04;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,23:45:99:795,0,623 -chr1 88242 . A C 1458.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=59.07;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1487,111,0 -chr1 88243 . G A 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.274;DP=40;Dels=0.00;FS=2.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.465;QD=19.67;ReadPosRankSum=-2.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:815,0,487 -chr1 88460 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.222;DP=41;Dels=0.00;FS=4.561;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.874;QD=15.80;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:676,0,700 -chr1 88534 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=50;Dels=0.00;FS=13.391;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.545;QD=14.54;ReadPosRankSum=-1.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1964|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_88510_88890) GT:AD:DP:GQ:PL 0/1:27,23:50:99:755,0,913 -chr1 88912 . A C 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.131;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-1.268;QD=13.31;ReadPosRankSum=-0.971;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:627,0,862 -chr1 88959 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.476;DP=56;Dels=0.00;FS=9.559;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.590;QD=15.78;ReadPosRankSum=0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:912,0,1002 -chr1 88961 . C G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=58;Dels=0.00;FS=11.723;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.661;QD=17.50;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,950 -chr1 88987 . A G 2405.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=30.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2434,184,0 -chr1 89344 . G C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=61;Dels=0.00;FS=5.322;HaplotypeScore=2.9937;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=1;MQRankSum=-0.052;QD=16.77;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1051,0,895 -chr1 89418 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.659;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=0.521;QD=18.45;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1793|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89391_89495) GT:AD:DP:GQ:PL 0/1:19,25:44:99:840,0,514 -chr1 89522 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.620;DP=45;Dels=0.00;FS=11.478;HaplotypeScore=103.5819;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.517;QD=13.15;ReadPosRankSum=-1.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:620,0,881 -chr1 89531 . A G 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=114.0798;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=1;MQRankSum=-0.041;QD=1.14;ReadPosRankSum=-1.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,9:50:85:85,0,1381 -chr1 89635 . T G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.207;DP=56;Dels=0.00;FS=7.797;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.737;QD=18.12;ReadPosRankSum=0.339;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N1762H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1043,0,749 -chr1 89720 . T C 1891.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.88;MQ0=0;QD=30.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1733|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1920,144,0 -chr1 89745 . A G 1759.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M1725T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1788,135,0 -chr1 89792 . G A 2016.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V1709|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2045,159,0 -chr1 89954 . T C 1227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.449;DP=64;Dels=0.00;FS=2.069;HaplotypeScore=2.6551;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.884;QD=19.18;ReadPosRankSum=1.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,37:64:99:1256,0,894 -chr1 90005 . A G 1150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=58;Dels=0.00;FS=3.623;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.523;QD=19.84;ReadPosRankSum=0.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1179,0,842 -chr1 90289 . C T 1801.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1597T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1830,141,0 -chr1 90303 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.343;DP=46;Dels=0.00;FS=5.030;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.388;QD=13.49;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I1592T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 0/1:26,20:46:99:649,0,883 -chr1 90520 . C T 496.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=7.375;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-0.693;QD=23.66;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:18:525,0,18 -chr1 90521 . C T 488.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;DP=21;Dels=0.00;FS=8.316;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-1.197;QD=23.24;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:12:516,0,12 -chr1 90525 . C T 577.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=43.4929;MLEAC=2;MLEAF=1.00;MQ=55.62;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,18:19:51:606,51,0 -chr1 90567 . G A 583.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=15.0334;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=34.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:612,48,0 -chr1 90588 . A G 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.589;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.768;QD=8.06;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:262,0,686 -chr1 90590 . T C 1086.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1115,84,0 -chr1 90591 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.430;DP=30;Dels=0.00;FS=1.987;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.387;QD=21.59;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,19:30:99:676,0,304 -chr1 90977 . G T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.999;DP=45;Dels=0.00;FS=4.453;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.857;QD=13.48;ReadPosRankSum=-1.633;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:635,0,845 -chr1 90985 . T C 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=47;Dels=0.00;FS=4.385;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.160;QD=12.29;ReadPosRankSum=0.228;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:606,0,909 -chr1 91106 . T C 1596.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.51;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1625,120,0 -chr1 91526 . G C 509.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=2.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.065;QD=12.14;ReadPosRankSum=-0.842;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:538,0,882 -chr1 91614 . A C 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.445;QD=17.90;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:1013,0,821 -chr1 91617 . T A 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.288;QD=18.19;ReadPosRankSum=1.043;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1047,0,834 -chr1 91650 . C A 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=42;Dels=0.00;FS=1.831;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.893;QD=0.88;ReadPosRankSum=-2.796;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q1346H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:37,5:42:65:65,0,1325 -chr1 91722 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.741;DP=50;Dels=0.00;FS=4.367;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.000;QD=10.08;ReadPosRankSum=0.676;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1322|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:33,17:50:99:532,0,996 -chr1 91774 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.765;QD=13.25;ReadPosRankSum=-1.230;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:823,0,1195 -chr1 91973 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.239;QD=15.71;ReadPosRankSum=-1.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1269|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:20,22:42:99:688,0,658 -chr1 91976 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.609;DP=46;Dels=0.00;FS=6.133;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.277;QD=12.97;ReadPosRankSum=2.338;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1268|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:26,20:46:99:625,0,846 -chr1 92011 . A C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=56;Dels=0.00;FS=7.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.813;QD=19.53;ReadPosRankSum=1.995;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1257A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1122,0,788 -chr1 92186 . G A 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;DP=35;Dels=0.00;FS=5.368;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.083;QD=16.51;ReadPosRankSum=-0.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1198|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:16,19:35:99:606,0,541 -chr1 92279 . A G 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=41;Dels=0.00;FS=6.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.090;QD=18.92;ReadPosRankSum=0.775;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:804,0,592 -chr1 92300 . C G 1407.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.55;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1436,108,0 -chr1 92325 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.810;DP=44;Dels=0.00;FS=6.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.692;QD=16.40;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:750,0,740 -chr1 92362 . A G 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.701;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.214;QD=14.48;ReadPosRankSum=0.097;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:752,0,920 -chr1 92420 . A C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=46;Dels=0.00;FS=6.635;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.404;QD=10.39;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,16:46:99:506,0,1054 -chr1 92426 . C T 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=42;Dels=0.00;FS=9.664;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.680;QD=9.99;ReadPosRankSum=0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:448,0,1021 -chr1 92459 . G A 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=41;Dels=0.00;FS=2.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.521;QD=11.87;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:515,0,892 -chr1 92463 . G A 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=43;Dels=0.00;FS=2.743;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.406;QD=12.99;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:587,0,880 -chr1 92529 . T A 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=1.253;QD=16.77;ReadPosRankSum=0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:984,0,918 -chr1 92647 . A G 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.840;QD=9.40;ReadPosRankSum=0.680;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:423,0,976 -chr1 92758 . T A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.338;DP=53;Dels=0.00;FS=3.955;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.930;QD=10.18;ReadPosRankSum=1.380;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:568,0,1136 -chr1 92787 . A G 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=68;Dels=0.00;FS=3.335;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.142;QD=13.50;ReadPosRankSum=0.377;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:946,0,1223 -chr1 92856 . G C 2242.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.58;MQ0=1;QD=29.11;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2271,172,0 -chr1 92881 . G T 1034.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.472;DP=57;Dels=0.00;FS=9.783;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=1.051;QD=18.15;ReadPosRankSum=-0.803;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1063,0,740 -chr1 92887 . A G 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.408;DP=56;Dels=0.00;FS=2.506;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=1;MQRankSum=0.126;QD=15.62;ReadPosRankSum=0.008;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:903,0,715 -chr1 92906 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=64;Dels=0.00;FS=2.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=2;MQRankSum=1.450;QD=13.48;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,30:64:99:891,0,1127 -chr1 93051 . G C 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=67;Dels=0.00;FS=0.945;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.436;QD=19.41;ReadPosRankSum=-0.576;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,38:67:99:1329,0,959 -chr1 93126 . T G 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.349;QD=21.83;ReadPosRankSum=-0.099;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1207,0,605 -chr1 93129 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=0.905;QD=22.01;ReadPosRankSum=0.242;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1217,0,604 -chr1 93143 . G C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.109;DP=51;Dels=0.00;FS=2.448;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.287;QD=11.86;ReadPosRankSum=-1.357;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:51:99:633,0,1071 -chr1 93221 . G C 960.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=59;Dels=0.00;FS=0.998;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.371;QD=16.28;ReadPosRankSum=0.387;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:989,0,965 -chr1 93235 . G A 1138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=63;Dels=0.00;FS=2.089;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=1.110;QD=18.08;ReadPosRankSum=-0.779;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,34:63:99:1167,0,900 -chr1 93270 . T C 2111.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.10;MQ0=0;QD=30.32;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2140,160,0 -chr1 93280 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.487;DP=52;Dels=0.00;FS=4.010;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.194;QD=13.11;ReadPosRankSum=3.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:710,0,1066 -chr1 93282 . G C 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.616;DP=49;Dels=0.00;FS=4.055;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.636;QD=14.02;ReadPosRankSum=3.222;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:715,0,961 -chr1 93283 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.394;DP=50;Dels=0.00;FS=2.447;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.10;MQ0=0;MQRankSum=-1.065;QD=14.36;ReadPosRankSum=2.746;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:746,0,976 -chr1 93306 . A T 2098.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.20;MQ0=0;QD=32.01;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2127,160,0 -chr1 93333 . C T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.258;DP=53;Dels=0.00;FS=5.940;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=0.454;QD=15.32;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:840,0,924 -chr1 93352 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=57;Dels=0.00;FS=11.817;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.745;QD=15.03;ReadPosRankSum=1.402;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:885,0,1090 -chr1 93358 . A C 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.132;DP=56;Dels=0.00;FS=12.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.231;QD=14.50;ReadPosRankSum=1.615;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,1093 -chr1 93504 . G A 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.233;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.560;QD=16.00;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,29:59:99:972,0,962 -chr1 93508 . G C 2130.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.9988;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.10;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2159,163,0 -chr1 93567 . A G 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=59;Dels=0.00;FS=2.347;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.177;QD=9.56;ReadPosRankSum=0.344;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,20:59:99:592,0,1326 -chr1 93595 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=4.620;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=7.95;ReadPosRankSum=-0.586;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,14:49:99:418,0,1282 -chr1 93676 . A G 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.019;QD=17.14;ReadPosRankSum=1.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1167|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93628_93699) GT:AD:DP:GQ:PL 0/1:27,28:55:99:971,0,908 -chr1 93754 . T A 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.413;DP=58;Dels=0.00;FS=5.597;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=11.58;ReadPosRankSum=-0.111;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,23:58:99:700,0,1216 -chr1 93879 . T C 1833.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.96;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1137|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1862,141,0 -chr1 93903 . G T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.782;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.011;QD=16.62;ReadPosRankSum=-0.261;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I1129|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:22,23:45:99:776,0,668 -chr1 93906 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=1.9830;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.098;QD=14.46;ReadPosRankSum=0.309;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1128|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:25,22:47:99:708,0,860 -chr1 93998 . A G 2112.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=2.5774;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.68;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2141,163,0 -chr1 94001 . A G 893.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=53;Dels=0.00;FS=2.323;HaplotypeScore=1.5782;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.240;QD=16.86;ReadPosRankSum=0.827;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:922,0,890 -chr1 94020 . G C 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.912;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.331;QD=15.44;ReadPosRankSum=1.733;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:785,0,888 -chr1 94164 . A G 839.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.879;QD=15.00;ReadPosRankSum=-0.501;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1084|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94102_94193) GT:AD:DP:GQ:PL 0/1:30,26:56:99:868,0,1033 -chr1 94307 . G A 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.403;QD=17.66;ReadPosRankSum=-0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:876,0,754 -chr1 94331 . G T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.887;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.692;QD=15.95;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:714,0,748 -chr1 94476 . G T 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.404;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=1;MQRankSum=0.350;QD=18.87;ReadPosRankSum=-1.498;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1047,0,739 -chr1 94499 . C T 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.740;DP=55;Dels=0.00;FS=1.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.531;QD=13.83;ReadPosRankSum=0.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:789,0,1061 -chr1 94679 . A G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.046;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.70;ReadPosRankSum=-0.198;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1005|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94543_94708) GT:AD:DP:GQ:PL 0/1:26,25:51:99:829,0,859 -chr1 94743 . G A 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.225;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-1.258;QD=9.38;ReadPosRankSum=3.272;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:366,0,807 -chr1 94753 . A C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.8896;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-0.225;QD=9.94;ReadPosRankSum=0.898;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:386,0,718 -chr1 94840 . A C 753.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.135;DP=58;Dels=0.00;FS=0.999;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.272;QD=13.00;ReadPosRankSum=-0.455;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S985A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:33,25:58:99:782,0,1167 -chr1 94856 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.040;QD=18.01;ReadPosRankSum=0.523;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L979|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1055,0,767 -chr1 94898 . G A 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.088;DP=57;Dels=0.00;FS=2.219;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.679;QD=16.35;ReadPosRankSum=-2.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L965|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:27,30:57:99:960,0,917 -chr1 94963 . C A 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.668;QD=16.69;ReadPosRankSum=-0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:896,0,874 -chr1 94973 . A T 2138.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2167,163,0 -chr1 95134 . T C 2154.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T933A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95058_95208) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2183,169,0 -chr1 95594 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;DP=53;Dels=0.00;FS=5.738;HaplotypeScore=2.6552;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=0.085;QD=17.22;ReadPosRankSum=0.349;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G817|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95323_95596) GT:AD:DP:GQ:PL 0/1:24,28:53:99:941,0,742 -chr1 95809 . G A 1511.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.57;MQ0=0;QD=34.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1540,114,0 -chr1 96016 . C T 1313.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1342,99,0 -chr1 96111 . A C 1249.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.76;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1278,96,0 -chr1 96124 . A G 1357.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.72;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1386,105,0 -chr1 96214 . A T 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.364;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.622;QD=15.04;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1036,0,1067 -chr1 96224 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.656;QD=15.16;ReadPosRankSum=-2.171;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:953,0,1050 -chr1 96308 . T C 2053.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.62;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2082,154,0 -chr1 96309 . A G 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.522;DP=54;Dels=0.00;FS=7.971;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.262;QD=13.66;ReadPosRankSum=-2.029;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:766,0,1037 -chr1 96335 . G T 1948.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;QD=30.44;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1977,147,0 -chr1 96360 . G A 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.447;DP=58;Dels=0.00;FS=3.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=1.081;QD=15.86;ReadPosRankSum=-0.864;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,883 -chr1 96399 . T G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=51;Dels=0.00;FS=8.273;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.902;QD=17.76;ReadPosRankSum=1.618;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:934,0,788 -chr1 96448 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.536;DP=51;Dels=0.00;FS=4.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.121;QD=17.09;ReadPosRankSum=-1.479;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:900,0,792 -chr1 96485 . A T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=44;Dels=0.00;FS=2.672;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=0.141;QD=15.77;ReadPosRankSum=0.987;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T806|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:23,21:44:99:722,0,775 -chr1 96530 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.746;QD=18.04;ReadPosRankSum=0.526;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N791|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:19,24:43:99:804,0,602 -chr1 96637 . G A 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.628;QD=15.17;ReadPosRankSum=-1.798;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:741,0,788 -chr1 96789 . C T 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;DP=69;Dels=0.00;FS=0.918;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=1;MQRankSum=0.417;QD=15.65;ReadPosRankSum=1.436;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1108,0,1126 -chr1 96791 . T C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=1.110;QD=15.59;ReadPosRankSum=1.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:1057,0,1086 -chr1 96809 . C T 2747.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=1;QD=26.52;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2776,205,0 -chr1 96822 . T G 1272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=73;Dels=0.00;FS=1.969;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=1;MQRankSum=-0.475;QD=17.44;ReadPosRankSum=-0.328;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,40:73:99:1301,0,1128 -chr1 96868 . A T 1270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=72;Dels=0.00;FS=7.826;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.620;QD=17.65;ReadPosRankSum=0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1299,0,1177 -chr1 96880 . C T 1144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;DP=65;Dels=0.00;FS=3.414;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.795;QD=17.61;ReadPosRankSum=-0.729;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1173,0,1062 -chr1 96881 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.233;DP=62;Dels=0.00;FS=4.010;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.752;QD=8.00;ReadPosRankSum=0.101;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,18:62:99:524,0,1555 -chr1 96885 . G T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=2.212;HaplotypeScore=11.9973;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.053;QD=17.23;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1045,0,994 -chr1 97080 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.185;DP=53;Dels=0.00;FS=3.844;HaplotypeScore=4.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.312;QD=15.58;ReadPosRankSum=-1.630;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L759S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:28,25:53:99:854,0,987 -chr1 97141 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.017;DP=35;Dels=0.00;FS=7.260;HaplotypeScore=3.5776;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.183;QD=19.31;ReadPosRankSum=2.450;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P739S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:15,20:35:99:704,0,461 -chr1 97145 . G A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=37;Dels=0.00;FS=2.995;HaplotypeScore=5.4724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.461;QD=20.48;ReadPosRankSum=1.021;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P737|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:13,23:37:99:786,0,395 -chr1 97223 . A C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=0.412;QD=14.31;ReadPosRankSum=0.443;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,28:58:99:858,0,1018 -chr1 97268 . G T 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.938;DP=63;Dels=0.00;FS=2.132;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.326;QD=12.76;ReadPosRankSum=-0.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:832,0,1288 -chr1 97299 . A G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.648;QD=14.48;ReadPosRankSum=-0.290;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,28:62:99:926,0,1199 -chr1 97312 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.498;DP=67;Dels=0.00;FS=0.988;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.608;QD=13.74;ReadPosRankSum=1.761;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1344 -chr1 97491 . T G 2512.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7219;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=30.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2541,193,0 -chr1 97631 . G C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.243;DP=55;Dels=0.00;FS=2.478;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.377;QD=11.76;ReadPosRankSum=-0.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A723G|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97615_97666) GT:AD:DP:GQ:PL 0/1:34,21:55:99:675,0,1153 -chr1 97696 . C T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.902;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.101;QD=12.26;ReadPosRankSum=1.362;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,18:46:99:592,0,888 -chr1 97749 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.914;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.748;QD=13.02;ReadPosRankSum=-0.831;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:653,0,801 -chr1 97919 . A T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=46;Dels=0.00;FS=4.288;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.066;QD=16.41;ReadPosRankSum=-0.945;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:783,0,771 -chr1 97946 . C G 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.771;DP=41;Dels=0.00;FS=2.814;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.879;QD=14.68;ReadPosRankSum=-1.799;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,20:41:99:630,0,670 -chr1 98038 . A G 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.277;DP=50;Dels=0.00;FS=1.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.019;QD=17.68;ReadPosRankSum=0.564;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:912,0,770 -chr1 98051 . A T 1890.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.05;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1919,144,0 -chr1 98140 . A G 1419.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=31.65;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1448,108,0 -chr1 98179 . G T 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.164;DP=54;Dels=0.00;FS=3.840;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.099;QD=16.44;ReadPosRankSum=1.013;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:916,0,864 -chr1 98231 . T A 2348.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.96;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2377,178,0 -chr1 98270 . A T 2354.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2383,178,0 -chr1 98294 . A G 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=52;Dels=0.00;FS=8.574;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-1.000;QD=15.21;ReadPosRankSum=0.707;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:819,0,922 -chr1 98466 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.245;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.607;QD=15.61;ReadPosRankSum=-2.224;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:762,0,808 -chr1 98495 . G A 994.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.390;QD=19.51;ReadPosRankSum=-1.113;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:1023,0,696 -chr1 98562 . A C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=55;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.698;QD=12.67;ReadPosRankSum=-0.572;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:725,0,1123 -chr1 98613 . T C 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=41;Dels=0.00;FS=4.457;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.327;QD=14.31;ReadPosRankSum=1.011;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:615,0,801 -chr1 98666 . A T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.742;DP=47;Dels=0.00;FS=2.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=1.116;QD=18.97;ReadPosRankSum=-3.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:920,0,631 -chr1 98933 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=1;MQRankSum=-0.034;QD=16.22;ReadPosRankSum=0.612;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1066,0,1072 -chr1 99114 . A T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.229;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.092;QD=14.05;ReadPosRankSum=-1.037;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I608|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:28,24:52:99:759,0,894 -chr1 99351 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=45;Dels=0.00;FS=2.527;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.683;QD=11.93;ReadPosRankSum=0.637;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L529|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,18:45:99:565,0,935 -chr1 99567 . T G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=12.036;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=0;MQRankSum=0.412;QD=14.02;ReadPosRankSum=-0.533;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E457D|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,22:49:99:715,0,877 -chr1 99633 . A G 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.770;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9944;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=1.259;QD=13.09;ReadPosRankSum=-0.599;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S435|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,731 -chr1 99642 . C T 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.702;QD=11.25;ReadPosRankSum=-0.579;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V432|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:25,18:43:99:512,0,818 -chr1 99729 . G A 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.652;DP=53;Dels=0.00;FS=3.841;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.298;QD=18.45;ReadPosRankSum=-1.670;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G403|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1006,0,723 -chr1 99861 . A G 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.654;DP=48;Dels=0.00;FS=2.555;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.822;QD=18.89;ReadPosRankSum=-1.581;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S359|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:19,29:48:99:935,0,572 -chr1 100026 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=-0.156;QD=20.77;ReadPosRankSum=-0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:859,0,407 -chr1 100458 . A C 2457.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F240L|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100334_100464) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2486,187,0 -chr1 100484 . A C 2630.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2659,199,0 -chr1 100660 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.981;QD=10.20;ReadPosRankSum=1.005;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:569,0,1225 -chr1 100710 . A C 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.633;DP=58;Dels=0.00;FS=1.023;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.213;QD=16.46;ReadPosRankSum=-1.944;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F235C|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,29:58:99:983,0,1001 -chr1 100778 . A T 1005.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=60;Dels=0.00;FS=2.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.139;QD=16.76;ReadPosRankSum=0.888;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A212|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1034,0,964 -chr1 100875 . C A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=46;Dels=0.00;FS=1.178;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.963;QD=14.84;ReadPosRankSum=-0.794;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:711,0,861 -chr1 100917 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.969;DP=54;Dels=0.00;FS=3.266;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.189;QD=3.81;ReadPosRankSum=-3.129;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:234,0,1538 -chr1 101397 . A G 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.492;QD=15.28;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:899,0,799 -chr1 101547 . A G 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=65;Dels=0.00;FS=10.521;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.833;QD=15.89;ReadPosRankSum=-0.151;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1061,0,1064 -chr1 101623 . T C 2368.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=24.90;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2397,181,0 -chr1 101683 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.992;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.040;QD=12.41;ReadPosRankSum=0.437;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:537,0,822 -chr1 101684 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.439;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.910;QD=13.31;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:534,0,741 -chr1 101745 . G A 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.536;DP=56;Dels=0.00;FS=3.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.107;QD=15.39;ReadPosRankSum=0.715;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:890,0,1039 -chr1 101797 . C A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=66;Dels=0.00;FS=0.940;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.032;QD=16.34;ReadPosRankSum=-0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1107,0,1179 -chr1 101798 . C T 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=69;Dels=0.00;FS=1.986;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=16.27;ReadPosRankSum=-0.582;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:69:99:1151,0,1212 -chr1 101823 . C T 2664.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.40;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2693,202,0 -chr1 101901 . C T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.165;DP=38;Dels=0.00;FS=6.942;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.407;QD=20.49;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:807,0,440 -chr1 101928 . T A 1680.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=38.41;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1709,129,0 -chr1 101943 . G C 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.433;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.144;QD=21.97;ReadPosRankSum=-0.445;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,30:45:99:1017,0,464 -chr1 101964 . A T 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.379;QD=14.30;ReadPosRankSum=-0.037;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:643,0,818 -chr1 102084 . T C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.787;DP=61;Dels=0.00;FS=0.974;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.816;QD=16.77;ReadPosRankSum=0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1051,0,930 -chr1 102113 . A C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=-1.220;QD=15.40;ReadPosRankSum=0.579;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:860,0,828 -chr1 102117 . C A 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=55;Dels=0.00;FS=2.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=1;MQRankSum=-1.307;QD=14.85;ReadPosRankSum=1.030;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:845,0,861 -chr1 102158 . T C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=54;Dels=0.00;FS=2.323;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=1;MQRankSum=1.951;QD=15.22;ReadPosRankSum=0.526;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:850,0,846 -chr1 102167 . G A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=57;Dels=0.00;FS=5.494;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=2;MQRankSum=0.806;QD=16.59;ReadPosRankSum=-2.418;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:974,0,828 -chr1 102180 . T A 2213.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=2;QD=25.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2242,166,0 -chr1 102205 . T C 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=59;Dels=0.00;FS=1.030;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-0.661;QD=15.50;ReadPosRankSum=0.770;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:943,0,978 -chr1 102214 . G C 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-2.208;QD=15.30;ReadPosRankSum=-1.135;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:931,0,1005 -chr1 102348 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=44;Dels=0.00;FS=11.766;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.295;QD=18.20;ReadPosRankSum=-0.554;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:829,0,650 -chr1 102411 . T A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.145;DP=43;Dels=0.00;FS=2.999;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.308;QD=18.02;ReadPosRankSum=-0.382;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:803,0,602 -chr1 102443 . C T 1665.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=69.5886;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=30.29;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1694,126,0 -chr1 102454 . T A 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.682;DP=46;Dels=0.00;FS=19.456;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=1.572;QD=16.93;ReadPosRankSum=-1.352;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:807,0,705 -chr1 102506 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.117;DP=36;Dels=0.00;FS=5.231;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=-1.950;QD=17.69;ReadPosRankSum=0.317;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:665,0,522 -chr1 102514 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;DP=39;Dels=0.00;FS=7.216;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=1;MQRankSum=0.617;QD=14.10;ReadPosRankSum=-0.264;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:578,0,741 -chr1 102576 . C G 1795.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.71;MQ0=2;QD=31.84;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1824,135,0 -chr1 102597 . T A 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.154;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=-0.495;QD=17.25;ReadPosRankSum=1.374;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:839,0,693 -chr1 102632 . G A 1747.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=1;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1776,135,0 -chr1 102685 . T C 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=48;Dels=0.00;FS=11.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-2.270;QD=15.41;ReadPosRankSum=-0.310;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:768,0,789 -chr1 102745 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=57;Dels=0.00;FS=1.037;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.626;QD=12.54;ReadPosRankSum=0.203;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:743,0,1192 -chr1 102828 . T A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.556;QD=13.44;ReadPosRankSum=-1.748;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:687,0,969 -chr1 102840 . C T 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.773;DP=49;Dels=0.00;FS=2.600;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.317;QD=11.49;ReadPosRankSum=-0.425;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:591,0,1069 -chr1 102853 . A T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=51;Dels=0.00;FS=4.012;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.453;QD=20.98;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1098,0,644 -chr1 103138 . A T 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=57;Dels=0.00;FS=3.801;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.010;QD=17.93;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1050,0,812 -chr1 103150 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=53;Dels=0.00;FS=2.466;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=2;MQRankSum=0.274;QD=14.58;ReadPosRankSum=-0.632;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:801,0,943 -chr1 103189 . A G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=55;Dels=0.00;FS=4.291;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=1;MQRankSum=0.854;QD=12.70;ReadPosRankSum=1.329;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:727,0,1140 -chr1 103225 . G A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.322;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=1;MQRankSum=1.023;QD=15.72;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:877,0,949 -chr1 103405 . C T 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=57;Dels=0.00;FS=2.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.280;QD=17.24;ReadPosRankSum=1.223;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1011,0,920 -chr1 103515 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=2.536;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.222;QD=13.79;ReadPosRankSum=-0.778;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:704,0,944 -chr1 103542 . G C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229;DP=44;Dels=0.00;FS=2.800;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=19.31;ReadPosRankSum=-1.492;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:878,0,558 -chr1 103599 . C G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.7842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.583;QD=15.71;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,22:46:99:751,0,773 -chr1 103609 . A C 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=48;Dels=0.00;FS=4.201;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.330;QD=16.89;ReadPosRankSum=-1.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:839,0,793 -chr1 103612 . C T 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=49;Dels=0.00;FS=1.101;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.130;QD=17.30;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:876,0,826 -chr1 103621 . G T 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;QD=17.70;ReadPosRankSum=-1.915;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:931,0,802 -chr1 103691 . C A 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=60;Dels=0.00;FS=2.252;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.061;QD=21.20;ReadPosRankSum=2.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,37:60:99:1300,0,754 -chr1 103828 . C G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=55;Dels=0.00;FS=7.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=0.227;QD=17.23;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:976,0,894 -chr1 103856 . C T 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=49;Dels=0.00;FS=16.948;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=-1.149;QD=12.02;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:617,0,1000 -chr1 103995 . G A 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.761;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.440;QD=12.81;ReadPosRankSum=-0.510;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,26:63:99:835,0,1325 -chr1 104120 . C G 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=54;Dels=0.00;FS=5.785;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.227;QD=12.09;ReadPosRankSum=-1.032;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:681,0,1040 -chr1 104149 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=51;Dels=0.00;FS=2.555;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.048;QD=19.29;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1012,0,605 -chr1 104155 . A G 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.401;DP=49;Dels=0.00;FS=4.412;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.798;QD=10.73;ReadPosRankSum=2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,17:49:99:554,0,1041 -chr1 104159 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=51;Dels=0.00;FS=4.244;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-1.120;QD=11.25;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:602,0,1079 -chr1 104167 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=2.473;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.109;QD=12.25;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,20:51:99:653,0,1056 -chr1 104213 . C T 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.709;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.104;QD=13.73;ReadPosRankSum=-1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:756,0,1034 -chr1 104372 . G A 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,156,0 -chr1 104376 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=53;Dels=0.00;FS=10.088;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.367;QD=18.28;ReadPosRankSum=-1.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,29:53:99:997,0,714 -chr1 104545 . A C 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.847;QD=17.70;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1108,0,937 -chr1 104549 . C A 2426.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2455,184,0 -chr1 104570 . G T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.314;DP=66;Dels=0.00;FS=2.084;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.212;QD=16.97;ReadPosRankSum=0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1148,0,1049 -chr1 104631 . T A 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.341;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.7461;MLEAC=1;MLEAF=0.500;MQ=60.16;MQ0=0;MQRankSum=-1.676;QD=15.18;ReadPosRankSum=-0.596;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:1045,0,1181 -chr1 104738 . A T 1287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=70;Dels=0.00;FS=10.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.242;QD=18.40;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1316,0,1019 -chr1 104775 . C A 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=61;Dels=0.00;FS=2.287;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.380;QD=20.29;ReadPosRankSum=0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,37:61:99:1266,0,700 -chr1 104901 . T G 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.076;DP=55;Dels=0.00;FS=2.401;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.582;QD=18.03;ReadPosRankSum=0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1020,0,851 -chr1 104914 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.187;QD=15.35;ReadPosRankSum=-0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,26:54:99:857,0,929 -chr1 105215 . A G 1426.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1455,111,0 -chr1 105276 . A G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=49;Dels=0.02;FS=1.174;HaplotypeScore=2.9659;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.120;QD=20.71;ReadPosRankSum=0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:48:99:1043,0,542 -chr1 105289 . C A 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=0.027;QD=19.57;ReadPosRankSum=0.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1085,0,685 -chr1 105333 . G A 2241.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=1;QD=30.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2270,169,0 -chr1 105363 . G A 2110.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=1;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2139,160,0 -chr1 105391 . A G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=59;Dels=0.00;FS=7.470;HaplotypeScore=3.5213;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=12.00;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,23:59:99:736,0,1250 -chr1 105594 . A G 2739.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=3.2358;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2768,214,0 -chr1 105636 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=70;Dels=0.00;FS=8.071;HaplotypeScore=4.6697;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.786;QD=15.83;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:70:99:1136,0,1128 -chr1 105656 . G A 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;DP=63;Dels=0.00;FS=6.709;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-1.218;QD=15.63;ReadPosRankSum=-0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1013,0,1033 -chr1 105661 . T A 1957.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=36.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1986,147,0 -chr1 105662 . T A 2023.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=25.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2052,153,0 -chr1 105733 . T G 2248.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.503;DP=62;Dels=0.00;FS=3.153;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;MQRankSum=0.335;QD=30.29;ReadPosRankSum=1.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,61:62:99:2277,135,0 -chr1 105750 . C T 2320.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2349,175,0 -chr1 105769 . C G 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=68;Dels=0.00;FS=3.397;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.071;QD=13.58;ReadPosRankSum=1.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,31:68:99:952,0,1291 -chr1 105775 . A G 1185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=2.634;QD=17.97;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1214,0,951 -chr1 105776 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.385;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.105;QD=13.42;ReadPosRankSum=0.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:914,0,1186 -chr1 105815 . C A 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;DP=65;Dels=0.00;FS=2.177;HaplotypeScore=2.3346;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=0.388;QD=17.30;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1153,0,982 -chr1 105914 . A G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.125;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.402;QD=19.33;ReadPosRankSum=1.939;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1014,0,607 -chr1 105940 . A G 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.169;DP=55;Dels=0.00;FS=1.036;HaplotypeScore=6.1984;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.580;QD=11.83;ReadPosRankSum=1.117;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,21:55:99:679,0,1160 -chr1 106000 . G A 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.619;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.475;QD=15.08;ReadPosRankSum=-0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,23:48:99:752,0,840 -chr1 106003 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.730;QD=15.87;ReadPosRankSum=-0.650;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,24:49:99:806,0,839 -chr1 106222 . A T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.445;DP=56;Dels=0.00;FS=3.858;HaplotypeScore=2.9889;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.294;QD=10.64;ReadPosRankSum=-1.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,22:56:99:624,0,1107 -chr1 106301 . G A 1226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=76;Dels=0.00;FS=3.172;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.057;QD=16.14;ReadPosRankSum=-0.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,38:76:99:1255,0,1277 -chr1 106304 . C T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.244;DP=75;Dels=0.00;FS=3.136;HaplotypeScore=1.6988;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.178;QD=14.90;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,36:75:99:1146,0,1287 -chr1 106352 . T A 2717.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2746,208,0 -chr1 106447 . C A 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;DP=58;Dels=0.00;FS=3.667;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=1.169;QD=15.17;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:908,0,1064 -chr1 106476 . T G 1349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=77;Dels=0.00;FS=16.431;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=1.137;QD=17.53;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,40:77:99:1378,0,1148 -chr1 106481 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=76;Dels=0.00;FS=14.274;HaplotypeScore=3.8312;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.091;QD=12.37;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,32:76:99:968,0,1489 -chr1 106482 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=76;Dels=0.00;FS=17.089;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.404;QD=12.63;ReadPosRankSum=0.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,32:76:99:988,0,1538 -chr1 106502 . C T 1216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=80;Dels=0.00;FS=9.385;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.833;QD=15.21;ReadPosRankSum=0.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,38:80:99:1245,0,1351 -chr1 106522 . G C 1262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=73;Dels=0.00;FS=7.905;HaplotypeScore=3.1224;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.745;QD=17.30;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,37:73:99:1291,0,1178 -chr1 106546 . A T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=68;Dels=0.00;FS=21.595;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.577;QD=16.29;ReadPosRankSum=0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,35:68:99:1136,0,1064 -chr1 106547 . T A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.040;DP=65;Dels=0.00;FS=19.861;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.581;QD=13.38;ReadPosRankSum=0.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,32:65:99:898,0,1081 -chr1 106583 . A C 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=51;Dels=0.00;FS=1.066;HaplotypeScore=1.8313;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.161;QD=18.17;ReadPosRankSum=-1.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:955,0,750 -chr1 106636 . C G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.551;DP=53;Dels=0.00;FS=4.175;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.208;QD=12.96;ReadPosRankSum=0.713;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:715,0,996 -chr1 106713 . G T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.015;DP=52;Dels=0.00;FS=10.628;HaplotypeScore=24.7277;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.007;QD=15.17;ReadPosRankSum=0.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:817,0,902 -chr1 106753 . T A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=40;Dels=0.00;FS=2.183;HaplotypeScore=19.7108;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.900;QD=0.26;ReadPosRankSum=-1.963;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,5:40:38:38,0,1284 -chr1 106797 . G A 1867.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1896,141,0 -chr1 106811 . G A,C 1402.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,27,16:43:99:1616,598,517,1018,0,970 -chr1 106817 . C T 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=40;Dels=0.00;FS=2.928;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.801;QD=23.29;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:960,0,454 -chr1 106840 . C T 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.801;QD=25.20;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,31:44:99:1137,0,394 -chr1 106843 . G C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.852;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.206;QD=8.09;ReadPosRankSum=-1.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:384,0,1140 -chr1 106856 . G A 1422.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1451,108,0 -chr1 106885 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.646;QD=22.57;ReadPosRankSum=0.921;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,23:33:99:773,0,304 -chr1 106934 . T A 450.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=34.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:479,36,0 -chr1 106992 . T C 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0 -chr1 106996 . C T 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0 -chr1 107014 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,6:7:12:149,12,0 -chr1 107015 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,5:6:12:149,12,0 -chr1 107020 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:6:12:149,12,0 -chr1 107021 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:149,12,0 -chr1 107045 . G A 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:2,5:7:12:149,12,0 -chr1 107068 . G A 83.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.13;MQ0=1;QD=16.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:111,9,0 -chr1 107156 . A T 10.9 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.26;MQ0=3;MQRankSum=0.736;QD=1.82;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:4,2:6:3:37,3,0 -chr1 107197 . C T 120.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.887;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.4725;MLEAC=2;MLEAF=1.00;MQ=12.97;MQ0=14;MQRankSum=2.957;QD=3.75;ReadPosRankSum=1.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:12:148,12,0 -chr1 107202 . G A 116.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.449;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.5362;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=13;MQRankSum=2.654;QD=3.63;ReadPosRankSum=1.674;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,14:32:12:144,12,0 -chr1 107216 . G T 87.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.623;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.1146;MLEAC=2;MLEAF=1.00;MQ=12.19;MQ0=12;MQRankSum=1.535;QD=2.73;ReadPosRankSum=0.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,6:32:9:115,9,0 -chr1 107223 . G A 78.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.529;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=3.0304;MLEAC=2;MLEAF=1.00;MQ=12.37;MQ0=12;MQRankSum=2.646;QD=2.45;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:9:106,9,0 -chr1 107234 . T C 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.256;DP=34;Dels=0.00;FS=10.000;HaplotypeScore=3.3679;MLEAC=1;MLEAF=0.500;MQ=15.56;MQ0=13;MQRankSum=2.161;QD=1.99;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,4:34:58:96,0,58 -chr1 107332 . A G 264.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.49;MQ0=1;QD=24.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:293,24,0 -chr1 107410 . T G 122.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.550;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.88;MQ0=4;MQRankSum=1.754;QD=11.09;ReadPosRankSum=-1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:7,4:11:12:150,12,0 -chr1 107457 . G A 251.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.263;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=2;MLEAF=1.00;MQ=19.81;MQ0=12;MQRankSum=3.308;QD=8.99;ReadPosRankSum=0.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,8:28:21:280,21,0 -chr1 107475 . G T 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.088;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.53;MQ0=12;MQRankSum=3.532;QD=9.13;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,9:30:24:302,24,0 -chr1 107492 . A G 271.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.144;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.9159;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.416;QD=9.37;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,9:29:24:300,24,0 -chr1 107493 . A C 268.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.847;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8490;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.281;QD=9.27;ReadPosRankSum=0.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,9:29:24:297,24,0 -chr1 107755 . G A 128.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.00;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr1 107795 . G T 489.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=1;QD=34.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:518,39,0 -chr1 107900 . T C 502.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=33.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:531,42,0 -chr1 107903 . A G 489.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=32.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:518,42,0 -chr1 108008 . A T 911.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.22;MQ0=0;QD=25.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:72:940,72,0 -chr1 108057 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=2.204;QD=13.15;ReadPosRankSum=3.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:620,0,784 -chr1 108058 . C T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=-1.780;QD=17.55;ReadPosRankSum=-2.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:818,0,619 -chr1 108069 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.51;MQ0=1;QD=25.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:901,66,0 -chr1 108088 . C T 944.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:973,72,0 -chr1 108089 . A G 933.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:962,72,0 -chr1 108104 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.48;MQ0=0;MQRankSum=-4.097;QD=14.00;ReadPosRankSum=-5.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:686,0,806 -chr1 108110 . C T 1376.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.31;MQ0=0;QD=34.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1405,114,0 -chr1 108111 . A G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.878;QD=9.97;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:427,0,745 -chr1 108112 . G A 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.496;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.793;QD=9.94;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:426,0,750 -chr1 108120 . A C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=48;Dels=0.00;FS=2.509;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.28;MQ0=0;MQRankSum=-2.348;QD=14.56;ReadPosRankSum=0.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:727,0,612 -chr1 108125 . T C 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=46;Dels=0.00;FS=2.597;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=33.80;MQ0=0;MQRankSum=1.807;QD=11.10;ReadPosRankSum=-1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:539,0,755 -chr1 108127 . C T 1486.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1515,126,0 -chr1 108128 . A G 1489.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1518,126,0 -chr1 108131 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.573;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.012;QD=13.32;ReadPosRankSum=2.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:721,0,597 -chr1 108137 . T A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.072;QD=13.30;ReadPosRankSum=4.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:720,0,593 -chr1 108138 . G C 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.272;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=0.952;QD=10.88;ReadPosRankSum=-4.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:594,0,722 -chr1 108168 . G A 896.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.18;MQ0=3;QD=25.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:81:925,81,0 -chr1 108170 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQ0=3;MQRankSum=0.019;QD=7.68;ReadPosRankSum=2.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:297,0,467 -chr1 108172 . A T 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.052;DP=34;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=3;MQRankSum=0.020;QD=7.99;ReadPosRankSum=2.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:300,0,431 -chr1 108179 . A T 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=31;Dels=0.00;FS=1.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.94;MQ0=3;MQRankSum=-0.092;QD=7.67;ReadPosRankSum=3.271;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:266,0,355 -chr1 108237 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.136;DP=52;Dels=0.00;FS=1.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=0.076;QD=2.84;ReadPosRankSum=-3.358;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:176,0,1420 -chr1 108244 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.012;DP=52;Dels=0.00;FS=3.548;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.507;QD=3.19;ReadPosRankSum=-2.533;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:194,0,1435 -chr1 108245 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=52;Dels=0.00;FS=3.605;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.358;QD=3.17;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:193,0,1432 -chr1 108320 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.061;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=0;MQRankSum=-1.995;QD=13.85;ReadPosRankSum=-0.737;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:804,0,1051 -chr1 108356 . C A 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=72;Dels=0.00;FS=1.099;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=1.076;QD=7.89;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:596,0,1658 -chr1 108358 . G C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.113;DP=72;Dels=0.00;FS=2.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=0.603;QD=8.11;ReadPosRankSum=-0.180;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:612,0,1682 -chr1 108381 . C G 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=57;Dels=0.00;FS=2.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=1.583;QD=9.47;ReadPosRankSum=-0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,19:57:99:568,0,1331 -chr1 108383 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.245;DP=59;Dels=0.00;FS=2.367;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.657;QD=10.86;ReadPosRankSum=-0.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:669,0,1309 -chr1 108421 . T C 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=54;Dels=0.00;FS=5.922;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.455;QD=12.48;ReadPosRankSum=-1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:702,0,1090 -chr1 108425 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.158;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.604;QD=12.76;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:666,0,1049 -chr1 108449 . A G 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.445;DP=52;Dels=0.00;FS=6.027;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=1.139;QD=12.59;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:683,0,1017 -chr1 108459 . T C 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=57;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=1;MQRankSum=-0.379;QD=17.36;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1018,0,841 -chr1 108471 . G A 2484.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=1;QD=27.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2513,190,0 -chr1 108482 . T C 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=70;Dels=0.00;FS=6.663;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=1;MQRankSum=-0.510;QD=11.90;ReadPosRankSum=-0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,28:70:99:861,0,1470 -chr1 108528 . T A 1085.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.439;DP=90;Dels=0.00;FS=2.962;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=3;MQRankSum=-0.509;QD=12.06;ReadPosRankSum=-0.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,37:90:99:1114,0,1842 -chr1 108603 . T C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=72;Dels=0.00;FS=5.096;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-1.165;QD=10.07;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:48,24:72:99:753,0,1647 -chr1 108612 . T C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=75;Dels=0.00;FS=7.991;HaplotypeScore=66.7830;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.528;QD=11.52;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:46,29:75:99:892,0,1572 -chr1 108628 . A C 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.110;DP=62;Dels=0.00;FS=2.268;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-0.346;QD=10.00;ReadPosRankSum=1.802;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:648,0,1375 -chr1 108660 . G A 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.575;QD=16.15;ReadPosRankSum=-1.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:852,0,837 -chr1 108664 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=49;Dels=0.00;FS=2.568;HaplotypeScore=1.7820;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.551;QD=15.63;ReadPosRankSum=-1.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:794,0,758 -chr1 108691 . A T 981.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1010,78,0 -chr1 108698 . C G 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=38;Dels=0.00;FS=8.656;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.27;MQ0=0;MQRankSum=0.998;QD=13.70;ReadPosRankSum=-4.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:549,0,669 -chr1 108709 . A C 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=37;Dels=0.00;FS=12.587;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=0.442;QD=13.97;ReadPosRankSum=-0.411;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:545,0,634 -chr1 108759 . T A 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.087;DP=55;Dels=0.00;FS=33.086;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.45;MQ0=0;MQRankSum=1.155;QD=14.38;ReadPosRankSum=0.868;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:819,0,968 -chr1 108772 . G A 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=54;Dels=0.00;FS=28.588;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-1.120;QD=13.33;ReadPosRankSum=-0.805;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:748,0,1076 -chr1 108785 . C G 1842.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=29.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1871,141,0 -chr1 108796 . C T 1158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176;DP=42;Dels=0.00;FS=2.508;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.950;QD=27.59;ReadPosRankSum=-0.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,33:42:99:1187,0,248 -chr1 108799 . G A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.972;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.684;QD=26.97;ReadPosRankSum=-0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,31:40:99:1107,0,249 -chr1 108827 . C T 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074;DP=32;Dels=0.00;FS=27.227;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-3.223;QD=11.99;ReadPosRankSum=-0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:412,0,643 -chr1 108889 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=18;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-1.616;QD=26.71;ReadPosRankSum=-1.335;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,16:18:33:509,0,33 -chr1 108893 . A G 636.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.770;DP=22;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.400;QD=28.95;ReadPosRankSum=-1.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,20:22:18:665,0,18 -chr1 108940 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=35;Dels=0.00;FS=14.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.160;QD=22.74;ReadPosRankSum=1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:824,0,345 -chr1 108944 . A G 1416.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1445,108,0 -chr1 108956 . G A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=38;Dels=0.00;FS=10.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.354;QD=23.86;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,27:38:99:935,0,334 -chr1 108987 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=30;Dels=0.00;FS=5.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.022;QD=9.69;ReadPosRankSum=-0.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:319,0,707 -chr1 108988 . A G,T 817.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=31.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:981,597,567,383,0,335 -chr1 108990 . G A,T 801.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=30.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:964,583,553,382,0,333 -chr1 109006 . G A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.423;DP=30;Dels=0.00;FS=9.472;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.963;QD=18.89;ReadPosRankSum=2.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:595,0,411 -chr1 109022 . A G 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=22;Dels=0.00;FS=2.126;HaplotypeScore=3.9974;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.672;QD=19.94;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,14:22:99:467,0,255 -chr1 109058 . A C 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=6.641;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-4.308;QD=19.07;ReadPosRankSum=0.467;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:524,0,360 -chr1 109062 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=27;Dels=0.00;FS=9.864;HaplotypeScore=13.9930;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=0;MQRankSum=-4.440;QD=16.55;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:475,0,443 -chr1 109083 . T C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.570;DP=34;Dels=0.00;FS=14.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=-3.295;QD=14.64;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:526,0,626 -chr1 109085 . G A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.173;DP=37;Dels=0.00;FS=16.965;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-3.692;QD=15.80;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:613,0,599 -chr1 109091 . G A 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=18.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-1.845;QD=17.92;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:781,0,633 -chr1 109097 . T A 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.958;DP=44;Dels=0.00;FS=18.557;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.652;QD=15.47;ReadPosRankSum=-1.072;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:709,0,666 -chr1 109115 . C T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=42;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=-1.862;QD=16.52;ReadPosRankSum=-1.233;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:722,0,721 -chr1 109169 . G C 974.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=21.19;ReadPosRankSum=-0.979;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:1003,0,590 -chr1 109252 . C T 1130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.266;DP=54;Dels=0.00;FS=7.888;HaplotypeScore=2.6437;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.461;QD=20.94;ReadPosRankSum=-0.763;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1159,0,672 -chr1 109254 . G A 2185.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.6648;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=32.54;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2214,166,0 -chr1 109269 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.574;DP=54;Dels=0.00;FS=15.735;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.175;QD=11.68;ReadPosRankSum=0.455;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:659,0,1060 -chr1 109311 . T A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.952;QD=14.86;ReadPosRankSum=-0.651;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,26:50:99:771,0,715 -chr1 109317 . T C 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=48;Dels=0.00;FS=1.079;HaplotypeScore=2.3119;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.702;QD=13.12;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:658,0,763 -chr1 109405 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=42;Dels=0.00;FS=6.930;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=2;MQRankSum=-0.585;QD=15.68;ReadPosRankSum=-0.938;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:687,0,600 -chr1 109412 . C A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.217;DP=47;Dels=0.00;FS=6.249;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.422;QD=16.31;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:795,0,679 -chr1 109420 . A T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=50;Dels=0.00;FS=1.145;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=2;MQRankSum=1.148;QD=15.90;ReadPosRankSum=-0.010;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:823,0,754 -chr1 109464 . C T 986.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=60;Dels=0.00;FS=7.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=3;MQRankSum=-1.214;QD=16.45;ReadPosRankSum=-0.217;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1015,0,831 -chr1 109479 . G A 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=53;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=3;MQRankSum=2.123;QD=17.43;ReadPosRankSum=-1.356;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:952,0,701 -chr1 109530 . G A 1926.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=1;QD=29.57;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1955,147,0 -chr1 109539 . T C 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=51;Dels=0.00;FS=2.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=1.378;QD=17.49;ReadPosRankSum=-0.518;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:920,0,726 -chr1 109549 . C T 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.389;DP=60;Dels=0.00;FS=1.044;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-0.603;QD=13.80;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1084 -chr1 109620 . A T 2529.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.89;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2558,199,0 -chr1 109646 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.471;QD=16.52;ReadPosRankSum=0.311;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:970,0,961 -chr1 109673 . A T 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.120;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.499;QD=14.44;ReadPosRankSum=1.382;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:909,0,993 -chr1 109689 . C T 2343.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=36.47;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2372,175,0 -chr1 109734 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.181;DP=56;Dels=0.00;FS=2.436;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=0.033;QD=14.01;ReadPosRankSum=0.115;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:813,0,1012 -chr1 109767 . C T 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=-0.035;QD=13.44;ReadPosRankSum=1.596;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:754,0,928 -chr1 109788 . T C 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-3.116;QD=5.73;ReadPosRankSum=2.141;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:269,0,1133 -chr1 109814 . C T 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.124;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.18;MQ0=0;MQRankSum=-4.437;QD=10.59;ReadPosRankSum=-1.494;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,18:47:99:526,0,933 -chr1 109855 . C G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1986;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-5.305;QD=11.95;ReadPosRankSum=1.686;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:542,0,816 -chr1 109898 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.567;DP=42;Dels=0.00;FS=4.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=-4.596;QD=14.49;ReadPosRankSum=-0.038;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:637,0,754 -chr1 109948 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.655;DP=45;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.56;MQ0=0;MQRankSum=-4.171;QD=13.66;ReadPosRankSum=-0.931;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,26:45:99:643,0,655 -chr1 109992 . C G 1090.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=20.2910;MLEAC=2;MLEAF=1.00;MQ=38.79;MQ0=0;QD=25.97;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:90:1119,90,0 -chr1 110000 . T C 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.991;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=3.3547;MLEAC=1;MLEAF=0.500;MQ=40.16;MQ0=0;MQRankSum=-3.699;QD=6.42;ReadPosRankSum=0.672;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:330,0,703 -chr1 110006 . A G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.955;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.5657;MLEAC=1;MLEAF=0.500;MQ=41.04;MQ0=0;MQRankSum=-3.990;QD=5.89;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:317,0,813 -chr1 110065 . T G 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.35;ReadPosRankSum=-1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:38:38,0,838 -chr1 110066 . T G 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.38;ReadPosRankSum=-1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:39:39,0,891 -chr1 110176 . A G 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=39;Dels=0.00;FS=2.780;HaplotypeScore=3.5109;MLEAC=1;MLEAF=0.500;MQ=46.75;MQ0=0;MQRankSum=-0.407;QD=13.61;ReadPosRankSum=-0.014;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T411|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:559,0,657 -chr1 110245 . A G 456.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.065;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=-0.531;QD=10.88;ReadPosRankSum=-0.142;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y388|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:485,0,885 -chr1 110253 . A C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.29;MQ0=0;MQRankSum=-0.744;QD=10.27;ReadPosRankSum=0.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S386A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,16:44:99:480,0,992 -chr1 110499 . C A 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.668;DP=57;Dels=0.00;FS=7.487;HaplotypeScore=1.9858;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.040;QD=15.54;ReadPosRankSum=1.365;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:914,0,969 -chr1 110535 . G A 2517.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=0;QD=29.61;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2546,193,0 -chr1 110567 . C A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=12.462;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.072;QD=17.29;ReadPosRankSum=-0.965;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1152,0,1057 -chr1 110655 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=49;Dels=0.00;FS=10.545;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.344;QD=18.79;ReadPosRankSum=-0.414;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:949,0,664 -chr1 110660 . G C 1835.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.79;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1864,141,0 -chr1 110836 . G C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.256;QD=13.11;ReadPosRankSum=0.128;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:579,0,858 -chr1 110841 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=42;Dels=0.00;FS=1.210;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.025;QD=14.76;ReadPosRankSum=-0.783;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,793 -chr1 110897 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.379;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=-0.138;QD=16.14;ReadPosRankSum=-0.344;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:577,0,566 -chr1 110902 . G A 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=36;Dels=0.00;FS=1.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.792;QD=15.33;ReadPosRankSum=-0.032;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:580,0,630 -chr1 110931 . T A 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=46;Dels=0.00;FS=4.246;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.242;QD=17.30;ReadPosRankSum=-1.440;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:824,0,677 -chr1 110948 . T A 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=55;Dels=0.00;FS=1.028;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=0;MQRankSum=0.416;QD=17.70;ReadPosRankSum=-0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|atA/atT|I314|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:1002,0,664 -chr1 110974 . T G 1390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=77;Dels=0.00;FS=4.904;HaplotypeScore=1.9464;MLEAC=1;MLEAF=0.500;MQ=54.88;MQ0=3;MQRankSum=-1.165;QD=18.06;ReadPosRankSum=-0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R306|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,49:77:99:1419,0,866 -chr1 111002 . G A 3102.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=52.54;MQ0=3;QD=33.73;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G296|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3131,241,0 -chr1 111012 . A G 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.621;DP=99;Dels=0.00;FS=4.879;HaplotypeScore=1.9775;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=2;MQRankSum=-2.017;QD=1.50;ReadPosRankSum=1.985;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I293T|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:177,0,2833 -chr1 111037 . C T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.209;DP=91;Dels=0.00;FS=27.980;HaplotypeScore=5.8656;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=1;MQRankSum=-5.776;QD=7.67;ReadPosRankSum=1.097;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G285R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,30:91:99:726,0,2033 -chr1 111047 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.018;DP=95;Dels=0.00;FS=36.143;HaplotypeScore=18.9090;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=2;MQRankSum=-6.952;QD=8.96;ReadPosRankSum=-0.167;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L281|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,39:95:99:879,0,1831 -chr1 111053 . G A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.068;DP=94;Dels=0.00;FS=22.160;HaplotypeScore=52.4073;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=2;MQRankSum=2.884;QD=5.07;ReadPosRankSum=-0.550;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y279|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:75,19:94:99:505,0,2239 -chr1 111063 . G A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=88;Dels=0.00;FS=26.842;HaplotypeScore=20.7019;MLEAC=1;MLEAF=0.500;MQ=49.44;MQ0=2;MQRankSum=-5.090;QD=3.58;ReadPosRankSum=-0.104;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,21:88:99:343,0,2305 -chr1 111093 . T G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;DP=72;Dels=0.00;FS=18.592;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.32;MQ0=2;MQRankSum=-5.719;QD=9.66;ReadPosRankSum=1.059;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:72:99:724,0,1232 -chr1 111097 . C T 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.318;DP=72;Dels=0.00;FS=35.215;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.27;MQ0=2;MQRankSum=-6.753;QD=9.77;ReadPosRankSum=1.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,35:72:99:732,0,1245 -chr1 111100 . A G 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=71;Dels=0.00;FS=28.661;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.11;MQ0=2;MQRankSum=-5.937;QD=9.72;ReadPosRankSum=0.950;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:71:99:718,0,1230 -chr1 111136 . T C 1449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=59.2005;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-5.507;QD=20.14;ReadPosRankSum=1.606;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,49:72:99:1478,0,710 -chr1 111137 . T A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=58.2007;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=5.353;QD=9.45;ReadPosRankSum=-1.274;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:49,22:71:99:699,0,1451 -chr1 111146 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=19.0679;MLEAC=1;MLEAF=0.500;MQ=51.24;MQ0=1;MQRankSum=-5.478;QD=4.65;ReadPosRankSum=0.664;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:372,0,1862 -chr1 111162 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=77;Dels=0.00;FS=4.192;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=1;MQRankSum=-4.854;QD=3.78;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:57,20:77:99:319,0,1968 -chr1 111178 . A G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.787;DP=88;Dels=0.00;FS=4.774;HaplotypeScore=23.6084;MLEAC=1;MLEAF=0.500;MQ=51.68;MQ0=1;MQRankSum=-2.409;QD=9.66;ReadPosRankSum=0.590;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:878,0,1739 -chr1 111187 . C T 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713;DP=91;Dels=0.00;FS=21.798;HaplotypeScore=61.2603;MLEAC=1;MLEAF=0.500;MQ=52.52;MQ0=1;MQRankSum=-5.366;QD=4.35;ReadPosRankSum=-0.991;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),SPLICE_SITE_DONOR(HIGH||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:69,22:91:99:424,0,2409 -chr1 111193 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=1;MQRankSum=-4.830;QD=5.18;ReadPosRankSum=-0.680;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Agg|W268R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:479,0,2299 -chr1 111194 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=1;MQRankSum=-4.830;QD=5.11;ReadPosRankSum=-0.649;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y267|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:473,0,2303 -chr1 111218 . A G 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.345;DP=85;Dels=0.00;FS=28.288;HaplotypeScore=40.8045;MLEAC=1;MLEAF=0.500;MQ=53.15;MQ0=1;MQRankSum=-6.832;QD=18.02;ReadPosRankSum=0.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D259|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,50:85:99:1560,0,1149 -chr1 111221 . A G 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.974;DP=85;Dels=0.00;FS=2.368;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-0.591;QD=5.79;ReadPosRankSum=0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G258|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,21:85:99:520,0,2174 -chr1 111222 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=85;Dels=0.00;FS=52.665;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-6.297;QD=9.76;ReadPosRankSum=-0.509;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G258D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,30:85:99:858,0,1882 -chr1 111233 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=8.074;HaplotypeScore=21.7535;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=0.985;QD=6.33;ReadPosRankSum=-0.484;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P254|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:554,0,2166 -chr1 111239 . C T 1826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=83;Dels=0.00;FS=18.536;HaplotypeScore=20.7540;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-5.866;QD=22.01;ReadPosRankSum=-0.753;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,56:83:99:1855,0,817 -chr1 111265 . T C 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=74;Dels=0.00;FS=53.983;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.93;MQ0=0;MQRankSum=-6.988;QD=12.77;ReadPosRankSum=2.319;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,32:74:99:973,0,1429 -chr1 111274 . T C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=65;Dels=0.00;FS=22.427;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=4.440;QD=9.60;ReadPosRankSum=-1.326;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:652,0,1525 -chr1 111296 . T A 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.855;DP=60;Dels=0.00;FS=47.063;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-6.194;QD=11.68;ReadPosRankSum=-0.038;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:729,0,1223 -chr1 111307 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.080;DP=61;Dels=0.00;FS=45.484;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-6.030;QD=8.75;ReadPosRankSum=-0.269;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:562,0,1377 -chr1 111315 . A T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.943;DP=53;Dels=0.00;FS=25.441;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-4.672;QD=4.07;ReadPosRankSum=-2.694;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:244,0,1509 -chr1 111318 . C T 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=50;Dels=0.00;FS=22.968;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-4.247;QD=3.04;ReadPosRankSum=-2.686;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,8:50:99:180,0,1475 -chr1 111328 . C T 2042.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.58;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2071,162,0 -chr1 111397 . G A 2124.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.93;MQ0=1;QD=28.28;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2153,166,0 -chr1 111485 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.983;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=-1.024;QD=15.81;ReadPosRankSum=1.190;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q223|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111401_111565) GT:AD:DP:GQ:PL 0/1:23,26:49:99:803,0,742 -chr1 111592 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=60;Dels=0.00;FS=3.582;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.112;QD=13.36;ReadPosRankSum=-0.246;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:830,0,1146 -chr1 111732 . A G 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.751;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=-1.026;QD=14.15;ReadPosRankSum=1.868;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:764,0,902 -chr1 111733 . G A 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.217;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=2.274;QD=17.17;ReadPosRankSum=-2.142;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:904,0,661 -chr1 111744 . G A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.681;DP=48;Dels=0.00;FS=2.691;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=0.557;QD=16.14;ReadPosRankSum=-0.227;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:803,0,707 -chr1 111927 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;DP=61;Dels=0.00;FS=8.983;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.791;QD=18.34;ReadPosRankSum=0.399;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q139|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1147,0,896 -chr1 111933 . G A 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=59;Dels=0.00;FS=11.534;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.586;QD=18.06;ReadPosRankSum=0.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I137|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,32:59:99:1094,0,890 -chr1 112070 . T C 1601.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.25;MQ0=0;QD=27.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I92V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1630,123,0 -chr1 112145 . T C 969.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=47;Dels=0.00;FS=8.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-2.922;QD=20.63;ReadPosRankSum=0.908;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:998,0,587 -chr1 112157 . A T 1725.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=24.4498;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1754,129,0 -chr1 112214 . G A 579.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.778;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=2;MQRankSum=0.106;QD=14.87;ReadPosRankSum=-2.021;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:608,0,645 -chr1 112312 . C G 1042.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=44;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.391;QD=23.70;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,30:44:99:1071,0,416 -chr1 112332 . G A 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.961;QD=7.80;ReadPosRankSum=-0.320;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:356,0,1063 -chr1 112390 . A T 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.639;DP=47;Dels=0.00;FS=2.499;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.835;QD=11.10;ReadPosRankSum=-0.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:550,0,929 -chr1 112486 . A C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.749;DP=57;Dels=0.00;FS=12.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.008;QD=12.10;ReadPosRankSum=-1.976;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:718,0,1139 -chr1 112608 . A G 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.596;QD=13.66;ReadPosRankSum=-0.185;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,27:62:99:875,0,1208 -chr1 112714 . A C 1539.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=44;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;MQRankSum=-0.873;QD=34.99;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,42:44:59:1568,59,0 -chr1 112726 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=45;Dels=0.00;FS=1.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.059;QD=10.97;ReadPosRankSum=-0.925;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:522,0,972 -chr1 112738 . A G 1769.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.86;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1798,138,0 -chr1 112792 . A G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=41;Dels=0.00;FS=7.053;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.535;QD=16.53;ReadPosRankSum=0.561;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L68|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:20,21:41:99:706,0,681 -chr1 112909 . A C 1038.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=31.52;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L29V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1067,81,0 -chr1 112926 . A T 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.603;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=24.1961;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.021;QD=14.43;ReadPosRankSum=-3.139;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V23D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,16:30:99:461,0,376 -chr1 112983 . A G 1239.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.7883;MLEAC=2;MLEAF=1.00;MQ=57.43;MQ0=0;QD=33.51;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V4A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1268,99,0 -chr1 112990 . T C 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.3109;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.352;QD=7.05;ReadPosRankSum=-0.185;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T2A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:24,12:36:99:282,0,828 -chr1 112999 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.4558;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.333;QD=22.16;ReadPosRankSum=-0.622;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:11,24:35:99:804,0,241 -chr1 113028 . T C 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.3184;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.835;QD=9.35;ReadPosRankSum=0.000;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:17,11:28:99:290,0,593 -chr1 113037 . G T 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.102;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=20.2844;MLEAC=1;MLEAF=0.500;MQ=56.42;MQ0=0;MQRankSum=-2.110;QD=8.84;ReadPosRankSum=-0.220;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,9:25:99:258,0,479 -chr1 113038 . A T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.888;DP=25;Dels=0.04;FS=0.000;HaplotypeScore=19.2851;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-0.827;QD=7.51;ReadPosRankSum=0.582;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:16,8:24:99:216,0,560 -chr1 113090 . A C 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.412;DP=41;Dels=0.00;FS=2.417;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=55.93;MQ0=2;MQRankSum=0.949;QD=0.51;ReadPosRankSum=-0.532;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:37,4:41:49:49,0,1144 -chr1 113092 . C T 1222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.600;DP=42;Dels=0.00;FS=2.442;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=2;MQRankSum=-1.195;QD=29.11;ReadPosRankSum=0.789;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:4,38:42:40:1251,0,40 -chr1 113105 . T A 1562.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.66;MQ0=2;QD=30.97;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1591,117,0 -chr1 113115 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=2;MQRankSum=1.145;QD=17.44;ReadPosRankSum=-0.628;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,27:45:99:813,0,572 -chr1 113119 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=45;Dels=0.00;FS=2.776;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=2;MQRankSum=0.335;QD=11.11;ReadPosRankSum=0.907;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:28,17:45:99:528,0,850 -chr1 113161 . C T 1227.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=2.5015;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=29.79;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1256,96,0 -chr1 113173 . T C 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.461;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=1.037;QD=10.59;ReadPosRankSum=0.148;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,12:30:99:346,0,540 -chr1 113177 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=25.30;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1027,78,0 -chr1 113178 . G A 1046.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=29.64;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1075,81,0 -chr1 113190 . C G 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=1.585;HaplotypeScore=1.7883;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.665;QD=8.34;ReadPosRankSum=-1.996;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:19,10:29:99:270,0,614 -chr1 113238 . G A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.041;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=20.8374;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.586;QD=3.57;ReadPosRankSum=2.277;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,5:26:99:121,0,747 -chr1 113268 . T G 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=36;Dels=0.00;FS=5.290;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.353;QD=10.83;ReadPosRankSum=-0.257;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,15:36:99:418,0,717 -chr1 113287 . A C 1111.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.97;MQ0=0;QD=29.47;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1140,90,0 -chr1 113306 . A C 1268.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=31.06;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1297,99,0 -chr1 113324 . C A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=34;Dels=0.00;FS=1.524;HaplotypeScore=1.9977;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.248;QD=20.79;ReadPosRankSum=0.071;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:13,21:34:99:735,0,408 -chr1 113358 . G A 385.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.134;QD=29.68;ReadPosRankSum=1.470;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:1,12:13:2:412,0,2 -chr1 113386 . A G 130.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.51;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0 -chr1 113396 . T C 43.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=21.87;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr1 113410 . A T 156.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.38;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,5:5:15:185,15,0 -chr1 113431 . A G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=0;MQRankSum=1.920;QD=18.85;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,5:8:82:179,0,82 -chr1 113440 . T A 180.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0 -chr1 113444 . T A 178.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:207,15,0 -chr1 113446 . A C 181.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=27.48;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:210,15,0 -chr1 113450 . A T 214.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.19;MQ0=0;QD=31.14;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:243,18,0 -chr1 113468 . G C 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.78;MQ0=0;MQRankSum=-2.670;QD=1.59;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,3:15:52:52,0,418 -chr1 113483 . T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.061;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=0;MQRankSum=-0.354;QD=1.10;ReadPosRankSum=-2.239;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,2:11:40:40,0,313 -chr1 113488 . T C 240.8 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=30.10;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:21:269,21,0 -chr1 113492 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=33.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:298,24,0 -chr1 113500 . T C 242.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=34.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:271,21,0 -chr1 113503 . T C 254.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=27.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:283,21,0 -chr1 113505 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:266,21,0 -chr1 113522 . T C 153.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.02;MQ0=0;QD=30.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:182,15,0 -chr1 114239 . A C 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=28.37;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr1 114264 . C G 551.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=32.00;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:580,42,0 -chr1 114287 . G A 771.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=28.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:800,63,0 -chr1 114304 . A G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;DP=21;Dels=0.00;FS=5.898;HaplotypeScore=11.6441;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-2.064;QD=10.66;ReadPosRankSum=-1.195;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,8:21:99:252,0,383 -chr1 114311 . G A 481.18 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.217;DP=16;Dels=0.00;FS=7.270;HaplotypeScore=3.6636;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;MQRankSum=-0.868;QD=30.07;ReadPosRankSum=1.302;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:1,15:16:10:509,10,0 -chr1 114312 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.329;DP=16;Dels=0.00;FS=6.726;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-2.223;QD=11.05;ReadPosRankSum=-1.799;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:205,0,294 -chr1 114313 . G C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=0.722;QD=13.40;ReadPosRankSum=2.646;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:256,0,295 -chr1 114326 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=0.249;QD=12.27;ReadPosRankSum=0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:286,0,380 -chr1 114330 . T C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-0.462;QD=16.94;ReadPosRankSum=-0.320;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,12:21:99:384,0,253 -chr1 114353 . C A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.002;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-1.591;QD=11.18;ReadPosRankSum=-0.648;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:196,0,307 -chr1 114354 . A T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.945;QD=18.85;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:311,0,195 -chr1 114356 . G T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.120;QD=18.92;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:312,0,191 -chr1 114371 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.9971;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.899;QD=13.75;ReadPosRankSum=0.417;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:427,0,524 -chr1 114439 . T C 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.119;DP=37;Dels=0.00;FS=3.179;HaplotypeScore=1.5781;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=0.445;QD=17.07;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:660,0,452 -chr1 114460 . C A 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.748;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.398;QD=13.74;ReadPosRankSum=-1.894;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:523,0,607 -chr1 114463 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.778;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.579;QD=14.34;ReadPosRankSum=2.434;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,19:35:99:530,0,535 -chr1 114470 . T G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.856;DP=26;Dels=0.00;FS=7.707;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=1.004;QD=4.38;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,6:26:99:142,0,623 -chr1 114472 . A C 864.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.84;MQ0=0;QD=34.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:893,69,0 -chr1 114475 . A G 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.177;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.350;QD=5.47;ReadPosRankSum=1.813;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:165,0,582 -chr1 114476 . G C 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.686;DP=25;Dels=0.00;FS=7.908;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.223;QD=5.75;ReadPosRankSum=2.004;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:172,0,560 -chr1 114480 . C A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.623;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-1.304;QD=5.71;ReadPosRankSum=2.450;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:171,0,583 -chr1 114486 . T G 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.268;DP=31;Dels=0.00;FS=17.994;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=0.434;QD=8.86;ReadPosRankSum=0.681;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:303,0,607 -chr1 114494 . C G 1000.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=30.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1029,78,0 -chr1 114501 . G A 815.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.64;MQ0=0;QD=33.99;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:844,66,0 -chr1 114552 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=25;Dels=0.00;FS=11.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=0.245;QD=17.19;ReadPosRankSum=1.006;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:458,0,356 -chr1 114576 . A T 643.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.58;MQ0=0;QD=37.73;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:672,51,0 -chr1 114578 . T C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=4.533;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=0;MQRankSum=0.381;QD=7.32;ReadPosRankSum=1.778;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:204,0,601 -chr1 114603 . A C 1082.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.79;MQ0=0;QD=29.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1111,84,0 -chr1 114617 . G A 1458.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=28.9952;MLEAC=2;MLEAF=1.00;MQ=46.56;MQ0=0;QD=27.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1487,114,0 -chr1 114621 . G A 1401.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.91;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1430,111,0 -chr1 114645 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=37.7265;MLEAC=1;MLEAF=0.500;MQ=45.53;MQ0=0;MQRankSum=-1.288;QD=20.49;ReadPosRankSum=1.767;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,23:34:99:725,0,274 -chr1 114719 . A G 12.77 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:39,3,0 -chr1 114726 . A G 10.9 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:37,3,0 -chr1 114739 . T C 14.68 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.89;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:41,3,0 -chr1 114740 . C T 11.83 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:38,3,0 -chr1 114744 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0 -chr1 114746 . A G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0 -chr1 114752 . A G 13.72 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:40,3,0 -chr1 114770 . G C 44.74 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.49;MQ0=0;QD=8.95;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:6:72,6,0 -chr1 114788 . T C 46.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.96;MQ0=0;QD=11.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:4:6:74,6,0 -chr1 114810 . T G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.41;MQ0=0;QD=7.83;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:3:42,3,0 -chr1 114906 . T G 147.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=21.13;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:176,15,0 -chr1 114967 . A T 395.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.734;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.69;MQ0=0;MQRankSum=2.100;QD=28.28;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,12:14:15:424,15,0 -chr1 115005 . G A 307.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.086;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=29.1197;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=23.64;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:335,9,0 -chr1 115006 . C T 312.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.099;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=33.6508;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=24.02;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:340,9,0 -chr1 115080 . G A 659.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.90;MQ0=0;QD=24.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:688,51,0 -chr1 115081 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=17;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=0.433;QD=16.63;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,275 -chr1 115090 . T C 776.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:805,60,0 -chr1 115098 . G T 841.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.28;MQ0=0;QD=32.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:870,66,0 -chr1 115143 . A G 816.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;QD=26.49;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:845,63,0 -chr1 115156 . A G 687.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.36;MQ0=0;QD=31.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:716,54,0 -chr1 115169 . T C 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=0;QD=28.56;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:60:808,60,0 -chr1 115181 . T G 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=34.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0 -chr1 115198 . A G 817.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.246;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;MQRankSum=-1.201;QD=34.05;ReadPosRankSum=2.246;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,22:24:11:845,11,0 -chr1 115206 . C T 1077.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1106,81,0 -chr1 115249 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=53;Dels=0.00;FS=9.816;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.278;QD=13.15;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:725,0,1025 -chr1 115259 . A G 2107.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.59;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2136,166,0 -chr1 115271 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.303;DP=57;Dels=0.00;FS=11.864;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.031;QD=16.42;ReadPosRankSum=-3.364;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:964,0,858 -chr1 115276 . G T 881.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;DP=60;Dels=0.00;FS=6.930;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=0.956;QD=14.70;ReadPosRankSum=-2.838;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:910,0,1060 -chr1 115303 . C T 2271.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2300,172,0 -chr1 115305 . A G 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;DP=56;Dels=0.00;FS=5.501;HaplotypeScore=51.1251;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=3.741;QD=14.66;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:849,0,1091 -chr1 115352 . T C 875.96 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.787;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.250;QD=32.44;ReadPosRankSum=2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:5:903,5,0 -chr1 115355 . A G 885.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.694;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.157;QD=32.81;ReadPosRankSum=1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:6:913,6,0 -chr1 115360 . T C 783.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=-1.129;QD=31.34;ReadPosRankSum=1.965;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,22:25:7:811,0,7 -chr1 115381 . A G 1182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.28;MQ0=1;MQRankSum=4.365;QD=21.12;ReadPosRankSum=5.503;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1211,0,406 -chr1 115385 . C T 2076.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=1;QD=35.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2105,160,0 -chr1 115399 . G T 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.993;DP=58;Dels=0.00;FS=5.640;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-3.684;QD=11.55;ReadPosRankSum=-2.448;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:698,0,1158 -chr1 115400 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.919;DP=58;Dels=0.00;FS=5.893;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-2.871;QD=11.38;ReadPosRankSum=-2.415;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:688,0,1133 -chr1 115414 . A G 1203.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=64;Dels=0.00;FS=3.517;HaplotypeScore=52.2248;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=2.511;QD=18.81;ReadPosRankSum=-0.519;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1232,0,864 -chr1 115418 . T C 1129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.624;DP=66;Dels=0.00;FS=0.952;HaplotypeScore=30.9607;MLEAC=1;MLEAF=0.500;MQ=55.61;MQ0=1;MQRankSum=3.185;QD=17.12;ReadPosRankSum=0.112;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1158,0,983 -chr1 115440 . A C 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.049;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=0.387;QD=14.95;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:970,0,1095 -chr1 115476 . T C 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.880;QD=13.59;ReadPosRankSum=1.676;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:735,0,938 -chr1 115480 . C A 1943.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.95;MQ0=0;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1972,150,0 -chr1 115485 . T C 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.179;QD=16.48;ReadPosRankSum=0.288;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:984,0,900 -chr1 115540 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=54;Dels=0.00;FS=4.135;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=-0.444;QD=11.44;ReadPosRankSum=-1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:646,0,1164 -chr1 115548 . T C 2024.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=26.84;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2053,157,0 -chr1 115568 . T A 987.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=26.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:1016,75,0 -chr1 115569 . G A 945.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=25.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:974,72,0 -chr1 115571 . T A 938.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:967,75,0 -chr1 115574 . C T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=37;Dels=0.00;FS=4.170;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.454;QD=3.64;ReadPosRankSum=1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,7:37:99:163,0,1074 -chr1 115602 . G C 1954.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.30;MQ0=0;QD=29.47;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1983,147,0 -chr1 115617 . C T 2393.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.55;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2422,184,0 -chr1 115730 . A G 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;DP=35;Dels=0.00;FS=8.346;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.007;QD=16.96;ReadPosRankSum=-1.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:622,0,576 -chr1 115732 . G A 512.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;DP=34;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.103;QD=15.08;ReadPosRankSum=-1.033;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:541,0,583 -chr1 115738 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.838;DP=37;Dels=0.00;FS=5.540;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-0.229;QD=16.99;ReadPosRankSum=-2.088;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:657,0,575 -chr1 115746 . A C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=38;Dels=0.00;FS=7.279;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.905;QD=15.23;ReadPosRankSum=-1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:607,0,655 -chr1 115752 . C A 1480.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=34.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1509,114,0 -chr1 115793 . G A 2310.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.47;MQ0=0;QD=27.91;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2339,175,0 -chr1 115811 . T G 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.283;QD=12.62;ReadPosRankSum=2.897;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1114 -chr1 115814 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.500;QD=12.67;ReadPosRankSum=2.987;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:700,0,1111 -chr1 115817 . A C 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.839;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.670;QD=12.35;ReadPosRankSum=3.005;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:683,0,1076 -chr1 115818 . G A 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.244;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.507;QD=12.73;ReadPosRankSum=2.771;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:703,0,1078 -chr1 115819 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.977;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.995;QD=12.52;ReadPosRankSum=2.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:692,0,1062 -chr1 115824 . T C 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=64;Dels=0.00;FS=0.970;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=3.857;QD=14.17;ReadPosRankSum=1.430;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,29:64:99:935,0,1177 -chr1 115872 . T C 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=37;Dels=0.00;FS=13.443;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=56.26;MQ0=0;MQRankSum=-0.564;QD=17.59;ReadPosRankSum=2.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:679,0,570 -chr1 115884 . G T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=32;Dels=0.00;FS=10.606;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.397;QD=13.49;ReadPosRankSum=-2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:460,0,582 -chr1 115887 . A T 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.104;DP=30;Dels=0.00;FS=8.202;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.395;QD=16.23;ReadPosRankSum=2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:515,0,435 -chr1 115890 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.658;DP=29;Dels=0.00;FS=5.988;HaplotypeScore=5.4965;MLEAC=1;MLEAF=0.500;MQ=56.14;MQ0=0;MQRankSum=-1.060;QD=15.58;ReadPosRankSum=2.211;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,15:29:99:480,0,414 -chr1 115900 . C A 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.934;DP=29;Dels=0.00;FS=2.129;HaplotypeScore=9.4946;MLEAC=1;MLEAF=0.500;MQ=56.43;MQ0=0;MQRankSum=0.375;QD=1.51;ReadPosRankSum=-2.050;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,5:29:72:72,0,793 -chr1 115966 . T A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=2;MQRankSum=0.798;QD=14.42;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:735,0,712 -chr1 115983 . T C 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=55;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.139;QD=17.10;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:969,0,769 -chr1 115998 . C G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=62;Dels=0.00;FS=5.215;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=0.776;QD=15.22;ReadPosRankSum=-0.747;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:972,0,1040 -chr1 116012 . A T 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=65;Dels=0.00;FS=1.013;HaplotypeScore=4.5213;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=1;MQRankSum=0.189;QD=14.12;ReadPosRankSum=0.486;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:946,0,1099 -chr1 116022 . G C 2223.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.7333;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=1;QD=34.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:64:99:2252,175,0 -chr1 116026 . T A 1054.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.724;DP=65;Dels=0.00;FS=2.157;HaplotypeScore=2.6644;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=1;MQRankSum=-0.182;QD=16.23;ReadPosRankSum=-0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1083,0,932 -chr1 116035 . G T 2393.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=3.3036;MLEAC=2;MLEAF=1.00;MQ=57.52;MQ0=1;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2422,181,0 -chr1 116068 . A G 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.699;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-1.678;QD=17.75;ReadPosRankSum=-0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:898,0,730 -chr1 116073 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.379;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=0;MQRankSum=-1.194;QD=15.54;ReadPosRankSum=0.884;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:805,0,790 -chr1 116082 . G A 1794.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=40.8500;MLEAC=2;MLEAF=1.00;MQ=57.87;MQ0=0;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1823,138,0 -chr1 116106 . C T 1595.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=57.28;MQ0=0;QD=30.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1624,120,0 -chr1 116191 . G A 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.858;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=3.7255;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=0.684;QD=10.49;ReadPosRankSum=-2.599;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:448,0,731 -chr1 116284 . G T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.326;DP=43;Dels=0.00;FS=1.216;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.07;MQ0=2;MQRankSum=-1.787;QD=15.72;ReadPosRankSum=-0.352;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,696 -chr1 116327 . C T 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=46.31;MQ0=1;MQRankSum=-3.916;QD=5.32;ReadPosRankSum=0.305;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:193,0,788 -chr1 116350 . T G 775.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=0;QD=33.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:804,60,0 -chr1 116354 . A G 750.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.28;MQ0=0;QD=33.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:779,57,0 -chr1 116368 . G T 687.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=24;Dels=0.00;FS=2.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.36;MQ0=0;MQRankSum=2.706;QD=28.66;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,21:24:26:716,0,26 -chr1 116375 . G A 873.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.89;MQ0=0;QD=33.23;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:902,69,0 -chr1 116391 . T A 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.605;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-2.880;QD=4.61;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:162,0,816 -chr1 116393 . A T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.688;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-3.134;QD=4.65;ReadPosRankSum=-0.127;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:163,0,804 -chr1 116410 . T C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.59;MQ0=0;QD=30.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0 -chr1 116422 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.301;DP=31;Dels=0.00;FS=12.035;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-3.613;QD=9.83;ReadPosRankSum=1.590;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:333,0,662 -chr1 116436 . T G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;DP=37;Dels=0.00;FS=10.037;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.32;MQ0=0;MQRankSum=-1.109;QD=14.97;ReadPosRankSum=-0.957;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:582,0,665 -chr1 116453 . C T 1640.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.49;MQ0=0;QD=26.27;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1669,123,0 -chr1 116488 . G A 1609.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.82;MQ0=0;QD=32.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1638,123,0 -chr1 116492 . T C 1557.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=31.39;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:40:99:1586,117,0 -chr1 116493 . C T 555.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.670;QD=13.56;ReadPosRankSum=-2.010;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:584,0,810 -chr1 116506 . A G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=41;Dels=0.00;FS=2.694;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-2.600;QD=16.68;ReadPosRankSum=-2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,21:41:99:712,0,659 -chr1 116529 . G A 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-3.948;QD=16.90;ReadPosRankSum=2.053;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:755,0,724 -chr1 116532 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=3.827;QD=15.97;ReadPosRankSum=-2.199;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:715,0,752 -chr1 116537 . C T 1663.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=26.41;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1692,126,0 -chr1 116554 . A C 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.179;DP=42;Dels=0.00;FS=9.199;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.68;MQ0=0;MQRankSum=-3.792;QD=19.64;ReadPosRankSum=0.436;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:853,0,555 -chr1 116565 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=41;Dels=0.00;FS=6.909;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-3.782;QD=20.31;ReadPosRankSum=-0.628;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:861,0,489 -chr1 116576 . G A 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=44;Dels=0.02;FS=4.546;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-3.188;QD=18.47;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:841,0,592 -chr1 116582 . A T 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=48;Dels=0.00;FS=2.552;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=0;MQRankSum=-2.973;QD=19.66;ReadPosRankSum=-0.611;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:972,0,614 -chr1 116595 . T G 1623.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.42;MQ0=0;QD=28.53;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1652,129,0 -chr1 116602 . A C 1697.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=57.59;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1726,138,0 -chr1 116621 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.163;DP=41;Dels=0.00;FS=2.820;HaplotypeScore=1.9914;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=1.938;QD=12.04;ReadPosRankSum=-1.029;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:522,0,880 -chr1 116650 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.47;MQ0=1;QD=28.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1552,117,0 -chr1 116679 . C T 1348.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.24;MQ0=1;QD=35.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1377,105,0 -chr1 116681 . A G 1459.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.89;MQ0=1;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1488,114,0 -chr1 116708 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.97;MQ0=0;MQRankSum=-0.735;QD=6.64;ReadPosRankSum=0.035;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:181,0,612 -chr1 116711 . T C 651.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=30.82;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:680,51,0 -chr1 116712 . G A 681.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=29.36;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:710,54,0 -chr1 116724 . T A 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.705;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-0.054;QD=21.55;ReadPosRankSum=-2.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,10:16:99:373,0,200 -chr1 116728 . T A 622.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=28.11;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:651,48,0 -chr1 116732 . A G 647.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.89;MQ0=0;QD=27.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:676,51,0 -chr1 116749 . A T 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.553;QD=15.18;ReadPosRankSum=0.456;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:787,0,824 -chr1 116757 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.743;QD=12.68;ReadPosRankSum=1.259;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:637,0,796 -chr1 116793 . G C 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=26.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,120,0 -chr1 116804 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.704;QD=12.06;ReadPosRankSum=0.418;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:559,0,846 -chr1 116809 . G A 1767.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=35.74;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1796,138,0 -chr1 116816 . A T 1677.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=29.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,129,0 -chr1 116822 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.282;DP=39;Dels=0.00;FS=1.310;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.493;QD=13.92;ReadPosRankSum=1.507;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:571,0,715 -chr1 116824 . T C 1298.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=28.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1327,99,0 -chr1 116906 . C A 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.149;QD=12.02;ReadPosRankSum=-2.562;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:569,0,916 -chr1 116917 . A G 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610;DP=47;Dels=0.00;FS=1.154;HaplotypeScore=1.9931;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-0.501;QD=12.89;ReadPosRankSum=-2.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:634,0,880 -chr1 116943 . A G 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.102;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.695;QD=18.14;ReadPosRankSum=-2.536;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:881,0,663 -chr1 116949 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=0.854;QD=13.97;ReadPosRankSum=3.146;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:713,0,926 -chr1 116959 . G A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=55;Dels=0.00;FS=1.029;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.355;QD=14.94;ReadPosRankSum=2.113;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:850,0,924 -chr1 116971 . G A 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.651;DP=50;Dels=0.00;FS=2.386;HaplotypeScore=3.2789;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-0.283;QD=17.90;ReadPosRankSum=0.870;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:923,0,717 -chr1 117007 . C T 1395.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.49;MQ0=0;QD=29.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1424,114,0 -chr1 117050 . G A 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.324;QD=6.57;ReadPosRankSum=-1.528;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,5:19:99:153,0,501 -chr1 117051 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.267;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.099;QD=7.10;ReadPosRankSum=-1.971;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:156,0,470 -chr1 117054 . T G 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.971;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.887;QD=7.26;ReadPosRankSum=-1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:159,0,429 -chr1 117071 . G A 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.080;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.164;QD=9.79;ReadPosRankSum=0.783;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:322,0,621 -chr1 117077 . G C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=33;Dels=0.00;FS=1.434;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=1.029;QD=10.75;ReadPosRankSum=1.740;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:383,0,738 -chr1 117104 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-2.211;QD=13.17;ReadPosRankSum=-0.335;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:700,0,1034 -chr1 117130 . C A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.251;DP=72;Dels=0.00;FS=18.205;HaplotypeScore=5.9991;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=4;MQRankSum=-4.097;QD=0.80;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:61,11:72:86:86,0,2246 -chr1 117148 . G T 1083.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.492;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=1;MQRankSum=0.824;QD=14.65;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:39,35:74:99:1112,0,1310 -chr1 117150 . C T 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=75;Dels=0.00;FS=0.883;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.114;QD=14.84;ReadPosRankSum=1.763;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:40,35:75:99:1141,0,1350 -chr1 117157 . A G 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=75;Dels=0.00;FS=1.938;HaplotypeScore=5.7880;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.827;QD=16.04;ReadPosRankSum=2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:38,37:75:99:1231,0,1283 -chr1 117161 . G A 1326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=76;Dels=0.00;FS=3.158;HaplotypeScore=3.9994;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.545;QD=17.46;ReadPosRankSum=0.900;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,40:76:99:1355,0,1228 -chr1 117175 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=78;Dels=0.00;FS=22.021;HaplotypeScore=9.9969;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.164;QD=3.19;ReadPosRankSum=-2.376;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:58,12:78:99:277,0,2135 -chr1 117193 . G A 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=65;Dels=0.00;FS=7.705;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.404;QD=13.73;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,28:65:99:921,0,1261 -chr1 117202 . G T 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=61;Dels=0.00;FS=10.025;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=1.292;QD=12.16;ReadPosRankSum=0.170;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,24:61:99:770,0,1299 -chr1 117240 . G A 248.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.71;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:277,21,0 -chr1 117248 . A G 170.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.18;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:199,15,0 -chr1 117260 . C G 86.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:114,9,0 -chr1 117286 . A G 714.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.70;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:743,57,0 -chr1 117350 . A T 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.016;DP=63;Dels=0.00;FS=4.058;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-6.819;QD=13.96;ReadPosRankSum=-3.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,30:63:99:908,0,1176 -chr1 117353 . G A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.169;DP=62;Dels=0.00;FS=6.115;HaplotypeScore=4.6334;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=6.744;QD=18.04;ReadPosRankSum=2.271;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,33:62:99:1147,0,898 -chr1 117361 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.041;DP=50;Dels=0.00;FS=2.729;HaplotypeScore=10.5317;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-5.755;QD=9.76;ReadPosRankSum=1.270;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:516,0,1175 -chr1 117411 . T C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=23;Dels=0.00;FS=39.846;HaplotypeScore=10.9973;MLEAC=1;MLEAF=0.500;MQ=46.04;MQ0=1;MQRankSum=-3.989;QD=6.82;ReadPosRankSum=-2.011;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,11:23:99:185,0,421 -chr1 117420 . A T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=-0.092;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,370 -chr1 117422 . G T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.523;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=0.215;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,369 -chr1 117438 . G C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.413;DP=32;Dels=0.00;FS=52.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.12;MQ0=1;MQRankSum=-3.851;QD=17.24;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,23:32:99:580,0,237 -chr1 117455 . T A,G 486.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.25;MQ0=1;QD=24.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,9,11:20:99:628,311,284,317,0,287 -chr1 117461 . G C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.770;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.298;QD=9.92;ReadPosRankSum=1.591;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,309 -chr1 117462 . T C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.123;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.887;QD=9.92;ReadPosRankSum=1.827;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117464 . C T 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.652;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.652;QD=9.92;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117465 . T A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.416;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.062;QD=9.86;ReadPosRankSum=1.355;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:186,0,295 -chr1 117467 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.550;DP=18;Dels=0.00;FS=28.543;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=1;MQRankSum=-3.224;QD=12.82;ReadPosRankSum=0.241;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,9:18:99:259,0,257 -chr1 117527 . C A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.031;DP=38;Dels=0.00;FS=14.618;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=2;MQRankSum=-4.256;QD=7.26;ReadPosRankSum=2.631;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:304,0,852 -chr1 117551 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.950;DP=19;Dels=0.00;FS=5.815;HaplotypeScore=15.9941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.750;QD=3.88;ReadPosRankSum=-1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:15,4:19:99:102,0,544 -chr1 117615 . A C 375.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=23.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:404,30,0 -chr1 117624 . G A 445.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:474,36,0 -chr1 117647 . T G 493.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.12;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:522,39,0 -chr1 117656 . A G 537.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:566,42,0 -chr1 117663 . A T 499.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:528,39,0 -chr1 117688 . T C 420.53 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;QD=32.35;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:13:36:488,36,0 -chr1 117772 . T G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117777 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117778 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117787 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.86;MQ0=2;QD=21.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,9:9:18:224,18,0 -chr1 117923 . C T 159.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.922;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.24;MQ0=3;MQRankSum=1.495;QD=15.99;ReadPosRankSum=-1.495;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:5,5:10:15:188,15,0 -chr1 117938 . T A 245.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=24.58;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:21:274,21,0 -chr1 117939 . T C 282.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=28.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:24:311,24,0 -chr1 117954 . T G 632.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.29;MQ0=2;QD=33.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:661,51,0 -chr1 117967 . C T 371.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.351;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.465;QD=11.99;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:400,0,581 -chr1 117972 . C G 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.218;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.686;QD=12.02;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:401,0,578 -chr1 117996 . T C 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.341;DP=34;Dels=0.00;FS=8.609;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=2;MQRankSum=-1.468;QD=9.26;ReadPosRankSum=0.635;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:343,0,658 -chr1 118063 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=3.026;QD=21.04;ReadPosRankSum=3.377;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,13:19:36:428,0,36 -chr1 118067 . T A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.792;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.566;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:60:418,0,60 -chr1 118068 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.426;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.487;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:69:418,0,69 -chr1 118069 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.541;QD=1.07;ReadPosRankSum=-1.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,7:25:55:55,0,547 -chr1 118098 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=17.1556;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=3.923;QD=21.06;ReadPosRankSum=-0.468;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:10,22:32:99:702,0,186 -chr1 118118 . A G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.220;DP=42;Dels=0.00;FS=2.745;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.888;QD=19.30;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:839,0,403 -chr1 118122 . C A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.130;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-1.111;QD=9.81;ReadPosRankSum=-0.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:411,0,831 -chr1 118131 . A G 556.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;DP=44;Dels=0.00;FS=2.548;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.24;MQ0=0;MQRankSum=-0.837;QD=12.65;ReadPosRankSum=-1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:585,0,736 -chr1 118140 . T A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-3.047;QD=12.91;ReadPosRankSum=-0.299;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:622,0,857 -chr1 118262 . C A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;QD=21.49;ReadPosRankSum=2.452;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:974,0,497 -chr1 118324 . A G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-1.355;QD=10.63;ReadPosRankSum=-2.135;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:528,0,851 -chr1 118347 . T A 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=42;Dels=0.00;FS=5.576;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.125;QD=22.54;ReadPosRankSum=0.181;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,30:42:99:975,0,281 -chr1 118393 . C G 1571.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1872;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1600,120,0 -chr1 118394 . C G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=43;Dels=0.00;FS=9.242;HaplotypeScore=4.1872;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=1.960;QD=15.99;ReadPosRankSum=0.524;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:716,0,621 -chr1 118403 . G A 1580.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=41.1140;MLEAC=2;MLEAF=1.00;MQ=57.24;MQ0=0;QD=27.67;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1609,123,0 -chr1 118423 . C A,T 1500.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.60;MQ0=0;QD=30.62;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,26,23:49:99:1727,749,670,978,0,915 -chr1 118436 . T A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.005;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=2.6648;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.756;QD=14.47;ReadPosRankSum=-1.770;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,26:53:99:795,0,854 -chr1 118461 . T C 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=3;MQRankSum=1.167;QD=15.68;ReadPosRankSum=-1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,27:47:99:765,0,667 -chr1 118483 . G C 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=44;Dels=0.00;FS=4.457;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=3;MQRankSum=-1.011;QD=12.18;ReadPosRankSum=0.197;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,21:44:99:564,0,783 -chr1 118552 . C T 844.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:66:873,66,0 -chr1 118569 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=29;Dels=0.00;FS=5.142;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=-3.742;QD=0.68;ReadPosRankSum=-3.419;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,6:29:48:48,0,779 -chr1 118577 . A G 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.12;MQ0=0;MQRankSum=-3.972;QD=1.53;ReadPosRankSum=-1.520;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,7:30:74:74,0,821 -chr1 118586 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.704;DP=28;Dels=0.00;FS=1.906;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-4.094;QD=3.21;ReadPosRankSum=-0.992;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,8:28:99:118,0,717 -chr1 118591 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;DP=26;Dels=0.00;FS=4.471;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=3.972;QD=23.84;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,18:26:99:648,0,124 -chr1 118613 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.81;MQ0=0;MQRankSum=-3.748;QD=6.56;ReadPosRankSum=3.244;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:179,0,510 -chr1 118618 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=-3.181;QD=6.60;ReadPosRankSum=3.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:180,0,492 -chr1 118625 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=18;Dels=0.00;FS=4.708;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-2.950;QD=6.32;ReadPosRankSum=2.763;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,6:18:99:142,0,434 -chr1 118632 . G T 625.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=2.6647;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=34.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:654,51,0 -chr1 118676 . G T 1157.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=30.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1186,90,0 -chr1 118776 . A G 1200.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=23.9732;MLEAC=2;MLEAF=1.00;MQ=59.04;MQ0=0;QD=33.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:36:99:1229,99,0 -chr1 118792 . T A 957.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=28.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:986,75,0 -chr1 118793 . T A 946.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=32.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:975,75,0 -chr1 118806 . G A 1063.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.10;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1092,84,0 -chr1 118812 . G A 1035.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=24.64;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1064,84,0 -chr1 118868 . G A 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.576;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-4.743;QD=17.09;ReadPosRankSum=1.211;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,17:31:99:558,0,461 -chr1 118880 . C T 637.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=0;QD=33.88;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:666,51,0 -chr1 118885 . A G 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=1.002;QD=15.42;ReadPosRankSum=-0.530;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,9:16:99:275,0,201 -chr1 118899 . A G 656.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=30.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:685,51,0 -chr1 118943 . A G 601.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.62;MQ0=6;QD=23.14;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,21:26:48:630,48,0 -chr1 118947 . T A 569.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.71;MQ0=6;QD=22.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:45:598,45,0 -chr1 118954 . C T 416.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.33;MQ0=6;QD=19.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,16:21:33:445,33,0 -chr1 118958 . C T 374.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.73;MQ0=6;QD=18.74;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,15:20:30:403,30,0 -chr1 118973 . C T 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.10;MQ0=1;MQRankSum=-0.456;QD=17.38;ReadPosRankSum=2.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,13:15:48:289,0,48 -chr1 118991 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.347;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.50;MQ0=1;MQRankSum=1.561;QD=10.94;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,20:21:33:258,33,0 -chr1 119018 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.520;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.12;MQ0=5;MQRankSum=1.561;QD=9.19;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:33:258,33,0 -chr1 119028 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.598;DP=28;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.29;MQ0=5;MQRankSum=2.693;QD=1.21;ReadPosRankSum=-2.784;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,3:28:62:62,0,217 -chr1 119038 . C G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.913;DP=27;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.72;MQ0=5;MQRankSum=2.679;QD=2.07;ReadPosRankSum=-2.775;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,3:27:84:84,0,217 -chr1 119044 . T A 84.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.19;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:27:113,0,27 -chr1 119050 . A T 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28 -chr1 119051 . C G 125.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.26;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,4:4:12:153,12,0 -chr1 119228 . A C 261.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=30.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:21:290,21,0 -chr1 119229 . G A 301.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=33.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:330,24,0 -chr1 119234 . G A 305.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=26.59;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:334,24,0 -chr1 119294 . T A 812.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.23;MQ0=0;QD=26.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:841,63,0 -chr1 119318 . T C 804.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9457;MLEAC=2;MLEAF=1.00;MQ=58.88;MQ0=0;QD=34.99;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:63:833,63,0 -chr1 119339 . A G 715.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=23.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:57:744,57,0 -chr1 119555 . C A 1140.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.628;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.523;QD=34.57;ReadPosRankSum=-1.628;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,32:33:96:1169,96,0 -chr1 119677 . C T 48.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.65;MQ0=0;MQRankSum=0.736;QD=16.25;ReadPosRankSum=-0.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,2:3:6:76,6,0 -chr1 119803 . C T 34.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=17.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr1 119816 . G A 33.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr1 119819 . C T 32.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 -chr1 119830 . A G 36.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=18.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr1 119840 . C T 68.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=22.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:96,9,0 -chr1 119841 . T C 65.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=21.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr1 119862 . G T 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr1 119869 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr1 119921 . A T 289.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.65;MQ0=0;QD=30.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:318,24,0 -chr1 119961 . G C 77.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=65.19;MQ0=0;MQRankSum=0.727;QD=19.44;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:26:106,0,26 -chr1 119977 . T G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=13;Dels=0.00;FS=9.792;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.49;MQ0=0;MQRankSum=-1.466;QD=19.52;ReadPosRankSum=0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,9:13:99:282,0,121 -chr1 120103 . C G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=41;Dels=0.00;FS=9.770;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.26;MQ0=0;MQRankSum=0.468;QD=3.29;ReadPosRankSum=1.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,7:41:99:163,0,1266 -chr1 120119 . G A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=37;Dels=0.00;FS=4.862;HaplotypeScore=2.9458;MLEAC=1;MLEAF=0.500;MQ=60.29;MQ0=0;MQRankSum=0.258;QD=14.67;ReadPosRankSum=-0.623;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,19:37:99:571,0,599 -chr1 120128 . T C 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=1.9459;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=1.099;QD=15.88;ReadPosRankSum=-0.594;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,18:34:99:568,0,540 -chr1 120143 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=27;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=1;MQRankSum=1.487;QD=14.95;ReadPosRankSum=0.154;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:432,0,438 -chr1 120179 . C T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=1;MQRankSum=-0.517;QD=13.45;ReadPosRankSum=0.680;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:378,0,440 -chr1 120186 . T C 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.610;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=1;MQRankSum=-0.268;QD=12.74;ReadPosRankSum=0.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,12:28:99:385,0,463 -chr1 120227 . C T 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140;DP=38;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=1;MQRankSum=1.322;QD=15.28;ReadPosRankSum=-1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,18:38:99:609,0,620 -chr1 120238 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=41;Dels=0.00;FS=7.160;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.231;QD=16.41;ReadPosRankSum=0.177;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,23:41:99:701,0,597 -chr1 120278 . C A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=49;Dels=0.00;FS=4.269;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=1;MQRankSum=0.282;QD=18.55;ReadPosRankSum=-0.366;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,29:49:99:937,0,665 -chr1 120311 . T C 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.855;DP=42;Dels=0.00;FS=1.163;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.780;QD=16.54;ReadPosRankSum=0.101;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:723,0,713 -chr1 120315 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.036;QD=15.72;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,762 -chr1 120371 . T C 692.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.27;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:54:721,54,0 -chr1 120437 . C T 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.001;DP=32;Dels=0.00;FS=22.212;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=0;MQRankSum=-1.284;QD=14.02;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:477,0,541 -chr1 120508 . C T 1393.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.10;MQ0=0;QD=30.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1422,108,0 -chr1 120513 . C G 436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=35;Dels=0.00;FS=5.287;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-1.317;QD=12.48;ReadPosRankSum=0.883;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:35:99:465,0,629 -chr1 120525 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=32;Dels=0.00;FS=5.486;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=55.77;MQ0=1;MQRankSum=0.337;QD=12.46;ReadPosRankSum=0.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:427,0,557 -chr1 120532 . T A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=34;Dels=0.00;FS=7.806;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=55.37;MQ0=1;MQRankSum=-0.055;QD=11.26;ReadPosRankSum=0.856;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,15:34:99:411,0,622 -chr1 120546 . C A 1112.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.7256;MLEAC=2;MLEAF=1.00;MQ=55.59;MQ0=1;QD=34.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1141,90,0 -chr1 120550 . C G 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.115;DP=33;Dels=0.00;FS=3.269;HaplotypeScore=2.4595;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-0.422;QD=10.60;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:378,0,603 -chr1 120567 . A T 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=25;Dels=0.00;FS=2.671;HaplotypeScore=15.7066;MLEAC=1;MLEAF=0.500;MQ=53.60;MQ0=1;MQRankSum=-2.312;QD=2.43;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,5:25:89:89,0,628 -chr1 120592 . G C 609.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=2;MLEAF=1.00;MQ=55.83;MQ0=0;QD=31.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:638,51,0 -chr1 120670 . A G 746.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:60:775,60,0 -chr1 120698 . C T 666.53 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.689;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=2.693;QD=28.98;ReadPosRankSum=0.959;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,20:23:3:693,0,3 -chr1 120702 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.6006;MLEAC=2;MLEAF=1.00;MQ=50.14;MQ0=0;QD=34.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:784,63,0 -chr1 120717 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=0;QD=34.34;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,20:20:57:715,57,0 -chr1 120722 . T C 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=3.000;QD=28.23;ReadPosRankSum=-0.403;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,17:21:43:621,0,43 -chr1 120723 . G T 738.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=46.92;MQ0=0;QD=32.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,21:21:60:767,60,0 -chr1 120725 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=-3.090;QD=0.71;ReadPosRankSum=0.224;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,4:21:43:43,0,578 -chr1 120730 . T C 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;DP=23;Dels=0.00;FS=1.935;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.58;MQ0=0;MQRankSum=-2.065;QD=3.77;ReadPosRankSum=-0.805;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,6:23:99:115,0,600 -chr1 120744 . C A 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.752;DP=27;Dels=0.00;FS=1.574;HaplotypeScore=6.9985;MLEAC=1;MLEAF=0.500;MQ=46.78;MQ0=0;MQRankSum=1.604;QD=19.32;ReadPosRankSum=0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,16:27:99:550,0,301 -chr1 120759 . T C 295.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.164;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-0.367;QD=15.57;ReadPosRankSum=-1.347;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:324,0,285 -chr1 120764 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=0;MQRankSum=-0.599;QD=13.70;ReadPosRankSum=0.951;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,10:21:99:316,0,375 -chr1 120777 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.459;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=1.257;QD=12.14;ReadPosRankSum=-0.018;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:429,0,613 -chr1 120780 . G A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.623;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=0;MQRankSum=0.960;QD=11.94;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:446,0,633 -chr1 120787 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.328;DP=39;Dels=0.00;FS=1.273;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=0;MQRankSum=-1.898;QD=14.64;ReadPosRankSum=2.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,19:39:99:599,0,603 -chr1 120802 . T C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=45;Dels=0.00;FS=2.555;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=0;MQRankSum=-3.970;QD=16.39;ReadPosRankSum=1.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,24:45:99:766,0,656 -chr1 120813 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=4.507;QD=14.68;ReadPosRankSum=-0.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,22:45:99:689,0,762 -chr1 120816 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=51.82;MQ0=0;MQRankSum=-4.264;QD=15.31;ReadPosRankSum=0.639;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:656,0,729 -chr1 120820 . T C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=40;Dels=0.00;FS=2.785;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-4.361;QD=15.12;ReadPosRankSum=1.517;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,684 -chr1 120826 . A G 1504.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=13.9933;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=34.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1533,114,0 -chr1 120838 . A C 1759.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.71;MQ0=1;QD=34.54;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1788,135,0 -chr1 120862 . T C 1676.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.45;MQ0=1;QD=31.05;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1705,132,0 -chr1 120875 . C T 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.870;DP=43;Dels=0.00;FS=4.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=1;MQRankSum=-5.022;QD=11.48;ReadPosRankSum=2.076;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,18:43:99:522,0,781 -chr1 120891 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.826;DP=23;Dels=0.00;FS=9.132;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=0;MQRankSum=-3.019;QD=3.16;ReadPosRankSum=1.155;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,5:23:99:101,0,602 -chr1 120906 . C A 986.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.7330;MLEAC=2;MLEAF=1.00;MQ=54.05;MQ0=1;QD=27.45;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1015,78,0 -chr1 120925 . T A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.177;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.81;MQ0=1;MQRankSum=-1.123;QD=12.24;ReadPosRankSum=0.578;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:99:481,0,688 -chr1 120936 . T A 1380.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.96;MQ0=1;QD=27.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1409,108,0 -chr1 120960 . G C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.936;DP=43;Dels=0.00;FS=2.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=1;MQRankSum=-1.055;QD=18.34;ReadPosRankSum=-1.309;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:817,0,617 -chr1 120966 . T C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=-1.213;QD=16.55;ReadPosRankSum=-0.480;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:740,0,631 -chr1 120969 . G A 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.851;DP=43;Dels=0.00;FS=1.149;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=1.322;QD=15.13;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:679,0,731 -chr1 120992 . C T 1474.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=1;QD=25.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1503,111,0 -chr1 120994 . C G 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=33.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0 -chr1 121003 . A G 1781.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=30.81;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1810,135,0 -chr1 121015 . T C 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.582;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.989;QD=17.38;ReadPosRankSum=0.659;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:932,0,820 -chr1 121034 . T C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.450;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.850;QD=16.97;ReadPosRankSum=0.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,25:49:99:860,0,817 -chr1 121052 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=46;Dels=0.00;FS=8.862;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.022;QD=16.80;ReadPosRankSum=0.681;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,23:46:99:801,0,734 -chr1 121087 . G T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=40;Dels=0.00;FS=5.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.924;QD=8.42;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,16:40:99:365,0,767 -chr1 121102 . G T 1242.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=33.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1271,99,0 -chr1 121118 . T A 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=7.025;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-0.692;QD=16.94;ReadPosRankSum=0.890;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,12:22:99:401,0,296 -chr1 121148 . G A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=27;Dels=0.00;FS=9.204;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.655;QD=15.92;ReadPosRankSum=-0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:458,0,425 -chr1 121152 . T C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.256;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.923;QD=15.84;ReadPosRankSum=-0.821;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:440,0,417 -chr1 121153 . C T 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.615;QD=15.76;ReadPosRankSum=-0.872;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:438,0,430 -chr1 121409 . T C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.00;MQ0=0;QD=11.83;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr1 121415 . G A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.544;DP=32;Dels=0.00;FS=8.557;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-2.657;QD=11.24;ReadPosRankSum=-0.094;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,16:32:99:388,0,539 -chr1 121429 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=46.16;MQ0=0;QD=22.24;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1604,126,0 -chr1 121448 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=3.811;QD=14.79;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,20:43:99:664,0,751 -chr1 121451 . G A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=-3.859;QD=16.34;ReadPosRankSum=0.816;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:731,0,659 -chr1 121462 . T A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=40;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-4.391;QD=16.62;ReadPosRankSum=0.204;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,22:40:99:693,0,595 -chr1 121471 . G C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.49;MQ0=14;QD=0.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:14,1:15:3:38,3,0 -chr1 122095 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr1 122148 . T G 1209.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=35.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1238,93,0 -chr1 122173 . G T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.745;DP=41;Dels=0.00;FS=1.248;HaplotypeScore=3.6993;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=0.176;QD=15.77;ReadPosRankSum=0.311;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,20:41:99:675,0,610 -chr1 122179 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=44;Dels=0.00;FS=2.744;HaplotypeScore=2.7126;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-0.813;QD=14.45;ReadPosRankSum=1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:664,0,726 -chr1 122203 . A C 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.560;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.51;MQ0=0;MQRankSum=-2.415;QD=16.76;ReadPosRankSum=0.352;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:732,0,674 -chr1 122216 . C G 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.587;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=32.8942;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-1.343;QD=15.60;ReadPosRankSum=-0.117;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:668,0,646 -chr1 122277 . T C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.946;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.4826;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.650;QD=9.49;ReadPosRankSum=2.750;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,10:30:99:313,0,658 -chr1 122295 . G A 1172.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.24;MQ0=0;QD=26.60;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1201,90,0 -chr1 122297 . G A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.136;DP=32;Dels=0.00;FS=3.151;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.564;QD=11.15;ReadPosRankSum=2.511;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,12:32:99:385,0,654 -chr1 122301 . C T 1251.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.50;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1280,93,0 -chr1 122383 . C T 1913.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=25.00;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1942,144,0 -chr1 122415 . G A 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=43;Dels=0.00;FS=2.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.30;MQ0=0;MQRankSum=-0.135;QD=13.41;ReadPosRankSum=-0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:605,0,828 -chr1 122424 . G A 1618.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;QD=29.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1647,129,0 -chr1 122430 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=43;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.37;MQ0=1;MQRankSum=0.216;QD=18.23;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:812,0,558 -chr1 122455 . G A,T 921.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=45.04;MQ0=2;QD=24.90;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,20,17:37:99:1105,544,493,561,0,513 -chr1 122456 . G T 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=37;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=2;MQRankSum=-0.480;QD=12.51;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,20:37:99:491,0,496 -chr1 122464 . G A 961.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.23;MQ0=2;QD=30.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:84:990,84,0 -chr1 122469 . A G 726.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=37.29;MQ0=2;QD=27.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,26:26:66:755,66,0 -chr1 122471 . G A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=26;Dels=0.00;FS=3.892;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=37.29;MQ0=2;MQRankSum=1.101;QD=11.64;ReadPosRankSum=-0.811;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:331,0,295 -chr1 122483 . G A 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.303;DP=23;Dels=0.00;FS=4.036;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=35.66;MQ0=2;MQRankSum=-2.429;QD=8.34;ReadPosRankSum=2.429;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,12:23:99:220,0,312 -chr1 122487 . T A 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=20;Dels=0.05;FS=1.957;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=31.84;MQ0=2;MQRankSum=-2.454;QD=6.64;ReadPosRankSum=2.742;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:161,0,242 -chr1 122498 . T C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.9968;MLEAC=1;MLEAF=0.500;MQ=48.55;MQ0=1;MQRankSum=0.407;QD=14.02;ReadPosRankSum=-0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,19:42:99:617,0,646 -chr1 122513 . T G 1544.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=1;QD=34.33;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1573,120,0 -chr1 122548 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=35;Dels=0.00;FS=1.445;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.791;QD=19.42;ReadPosRankSum=2.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,21:35:99:708,0,420 -chr1 122565 . A T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.454;DP=37;Dels=0.00;FS=7.957;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.391;QD=20.07;ReadPosRankSum=-0.673;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,23:37:99:771,0,457 -chr1 122594 . G T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=54;Dels=0.00;FS=2.373;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=0.177;QD=12.25;ReadPosRankSum=2.129;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,21:54:99:690,0,1043 -chr1 122607 . G C 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=3.662;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.387;QD=15.56;ReadPosRankSum=-0.751;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,28:59:99:946,0,1029 -chr1 122655 . T G 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=64;Dels=0.00;FS=1.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.915;QD=9.84;ReadPosRankSum=1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,21:64:99:658,0,1417 -chr1 122658 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=63;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.303;QD=9.33;ReadPosRankSum=1.676;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,20:63:99:616,0,1391 -chr1 122661 . C T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=59;Dels=0.00;FS=3.946;HaplotypeScore=7.7321;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-0.511;QD=9.88;ReadPosRankSum=1.371;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,19:59:99:611,0,1272 -chr1 122745 . C A 1546.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=2;MLEAF=1.00;MQ=56.58;MQ0=0;QD=35.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1575,120,0 -chr1 122757 . A C,G 1142.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.27;MQ0=0;QD=30.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,15,22:37:99:1336,829,786,508,0,441 -chr1 122760 . T G 1421.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.36;MQ0=0;QD=30.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1450,108,0 -chr1 122767 . A C 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-5.113;QD=8.09;ReadPosRankSum=2.844;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:360,0,994 -chr1 122789 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-4.915;QD=8.73;ReadPosRankSum=1.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,12:38:99:360,0,925 -chr1 122826 . G A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.987;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.84;MQ0=0;MQRankSum=-3.853;QD=3.02;ReadPosRankSum=1.957;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,6:37:99:140,0,1158 -chr1 122828 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=40;Dels=0.00;FS=1.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.688;QD=4.42;ReadPosRankSum=0.423;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,8:40:99:205,0,1171 -chr1 122865 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=49;Dels=0.00;FS=14.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=0.373;QD=9.81;ReadPosRankSum=0.501;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,16:49:99:509,0,1184 -chr1 122905 . C T 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.019;DP=42;Dels=0.00;FS=5.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.989;QD=6.14;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,10:42:99:286,0,1168 -chr1 122938 . C T 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.284;DP=41;Dels=0.00;FS=5.664;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=1;MQRankSum=-4.235;QD=7.65;ReadPosRankSum=-3.497;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:342,0,1011 -chr1 122969 . T C 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=52;Dels=0.00;FS=11.610;HaplotypeScore=2.8266;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=-5.166;QD=13.00;ReadPosRankSum=1.641;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,21:52:99:704,0,1092 -chr1 122976 . C T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=49;Dels=0.00;FS=12.245;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-3.283;QD=13.83;ReadPosRankSum=2.879;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:706,0,952 -chr1 122990 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.759;DP=52;Dels=0.00;FS=15.894;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-4.241;QD=12.23;ReadPosRankSum=3.207;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:664,0,1073 -chr1 123012 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.417;DP=52;Dels=0.00;FS=6.555;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-3.786;QD=11.46;ReadPosRankSum=0.019;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:624,0,1045 -chr1 123034 . T C 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.523;DP=46;Dels=0.00;FS=4.428;HaplotypeScore=3.8314;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-1.707;QD=10.23;ReadPosRankSum=-1.707;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,17:46:99:499,0,1020 -chr1 123098 . A G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=38;Dels=0.00;FS=7.718;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=1;MQRankSum=1.769;QD=9.86;ReadPosRankSum=-1.613;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:403,0,787 -chr1 123121 . C T 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.802;DP=35;Dels=0.00;FS=3.247;HaplotypeScore=1.8273;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=1;MQRankSum=-1.207;QD=9.59;ReadPosRankSum=-1.907;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:364,0,645 -chr1 123176 . A T 1326.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.74;MQ0=0;QD=34.79;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1355,102,0 -chr1 123262 . G A 661.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=10.6984;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:690,51,0 -chr1 123294 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=22;Dels=0.00;FS=6.897;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.901;QD=10.03;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:249,0,484 -chr1 123320 . T A 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.094;DP=23;Dels=0.00;FS=7.060;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.409;QD=11.56;ReadPosRankSum=2.425;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,9:23:99:294,0,487 -chr1 123328 . G C 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=25;Dels=0.00;FS=6.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.878;QD=9.19;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:258,0,573 -chr1 123528 . G T 563.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.41;MQ0=3;QD=31.32;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,15:18:45:592,45,0 -chr1 123588 . T C 848.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.28;MQ0=3;QD=33.95;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,22:25:66:877,66,0 -chr1 123694 . A G 697.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.64;MQ0=0;QD=34.89;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:726,54,0 -chr1 123730 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=23;Dels=0.00;FS=5.969;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.502;QD=1.34;ReadPosRankSum=-0.411;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,3:23:59:59,0,664 -chr1 123755 . C A 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=28;Dels=0.00;FS=5.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=0.624;QD=2.21;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,4:28:90:90,0,768 -chr1 123843 . T C 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=0.889;QD=7.57;ReadPosRankSum=-0.191;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:210,0,577 -chr1 123903 . T A 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.580;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.500;QD=11.77;ReadPosRankSum=1.221;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:393,0,627 -chr1 123904 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.941;QD=11.67;ReadPosRankSum=1.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:390,0,619 -chr1 123916 . T G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.496;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.276;QD=10.49;ReadPosRankSum=0.390;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:385,0,693 -chr1 123923 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.329;QD=9.32;ReadPosRankSum=-0.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:373,0,791 -chr1 123947 . C A 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=1.259;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.321;QD=9.66;ReadPosRankSum=-0.867;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:434,0,970 -chr1 123966 . G A 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=11.9954;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.893;QD=8.91;ReadPosRankSum=-0.275;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:349,0,885 -chr1 123975 . T A 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=41;Dels=0.00;FS=1.345;HaplotypeScore=13.9928;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.124;QD=9.60;ReadPosRankSum=1.113;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:422,0,967 -chr1 124035 . T C 365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.216;DP=34;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-0.378;QD=10.76;ReadPosRankSum=1.423;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:394,0,689 -chr1 124057 . G A 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=38;Dels=0.00;FS=1.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.990;QD=12.70;ReadPosRankSum=0.754;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:511,0,655 -chr1 124075 . T G 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-0.800;QD=11.92;ReadPosRankSum=1.082;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:362,0,542 -chr1 124090 . T C 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.741;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-3.362;QD=13.27;ReadPosRankSum=0.703;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:453,0,623 -chr1 124097 . G A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=-3.549;QD=10.19;ReadPosRankSum=0.669;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:344,0,678 -chr1 124108 . A G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=29;Dels=0.00;FS=3.834;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.061;QD=9.68;ReadPosRankSum=1.124;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,669 -chr1 124113 . C A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.297;DP=32;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.25;MQ0=0;MQRankSum=-3.923;QD=8.52;ReadPosRankSum=1.159;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:301,0,784 -chr1 124123 . A C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.866;DP=31;Dels=0.00;FS=6.205;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.867;QD=8.61;ReadPosRankSum=-0.063;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:295,0,742 -chr1 124134 . C T 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=29;Dels=0.00;FS=10.056;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=3.001;QD=23.82;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:8,21:29:99:719,0,221 -chr1 124151 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=0;MQRankSum=1.104;QD=10.27;ReadPosRankSum=1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:285,0,486 -chr1 124152 . A G 916.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.49;MQ0=0;QD=27.62;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:945,72,0 -chr1 124168 . C T 879.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.592;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=3.4667;MLEAC=2;MLEAF=1.00;MQ=42.46;MQ0=2;MQRankSum=2.281;QD=28.38;ReadPosRankSum=1.764;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:72:908,72,0 -chr1 124203 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.72;MQ0=2;QD=25.33;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:66:788,66,0 -chr1 124205 . A G 777.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.764;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.60;MQ0=2;MQRankSum=2.281;QD=25.09;ReadPosRankSum=-2.195;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:69:806,69,0 -chr1 124243 . G C 675.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.16;MQ0=2;QD=28.16;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:57:704,57,0 -chr1 124267 . G A 818.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.25;MQ0=0;QD=34.12;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:847,66,0 -chr1 124277 . A C 856.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.91;MQ0=0;QD=34.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:885,69,0 -chr1 124284 . C T 947.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.04;MQ0=0;QD=33.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:976,78,0 -chr1 124321 . C T 993.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.624;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.37;MQ0=0;MQRankSum=2.203;QD=33.13;ReadPosRankSum=1.788;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,28:30:78:1022,78,0 -chr1 124337 . C T 1115.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.315;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.29;MQ0=0;MQRankSum=2.239;QD=31.88;ReadPosRankSum=-0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,33:35:90:1144,90,0 -chr1 124376 . A T 778.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.420;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.24;MQ0=2;MQRankSum=1.850;QD=25.12;ReadPosRankSum=-0.645;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:66:807,66,0 -chr1 124388 . C T 51.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.026;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.51;MQ0=0;MQRankSum=1.026;QD=12.94;ReadPosRankSum=-1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,2:4:6:79,6,0 -chr1 124423 . T A 12.77 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.97;MQ0=9;QD=1.28;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:9,1:10:3:39,3,0 -chr1 124467 . G T 1086.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.37;MQ0=10;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,33:40:84:1115,84,0 -chr1 124471 . G A 1113.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=8;QD=29.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,31:38:87:1142,87,0 -chr1 124494 . G A 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.11;MQ0=0;MQRankSum=2.064;QD=19.94;ReadPosRankSum=4.069;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1025,0,663 -chr1 124512 . A C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.557;QD=13.28;ReadPosRankSum=1.261;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:692,0,960 -chr1 124607 . T C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.445;DP=50;Dels=0.00;FS=19.947;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.175;QD=16.82;ReadPosRankSum=1.106;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:869,0,855 -chr1 124731 . C A 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=30;Dels=0.00;FS=18.572;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.727;QD=1.29;ReadPosRankSum=-2.688;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,4:30:67:67,0,818 -chr1 124820 . A T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.600;QD=13.31;ReadPosRankSum=1.683;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:667,0,918 -chr1 124864 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.180;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.318;QD=14.06;ReadPosRankSum=-2.039;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:647,0,835 -chr1 124901 . T G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.761;QD=16.06;ReadPosRankSum=0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:751,0,736 -chr1 124917 . A T 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.090;DP=40;Dels=0.00;FS=2.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=0.251;QD=11.29;ReadPosRankSum=-1.145;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:480,0,891 -chr1 124920 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.054;QD=10.47;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:405,0,807 -chr1 125002 . T C 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.594;DP=49;Dels=0.00;FS=1.202;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.069;QD=9.57;ReadPosRankSum=-1.460;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:497,0,1178 -chr1 125004 . A G 1137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.804;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=1.148;QD=23.22;ReadPosRankSum=1.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,32:49:99:1166,0,460 -chr1 125020 . A T 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.617;DP=46;Dels=0.00;FS=1.204;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-1.547;QD=9.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:486,0,1126 -chr1 125046 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=1.788;QD=12.74;ReadPosRankSum=0.293;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:627,0,985 -chr1 125096 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.345;HaplotypeScore=2.7212;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.887;QD=16.57;ReadPosRankSum=0.553;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:724,0,731 -chr1 125124 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.683;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=3.985;QD=26.36;ReadPosRankSum=0.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:7,26:33:99:898,0,147 -chr1 125126 . T C 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.859;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.029;QD=3.63;ReadPosRankSum=0.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:148,0,866 -chr1 125128 . G A 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.011;QD=2.63;ReadPosRankSum=2.370;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,7:33:99:115,0,854 -chr1 125133 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.992;QD=3.99;ReadPosRankSum=2.622;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:152,0,843 -chr1 125134 . A G 1101.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=54.91;MQ0=0;QD=25.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1130,90,0 -chr1 125142 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=52.83;MQ0=0;MQRankSum=4.377;QD=22.16;ReadPosRankSum=-1.254;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,20:30:99:693,0,230 -chr1 125149 . G A 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=28;Dels=0.00;FS=1.690;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=50.58;MQ0=0;MQRankSum=-4.514;QD=12.42;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:376,0,460 -chr1 125166 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=-4.339;QD=9.10;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:283,0,577 -chr1 125168 . C T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=1.805;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.84;MQ0=0;MQRankSum=4.551;QD=18.83;ReadPosRankSum=0.826;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,18:30:99:593,0,339 -chr1 125175 . A G 1245.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=23.30;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1274,102,0 -chr1 125190 . C T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=37;Dels=0.00;FS=4.233;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=0;MQRankSum=-5.120;QD=10.53;ReadPosRankSum=0.820;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:418,0,736 -chr1 125195 . C T 1518.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.9963;MLEAC=2;MLEAF=1.00;MQ=51.70;MQ0=0;QD=25.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1547,123,0 -chr1 125207 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.99;ReadPosRankSum=2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:379,0,880 -chr1 125210 . C T 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.89;ReadPosRankSum=2.309;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:375,0,828 -chr1 125216 . G C 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.307;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.26;MQ0=0;MQRankSum=-5.080;QD=8.81;ReadPosRankSum=1.918;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:372,0,862 -chr1 125248 . T C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=49;Dels=0.00;FS=1.304;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=1;MQRankSum=-3.990;QD=12.14;ReadPosRankSum=-0.686;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:623,0,932 -chr1 125250 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.022;DP=47;Dels=0.00;FS=2.895;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.33;MQ0=1;MQRankSum=4.261;QD=18.97;ReadPosRankSum=0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:920,0,541 -chr1 125267 . T C 1345.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.3302;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=32.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1374,111,0 -chr1 125269 . T C 1426.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=34.80;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1455,114,0 -chr1 125274 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=3.553;QD=15.80;ReadPosRankSum=0.624;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:755,0,576 -chr1 125306 . A T 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=36;Dels=0.00;FS=1.377;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=1;MQRankSum=-2.732;QD=11.44;ReadPosRankSum=1.772;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:440,0,654 -chr1 125310 . C T 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.769;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=1;MQRankSum=3.388;QD=16.64;ReadPosRankSum=-1.600;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:544,0,362 -chr1 125319 . C T 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.05;MQ0=1;MQRankSum=-3.282;QD=8.96;ReadPosRankSum=2.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:279,0,506 -chr1 125322 . T A 873.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.64;MQ0=1;QD=32.36;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:902,72,0 -chr1 125330 . T A 876.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.42;MQ0=1;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:72:905,72,0 -chr1 125345 . C T 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=23;Dels=0.00;FS=1.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.96;MQ0=0;MQRankSum=-3.132;QD=9.86;ReadPosRankSum=-0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:255,0,427 -chr1 125408 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:224,18,0 -chr1 125409 . C G 191.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=31.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:220,18,0 -chr1 125410 . C G 194.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:223,18,0 -chr1 125416 . G T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=14;Dels=0.00;FS=2.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=1.734;QD=1.00;ReadPosRankSum=-0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,2:14:42:42,0,418 -chr1 125441 . A G 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=24;Dels=0.00;FS=1.760;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=1;MQRankSum=-3.324;QD=4.32;ReadPosRankSum=-3.905;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:132,0,545 -chr1 125444 . C T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=26;Dels=0.00;FS=1.697;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.30;MQ0=1;MQRankSum=3.652;QD=21.11;ReadPosRankSum=2.746;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:577,0,160 -chr1 125447 . G A 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.535;DP=24;Dels=0.00;FS=1.744;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.32;MQ0=1;MQRankSum=-3.937;QD=6.12;ReadPosRankSum=-2.551;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:175,0,501 -chr1 125453 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.271;DP=24;Dels=0.00;FS=3.963;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.60;MQ0=1;MQRankSum=-4.062;QD=7.91;ReadPosRankSum=-2.946;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,11:24:99:218,0,462 -chr1 125481 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.995;DP=33;Dels=0.00;FS=3.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.76;MQ0=1;MQRankSum=-4.758;QD=8.93;ReadPosRankSum=2.724;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:323,0,666 -chr1 125491 . G C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.31;ReadPosRankSum=1.104;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:286,0,566 -chr1 125495 . G A 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.953;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.43;ReadPosRankSum=1.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:289,0,560 -chr1 125497 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.689;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.55;ReadPosRankSum=1.274;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:292,0,557 -chr1 125498 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.19;ReadPosRankSum=1.387;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:283,0,571 -chr1 125503 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=26;Dels=0.00;FS=1.657;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=0;MQRankSum=-4.042;QD=10.14;ReadPosRankSum=1.294;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:292,0,609 -chr1 125509 . C T 1210.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=28.40;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1239,93,0 -chr1 125530 . T C 1192.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;QD=25.52;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1221,93,0 -chr1 125548 . C A 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=29;Dels=0.00;FS=9.640;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=2.073;QD=16.13;ReadPosRankSum=0.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,15:29:99:496,0,417 -chr1 125550 . G A 1067.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.16;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1096,87,0 -chr1 125582 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.929;DP=28;Dels=0.00;FS=3.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=1;MQRankSum=0.386;QD=21.10;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,18:28:99:619,0,268 -chr1 125589 . A T 672.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=28.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:701,51,0 -chr1 125622 . A C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.336;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=1;MQRankSum=-0.542;QD=19.26;ReadPosRankSum=-0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:837,0,537 -chr1 125640 . G T 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=41;Dels=0.00;FS=2.681;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-1.405;QD=14.29;ReadPosRankSum=3.533;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:614,0,776 -chr1 125691 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=44;Dels=0.00;FS=4.165;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-2.085;QD=13.79;ReadPosRankSum=-0.308;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:635,0,863 -chr1 125721 . T G 219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=36;Dels=0.00;FS=1.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-1.754;QD=6.10;ReadPosRankSum=0.913;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,9:36:99:248,0,910 -chr1 125736 . T C 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-1.023;QD=7.61;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:264,0,762 -chr1 125740 . A G 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.249;QD=8.20;ReadPosRankSum=-1.014;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:266,0,653 -chr1 125759 . T C 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.697;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.079;QD=11.06;ReadPosRankSum=-0.652;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:349,0,542 -chr1 125772 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.466;DP=26;Dels=0.00;FS=8.852;HaplotypeScore=17.6766;MLEAC=1;MLEAF=0.500;MQ=55.71;MQ0=0;MQRankSum=-4.089;QD=13.88;ReadPosRankSum=-0.489;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:389,0,400 -chr1 125787 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=26;Dels=0.00;FS=12.825;HaplotypeScore=2.9982;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=1.463;QD=0.57;ReadPosRankSum=-2.801;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,3:26:43:43,0,723 -chr1 125794 . C T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.246;DP=25;Dels=0.00;FS=1.697;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-4.243;QD=12.43;ReadPosRankSum=1.670;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:339,0,466 -chr1 125810 . G T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.808;QD=9.17;ReadPosRankSum=1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:331,0,680 -chr1 125834 . T G 1147.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.621;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7719;MLEAC=2;MLEAF=1.00;MQ=58.76;MQ0=0;MQRankSum=-0.503;QD=26.31;ReadPosRankSum=-1.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,30:31:70:1176,70,0 -chr1 126025 . G A 1160.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=47.94;MQ0=0;QD=26.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1189,90,0 -chr1 126059 . T C 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.273;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.52;ReadPosRankSum=-2.721;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:590,0,540 -chr1 126061 . T A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.514;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.40;ReadPosRankSum=-3.341;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:586,0,522 -chr1 126072 . G A 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.927;DP=28;Dels=0.00;FS=6.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.25;MQ0=0;MQRankSum=-4.480;QD=11.53;ReadPosRankSum=1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:351,0,542 -chr1 126082 . A T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310;DP=19;Dels=0.00;FS=7.701;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=0;MQRankSum=-3.592;QD=9.46;ReadPosRankSum=1.479;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,7:19:99:208,0,430 -chr1 126524 . G A 622.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:651,51,0 -chr1 126529 . T A 646.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:675,51,0 -chr1 126531 . C T 649.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:678,51,0 -chr1 126536 . G A 653.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=25.84;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:682,51,0 -chr1 126547 . G A 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=25;Dels=0.00;FS=13.262;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.44;MQ0=0;MQRankSum=0.082;QD=16.95;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:452,0,359 -chr1 126551 . A G 380.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=25;Dels=0.00;FS=13.829;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.34;MQ0=0;MQRankSum=0.027;QD=15.23;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,12:25:99:409,0,391 -chr1 126556 . T C 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=24;Dels=0.00;FS=26.945;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-0.381;QD=12.41;ReadPosRankSum=4.070;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:326,0,444 -chr1 126572 . G C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=49;Dels=0.00;FS=4.366;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=0;MQRankSum=-3.829;QD=8.40;ReadPosRankSum=0.618;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,15:49:99:440,0,1091 -chr1 126583 . C T 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-1.853;QD=19.55;ReadPosRankSum=5.365;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:947,0,591 -chr1 126584 . G A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=47;Dels=0.00;FS=2.763;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-4.028;QD=8.53;ReadPosRankSum=1.677;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,15:47:99:429,0,1116 -chr1 126595 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=52;Dels=0.00;FS=2.606;HaplotypeScore=22.9737;MLEAC=1;MLEAF=0.500;MQ=51.73;MQ0=0;MQRankSum=-4.709;QD=8.67;ReadPosRankSum=2.092;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:479,0,1271 -chr1 126599 . G T 1355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=50;Dels=0.00;FS=1.289;HaplotypeScore=32.9690;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-2.510;QD=27.12;ReadPosRankSum=-1.715;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,38:50:99:1384,0,313 -chr1 126603 . A G 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=50;Dels=0.00;FS=2.527;HaplotypeScore=32.7034;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-4.690;QD=8.90;ReadPosRankSum=4.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:473,0,1206 -chr1 126605 . C T 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.369;HaplotypeScore=32.7046;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=3.501;QD=15.29;ReadPosRankSum=-4.331;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:808,0,893 -chr1 126609 . C T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.515;DP=50;Dels=0.00;FS=2.429;HaplotypeScore=30.7052;MLEAC=1;MLEAF=0.500;MQ=52.80;MQ0=0;MQRankSum=-2.243;QD=17.32;ReadPosRankSum=3.641;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:894,0,800 -chr1 126615 . T A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.333;DP=53;Dels=0.00;FS=8.297;HaplotypeScore=11.7855;MLEAC=1;MLEAF=0.500;MQ=54.30;MQ0=0;MQRankSum=-5.840;QD=8.94;ReadPosRankSum=4.602;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:502,0,1303 -chr1 126645 . G A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.603;HaplotypeScore=100.5169;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-5.977;QD=5.77;ReadPosRankSum=-1.607;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,16:65:99:403,0,1747 -chr1 126670 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=54;Dels=0.00;FS=1.105;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-1.100;QD=11.75;ReadPosRankSum=-0.710;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:663,0,1180 -chr1 126698 . T C 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.857;DP=55;Dels=0.00;FS=8.472;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=2.036;QD=22.43;ReadPosRankSum=2.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1262,0,539 -chr1 126702 . T C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=58;Dels=0.00;FS=16.756;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.515;QD=9.98;ReadPosRankSum=-2.609;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:38,20:58:99:607,0,1364 -chr1 126709 . C T 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=54;Dels=0.00;FS=4.827;HaplotypeScore=4.9981;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.447;QD=5.42;ReadPosRankSum=-0.697;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:42,12:54:99:321,0,1519 -chr1 126712 . A T 2169.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=9.9949;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;QD=27.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2198,166,0 -chr1 126725 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=57;Dels=0.00;FS=9.993;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.729;QD=12.00;ReadPosRankSum=-1.418;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:35,22:57:99:712,0,1228 -chr1 126730 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=53;Dels=0.00;FS=6.032;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.467;QD=9.18;ReadPosRankSum=-2.601;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:515,0,1208 -chr1 126761 . C A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=1.910;QD=16.77;ReadPosRankSum=-0.350;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:850,0,808 -chr1 126795 . T A 1211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=58;Dels=0.00;FS=1.054;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.462;QD=20.89;ReadPosRankSum=1.685;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1240,0,735 -chr1 126808 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=61;Dels=0.00;FS=3.491;HaplotypeScore=16.9835;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-3.792;QD=1.68;ReadPosRankSum=-0.502;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:53,8:61:99:131,0,1927 -chr1 126813 . C A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=62;Dels=0.00;FS=3.493;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.433;QD=1.59;ReadPosRankSum=0.304;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,8:62:99:127,0,1961 -chr1 126818 . A T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=60;Dels=0.00;FS=3.656;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=-1.381;QD=19.81;ReadPosRankSum=-0.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1217,0,765 -chr1 126828 . G A 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.847;DP=64;Dels=0.00;FS=3.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.035;QD=18.39;ReadPosRankSum=0.616;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1205,0,913 -chr1 126853 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=65;Dels=0.00;FS=24.367;HaplotypeScore=18.9957;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-2.099;QD=2.83;ReadPosRankSum=-0.102;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,11:65:99:212,0,1982 -chr1 126860 . A C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.719;DP=68;Dels=0.00;FS=20.308;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=1;MQRankSum=-1.259;QD=2.08;ReadPosRankSum=0.450;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,10:68:99:170,0,2073 -chr1 126861 . T A 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=69;Dels=0.00;FS=6.505;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=0.043;QD=15.01;ReadPosRankSum=1.333;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1064,0,1239 -chr1 126865 . G C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;DP=69;Dels=0.00;FS=24.072;HaplotypeScore=18.9966;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-0.684;QD=2.62;ReadPosRankSum=0.043;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,11:69:99:209,0,2116 -chr1 126883 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.091;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=0.724;QD=7.50;ReadPosRankSum=0.943;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:50,19:69:99:546,0,1802 -chr1 126896 . G T 1175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.676;DP=66;Dels=0.00;FS=6.828;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=1;MQRankSum=0.099;QD=17.81;ReadPosRankSum=-1.057;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1204,0,1011 -chr1 126923 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=68;Dels=0.00;FS=11.174;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=1;MQRankSum=1.555;QD=9.54;ReadPosRankSum=-1.395;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:46,22:68:99:677,0,1574 -chr1 126945 . A T 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.121;DP=63;Dels=0.00;FS=9.115;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.380;QD=4.79;ReadPosRankSum=0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,14:63:99:330,0,1740 -chr1 126957 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.697;DP=59;Dels=0.00;FS=5.370;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=0.773;QD=2.47;ReadPosRankSum=1.289;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,10:59:99:174,0,1767 -chr1 126959 . A G 174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=55;Dels=0.00;FS=5.678;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-0.116;QD=3.18;ReadPosRankSum=0.812;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:45,10:55:99:203,0,1601 -chr1 126963 . C A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=54;Dels=0.00;FS=19.876;HaplotypeScore=17.9934;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-0.135;QD=13.01;ReadPosRankSum=0.695;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:731,0,1059 -chr1 126974 . G A 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;DP=53;Dels=0.00;FS=4.336;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=1;MQRankSum=-0.448;QD=19.37;ReadPosRankSum=-0.858;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:1055,0,636 -chr1 126988 . T C 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=1;MQRankSum=-0.179;QD=1.42;ReadPosRankSum=-0.636;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:40,7:47:95:95,0,1426 -chr1 127068 . T C 919.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.25;MQ0=0;QD=27.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:948,72,0 -chr1 127210 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=1.8245;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=0;MQRankSum=1.532;QD=1.71;ReadPosRankSum=-1.296;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,2:11:47:47,0,276 -chr1 127231 . C A 235.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=33.69;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:264,21,0 -chr1 127271 . G A 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.262;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=2.262;QD=24.89;ReadPosRankSum=0.566;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,8:11:24:302,24,0 -chr1 127280 . C T 285.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.63;MQ0=2;QD=23.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:314,24,0 -chr1 127338 . C T 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.92;MQ0=0;MQRankSum=0.731;QD=15.01;ReadPosRankSum=0.731;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:1,4:5:12:103,0,12 -chr1 127348 . G A 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=6;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.23;MQ0=0;MQRankSum=0.720;QD=12.51;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:2,4:6:12:103,0,12 -chr1 127382 . C T 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;DP=10;Dels=0.00;FS=11.181;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=35.14;MQ0=0;MQRankSum=2.383;QD=9.08;ReadPosRankSum=-0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:6,4:10:43:119,0,43 -chr1 127438 . G T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=27;Dels=0.00;FS=15.441;HaplotypeScore=6.0290;MLEAC=1;MLEAF=0.500;MQ=25.45;MQ0=5;MQRankSum=2.404;QD=11.51;ReadPosRankSum=1.469;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,14:27:56:339,0,56 -chr1 127457 . C T 504.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.419;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.1428;MLEAC=2;MLEAF=1.00;MQ=26.11;MQ0=5;MQRankSum=0.959;QD=18.03;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:5,23:28:51:533,51,0 -chr1 127490 . G A 323.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.41;MQ0=1;MQRankSum=1.488;QD=21.58;ReadPosRankSum=1.240;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,14:15:36:352,36,0 -chr1 127515 . T C 221.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.49;MQ0=0;QD=24.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,9:9:24:250,24,0 -chr1 127567 . G A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=35;Dels=0.00;FS=6.623;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=2;MQRankSum=-4.564;QD=1.99;ReadPosRankSum=-3.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,12:35:98:98,0,737 -chr1 127579 . G C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=39;Dels=0.00;FS=3.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=2;MQRankSum=-4.786;QD=2.30;ReadPosRankSum=-2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:118,0,827 -chr1 127590 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=42;Dels=0.00;FS=4.107;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.59;MQ0=2;MQRankSum=-4.885;QD=1.95;ReadPosRankSum=1.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,13:42:99:110,0,969 -chr1 127595 . T G 1307.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.28;MQ0=2;QD=29.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1336,111,0 -chr1 127637 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.819;DP=40;Dels=0.00;FS=12.746;HaplotypeScore=2.4098;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-4.973;QD=2.04;ReadPosRankSum=-1.284;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:110,0,984 -chr1 127648 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.114;DP=35;Dels=0.00;FS=12.225;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=4.397;QD=25.96;ReadPosRankSum=3.076;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,26:35:99:937,0,111 -chr1 127656 . T C 1057.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1086,81,0 -chr1 127661 . C T 1052.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.96;MQ0=0;QD=32.43;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1081,81,0 -chr1 127677 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=30.02;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:27:75:1027,75,0 -chr1 127909 . T A 404.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.68;MQ0=5;QD=19.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:42:433,42,0 -chr1 127922 . T C 479.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.69;MQ0=4;QD=22.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:45:508,45,0 -chr1 127948 . A G 614.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.18;MQ0=4;QD=26.73;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:643,51,0 -chr1 128047 . A G 823.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=1;QD=29.22;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q26|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,23:23:63:852,63,0 -chr1 128090 . A T 825.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.66;MQ0=1;QD=25.81;EFF=STOP_GAINED(HIGH|NONSENSE|Aga/Tga|R41*|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,32:32:69:854,69,0 -chr1 128144 . C T 1024.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.67;MQ0=0;QD=31.05;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L59|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,33:33:81:1053,81,0 -chr1 128315 . C T 802.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=29.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:831,63,0 -chr1 128373 . T A 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.675;DP=31;Dels=0.00;FS=10.328;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=0;MQRankSum=-3.475;QD=1.64;ReadPosRankSum=-1.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,6:31:79:79,0,886 -chr1 128434 . A G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=34;Dels=0.00;FS=10.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=-4.271;QD=13.76;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:496,0,567 -chr1 128435 . C A 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.620;DP=34;Dels=0.00;FS=13.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=4.202;QD=15.61;ReadPosRankSum=-1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:559,0,495 -chr1 128484 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.879;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-4.478;QD=17.06;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:540,0,432 -chr1 128493 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.90;MQ0=0;MQRankSum=-4.008;QD=15.96;ReadPosRankSum=0.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,15:28:99:475,0,439 -chr1 128534 . G T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=28;Dels=0.00;FS=5.632;HaplotypeScore=18.3580;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.821;QD=1.99;ReadPosRankSum=-2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,4:28:84:84,0,841 -chr1 128588 . C T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=37;Dels=0.00;FS=28.800;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.381;QD=17.89;ReadPosRankSum=1.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:690,0,561 -chr1 128665 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.03;FS=0.000;HaplotypeScore=3.2953;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1204,93,0 -chr1 128691 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.043;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=4;MQRankSum=-0.764;QD=6.66;ReadPosRankSum=-0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:288,0,846 -chr1 128700 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=5;MQRankSum=-1.458;QD=4.21;ReadPosRankSum=-0.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:184,0,862 -chr1 128703 . A G 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.686;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-0.441;QD=4.19;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:175,0,799 -chr1 128705 . C T 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=5;MQRankSum=-0.969;QD=4.27;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:182,0,890 -chr1 128706 . A G 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.275;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-1.471;QD=4.59;ReadPosRankSum=0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:189,0,851 -chr1 128741 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=49;Dels=0.00;FS=18.338;HaplotypeScore=2.9979;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=3;MQRankSum=-1.889;QD=10.67;ReadPosRankSum=2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:551,0,903 -chr1 128751 . A G 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.379;DP=53;Dels=0.00;FS=22.251;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=3;MQRankSum=-1.700;QD=9.75;ReadPosRankSum=3.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:545,0,1055 -chr1 128795 . G A 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.675;DP=55;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-3.881;QD=14.92;ReadPosRankSum=-1.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:849,0,927 -chr1 128807 . T C 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=57;Dels=0.00;FS=5.835;HaplotypeScore=10.9974;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.485;QD=12.96;ReadPosRankSum=3.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:767,0,1052 -chr1 128808 . C T 2130.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=11.9972;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2159,165,0 -chr1 128816 . A G 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=56;Dels=0.00;FS=11.033;HaplotypeScore=23.9742;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.409;QD=5.35;ReadPosRankSum=-2.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:328,0,1466 -chr1 128821 . G T 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=54;Dels=0.00;FS=1.128;HaplotypeScore=13.9934;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=0;MQRankSum=-1.961;QD=19.50;ReadPosRankSum=3.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1081,0,641 -chr1 128823 . C T 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;DP=51;Dels=0.00;FS=1.146;HaplotypeScore=22.8239;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-0.718;QD=18.68;ReadPosRankSum=2.727;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:981,0,699 -chr1 128833 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.443;DP=53;Dels=0.00;FS=6.025;HaplotypeScore=10.8296;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=0;MQRankSum=-0.580;QD=3.51;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:214,0,1479 -chr1 128853 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=49;Dels=0.00;FS=11.665;HaplotypeScore=1.6634;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.294;QD=3.67;ReadPosRankSum=1.902;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:39,9:49:99:208,0,1382 -chr1 128899 . G A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.178;DP=38;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-3.084;QD=11.84;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:478,0,618 -chr1 128911 . T C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=51;Dels=0.00;FS=1.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.607;QD=3.39;ReadPosRankSum=-3.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:201,0,1364 -chr1 128916 . G A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-1.816;QD=3.41;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:202,0,1455 -chr1 128946 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=60;Dels=0.00;FS=2.267;HaplotypeScore=13.9962;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.741;QD=9.48;ReadPosRankSum=1.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:597,0,1331 -chr1 128948 . A C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.669;DP=62;Dels=0.00;FS=1.018;HaplotypeScore=31.9736;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-2.302;QD=9.50;ReadPosRankSum=1.640;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:617,0,1424 -chr1 128956 . C G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=47.9525;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=0.097;QD=7.15;ReadPosRankSum=1.620;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:493,0,1642 -chr1 128957 . T G 1312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=33.9668;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.149;QD=20.84;ReadPosRankSum=1.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1341,0,755 -chr1 128961 . G A 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.577;QD=19.96;ReadPosRankSum=1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1286,0,756 -chr1 128975 . G T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=33.8278;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.350;QD=10.39;ReadPosRankSum=-0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,23:68:99:735,0,1596 -chr1 128988 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.066;DP=73;Dels=0.00;FS=12.861;HaplotypeScore=23.3284;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.345;QD=5.52;ReadPosRankSum=1.976;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:55,17:73:99:431,0,2010 -chr1 129160 . A T 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-5.688;QD=4.52;ReadPosRankSum=-1.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,15:63:99:313,0,1702 -chr1 129165 . G T 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-5.619;QD=4.83;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,15:61:99:323,0,1605 -chr1 129168 . A G 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-5.671;QD=4.71;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:47,15:62:99:320,0,1616 -chr1 129170 . G T 2364.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.46;MQ0=0;QD=33.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2393,187,0 -chr1 129174 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.686;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-5.798;QD=4.36;ReadPosRankSum=1.384;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:50,16:66:99:316,0,1690 -chr1 129186 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.619;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQ0=1;MQRankSum=-6.469;QD=6.53;ReadPosRankSum=1.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,23:69:99:479,0,1553 -chr1 129201 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=58;Dels=0.00;FS=2.756;HaplotypeScore=12.9038;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=1;MQRankSum=1.307;QD=5.62;ReadPosRankSum=1.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,14:58:99:354,0,1347 -chr1 129215 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088;DP=44;Dels=0.00;FS=1.218;HaplotypeScore=9.9234;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.732;QD=10.43;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:487,0,829 -chr1 129227 . T C 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.3660;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=1;MQRankSum=-4.330;QD=5.34;ReadPosRankSum=1.719;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:199,0,742 -chr1 129279 . T G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;DP=43;Dels=0.00;FS=7.514;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=55.76;MQ0=2;MQRankSum=-0.257;QD=20.27;ReadPosRankSum=-4.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,28:43:99:900,0,484 -chr1 129287 . G A 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=45;Dels=0.00;FS=10.631;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.96;MQ0=2;MQRankSum=-1.076;QD=22.04;ReadPosRankSum=-3.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:14,31:45:99:1020,0,440 -chr1 129320 . T A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=51;Dels=0.00;FS=20.436;HaplotypeScore=2.9997;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=3;MQRankSum=0.864;QD=22.03;ReadPosRankSum=3.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1152,0,502 -chr1 129323 . A G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.889;DP=48;Dels=0.00;FS=17.838;HaplotypeScore=3.9996;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=0.605;QD=21.10;ReadPosRankSum=3.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1041,0,518 -chr1 129341 . C G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=57;Dels=0.00;FS=17.030;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=6;MQRankSum=-1.618;QD=3.28;ReadPosRankSum=-3.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,14:57:99:215,0,1547 -chr1 129364 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.104;DP=53;Dels=0.00;FS=30.019;HaplotypeScore=14.7852;MLEAC=1;MLEAF=0.500;MQ=56.85;MQ0=5;MQRankSum=-1.619;QD=5.17;ReadPosRankSum=0.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:37,16:53:99:302,0,1331 -chr1 129366 . C T 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.951;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=12.7857;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=5;MQRankSum=2.207;QD=16.03;ReadPosRankSum=-0.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,729 -chr1 129393 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=49;Dels=0.00;FS=6.439;HaplotypeScore=51.4904;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=-1.665;QD=10.87;ReadPosRankSum=1.560;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:561,0,1020 -chr1 129409 . C T 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=52;Dels=0.00;FS=15.514;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-1.292;QD=7.01;ReadPosRankSum=2.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:393,0,1247 -chr1 129415 . T G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=10.402;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-1.083;QD=4.57;ReadPosRankSum=1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,13:49:99:252,0,1255 -chr1 129421 . A G 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=47;Dels=0.00;FS=10.402;HaplotypeScore=14.7307;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.163;QD=4.36;ReadPosRankSum=1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,11:47:99:233,0,1272 -chr1 129428 . T A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=47;Dels=0.00;FS=11.605;HaplotypeScore=14.5195;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=0.749;QD=1.72;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:109,0,1365 -chr1 129430 . T C 1335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.868;DP=47;Dels=0.00;FS=14.700;HaplotypeScore=13.5208;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.941;QD=28.42;ReadPosRankSum=-1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,40:47:99:1364,0,151 -chr1 129470 . A G 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=34;Dels=0.00;FS=6.431;HaplotypeScore=3.9295;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=3.106;QD=26.23;ReadPosRankSum=3.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,26:34:99:920,0,161 -chr1 129498 . G A 174.9 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,6:6:15:203,15,0 -chr1 129499 . G A 154.94 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=4.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.736;QD=25.82;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:1,5:6:14:183,0,14 -chr1 129592 . A G 656.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.867;DP=20;Dels=0.00;FS=9.777;HaplotypeScore=22.2964;MLEAC=2;MLEAF=1.00;MQ=53.98;MQ0=0;MQRankSum=-1.387;QD=32.85;ReadPosRankSum=-1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,19:20:15:685,15,0 -chr1 129600 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.9992;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=1.557;QD=13.22;ReadPosRankSum=-0.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:372,0,498 -chr1 129610 . G T 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.411;DP=28;Dels=0.00;FS=28.641;HaplotypeScore=3.7875;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=-2.006;QD=30.10;ReadPosRankSum=0.446;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:3,25:28:36:871,0,36 -chr1 129625 . G A 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.306;DP=29;Dels=0.00;FS=12.308;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.476;QD=13.10;ReadPosRankSum=1.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,12:29:99:408,0,556 -chr1 129672 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=10;Dels=0.00;FS=11.761;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.898;QD=1.69;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,2:10:45:45,0,294 -chr1 129688 . T C 517.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:546,42,0 -chr1 129768 . T C 363.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.11;MQ0=0;QD=30.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:392,30,0 -chr1 129773 . T C 324.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.65;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:353,27,0 -chr1 129786 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129790 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129791 . T A 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129792 . C T 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129814 . A G 86.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.45;MQ0=0;QD=17.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:114,9,0 -chr1 129819 . A T 123.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:151,12,0 -chr1 129823 . T C 124.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:152,12,0 -chr1 129890 . C T 551.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.187;DP=39;Dels=0.00;FS=4.523;HaplotypeScore=2.9153;MLEAC=2;MLEAF=1.00;MQ=26.19;MQ0=13;MQRankSum=2.769;QD=14.15;ReadPosRankSum=-2.891;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:15,24:39:28:580,28,0 -chr1 129897 . C A 631.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.036;DP=42;Dels=0.00;FS=4.559;HaplotypeScore=4.7472;MLEAC=2;MLEAF=1.00;MQ=26.06;MQ0=14;MQRankSum=2.939;QD=15.04;ReadPosRankSum=-2.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:18,24:42:37:660,37,0 -chr1 129936 . C T 516.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.057;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=25.05;MQ0=5;MQRankSum=1.999;QD=19.14;ReadPosRankSum=1.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:6,21:27:48:545,48,0 -chr1 129979 . T C 255.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.81;MQ0=2;QD=21.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:27:284,27,0 -chr1 129983 . C T 208.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=18.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:237,24,0 -chr1 129984 . T C 217.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=19.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:246,24,0 -chr1 130090 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.290;QD=16.48;ReadPosRankSum=-1.448;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,11:12:21:226,21,0 -chr1 130092 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.752;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.752;QD=16.48;ReadPosRankSum=-0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:21:226,21,0 -chr1 130105 . T G 496.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=1.6988;MLEAC=2;MLEAF=1.00;MQ=30.50;MQ0=1;MQRankSum=1.449;QD=23.66;ReadPosRankSum=-1.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:3,18:21:45:525,45,0 -chr1 130186 . G A 309.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:338,30,0 -chr1 130188 . G A 307.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:336,30,0 -chr1 130195 . G A 303.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:332,30,0 -chr1 130203 . T C 188.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.02;MQ0=0;QD=26.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:217,21,0 -chr1 130297 . C T 396.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:425,33,0 -chr1 130299 . C T 391.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:420,33,0 -chr1 130317 . G A 482.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=28.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:511,39,0 -chr1 130321 . G A 485.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:514,39,0 -chr1 130322 . G A 476.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:505,39,0 -chr1 130326 . A G 488.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=27.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:517,39,0 -chr1 130345 . T C 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.48;MQ0=0;QD=32.54;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0 -chr1 130362 . C T 595.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.33;MQ0=0;QD=29.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:624,48,0 -chr1 130369 . A G 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=0;QD=34.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0 -chr1 130374 . T C 645.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.35;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:674,51,0 -chr1 130382 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.395;DP=19;Dels=0.00;FS=9.745;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=0;MQRankSum=-1.395;QD=20.51;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:418,0,230 -chr1 130392 . G A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=16;Dels=0.00;FS=10.532;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=0;MQRankSum=-1.059;QD=17.24;ReadPosRankSum=1.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:304,0,242 -chr1 130395 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=17;Dels=0.00;FS=10.843;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.81;MQ0=0;MQRankSum=-1.107;QD=16.63;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,277 -chr1 130406 . G A 733.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=0;QD=33.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:762,57,0 -chr1 130422 . G A 680.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=27.30;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:709,54,0 -chr1 130428 . C T 234.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=20;Dels=0.00;FS=13.778;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=0;MQRankSum=0.501;QD=11.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:12,8:20:99:263,0,382 -chr1 130463 . T A 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.131;DP=33;Dels=0.00;FS=33.092;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=1.767;QD=13.30;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:467,0,604 -chr1 130464 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.665;DP=34;Dels=0.00;FS=25.025;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-1.006;QD=16.52;ReadPosRankSum=-0.104;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:590,0,499 -chr1 130471 . G T 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=36;Dels=0.00;FS=24.517;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.430;QD=13.85;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:527,0,659 -chr1 130515 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.442;DP=43;Dels=0.00;FS=6.930;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.717;QD=16.53;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:739,0,723 -chr1 130542 . C T 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.025;DP=53;Dels=0.00;FS=1.790;HaplotypeScore=19.9950;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.161;QD=1.77;ReadPosRankSum=-3.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,8:53:99:122,0,1658 -chr1 130586 . C T 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.100;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.060;QD=18.68;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:962,0,598 -chr1 130630 . G A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=19.8889;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=0;MQRankSum=0.154;QD=17.07;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:745,0,563 -chr1 130682 . A C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.407;QD=11.69;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,21:55:99:671,0,1176 -chr1 130699 . G A 1434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.851;QD=23.14;ReadPosRankSum=-0.956;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,42:62:99:1463,0,623 -chr1 130768 . C T 1247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=53;Dels=0.00;FS=14.260;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.41;MQ0=0;MQRankSum=0.829;QD=23.54;ReadPosRankSum=-1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1276,0,522 -chr1 130839 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=2.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.222;QD=17.69;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:665,0,568 -chr1 130852 . C G 1575.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.648;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.127;QD=22.42;ReadPosRankSum=0.887;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,40:41:99:1604,120,0 -chr1 130914 . A G 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.017;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.258;QD=22.52;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1109,0,452 -chr1 130927 . A C 1100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;DP=48;Dels=0.00;FS=6.248;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.498;QD=22.93;ReadPosRankSum=2.329;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1129,0,467 -chr1 130951 . A G 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.242;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=26.1290;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.231;QD=23.90;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:1056,0,426 -chr1 130966 . A T 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=53;Dels=0.00;FS=6.248;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.819;QD=24.73;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,38:53:99:1339,0,440 -chr1 130976 . G C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.645;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-0.337;QD=9.57;ReadPosRankSum=1.048;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:526,0,1151 -chr1 130992 . C T 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.042;DP=57;Dels=0.00;FS=3.924;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.112;QD=21.72;ReadPosRankSum=-1.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,37:57:99:1266,0,611 -chr1 131017 . C G 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=49;Dels=0.00;FS=19.446;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.850;QD=16.36;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:830,0,803 -chr1 131080 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=9.7317;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-0.662;QD=13.66;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:561,0,711 -chr1 131092 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=2.039;QD=20.12;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,25:40:99:833,0,436 -chr1 131093 . A T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.421;DP=40;Dels=0.00;FS=5.618;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.234;QD=5.22;ReadPosRankSum=1.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:237,0,1057 -chr1 131106 . A G 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.361;DP=32;Dels=0.00;FS=8.080;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-2.945;QD=13.59;ReadPosRankSum=-0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:463,0,546 -chr1 131121 . C T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.467;DP=34;Dels=0.00;FS=5.188;HaplotypeScore=15.7761;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.640;QD=15.90;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:569,0,510 -chr1 131126 . C A 1433.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.7761;MLEAC=2;MLEAF=1.00;MQ=53.11;MQ0=0;QD=32.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1462,111,0 -chr1 131132 . C A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.426;DP=44;Dels=0.00;FS=15.097;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.78;MQ0=0;MQRankSum=4.844;QD=17.24;ReadPosRankSum=-1.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:787,0,609 -chr1 131154 . A T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=44;Dels=0.00;FS=23.397;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-4.184;QD=14.54;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:668,0,759 -chr1 131158 . C T 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.954;DP=41;Dels=0.00;FS=21.509;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.27;MQ0=0;MQRankSum=-3.830;QD=13.41;ReadPosRankSum=2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:578,0,692 -chr1 131163 . T C 1650.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4677;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=32.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1679,129,0 -chr1 131170 . T G 560.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=49;Dels=0.00;FS=38.825;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=-3.211;QD=11.44;ReadPosRankSum=1.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:589,0,938 -chr1 131184 . G A 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.436;DP=49;Dels=0.00;FS=38.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=2;MQRankSum=-3.020;QD=8.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:461,0,1001 -chr1 131207 . G T 418.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.185;DP=42;Dels=0.00;FS=27.416;HaplotypeScore=4.4038;MLEAC=1;MLEAF=0.500;MQ=48.07;MQ0=2;MQRankSum=-3.576;QD=9.97;ReadPosRankSum=-4.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:447,0,821 -chr1 131225 . C G 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.578;DP=40;Dels=0.00;FS=16.577;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.44;MQ0=3;MQRankSum=-2.808;QD=6.19;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:276,0,822 -chr1 131249 . C T 126.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.12;MQ0=0;MQRankSum=0.731;QD=25.21;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:1,4:5:12:154,12,0 -chr1 131267 . T A 654.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.56;MQ0=1;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:683,51,0 -chr1 131275 . T C 693.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.79;MQ0=1;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:722,54,0 -chr1 131301 . T C 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.737;DP=31;Dels=0.00;FS=14.239;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=3;MQRankSum=0.331;QD=6.41;ReadPosRankSum=-2.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:227,0,719 -chr1 131355 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=32;Dels=0.00;FS=6.200;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=1;MQRankSum=0.099;QD=15.24;ReadPosRankSum=0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:516,0,481 -chr1 131363 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.895;DP=30;Dels=0.00;FS=4.091;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=1;MQRankSum=-1.768;QD=15.03;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:479,0,438 -chr1 131370 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=35;Dels=0.00;FS=6.017;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=1;MQRankSum=2.012;QD=12.54;ReadPosRankSum=0.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:467,0,650 -chr1 131393 . T A 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.277;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-1.006;QD=16.68;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:612,0,506 -chr1 131394 . T G 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-2.497;QD=16.71;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:613,0,502 -chr1 131430 . C G 1471.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.04;MQ0=1;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1500,117,0 -chr1 131432 . G C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=42;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=1;MQRankSum=-1.274;QD=17.66;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:770,0,563 -chr1 131475 . G T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=48;Dels=0.00;FS=2.505;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.99;MQ0=1;MQRankSum=0.096;QD=15.00;ReadPosRankSum=0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:748,0,812 -chr1 131486 . C G 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=50;Dels=0.00;FS=2.434;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.59;MQ0=0;MQRankSum=0.601;QD=16.58;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:857,0,830 -chr1 131560 . C T 2155.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=30.7936;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=30.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2184,169,0 -chr1 131561 . A G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=33.7934;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=4.289;QD=12.63;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,25:63:99:824,0,1054 -chr1 131579 . T A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.134;DP=55;Dels=0.00;FS=1.050;HaplotypeScore=2.6642;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=3.452;QD=14.49;ReadPosRankSum=-1.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:825,0,902 -chr1 131583 . G A 2053.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6642;MLEAC=2;MLEAF=1.00;MQ=51.43;MQ0=0;QD=27.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2082,162,0 -chr1 131601 . G A 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=26.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:808,63,0 -chr1 131602 . T C 819.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=28.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:848,63,0 -chr1 131633 . G T 907.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.40;MQ0=0;QD=28.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:936,69,0 -chr1 131703 . T C 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=1;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:55:99:2139,160,0 -chr1 131720 . T C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.158;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.715;QD=13.65;ReadPosRankSum=4.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:779,0,1056 -chr1 131746 . G A 1546.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=2;QD=31.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,42:43:99:1575,120,0 -chr1 131760 . C T 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=39;Dels=0.00;FS=7.125;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=2;MQRankSum=1.717;QD=15.71;ReadPosRankSum=0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:641,0,573 -chr1 131770 . G A,C 1088.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.27;MQ0=3;QD=28.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/2:2,18,18:38:99:1278,681,630,597,0,543 -chr1 131775 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080;DP=35;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQ0=2;MQRankSum=-1.927;QD=13.85;ReadPosRankSum=-1.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:513,0,603 -chr1 131776 . G A 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.441;DP=33;Dels=0.00;FS=3.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQ0=2;MQRankSum=-2.203;QD=12.42;ReadPosRankSum=-0.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:438,0,599 -chr1 131796 . A G 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.532;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.71;MQ0=2;MQRankSum=-2.445;QD=10.05;ReadPosRankSum=0.780;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,14:36:99:390,0,704 -chr1 131801 . A G 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.91;MQ0=2;MQRankSum=2.114;QD=19.39;ReadPosRankSum=-1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:707,0,371 -chr1 131805 . G C 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=2.434;QD=19.64;ReadPosRankSum=-1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:39:99:794,0,392 -chr1 131806 . A G 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.239;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=-2.752;QD=9.10;ReadPosRankSum=1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:383,0,799 -chr1 131818 . T C 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=39;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.16;MQ0=2;MQRankSum=-2.677;QD=7.05;ReadPosRankSum=0.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:303,0,803 -chr1 131851 . A G 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=41;Dels=0.00;FS=5.599;HaplotypeScore=20.1968;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-3.302;QD=7.48;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:41:99:335,0,851 -chr1 131940 . C T 523.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=33;Dels=0.00;FS=13.038;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.25;MQ0=1;MQRankSum=0.537;QD=15.87;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:552,0,366 -chr1 131946 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.071;DP=33;Dels=0.00;FS=13.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.15;MQ0=1;MQRankSum=-0.754;QD=7.81;ReadPosRankSum=-0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:286,0,622 -chr1 131950 . G A 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.061;DP=33;Dels=0.00;FS=9.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=1;MQRankSum=-0.793;QD=6.69;ReadPosRankSum=-0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:249,0,652 -chr1 131964 . T C 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.757;DP=27;Dels=0.00;FS=4.809;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.64;MQ0=1;MQRankSum=-0.976;QD=1.70;ReadPosRankSum=-2.017;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,5:27:74:74,0,639 -chr1 131985 . A T 612.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.63;MQ0=1;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:51:641,51,0 -chr1 132042 . C T 418.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.17;MQ0=4;QD=19.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:36:447,36,0 -chr1 132048 . T A 299.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.822;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.89;MQ0=4;MQRankSum=1.734;QD=16.65;ReadPosRankSum=1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:6,12:18:27:328,27,0 -chr1 132089 . A T 110.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.747;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.9529;MLEAC=2;MLEAF=1.00;MQ=18.63;MQ0=4;MQRankSum=0.747;QD=9.17;ReadPosRankSum=-0.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:138,12,0 -chr1 132209 . C T 107.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=34.81;MQ0=0;QD=26.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:135,12,0 -chr1 132286 . C T 954.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.87;MQ0=1;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:78:983,78,0 -chr1 132307 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.61;MQ0=0;QD=29.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,25:26:63:788,63,0 -chr1 132327 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.844;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.266;QD=7.82;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,314 -chr1 132328 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.532;QD=7.82;ReadPosRankSum=1.644;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,315 -chr1 132332 . A T 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.400;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.355;QD=7.65;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:166,0,314 -chr1 132348 . G A 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=0;MQRankSum=1.431;QD=8.74;ReadPosRankSum=1.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:238,0,433 -chr1 132356 . A C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.968;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=14.3879;MLEAC=1;MLEAF=0.500;MQ=45.87;MQ0=0;MQRankSum=-2.087;QD=16.82;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,15:24:99:432,0,228 -chr1 132369 . A T 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.273;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.53;MQ0=0;MQRankSum=-0.634;QD=1.95;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,5:23:73:73,0,558 -chr1 132372 . A T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.52;ReadPosRankSum=2.068;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:40:40,0,597 -chr1 132376 . T A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.56;ReadPosRankSum=1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:41:41,0,600 -chr1 132383 . A C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.49;MQ0=0;MQRankSum=-0.142;QD=0.75;ReadPosRankSum=-0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,4:20:43:43,0,566 -chr1 132405 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.18;MQ0=2;QD=32.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:60:784,60,0 -chr1 132443 . C T 984.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.73;MQ0=2;QD=29.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1013,78,0 -chr1 132456 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=28;Dels=0.00;FS=1.941;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=50.78;MQ0=2;MQRankSum=0.212;QD=22.35;ReadPosRankSum=0.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,18:28:99:654,0,184 -chr1 132468 . C G 1263.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.51;MQ0=2;QD=32.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1292,99,0 -chr1 132478 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.382;DP=36;Dels=0.00;FS=3.155;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=2;MQRankSum=0.673;QD=9.83;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:382,0,743 -chr1 132621 . A G 898.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=1.9970;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;MQRankSum=-0.800;QD=34.57;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,25:26:42:927,42,0 -chr1 132697 . G T 1425.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=1;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1454,108,0 -chr1 132730 . G C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=40;Dels=0.00;FS=1.399;HaplotypeScore=2.7317;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=1;MQRankSum=-4.323;QD=6.12;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:273,0,1019 -chr1 132737 . C T 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=48;Dels=0.00;FS=1.273;HaplotypeScore=23.7282;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=2;MQRankSum=-4.842;QD=7.04;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,14:48:99:366,0,1103 -chr1 132780 . A G 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.056;DP=55;Dels=0.00;FS=28.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=1;MQRankSum=2.043;QD=6.52;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:387,0,1434 -chr1 132838 . G A 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;DP=60;Dels=0.00;FS=19.671;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.32;MQ0=0;MQRankSum=-0.669;QD=14.03;ReadPosRankSum=1.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:870,0,1128 -chr1 132869 . G T 2120.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.59;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2149,166,0 -chr1 132921 . T C 1226.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=47.64;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1255,96,0 -chr1 132922 . T C 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.652;QD=17.87;ReadPosRankSum=1.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:600,0,462 -chr1 132923 . G T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.842;QD=17.65;ReadPosRankSum=1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:593,0,451 -chr1 132956 . T C 1509.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=64.3730;MLEAC=2;MLEAF=1.00;MQ=53.28;MQ0=0;QD=28.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1538,117,0 -chr1 133042 . G A 1488.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.72;MQ0=0;QD=34.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1517,120,0 -chr1 133059 . C T 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;DP=46;Dels=0.00;FS=11.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=0;MQRankSum=-2.139;QD=15.34;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:734,0,651 -chr1 133068 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.081;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=0;MQRankSum=-2.420;QD=14.97;ReadPosRankSum=-0.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:687,0,652 -chr1 133104 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=47;Dels=0.00;FS=4.125;HaplotypeScore=2.9633;MLEAC=1;MLEAF=0.500;MQ=52.43;MQ0=0;MQRankSum=1.309;QD=14.85;ReadPosRankSum=-0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:726,0,732 -chr1 133115 . C G 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=46;Dels=0.00;FS=2.550;HaplotypeScore=2.9394;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-1.164;QD=15.49;ReadPosRankSum=0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:741,0,689 -chr1 133160 . A T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=24.1627;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=2.042;QD=14.09;ReadPosRankSum=0.744;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:592,0,613 -chr1 133168 . T A 1301.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=72.4881;MLEAC=2;MLEAF=1.00;MQ=50.41;MQ0=0;QD=30.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1330,105,0 -chr1 133318 . T G 1696.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1725,132,0 -chr1 133344 . T C 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.230;QD=15.59;ReadPosRankSum=0.150;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:792,0,735 -chr1 133348 . G T 1903.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.70;MQ0=0;QD=33.82;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1932,150,0 -chr1 133404 . G T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=49;Dels=0.00;FS=1.131;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=3.143;QD=19.20;ReadPosRankSum=0.559;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:20,29:49:99:969,0,589 -chr1 133419 . G C 1742.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=33.58;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1771,138,0 -chr1 133433 . G A 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-4.245;QD=8.51;ReadPosRankSum=0.593;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:27,12:39:99:360,0,943 -chr1 133435 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=26.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1302,102,0 -chr1 133436 . A T 1250.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.76;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1279,99,0 -chr1 133437 . G C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.96;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0 -chr1 133448 . C A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.362;DP=47;Dels=0.00;FS=1.146;HaplotypeScore=1.5317;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-4.461;QD=10.08;ReadPosRankSum=-0.365;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,17:47:99:502,0,1052 -chr1 133453 . C T 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.012;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=16.0294;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-4.142;QD=10.85;ReadPosRankSum=-0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,18:48:99:549,0,976 -chr1 133491 . T A,G 1599.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=57.45;MQ0=0;QD=30.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/2:0,20,32:52:99:1838,1129,1068,710,0,616 -chr1 133511 . T G 1608.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.68;MQ0=0;QD=27.83;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1637,126,0 -chr1 133553 . A G 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.865;DP=46;Dels=0.00;FS=8.994;HaplotypeScore=2.6278;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-4.347;QD=9.08;ReadPosRankSum=0.657;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,16:46:99:446,0,1041 -chr1 133580 . G T 655.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=46;Dels=0.00;FS=8.283;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=0;MQRankSum=-5.226;QD=14.26;ReadPosRankSum=-1.808;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,21:46:99:684,0,798 -chr1 133584 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=4.288;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-5.037;QD=13.24;ReadPosRankSum=-1.450;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,20:45:99:624,0,830 -chr1 133629 . G A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=53;Dels=0.00;FS=2.379;HaplotypeScore=3.9941;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.817;QD=14.45;ReadPosRankSum=0.793;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:28,25:53:99:794,0,922 -chr1 133703 . G A 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.177;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-5.657;QD=8.59;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:29,18:47:99:432,0,1026 -chr1 133708 . C T 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-4.162;QD=6.83;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:34,14:48:99:356,0,1139 -chr1 133768 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.666;DP=35;Dels=0.00;FS=3.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-3.499;QD=9.74;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:22,13:35:99:369,0,766 -chr1 133772 . T A 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.647;DP=31;Dels=0.00;FS=1.503;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.798;QD=11.86;ReadPosRankSum=-0.258;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:17,14:31:99:396,0,591 -chr1 133877 . G C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=64;Dels=0.00;FS=2.113;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=0;MQRankSum=-3.336;QD=12.97;ReadPosRankSum=1.698;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V19|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:858,0,1194 -chr1 133880 . T G 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.53;MQ0=0;MQRankSum=-1.770;QD=2.61;ReadPosRankSum=2.191;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S20|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,10:62:99:190,0,1843 -chr1 133924 . C T 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.234;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=14.4642;MLEAC=1;MLEAF=0.500;MQ=50.02;MQ0=1;MQRankSum=-2.145;QD=5.48;ReadPosRankSum=0.419;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P35L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:302,0,1267 -chr1 133955 . C G 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;DP=31;Dels=0.00;FS=1.768;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.62;MQ0=0;MQRankSum=-2.415;QD=5.06;ReadPosRankSum=-1.377;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D45E|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:185,0,789 -chr1 133985 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.181;DP=21;Dels=0.00;FS=15.849;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-2.976;QD=1.42;ReadPosRankSum=-2.032;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C55|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,5:21:58:58,0,571 -chr1 134007 . G T 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.146;DP=26;Dels=0.00;FS=3.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=1;MQRankSum=-3.466;QD=6.64;ReadPosRankSum=-0.903;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V63L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:201,0,596 -chr1 134011 . C T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=30;Dels=0.00;FS=3.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-3.372;QD=7.46;ReadPosRankSum=-0.619;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A64V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:252,0,660 -chr1 134033 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.577;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.69;MQ0=2;MQRankSum=-1.710;QD=0.33;ReadPosRankSum=-2.732;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L71|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,6:39:41:41,0,1056 -chr1 134148 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.729;DP=60;Dels=0.00;FS=15.632;HaplotypeScore=2.9570;MLEAC=1;MLEAF=0.500;MQ=39.89;MQ0=8;MQRankSum=1.349;QD=8.15;ReadPosRankSum=0.912;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R110C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,19:60:99:517,0,973 -chr1 134280 . A C 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=91;Dels=0.00;FS=2.074;HaplotypeScore=10.4073;MLEAC=1;MLEAF=0.500;MQ=34.28;MQ0=7;MQRankSum=1.802;QD=10.80;ReadPosRankSum=-0.414;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K154Q|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,38:91:99:1011,0,1041 -chr1 134333 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.529;DP=65;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.88;MQ0=7;MQRankSum=0.576;QD=10.38;ReadPosRankSum=0.734;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y171|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:703,0,1008 -chr1 134354 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.63;MQ0=7;MQRankSum=0.036;QD=9.56;ReadPosRankSum=-0.060;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A178|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:516,0,788 -chr1 134514 . T C 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.7876;MLEAC=1;MLEAF=0.500;MQ=37.13;MQ0=3;MQRankSum=-2.851;QD=7.28;ReadPosRankSum=-0.527;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C232R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:392,0,878 -chr1 134570 . T C 854.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.49;MQ0=0;MQRankSum=3.436;QD=19.43;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F250|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:883,0,419 -chr1 134580 . C T 1494.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.09;MQ0=0;QD=33.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P254S|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1523,117,0 -chr1 134603 . G T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.9762;MLEAC=1;MLEAF=0.500;MQ=42.98;MQ0=0;MQRankSum=-4.437;QD=12.42;ReadPosRankSum=-1.075;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T261|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:612,0,769 -chr1 134696 . G A 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;DP=25;Dels=0.00;FS=7.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.51;MQ0=1;MQRankSum=1.217;QD=13.63;ReadPosRankSum=-3.187;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R292|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:11,14:25:99:369,0,240 -chr1 134729 . G T 259.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.888;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=3.8313;MLEAC=2;MLEAF=1.00;MQ=20.10;MQ0=6;MQRankSum=1.678;QD=13.67;ReadPosRankSum=1.283;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G303|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,17:19:30:288,30,0 -chr1 134730 . T G 147.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=17;Dels=0.00;FS=9.031;HaplotypeScore=3.8313;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=6;MQRankSum=0.715;QD=8.70;ReadPosRankSum=1.931;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F304V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:3,14:17:2:174,0,2 -chr1 134755 . G C 619.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.70;MQ0=7;QD=20.66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S312T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:54:648,54,0 -chr1 134780 . T C 422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=42;Dels=0.00;FS=7.420;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=0.050;QD=10.07;ReadPosRankSum=1.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C320|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:451,0,502 -chr1 134807 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=53;Dels=0.00;FS=2.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.74;MQ0=5;MQRankSum=-1.432;QD=14.07;ReadPosRankSum=0.010;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I329|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:774,0,584 -chr1 134822 . T C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=52;Dels=0.00;FS=4.058;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=36.11;MQ0=1;MQRankSum=-2.231;QD=16.55;ReadPosRankSum=0.789;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I334|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,33:52:99:889,0,575 -chr1 134927 . G C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=5.3557;MLEAC=1;MLEAF=0.500;MQ=26.60;MQ0=9;MQRankSum=1.588;QD=7.44;ReadPosRankSum=-0.677;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E369D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:415,0,456 -chr1 135009 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=56;Dels=0.00;FS=9.949;HaplotypeScore=1.8154;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=-2.335;QD=0.23;ReadPosRankSum=-2.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T397A|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,6:56:41:41,0,1637 -chr1 135029 . G C 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=68;Dels=0.00;FS=9.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=1;MQRankSum=-1.650;QD=2.79;ReadPosRankSum=-0.245;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L403F|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,11:68:99:218,0,1758 -chr1 135042 . A G 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.577;DP=75;Dels=0.00;FS=8.931;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=39.96;MQ0=1;MQRankSum=3.045;QD=8.50;ReadPosRankSum=0.420;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N408D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,22:75:99:666,0,1347 -chr1 135055 . A G 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.310;DP=84;Dels=0.00;FS=10.873;HaplotypeScore=9.3239;MLEAC=1;MLEAF=0.500;MQ=36.61;MQ0=3;MQRankSum=0.553;QD=3.71;ReadPosRankSum=1.854;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E412G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:340,0,1652 -chr1 135124 . A G 1965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.982;DP=84;Dels=0.00;FS=3.513;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=2.897;QD=23.40;ReadPosRankSum=0.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q435R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,68:84:99:1994,0,139 -chr1 135152 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.499;DP=86;Dels=0.00;FS=1.215;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=3;MQRankSum=-0.614;QD=1.25;ReadPosRankSum=0.942;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D444|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:136,0,2271 -chr1 135153 . G A 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.997;DP=87;Dels=0.00;FS=1.186;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=3;MQRankSum=-0.409;QD=1.65;ReadPosRankSum=0.537;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V445M|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:172,0,2269 -chr1 135160 . C G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.067;DP=80;Dels=0.00;FS=2.719;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=38.64;MQ0=3;MQRankSum=0.297;QD=2.51;ReadPosRankSum=1.116;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S447C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:229,0,2067 -chr1 135180 . T A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.230;DP=74;Dels=0.00;FS=21.668;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.55;MQ0=0;MQRankSum=1.094;QD=3.70;ReadPosRankSum=1.690;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Att|F454I|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,13:74:99:302,0,1980 -chr1 135182 . T C 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=73;Dels=0.00;FS=22.648;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.76;MQ0=0;MQRankSum=-0.479;QD=10.89;ReadPosRankSum=1.077;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F454|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,29:73:99:823,0,1443 -chr1 135209 . A G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.127;DP=78;Dels=0.00;FS=18.781;HaplotypeScore=10.8281;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-2.484;QD=12.02;ReadPosRankSum=0.229;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A463|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:966,0,1557 -chr1 135218 . T C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=76;Dels=0.00;FS=7.732;HaplotypeScore=20.2693;MLEAC=1;MLEAF=0.500;MQ=49.54;MQ0=0;MQRankSum=-1.200;QD=6.59;ReadPosRankSum=-0.624;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S466|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,19:76:99:529,0,1942 -chr1 135220 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=77;Dels=0.00;FS=5.434;HaplotypeScore=9.4397;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-0.384;QD=6.30;ReadPosRankSum=-0.821;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E467G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:58,19:77:99:513,0,1945 -chr1 135242 . G T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;DP=84;Dels=0.00;FS=4.355;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-2.169;QD=10.69;ReadPosRankSum=-0.189;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P474|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,32:84:99:926,0,1735 -chr1 135249 . C A 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=83;Dels=0.00;FS=0.951;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=3.080;QD=7.48;ReadPosRankSum=1.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P477T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:649,0,2002 -chr1 135260 . G C 1586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=1.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=-0.838;QD=20.61;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A480|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,50:77:99:1615,0,861 -chr1 135276 . C T 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=78;Dels=0.00;FS=3.392;HaplotypeScore=25.9840;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=0.021;QD=9.15;ReadPosRankSum=0.503;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,25:78:99:742,0,1838 -chr1 135284 . A G 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;DP=83;Dels=0.00;FS=0.867;HaplotypeScore=45.6804;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=2.555;QD=10.96;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,30:83:99:938,0,1841 -chr1 135290 . A G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.543;DP=80;Dels=0.00;FS=3.316;HaplotypeScore=43.6813;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.055;QD=11.50;ReadPosRankSum=-0.730;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:948,0,1404 -chr1 135296 . T A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=77;Dels=0.00;FS=3.797;HaplotypeScore=25.7468;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.051;QD=7.83;ReadPosRankSum=0.366;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,22:77:99:631,0,2017 -chr1 135305 . C A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.358;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=18.7849;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.819;QD=2.55;ReadPosRankSum=-4.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:77,14:91:99:260,0,2802 -chr1 135319 . A G 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=101;Dels=0.00;FS=0.864;HaplotypeScore=3.9995;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.932;QD=7.50;ReadPosRankSum=-0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,27:101:99:786,0,2632 -chr1 135362 . G C 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;DP=104;Dels=0.00;FS=0.933;HaplotypeScore=3.5999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.569;QD=5.02;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,21:104:99:550,0,2813 -chr1 135376 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=104;Dels=0.00;FS=0.969;HaplotypeScore=2.8632;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-2.044;QD=4.12;ReadPosRankSum=0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:85,19:104:99:457,0,2999 -chr1 135384 . G A 3914.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=22.8484;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=33.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:3943,301,0 -chr1 135391 . T G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.718;DP=103;Dels=0.00;FS=2.944;HaplotypeScore=27.2496;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-0.169;QD=7.15;ReadPosRankSum=0.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:103:99:765,0,2417 -chr1 135400 . G A 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=108;Dels=0.00;FS=6.146;HaplotypeScore=26.0389;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-2.758;QD=15.78;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,52:108:99:1732,0,1799 -chr1 135425 . T C 2440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=100;Dels=0.00;FS=5.702;HaplotypeScore=37.9722;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-2.038;QD=24.41;ReadPosRankSum=-0.257;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,72:100:99:2469,0,843 -chr1 135428 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=96;Dels=0.00;FS=3.339;HaplotypeScore=38.9718;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-1.010;QD=4.73;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:482,0,2684 -chr1 135433 . G T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=100;Dels=0.00;FS=5.032;HaplotypeScore=76.9445;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-4.688;QD=4.05;ReadPosRankSum=0.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:433,0,2862 -chr1 135440 . A T 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=97;Dels=0.00;FS=0.920;HaplotypeScore=61.9081;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.804;QD=5.41;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:553,0,2671 -chr1 135443 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.451;DP=97;Dels=0.00;FS=2.004;HaplotypeScore=60.8069;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.533;QD=5.00;ReadPosRankSum=-0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:513,0,2730 -chr1 135446 . C T 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.176;DP=97;Dels=0.00;FS=2.653;HaplotypeScore=42.8139;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-7.372;QD=12.97;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,42:97:99:1286,0,1882 -chr1 135450 . C T 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=94;Dels=0.00;FS=2.740;HaplotypeScore=39.6045;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-7.169;QD=13.13;ReadPosRankSum=-0.593;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:54,40:94:99:1262,0,1853 -chr1 135469 . C T 1458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=101;Dels=0.00;FS=3.736;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-8.200;QD=14.44;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1487,0,1800 -chr1 135483 . A C 2726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.152;DP=96;Dels=0.00;FS=0.981;HaplotypeScore=66.5358;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=0;MQRankSum=-3.811;QD=28.40;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,75:96:99:2755,0,482 -chr1 135489 . T G 1566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;DP=97;Dels=0.00;FS=12.274;HaplotypeScore=43.2734;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-7.619;QD=16.15;ReadPosRankSum=1.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,47:97:99:1595,0,1719 -chr1 135492 . A G 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=97;Dels=0.00;FS=1.972;HaplotypeScore=44.2721;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-4.134;QD=6.52;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:661,0,2654 -chr1 135504 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.723;DP=98;Dels=0.00;FS=21.343;HaplotypeScore=21.9832;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-6.623;QD=15.06;ReadPosRankSum=2.581;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,45:98:99:1504,0,1796 -chr1 135514 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=97;Dels=0.00;FS=12.661;HaplotypeScore=41.9659;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=0;MQRankSum=-5.004;QD=6.73;ReadPosRankSum=0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:681,0,2606 -chr1 135517 . C T 1587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.502;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=21.9725;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=2.170;QD=16.71;ReadPosRankSum=1.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,48:95:99:1616,0,1560 -chr1 135526 . T G 3368.77 . AC=2;AF=1.00;AN=2;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=53.9823;MLEAC=2;MLEAF=1.00;MQ=57.70;MQ0=0;QD=26.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,85:85:99:3397,256,0 -chr1 135527 . T C 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.045;DP=85;Dels=0.00;FS=8.852;HaplotypeScore=80.9742;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-4.243;QD=2.79;ReadPosRankSum=1.642;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,13:85:99:265,0,2552 -chr1 135535 . G A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.892;DP=82;Dels=0.00;FS=8.551;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-5.078;QD=3.08;ReadPosRankSum=1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,13:82:99:281,0,2484 -chr1 135536 . C T 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=79;Dels=0.00;FS=4.308;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=-1.623;QD=4.20;ReadPosRankSum=1.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,14:79:99:360,0,1863 -chr1 135537 . A G 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.307;DP=78;Dels=0.00;FS=9.867;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.630;QD=11.14;ReadPosRankSum=1.297;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,28:78:99:897,0,1742 -chr1 135551 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=91;Dels=0.00;FS=9.889;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=-4.719;QD=8.24;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:63,27:91:99:778,0,2232 -chr1 135557 . A C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.109;DP=92;Dels=0.00;FS=11.651;HaplotypeScore=3.9926;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-3.944;QD=8.20;ReadPosRankSum=-1.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:783,0,2240 -chr1 135582 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.013;DP=97;Dels=0.00;FS=10.159;HaplotypeScore=29.4167;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-4.142;QD=6.48;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,24:97:99:657,0,2497 -chr1 135587 . G C 2286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.678;DP=96;Dels=0.00;FS=0.869;HaplotypeScore=28.5846;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=0.144;QD=23.82;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,67:96:99:2315,0,856 -chr1 135606 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.585;DP=96;Dels=0.00;FS=2.045;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.629;QD=4.78;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:487,0,2576 -chr1 135609 . C A 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.944;DP=93;Dels=0.00;FS=7.797;HaplotypeScore=83.8468;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=-3.424;QD=7.92;ReadPosRankSum=-0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,27:93:99:765,0,2259 -chr1 135618 . C T 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.853;DP=89;Dels=0.00;FS=1.036;HaplotypeScore=65.8507;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.727;QD=3.94;ReadPosRankSum=2.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,17:89:99:379,0,2429 -chr1 135632 . G C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=89;Dels=0.00;FS=3.725;HaplotypeScore=67.7422;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-1.496;QD=4.58;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,18:89:99:436,0,2397 -chr1 135636 . T C 2955.77 . AC=2;AF=1.00;AN=2;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=82.6805;MLEAC=2;MLEAF=1.00;MQ=58.77;MQ0=0;QD=24.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,78:79:99:2984,226,0 -chr1 135637 . A C 1811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.105;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=83.6799;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.341;QD=22.65;ReadPosRankSum=-0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,56:80:99:1840,0,664 -chr1 135639 . T G 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.448;DP=83;Dels=0.00;FS=11.996;HaplotypeScore=104.6691;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.923;QD=4.39;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,18:83:99:393,0,2312 -chr1 135641 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.648;QD=6.67;ReadPosRankSum=-0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:602,0,2169 -chr1 135642 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.954;QD=6.71;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:605,0,2180 -chr1 135643 . C T 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=90;Dels=0.00;FS=9.549;HaplotypeScore=115.6735;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-2.215;QD=4.20;ReadPosRankSum=0.801;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,19:90:99:406,0,2519 -chr1 135648 . G C 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=94;Dels=0.00;FS=0.939;HaplotypeScore=81.8473;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.363;QD=6.44;ReadPosRankSum=-0.062;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,23:94:99:634,0,2439 -chr1 135650 . G A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=98;Dels=0.00;FS=0.925;HaplotypeScore=85.9035;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.805;QD=6.04;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:620,0,2541 -chr1 135660 . T G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=101;Dels=0.00;FS=0.897;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.059;QD=6.71;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,25:101:99:706,0,2603 -chr1 135662 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.122;QD=6.70;ReadPosRankSum=0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,26:101:99:705,0,2524 -chr1 135693 . G A 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;DP=102;Dels=0.00;FS=1.895;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=1.915;QD=7.13;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:102:99:756,0,2603 -chr1 135705 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.990;QD=6.44;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,26:103:99:692,0,2558 -chr1 135724 . G A 3782.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=2;MLEAF=1.00;MQ=58.30;MQ0=1;QD=35.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3811,286,0 -chr1 135725 . C A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=2;MQRankSum=0.224;QD=6.62;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:677,0,2539 -chr1 135734 . C T 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=84;Dels=0.00;FS=9.368;HaplotypeScore=43.9728;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=3;MQRankSum=-0.578;QD=2.59;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:246,0,2508 -chr1 135736 . C G 2208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=87;Dels=0.00;FS=2.092;HaplotypeScore=32.9825;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=3;MQRankSum=-1.198;QD=25.39;ReadPosRankSum=-0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,66:87:99:2237,0,546 -chr1 135750 . A G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.586;DP=76;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=3;MQRankSum=-1.757;QD=1.50;ReadPosRankSum=2.431;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,10:76:99:142,0,2292 -chr1 135758 . G T 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=79;Dels=0.00;FS=5.453;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.66;MQ0=3;MQRankSum=-3.574;QD=4.98;ReadPosRankSum=-1.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:422,0,2063 -chr1 135778 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.029;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=-4.222;QD=5.93;ReadPosRankSum=2.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:224,0,882 -chr1 135782 . G T 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.47;MQ0=0;MQRankSum=-3.992;QD=5.41;ReadPosRankSum=3.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:196,0,843 -chr1 135800 . C T 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.440;DP=36;Dels=0.00;FS=3.702;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-4.077;QD=3.97;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:171,0,1061 -chr1 135819 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=52;Dels=0.00;FS=6.289;HaplotypeScore=11.8640;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.616;QD=8.25;ReadPosRankSum=-2.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:457,0,1294 -chr1 135828 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.663;DP=51;Dels=0.00;FS=8.174;HaplotypeScore=22.8565;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.593;QD=4.52;ReadPosRankSum=-0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,11:51:99:259,0,1414 -chr1 135836 . G T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.890;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=12.5980;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=4.353;QD=12.80;ReadPosRankSum=2.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:796,0,1231 -chr1 135848 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.467;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.656;QD=13.62;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1249 -chr1 135855 . T G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.541;DP=69;Dels=0.00;FS=0.917;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=1.635;QD=13.33;ReadPosRankSum=-2.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,29:69:99:948,0,1381 -chr1 135865 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=67;Dels=0.00;FS=2.217;HaplotypeScore=55.9758;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.993;QD=8.09;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,20:67:99:570,0,1674 -chr1 135868 . A T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.045;DP=65;Dels=0.00;FS=1.000;HaplotypeScore=20.9924;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.676;QD=9.50;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:646,0,1554 -chr1 135874 . T C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.590;DP=70;Dels=0.00;FS=0.954;HaplotypeScore=19.9927;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-2.097;QD=10.60;ReadPosRankSum=-0.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2S|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,26:70:99:770,0,1499 -chr1 135880 . T G 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.422;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-1.102;QD=10.01;ReadPosRankSum=0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F4C|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:45,24:69:99:719,0,1540 -chr1 135884 . T C 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.749;DP=70;Dels=0.00;FS=2.105;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.179;QD=10.03;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,24:70:99:730,0,1622 -chr1 135900 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.045;DP=74;Dels=0.00;FS=1.994;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.685;QD=10.38;ReadPosRankSum=0.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R11*|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,27:74:99:796,0,1573 -chr1 135922 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=92;Dels=0.00;FS=1.814;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.479;QD=9.52;ReadPosRankSum=0.760;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I18T|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,31:92:99:904,0,2103 -chr1 135936 . A G 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=84;Dels=0.00;FS=4.645;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=1.810;QD=9.10;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T23A|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,27:84:99:793,0,1944 -chr1 135937 . C T 1766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.487;QD=21.55;ReadPosRankSum=-0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T23I|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1795,0,896 -chr1 135938 . A G 1781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.486;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.699;QD=21.73;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T23|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1810,0,895 -chr1 135950 . G A 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.094;DP=83;Dels=0.00;FS=4.423;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.851;QD=9.73;ReadPosRankSum=-0.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K27|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,27:83:99:836,0,1943 -chr1 135990 . T G 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.534;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=18.3925;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.628;QD=8.58;ReadPosRankSum=0.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,21:67:99:603,0,1660 -chr1 135994 . A T 2749.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2778,211,0 -chr1 136009 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=44;Dels=0.00;FS=6.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.106;QD=14.20;ReadPosRankSum=-2.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:653,0,848 -chr1 136065 . A T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=46;Dels=0.00;FS=1.150;HaplotypeScore=1.7675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.035;QD=12.34;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,18:46:99:596,0,963 -chr1 136086 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.177;DP=51;Dels=0.00;FS=2.381;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.043;QD=12.07;ReadPosRankSum=0.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:644,0,1054 -chr1 136090 . A G 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.098;DP=50;Dels=0.00;FS=2.463;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-1.042;QD=12.52;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:654,0,1012 -chr1 136102 . G A 1209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=59;Dels=0.00;FS=2.203;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.365;QD=20.50;ReadPosRankSum=0.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,36:59:99:1238,0,690 -chr1 136134 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=52;Dels=0.00;FS=11.273;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.346;QD=8.28;ReadPosRankSum=1.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,17:52:99:459,0,1143 -chr1 136138 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=12.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-0.829;QD=7.34;ReadPosRankSum=1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:417,0,1249 -chr1 136150 . G C 528.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.335;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=17.3638;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-0.945;QD=10.37;ReadPosRankSum=-0.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:557,0,1120 -chr1 136165 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.333;DP=49;Dels=0.00;FS=8.545;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.736;QD=9.87;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:512,0,993 -chr1 136178 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=49;Dels=0.00;FS=8.560;HaplotypeScore=1.9248;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.250;QD=9.83;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:510,0,1040 -chr1 136208 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=40;Dels=0.00;FS=5.407;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-2.022;QD=7.12;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:313,0,1004 -chr1 136237 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.694;QD=3.25;ReadPosRankSum=1.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:142,0,1006 -chr1 136238 . T A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.197;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.423;QD=3.16;ReadPosRankSum=1.242;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:139,0,998 -chr1 136245 . A G 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.130;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.151;QD=3.26;ReadPosRankSum=1.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:152,0,1108 -chr1 136246 . G A 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.054;QD=3.39;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:157,0,1099 -chr1 136281 . A G 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=2.132;QD=20.72;ReadPosRankSum=1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1064,0,533 -chr1 136286 . T A 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=50;Dels=0.00;FS=1.154;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=1.147;QD=9.96;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:526,0,1136 -chr1 136296 . T C 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.294;DP=57;Dels=0.00;FS=2.395;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.166;QD=8.75;ReadPosRankSum=1.526;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:527,0,1372 -chr1 136297 . A C 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=57;Dels=0.00;FS=1.124;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.951;QD=8.80;ReadPosRankSum=1.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:530,0,1359 -chr1 136349 . A G 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.221;DP=55;Dels=0.00;FS=4.256;HaplotypeScore=2.8244;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.501;QD=7.32;ReadPosRankSum=-2.806;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:431,0,1458 -chr1 136355 . G A 2168.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.7122;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=25.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2197,163,0 -chr1 136407 . T A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.022;DP=36;Dels=0.00;FS=1.438;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-4.739;QD=7.63;ReadPosRankSum=1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:303,0,897 -chr1 136411 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.363;DP=35;Dels=0.00;FS=3.074;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-4.708;QD=7.94;ReadPosRankSum=1.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,11:35:99:306,0,864 -chr1 136414 . A G 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.761;DP=34;Dels=0.00;FS=1.456;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-4.675;QD=8.23;ReadPosRankSum=1.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:308,0,808 -chr1 136416 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.63;MQ0=0;MQRankSum=-4.640;QD=8.57;ReadPosRankSum=1.814;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:311,0,783 -chr1 136425 . A G 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=37;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-5.166;QD=12.29;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:483,0,735 -chr1 136429 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=39;Dels=0.00;FS=6.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=-5.339;QD=12.84;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:529,0,713 -chr1 136439 . C T 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-5.553;QD=13.61;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A37V|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:600,0,750 -chr1 136450 . C G 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.709;DP=44;Dels=0.00;FS=8.887;HaplotypeScore=14.9765;MLEAC=1;MLEAF=0.500;MQ=51.92;MQ0=0;MQRankSum=-5.669;QD=12.77;ReadPosRankSum=0.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H41D|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:590,0,832 -chr1 136462 . G A 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;DP=37;Dels=0.00;FS=5.041;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=51.93;MQ0=0;MQRankSum=-4.995;QD=9.59;ReadPosRankSum=1.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E45K|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:383,0,810 -chr1 136465 . T A 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.278;DP=36;Dels=0.00;FS=5.077;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.37;MQ0=0;MQRankSum=-5.070;QD=11.02;ReadPosRankSum=1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_LOST(HIGH|MISSENSE|Tga/Aga|*46R|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:425,0,704 -chr1 136487 . G T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.53;ReadPosRankSum=1.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:361,0,895 -chr1 136488 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.143;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.66;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:366,0,788 -chr1 136547 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.519;DP=52;Dels=0.00;FS=24.103;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=0.123;QD=15.98;ReadPosRankSum=1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I7M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,28:52:99:859,0,785 -chr1 136596 . A C 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-0.139;QD=18.76;ReadPosRankSum=-0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K24Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1004,0,696 -chr1 136655 . T A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.512;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.278;QD=15.84;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H43Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:18,20:38:99:630,0,576 -chr1 136658 . A G 1300.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I44M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,102,0 -chr1 136742 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.161;DP=48;Dels=0.00;FS=11.641;HaplotypeScore=1.8937;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.635;QD=17.29;ReadPosRankSum=-0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F72|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,27:48:99:858,0,624 -chr1 136752 . C T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=43;Dels=0.00;FS=4.498;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.528;QD=15.37;ReadPosRankSum=0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P76S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,24:43:99:689,0,591 -chr1 136754 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=45;Dels=0.00;FS=8.549;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.808;QD=15.51;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P76|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,24:45:99:726,0,665 -chr1 136841 . A G 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.684;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.110;QD=17.34;ReadPosRankSum=0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E105|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,25:46:99:826,0,691 -chr1 136898 . A G 1598.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E124|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1627,126,0 -chr1 136902 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.935;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.194;QD=13.13;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L126|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,20:46:99:632,0,609 -chr1 136996 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.141;HaplotypeScore=2.5774;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.082;QD=14.73;ReadPosRankSum=0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K157R|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:647,0,707 -chr1 137035 . T C 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.623;QD=14.32;ReadPosRankSum=1.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V170A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:29,27:56:99:830,0,902 -chr1 137064 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=65;Dels=0.00;FS=3.370;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;QD=16.57;ReadPosRankSum=0.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V180I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1105,0,993 -chr1 137119 . A G 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=59;Dels=0.00;FS=0.985;HaplotypeScore=3.6004;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.388;QD=18.93;ReadPosRankSum=-0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N198S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,34:59:99:1145,0,816 -chr1 137153 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.416;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=1;MQRankSum=2.932;QD=17.69;ReadPosRankSum=-0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S209|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1001,0,825 -chr1 137179 . A G 799.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=1.7878;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=-3.289;QD=13.79;ReadPosRankSum=-0.603;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E218G|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:828,0,1091 -chr1 137275 . G A 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=55;Dels=0.00;FS=4.048;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-2.535;QD=20.30;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R250K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,35:55:99:1145,0,643 -chr1 137372 . C T 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.028;QD=13.71;ReadPosRankSum=0.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V282|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1029,0,1332 -chr1 137373 . A G 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-2.632;QD=14.48;ReadPosRankSum=0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T283A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1085,0,1343 -chr1 137483 . G A 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-0.043;QD=11.64;ReadPosRankSum=-0.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M319I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,16:39:99:482,0,810 -chr1 137571 . A G 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=61;Dels=0.00;FS=1.046;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=55.97;MQ0=0;MQRankSum=-2.341;QD=13.06;ReadPosRankSum=-0.022;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N349D|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:35,26:61:99:825,0,1208 -chr1 137613 . C T 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.184;DP=57;Dels=0.00;FS=4.341;HaplotypeScore=3.9492;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-2.620;QD=14.84;ReadPosRankSum=-0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L363F|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:31,26:57:99:874,0,1052 -chr1 137666 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.663;DP=44;Dels=0.00;FS=1.184;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-0.687;QD=17.20;ReadPosRankSum=1.422;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C380|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,25:44:99:785,0,643 -chr1 137873 . T C 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=-1.416;QD=15.98;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V449|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,25:50:99:827,0,840 -chr1 137891 . C T 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.27;MQ0=0;MQRankSum=1.660;QD=16.26;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I455|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,26:50:99:841,0,766 -chr1 137927 . A T 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.120;QD=12.43;ReadPosRankSum=-0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P467|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:749,0,1114 -chr1 138034 . T C 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8939;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=0.781;QD=7.54;ReadPosRankSum=-1.513;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V503A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:33,13:46:99:375,0,1176 -chr1 138075 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;DP=48;Dels=0.00;FS=2.557;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.500;QD=14.02;ReadPosRankSum=-0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L517|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,22:48:99:701,0,894 -chr1 138170 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-3.956;QD=13.84;ReadPosRankSum=-0.258;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K548|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,18:40:99:582,0,750 -chr1 138221 . G A 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=49;Dels=0.00;FS=4.125;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=-4.650;QD=14.73;ReadPosRankSum=1.474;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K565|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,24:49:99:750,0,740 -chr1 138281 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.653;DP=47;Dels=0.00;FS=8.620;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-4.611;QD=12.82;ReadPosRankSum=0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T585|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,21:47:99:631,0,882 -chr1 138362 . T C 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.377;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-3.648;QD=16.45;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A612|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:719,0,680 -chr1 138386 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.181;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.153;QD=15.48;ReadPosRankSum=0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F620|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,20:43:99:694,0,739 -chr1 138609 . G A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.214;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-4.884;QD=12.04;ReadPosRankSum=0.573;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E695K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,24:50:99:630,0,897 -chr1 138660 . C A 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=0;MQRankSum=4.417;QD=18.88;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1010,0,467 -chr1 138683 . G T 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;DP=56;Dels=0.00;FS=2.284;HaplotypeScore=2.8620;MLEAC=1;MLEAF=0.500;MQ=46.57;MQ0=0;MQRankSum=-4.417;QD=10.00;ReadPosRankSum=-2.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:588,0,1019 -chr1 138698 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=58;Dels=0.00;FS=2.144;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-3.995;QD=10.77;ReadPosRankSum=-1.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:653,0,1080 -chr1 138718 . T C 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=53;Dels=0.00;FS=5.608;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=0;MQRankSum=-4.422;QD=13.60;ReadPosRankSum=-0.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:749,0,948 -chr1 138736 . T C 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=50;Dels=0.00;FS=10.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=-4.540;QD=16.34;ReadPosRankSum=-0.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:845,0,811 -chr1 138777 . T A 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.575;DP=53;Dels=0.00;FS=2.347;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=0;MQRankSum=-4.937;QD=16.24;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:889,0,952 -chr1 138778 . C T 2144.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=2;MLEAF=1.00;MQ=52.94;MQ0=0;QD=33.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2173,163,0 -chr1 138820 . A C 2124.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2153,160,0 -chr1 138922 . A T 728.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417;DP=57;Dels=0.00;FS=1.039;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=1;MQRankSum=-0.363;QD=12.79;ReadPosRankSum=-1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:757,0,1026 -chr1 138960 . T C 2157.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.52;MQ0=1;QD=28.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2186,172,0 -chr1 138982 . C A 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.642;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=1;MQRankSum=0.793;QD=17.38;ReadPosRankSum=0.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1036,0,849 -chr1 139024 . A T 1024.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=56;Dels=0.00;FS=5.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.72;MQ0=0;MQRankSum=-1.928;QD=18.30;ReadPosRankSum=0.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1053,0,858 -chr1 139066 . A G 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-3.328;QD=16.55;ReadPosRankSum=-0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:988,0,1020 -chr1 139093 . A G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=47;Dels=0.00;FS=4.452;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=-4.267;QD=16.85;ReadPosRankSum=-1.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:820,0,809 -chr1 139143 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=38;Dels=0.00;FS=2.742;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-4.926;QD=17.57;ReadPosRankSum=1.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:696,0,605 -chr1 139149 . A G 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=38;Dels=0.00;FS=2.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.61;MQ0=0;MQRankSum=-4.932;QD=18.23;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,21:38:99:721,0,567 -chr1 139163 . C T 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.156;QD=14.30;ReadPosRankSum=1.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:586,0,689 -chr1 139224 . A G 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=58;Dels=0.00;FS=3.833;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.755;QD=12.22;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:737,0,1030 -chr1 139254 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=60;Dels=0.00;FS=3.815;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.339;QD=14.35;ReadPosRankSum=-0.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:889,0,1036 -chr1 139269 . A G 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=58;Dels=0.00;FS=1.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-4.651;QD=14.17;ReadPosRankSum=0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:850,0,1089 -chr1 139286 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.863;DP=56;Dels=0.00;FS=3.856;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.836;QD=15.19;ReadPosRankSum=0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:879,0,1015 -chr1 139341 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=0;MQRankSum=-2.059;QD=15.48;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:725,0,819 -chr1 139358 . A T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.459;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.28;MQ0=0;MQRankSum=-2.238;QD=14.18;ReadPosRankSum=-0.694;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:737,0,962 -chr1 139417 . A C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.696;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.263;QD=8.24;ReadPosRankSum=-1.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:440,0,1164 -chr1 139435 . T G 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.343;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.55;MQ0=0;MQRankSum=-5.052;QD=4.45;ReadPosRankSum=0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:255,0,1407 -chr1 139441 . G A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.092;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=0;MQRankSum=-5.283;QD=5.05;ReadPosRankSum=0.845;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,13:52:99:291,0,1353 -chr1 139480 . A G 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-4.475;QD=2.29;ReadPosRankSum=1.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,9:47:99:136,0,1324 -chr1 139483 . T C 1251.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=5.087;QD=25.04;ReadPosRankSum=0.863;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1280,0,278 -chr1 139488 . T A 312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.71;MQ0=0;MQRankSum=-5.373;QD=6.01;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:341,0,1293 -chr1 139495 . G T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=50;Dels=0.00;FS=1.248;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=-5.314;QD=6.36;ReadPosRankSum=-1.207;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,1235 -chr1 139501 . T G 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.434;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.62;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:326,0,1098 -chr1 139502 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.066;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.55;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:323,0,1098 -chr1 139534 . T C 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=0;MQRankSum=-5.026;QD=15.83;ReadPosRankSum=-0.795;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,24:43:99:709,0,616 -chr1 139556 . A G 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=5.120;QD=12.09;ReadPosRankSum=-2.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:560,0,740 -chr1 139563 . T C 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-5.014;QD=18.81;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:856,0,472 -chr1 139576 . C A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.257;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=19.9086;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-4.247;QD=21.52;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:846,0,350 -chr1 139610 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=8.3569;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=-4.699;QD=13.06;ReadPosRankSum=-1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:603,0,686 -chr1 139650 . C A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=0;MQRankSum=-3.849;QD=15.37;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:720,0,755 -chr1 139666 . T A 1813.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=51.90;MQ0=0;QD=29.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,46:47:99:1842,138,0 -chr1 139700 . T C 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.796;DP=42;Dels=0.00;FS=2.709;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=1;MQRankSum=-4.603;QD=15.66;ReadPosRankSum=-0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:686,0,746 -chr1 139730 . T C 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;DP=44;Dels=0.00;FS=2.648;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.08;MQ0=1;MQRankSum=-5.150;QD=13.86;ReadPosRankSum=0.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:638,0,806 -chr1 139736 . A G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=47;Dels=0.00;FS=4.288;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=1;MQRankSum=-4.921;QD=13.97;ReadPosRankSum=-0.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:685,0,804 -chr1 139754 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=44;Dels=0.00;FS=9.774;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=1;MQRankSum=-5.101;QD=14.49;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:666,0,663 -chr1 139766 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.920;DP=47;Dels=0.00;FS=19.585;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=2;MQRankSum=-4.394;QD=11.61;ReadPosRankSum=0.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:574,0,790 -chr1 139816 . T A 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=40;Dels=0.00;FS=36.168;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.812;QD=18.44;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:766,0,353 -chr1 139888 . A G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.061;DP=34;Dels=0.00;FS=8.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.243;QD=5.49;ReadPosRankSum=-1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,8:34:99:215,0,931 -chr1 140035 . C T 1028.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.162;DP=30;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.59;MQ0=0;MQRankSum=1.764;QD=34.29;ReadPosRankSum=-0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,27:29:43:1057,43,0 -chr1 140037 . C T 1021.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=31;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=0;MQRankSum=1.271;QD=32.96;ReadPosRankSum=0.924;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,29:30:44:1050,44,0 -chr1 140066 . A G 1165.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1194,90,0 -chr1 140150 . A G 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0 -chr1 140265 . A T 876.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.93;MQ0=0;QD=24.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:905,69,0 -chr1 140358 . G A 1191.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1220,90,0 -chr1 140388 . T C 1024.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1053,78,0 -chr1 140546 . T C 430.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:459,36,0 -chr1 140560 . T C 561.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:590,45,0 -chr1 141091 . G A 812.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.5641;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=32.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:841,63,0 -chr1 141137 . A G 1166.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:32:90:1195,90,0 -chr1 141143 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1290,96,0 -chr1 141147 . C T 1086.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:31:84:1115,84,0 -chr1 141182 . C G 1085.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1114,84,0 -chr1 141263 . G A 1101.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1130,84,0 -chr1 141349 . C T 1090.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9990;MLEAC=2;MLEAF=1.00;MQ=59.61;MQ0=0;QD=30.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1119,84,0 -chr1 141378 . T C 1215.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=30.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1244,96,0 -chr1 141387 . C T 1141.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=27.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1170,90,0 -chr1 141396 . C T 955.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:984,75,0 -chr1 141400 . T C 1036.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=27.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1065,81,0 -chr1 141412 . T C 854.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=32.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:883,66,0 -chr1 141422 . G A 736.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=28.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,19:20:57:765,57,0 -chr1 141455 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;QD=26.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:833,63,0 -chr1 141471 . C T 759.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:788,60,0 -chr1 141498 . C A 891.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:920,69,0 -chr1 141507 . G C 961.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:990,75,0 -chr1 141536 . A G 1066.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1095,81,0 -chr1 141614 . A T 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0 -chr1 141636 . C A 434.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:463,39,0 -chr1 141654 . T A 544.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:573,45,0 -chr1 141655 . T A 534.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:563,45,0 -chr1 142437 . C T 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.548;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=-4.440;QD=13.66;ReadPosRankSum=-4.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:397,0,497 -chr1 142438 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=4.392;QD=16.73;ReadPosRankSum=4.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:480,0,389 -chr1 142481 . A G 1079.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.38;MQ0=0;QD=33.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1108,90,0 -chr1 142494 . T C 884.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.77;MQ0=0;QD=32.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:913,75,0 -chr1 142601 . A G 2064.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.05;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2093,165,0 -chr1 142776 . G A 1396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=67;Dels=0.00;FS=3.384;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.34;MQ0=0;MQRankSum=-3.183;QD=20.85;ReadPosRankSum=1.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,42:67:99:1425,0,774 -chr1 142787 . C T 2578.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.71;MQ0=0;QD=24.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2607,199,0 -chr1 142805 . A G 2382.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=29.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2411,184,0 -chr1 142821 . T A 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.014;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=43.83;MQ0=0;MQRankSum=-1.966;QD=20.30;ReadPosRankSum=-0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1287,0,713 -chr1 142863 . G A 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=51;Dels=0.00;FS=2.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.90;MQ0=0;MQRankSum=-0.161;QD=16.58;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:874,0,753 -chr1 142891 . A T 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=2.468;QD=17.49;ReadPosRankSum=-0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:955,0,777 -chr1 142898 . A G 956.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=0.197;QD=17.09;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,29:56:99:985,0,879 -chr1 142936 . A C 1403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=77;Dels=0.00;FS=0.875;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.936;QD=18.23;ReadPosRankSum=-0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,42:77:99:1432,0,1097 -chr1 142944 . T C 1485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.608;DP=75;Dels=0.00;FS=1.980;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.683;QD=19.81;ReadPosRankSum=-1.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,44:75:99:1514,0,922 -chr1 142972 . C T 1381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=75;Dels=0.00;FS=0.882;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.585;QD=18.42;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,42:75:99:1410,0,1088 -chr1 143047 . G C 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=57;Dels=0.00;FS=5.471;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=2;MQRankSum=-0.379;QD=14.84;ReadPosRankSum=0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:874,0,913 -chr1 143077 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=43;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.876;QD=14.32;ReadPosRankSum=-0.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:644,0,718 -chr1 143079 . T A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=44;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=1;MQRankSum=-1.497;QD=13.54;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:624,0,799 -chr1 143101 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.221;DP=58;Dels=0.00;FS=5.324;HaplotypeScore=5.2545;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.582;QD=15.00;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,28:58:99:898,0,920 -chr1 143121 . C T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.297;DP=78;Dels=0.00;FS=16.462;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-4.301;QD=1.05;ReadPosRankSum=-3.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:69,9:78:99:110,0,2263 -chr1 143129 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=82;Dels=0.00;FS=21.866;HaplotypeScore=20.8424;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-4.844;QD=1.53;ReadPosRankSum=-2.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,11:82:99:154,0,2388 -chr1 143138 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=85;Dels=0.00;FS=19.743;HaplotypeScore=26.7703;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.325;QD=10.00;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:51,34:85:99:878,0,1589 -chr1 143140 . C T 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=85;Dels=0.00;FS=27.442;HaplotypeScore=15.7969;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-4.591;QD=3.11;ReadPosRankSum=-1.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,14:85:99:293,0,2284 -chr1 143161 . G A 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=78;Dels=0.00;FS=0.906;HaplotypeScore=32.9944;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=1.886;QD=11.66;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:938,0,1383 -chr1 143163 . C A 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=33.0925;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.100;QD=10.32;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,31:78:99:833,0,1525 -chr1 143164 . G T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.056;DP=79;Dels=0.00;FS=32.060;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-4.706;QD=4.33;ReadPosRankSum=2.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:370,0,2093 -chr1 143165 . G A 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=79;Dels=0.00;FS=28.863;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-3.856;QD=3.93;ReadPosRankSum=2.881;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:339,0,2068 -chr1 143178 . C A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.003;DP=76;Dels=0.00;FS=33.120;HaplotypeScore=44.4775;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=-4.295;QD=4.14;ReadPosRankSum=3.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:62,14:76:99:343,0,1910 -chr1 143221 . A T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.319;DP=63;Dels=0.00;FS=19.029;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=2;MQRankSum=-2.568;QD=1.30;ReadPosRankSum=-0.916;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,9:63:99:110,0,1876 -chr1 143253 . G T 2036.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=42.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2065,159,0 -chr1 143376 . C G 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=51;Dels=0.00;FS=6.452;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=6;MQRankSum=2.251;QD=20.51;ReadPosRankSum=-0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1074,0,461 -chr1 143406 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=55;Dels=0.00;FS=3.966;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=2;MQRankSum=-1.903;QD=13.47;ReadPosRankSum=0.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:769,0,1020 -chr1 143414 . A G 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=56;Dels=0.00;FS=5.804;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-0.572;QD=12.89;ReadPosRankSum=1.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:750,0,1015 -chr1 143459 . G T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.432;DP=56;Dels=0.00;FS=5.668;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=2;MQRankSum=1.522;QD=11.17;ReadPosRankSum=0.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:654,0,1069 -chr1 143490 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-1.155;QD=11.50;ReadPosRankSum=0.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:649,0,1103 -chr1 143531 . G A 1174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=61;Dels=0.00;FS=2.178;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.591;QD=19.26;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,35:61:99:1203,0,835 -chr1 143603 . C T 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-1.269;QD=15.61;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:918,0,950 -chr1 143650 . T C 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.267;QD=17.93;ReadPosRankSum=1.209;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:871,0,713 -chr1 143705 . G A 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.934;DP=50;Dels=0.00;FS=10.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=1.538;QD=15.12;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:784,0,957 -chr1 143726 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=51;Dels=0.00;FS=4.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=0.349;QD=15.19;ReadPosRankSum=-1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:803,0,907 -chr1 143837 . A G 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.74;MQ0=0;MQRankSum=-3.207;QD=15.49;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:880,0,915 -chr1 143843 . G T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.62;MQ0=0;MQRankSum=-2.653;QD=15.86;ReadPosRankSum=1.953;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,954 -chr1 143851 . A T 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=55;Dels=0.00;FS=2.282;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=0;MQRankSum=-2.639;QD=17.25;ReadPosRankSum=0.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:977,0,823 -chr1 143867 . T A 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.451;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-2.076;QD=17.19;ReadPosRankSum=-0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1111,0,885 -chr1 143879 . A C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=66;Dels=0.00;FS=0.942;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.64;MQ0=0;MQRankSum=-1.603;QD=16.06;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,36:66:99:1088,0,1011 -chr1 143887 . C G 1133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=70;Dels=0.00;FS=0.918;HaplotypeScore=4.7286;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-0.633;QD=16.20;ReadPosRankSum=-1.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,38:70:99:1162,0,1037 -chr1 143960 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=49;Dels=0.00;FS=2.555;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.728;QD=12.06;ReadPosRankSum=-0.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:619,0,1001 -chr1 144130 . G A 1136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=62;Dels=0.00;FS=5.270;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.014;QD=18.33;ReadPosRankSum=-1.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1165,0,864 -chr1 144149 . G A 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=1.013;QD=17.25;ReadPosRankSum=-1.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1029,0,881 -chr1 144222 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.87;MQ0=0;MQRankSum=-2.776;QD=15.38;ReadPosRankSum=-0.729;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R143|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:859,0,804 -chr1 144255 . A G 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=54;Dels=0.00;FS=10.821;HaplotypeScore=2.7619;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=-5.069;QD=15.64;ReadPosRankSum=1.367;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T132|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:873,0,825 -chr1 144286 . C G 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=45;Dels=0.00;FS=1.238;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=-5.256;QD=15.22;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G122A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:713,0,730 -chr1 144294 . T A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.317;QD=16.47;ReadPosRankSum=0.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E119D|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:786,0,731 -chr1 144318 . G T 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=40;Dels=0.00;FS=5.217;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQ0=0;MQRankSum=-5.240;QD=14.62;ReadPosRankSum=-1.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R111|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:613,0,598 -chr1 144319 . C T 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=40;Dels=0.00;FS=2.910;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-5.180;QD=14.67;ReadPosRankSum=-1.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R111H|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:615,0,628 -chr1 144346 . G C 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-4.374;QD=17.19;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T102S|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:802,0,630 -chr1 144351 . A C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-4.499;QD=15.33;ReadPosRankSum=1.692;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P100|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:764,0,687 -chr1 144382 . T G 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=53;Dels=0.00;FS=2.371;HaplotypeScore=4.8928;MLEAC=1;MLEAF=0.500;MQ=56.28;MQ0=0;MQRankSum=-2.346;QD=14.58;ReadPosRankSum=2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D90A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:53:99:801,0,829 -chr1 144385 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.198;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=6.8884;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-2.125;QD=15.05;ReadPosRankSum=2.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D89G|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:811,0,831 -chr1 144434 . T A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=55;Dels=0.00;FS=1.039;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.232;QD=12.49;ReadPosRankSum=-0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N73Y|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:715,0,1146 -chr1 144525 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.856;QD=18.21;ReadPosRankSum=-0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R42|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:629,0,394 -chr1 144561 . C G 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.186;QD=18.71;ReadPosRankSum=1.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R30|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:758,0,482 -chr1 144564 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.541;QD=19.10;ReadPosRankSum=0.943;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q29|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:735,0,466 -chr1 144576 . C G 1458.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;QD=35.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L25F|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1487,114,0 -chr1 144606 . G C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.165;DP=54;Dels=0.00;FS=2.347;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.276;QD=16.09;ReadPosRankSum=-0.898;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S15|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,27:54:99:897,0,877 -chr1 144686 . T C 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=54;Dels=0.00;FS=1.047;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.788;QD=16.87;ReadPosRankSum=-1.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:26,28:54:99:939,0,867 -chr1 144759 . C G 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.336;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.833;QD=14.26;ReadPosRankSum=1.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:20,18:38:99:570,0,686 -chr1 144778 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=-1.949;QD=17.02;ReadPosRankSum=-1.535;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),START_GAINED(LOW||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:607,0,531 -chr1 144839 . C T 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-3.678;QD=8.56;ReadPosRankSum=-2.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:24,11:35:99:328,0,819 -chr1 144896 . C T 1822.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.76;MQ0=0;QD=33.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1851,138,0 -chr1 144909 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=44;Dels=0.00;FS=4.590;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=0.603;QD=20.77;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:942,0,494 -chr1 144934 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=38;Dels=0.00;FS=17.088;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.893;QD=21.31;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:838,0,442 -chr1 144950 . G A 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=38;Dels=0.00;FS=11.386;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.801;QD=22.23;ReadPosRankSum=0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,25:38:99:873,0,375 -chr1 144960 . A G 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=31;Dels=0.00;FS=13.484;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=0.675;QD=23.61;ReadPosRankSum=-0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:760,0,270 -chr1 144980 . T G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.632;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.879;QD=10.70;ReadPosRankSum=-0.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:317,0,537 -chr1 145002 . C G 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.427;QD=8.92;ReadPosRankSum=0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:269,0,580 -chr1 145030 . C T 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=27;Dels=0.00;FS=7.832;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-0.704;QD=15.14;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:437,0,486 -chr1 145051 . C T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=26;Dels=0.00;FS=10.770;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-0.571;QD=19.38;ReadPosRankSum=-1.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:532,0,376 -chr1 145056 . T C 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=25;Dels=0.00;FS=10.578;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.248;QD=12.11;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:331,0,511 -chr1 145062 . C T 1092.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1121,84,0 -chr1 145137 . A G 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=17.5729;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-3.783;QD=5.84;ReadPosRankSum=-3.420;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,7:26:99:180,0,645 -chr1 145149 . G C 959.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.936;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=2;MLEAF=1.00;MQ=52.35;MQ0=2;MQRankSum=1.244;QD=29.97;ReadPosRankSum=2.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,27:32:11:987,11,0 -chr1 145165 . C A 1164.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=50.22;MQ0=3;QD=33.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,35:35:96:1193,96,0 -chr1 145178 . T A 1075.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=3;QD=33.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:87:1104,87,0 -chr1 145196 . A T 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=31;Dels=0.00;FS=4.262;HaplotypeScore=15.6286;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=3;MQRankSum=-2.370;QD=20.54;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,19:31:99:665,0,196 -chr1 145230 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=40;Dels=0.00;FS=9.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=2;MQRankSum=1.303;QD=8.29;ReadPosRankSum=2.151;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:360,0,901 -chr1 145381 . T C 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.906;DP=37;Dels=0.03;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=1;MQRankSum=0.283;QD=22.64;ReadPosRankSum=-0.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,27:36:99:866,0,203 -chr1 145385 . A T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-0.159;QD=5.89;ReadPosRankSum=0.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,9:38:99:252,0,952 -chr1 145416 . T C 1041.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=23.0537;MLEAC=2;MLEAF=1.00;MQ=54.28;MQ0=1;QD=31.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1070,87,0 -chr1 145429 . C T 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=33;Dels=0.00;FS=4.709;HaplotypeScore=14.4456;MLEAC=1;MLEAF=0.500;MQ=53.98;MQ0=1;MQRankSum=-2.077;QD=14.17;ReadPosRankSum=1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:496,0,578 -chr1 145442 . C T 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.854;DP=28;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=1;MQRankSum=2.415;QD=17.49;ReadPosRankSum=-2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,16:28:99:518,0,409 -chr1 145448 . T C 377.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=31.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:406,30,0 -chr1 145453 . A G 385.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=26.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:414,30,0 -chr1 145503 . G A,C 789.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.79;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,8:27:99:956,264,207,691,0,667 -chr1 145509 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=1.970;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.472;QD=23.26;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:633,0,240 -chr1 145512 . C T 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.259;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.711;QD=9.29;ReadPosRankSum=-1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:242,0,524 -chr1 145513 . G A 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.226;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-1.904;QD=20.90;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:509,0,246 -chr1 145515 . G A 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.013;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.126;QD=10.13;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:251,0,503 -chr1 145531 . A G 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.177;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.288;QD=17.10;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,10:18:99:336,0,240 -chr1 145534 . C T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=2.518;QD=11.41;ReadPosRankSum=2.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,8:19:99:245,0,339 -chr1 145538 . T C 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.376;QD=16.92;ReadPosRankSum=-2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:299,0,219 -chr1 145544 . T C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=1.134;QD=11.81;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:99:170,0,230 -chr1 145555 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.470;QD=12.78;ReadPosRankSum=-2.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,5:10:99:156,0,173 -chr1 145615 . A C 535.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=2;MLEAF=1.00;MQ=55.87;MQ0=0;QD=32.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:564,42,0 -chr1 145642 . A G 1135.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.6529;MLEAC=2;MLEAF=1.00;MQ=54.53;MQ0=0;QD=31.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1164,87,0 -chr1 145654 . T C 490.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=1;MQRankSum=-2.198;QD=15.83;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:519,0,451 -chr1 145666 . G A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=33;Dels=0.00;FS=1.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.78;MQ0=2;MQRankSum=-1.364;QD=13.72;ReadPosRankSum=1.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:481,0,521 -chr1 145673 . T C 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=35;Dels=0.00;FS=1.624;HaplotypeScore=15.4641;MLEAC=1;MLEAF=0.500;MQ=52.28;MQ0=2;MQRankSum=0.955;QD=13.76;ReadPosRankSum=-0.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:510,0,570 -chr1 145676 . A G 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.570;DP=36;Dels=0.00;FS=1.666;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=2;MQRankSum=0.707;QD=13.02;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:497,0,607 -chr1 145688 . A G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.302;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=-0.944;QD=15.17;ReadPosRankSum=-0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:544,0,419 -chr1 145689 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=1.171;QD=11.67;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:425,0,541 -chr1 145706 . C T 986.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=2;QD=32.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:78:1015,78,0 -chr1 145712 . A G 1007.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.65;MQ0=2;QD=32.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:81:1036,81,0 -chr1 145783 . G A 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=19;Dels=0.00;FS=2.199;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.549;QD=19.15;ReadPosRankSum=2.409;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:392,0,216 -chr1 145845 . C T 1598.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.69;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1627,120,0 -chr1 145926 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.984;DP=43;Dels=0.00;FS=1.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=2.423;QD=15.23;ReadPosRankSum=0.621;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:683,0,719 -chr1 145928 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=41;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-0.745;QD=16.12;ReadPosRankSum=-0.588;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:689,0,634 -chr1 145949 . T C 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.879;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.907;QD=16.95;ReadPosRankSum=0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:791,0,650 -chr1 145950 . G C 1750.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=0;QD=26.60;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1779,135,0 -chr1 145957 . T C 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-2.937;QD=19.86;ReadPosRankSum=0.461;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:942,0,588 -chr1 145961 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=47;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=-3.067;QD=19.74;ReadPosRankSum=1.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:956,0,621 -chr1 145971 . T C 1794.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=30.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1823,135,0 -chr1 145982 . C T 1821.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1850,138,0 -chr1 145991 . T C 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=40;Dels=0.00;FS=2.157;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-0.969;QD=31.44;ReadPosRankSum=2.998;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,36:40:39:1286,0,39 -chr1 145995 . C T 1327.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.079;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.3985;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;MQRankSum=-0.621;QD=34.94;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,36:38:38:1356,38,0 -chr1 146000 . G A 1358.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=22.90;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1387,108,0 -chr1 146028 . T C 1707.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8730;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=27.76;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1736,135,0 -chr1 146053 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=42;Dels=0.00;FS=1.216;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.654;QD=14.85;ReadPosRankSum=-1.484;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:652,0,659 -chr1 146141 . G C 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.379;QD=16.12;ReadPosRankSum=0.093;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:915,0,948 -chr1 146183 . C T 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=61;Dels=0.00;FS=13.794;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=0.166;QD=14.73;ReadPosRankSum=1.165;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:927,0,1096 -chr1 146259 . G A 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;DP=50;Dels=0.00;FS=1.112;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.160;QD=13.60;ReadPosRankSum=0.225;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:708,0,962 -chr1 146273 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=47;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=-0.672;QD=14.27;ReadPosRankSum=0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:699,0,859 -chr1 146296 . T C 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123;DP=51;Dels=0.00;FS=2.461;HaplotypeScore=1.7074;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.406;QD=13.64;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:724,0,886 -chr1 146334 . G A 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.744;DP=54;Dels=0.00;FS=15.099;HaplotypeScore=4.3788;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=0.234;QD=13.53;ReadPosRankSum=-0.892;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:759,0,888 -chr1 146352 . A C 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.498;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.008;QD=16.62;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:876,0,875 -chr1 146412 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.096;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.487;QD=17.29;ReadPosRankSum=-0.974;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:841,0,718 -chr1 146446 . G T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-3.670;QD=13.83;ReadPosRankSum=-0.730;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:706,0,869 -chr1 146451 . T C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.785;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-1.455;QD=13.94;ReadPosRankSum=-0.796;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:725,0,868 -chr1 146456 . G C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.9978;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-3.167;QD=10.90;ReadPosRankSum=0.452;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:44:99:508,0,846 -chr1 146467 . C T 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=55.70;MQ0=0;MQRankSum=-3.722;QD=12.56;ReadPosRankSum=-0.562;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:493,0,671 -chr1 146489 . T A 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=6.7989;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-3.721;QD=8.78;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:362,0,945 -chr1 146502 . C T 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.559;DP=40;Dels=0.00;FS=2.861;HaplotypeScore=82.1865;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.486;QD=11.52;ReadPosRankSum=2.989;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:489,0,888 -chr1 146626 . C A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=0.151;QD=9.56;ReadPosRankSum=-0.179;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:420,0,892 -chr1 146707 . A T 748.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=51.1918;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-0.045;QD=14.13;ReadPosRankSum=-0.846;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:777,0,951 -chr1 146722 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.569;DP=53;Dels=0.00;FS=2.427;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-0.514;QD=12.00;ReadPosRankSum=0.966;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:664,0,1073 -chr1 146734 . G A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.057;QD=8.69;ReadPosRankSum=2.226;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:489,0,1193 -chr1 146736 . C T 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.906;QD=9.05;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:508,0,1187 -chr1 146737 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.038;QD=9.15;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:513,0,1186 -chr1 146738 . G A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.005;QD=8.94;ReadPosRankSum=2.470;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:502,0,1205 -chr1 146751 . T C 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.546;DP=56;Dels=0.00;FS=8.313;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=2.036;QD=19.41;ReadPosRankSum=-0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1115,0,613 -chr1 146757 . T C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=54;Dels=0.00;FS=8.599;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=1;MQRankSum=-1.537;QD=11.00;ReadPosRankSum=-0.118;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:622,0,1058 -chr1 146765 . T C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=50;Dels=0.00;FS=2.814;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.67;MQ0=1;MQRankSum=-1.838;QD=9.12;ReadPosRankSum=0.011;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:484,0,1120 -chr1 146805 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.862;DP=39;Dels=0.00;FS=3.130;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=0.738;QD=8.51;ReadPosRankSum=0.585;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:360,0,832 -chr1 146811 . A T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860;DP=41;Dels=0.00;FS=1.258;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.246;QD=10.92;ReadPosRankSum=-0.821;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:476,0,771 -chr1 146917 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=34;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.919;QD=22.14;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,22:34:99:781,0,382 -chr1 146962 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.455;DP=33;Dels=0.00;FS=8.473;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.387;QD=12.14;ReadPosRankSum=-0.387;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:429,0,656 -chr1 147004 . A G 326.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:355,27,0 -chr1 147012 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 147033 . A G 283.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.29;MQ0=0;QD=27.26;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:312,24,0 -chr1 147043 . G A 158.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.198;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=1;MQRankSum=1.495;QD=19.86;ReadPosRankSum=0.922;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,5:8:15:187,15,0 -chr1 147044 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.720;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.27;MQ0=1;MQRankSum=1.380;QD=18.86;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,4:7:12:160,12,0 -chr1 147046 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.638;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.75;MQ0=1;MQRankSum=2.017;QD=14.67;ReadPosRankSum=2.017;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,4:9:12:160,12,0 -chr1 147053 . C T 129.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.73;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:157,12,0 -chr1 147055 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.46;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:154,12,0 -chr1 147074 . G A 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=4.7802;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=1;MQRankSum=2.617;QD=5.25;ReadPosRankSum=-1.880;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:149,0,214 -chr1 147113 . A C 82.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=27.3842;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=3;MQRankSum=1.937;QD=2.30;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,6:36:99:111,0,296 -chr1 147139 . G A 323.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.091;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=16.6145;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=11;MQRankSum=2.940;QD=6.11;ReadPosRankSum=1.127;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:53:99:352,0,249 -chr1 147150 . T G 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=10.0978;MLEAC=1;MLEAF=0.500;MQ=26.62;MQ0=11;MQRankSum=-1.429;QD=2.04;ReadPosRankSum=-1.554;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:128,0,456 -chr1 147170 . G A 326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=42.8592;MLEAC=1;MLEAF=0.500;MQ=26.42;MQ0=13;MQRankSum=3.898;QD=6.95;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,13:47:99:355,0,181 -chr1 147223 . T C 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=20.60;MQ0=4;MQRankSum=-2.013;QD=3.22;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:112,0,126 -chr1 147226 . G C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.109;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=1.702;QD=2.41;ReadPosRankSum=1.702;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,8:24:86:86,0,115 -chr1 147227 . C A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=6.9023;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=0.910;QD=0.99;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,5:24:52:52,0,159 -chr1 147238 . A G 178.8 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=5.5670;MLEAC=2;MLEAF=1.00;MQ=23.04;MQ0=2;QD=10.52;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:21:207,21,0 -chr1 147243 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=22.90;MQ0=2;MQRankSum=0.755;QD=3.39;ReadPosRankSum=1.200;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,8:20:96:96,0,131 -chr1 147246 . A T 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.236;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=24.50;MQ0=1;MQRankSum=1.559;QD=2.56;ReadPosRankSum=-2.126;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,4:21:82:82,0,176 -chr1 147259 . A G 289.56 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.540;DP=19;Dels=0.00;FS=4.393;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.17;MQ0=1;MQRankSum=1.185;QD=15.24;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,16:19:7:317,7,0 -chr1 147272 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=16;Dels=0.00;FS=3.522;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=31.58;MQ0=1;MQRankSum=2.298;QD=9.11;ReadPosRankSum=-2.062;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,6:16:99:174,0,100 -chr1 147273 . T C 302.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=31.58;MQ0=1;QD=18.92;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,15:16:27:331,27,0 -chr1 147296 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=18;Dels=0.00;FS=7.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=3.532;QD=16.93;ReadPosRankSum=-0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:51:333,0,51 -chr1 147357 . A T 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=30;Dels=0.00;FS=28.709;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.13;MQ0=6;MQRankSum=-3.766;QD=4.79;ReadPosRankSum=-1.133;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,14:30:99:172,0,529 -chr1 147416 . T C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=10;Dels=0.00;FS=15.441;HaplotypeScore=26.0957;MLEAC=1;MLEAF=0.500;MQ=30.35;MQ0=3;MQRankSum=-1.754;QD=3.98;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,4:10:68:68,0,134 -chr1 147424 . A G 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=8;Dels=0.00;FS=11.761;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=30.85;MQ0=2;MQRankSum=1.380;QD=13.85;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,4:8:31:139,0,31 -chr1 147427 . T C 164.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=23.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:193,18,0 -chr1 147428 . T C 173.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=24.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:202,18,0 -chr1 147440 . C T 145.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=2;MQRankSum=2.219;QD=13.27;ReadPosRankSum=-0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,5:11:5:173,0,5 -chr1 147461 . G A 174.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=8.9694;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=2;MQRankSum=3.016;QD=11.65;ReadPosRankSum=-1.493;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,6:15:24:203,0,24 -chr1 147474 . C T 286.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=10.9207;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=2;MQRankSum=3.281;QD=15.94;ReadPosRankSum=-2.752;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:15:315,0,15 -chr1 147490 . G A 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=23;Dels=0.00;FS=3.834;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=2.760;QD=12.95;ReadPosRankSum=3.318;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:326,0,430 -chr1 147522 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=30;Dels=0.00;FS=1.449;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.65;MQ0=0;MQRankSum=-3.516;QD=17.83;ReadPosRankSum=-0.963;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:563,0,394 -chr1 147528 . A G 1043.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.18;MQ0=0;QD=31.37;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1072,81,0 -chr1 147529 . T C 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.492;DP=27;Dels=0.00;FS=1.598;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=3.380;QD=12.77;ReadPosRankSum=0.962;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,11:27:99:373,0,495 -chr1 147542 . C T 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=33;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.17;MQ0=0;MQRankSum=-2.900;QD=17.30;ReadPosRankSum=-0.234;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:599,0,528 -chr1 147543 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=34;Dels=0.00;FS=3.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=0;MQRankSum=-1.639;QD=17.52;ReadPosRankSum=-0.535;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:624,0,489 -chr1 147546 . G A 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=35;Dels=0.00;FS=3.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.560;QD=12.42;ReadPosRankSum=0.248;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:463,0,624 -chr1 147575 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=4.613;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-2.836;QD=20.26;ReadPosRankSum=-0.194;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:879,0,470 -chr1 147578 . A C 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=2.964;QD=10.43;ReadPosRankSum=0.744;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:456,0,851 -chr1 147586 . C T 1415.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=53.48;MQ0=0;QD=32.80;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1444,114,0 -chr1 147591 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=35;Dels=0.00;FS=1.344;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-2.317;QD=18.31;ReadPosRankSum=0.850;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:669,0,479 -chr1 147594 . G C,T 1053.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.02;MQ0=0;QD=30.98;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,15:34:99:1240,557,500,683,0,638 -chr1 147597 . A G 1257.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=52.79;MQ0=0;QD=24.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1286,99,0 -chr1 147598 . G A 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=33;Dels=0.00;FS=5.093;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-2.045;QD=19.33;ReadPosRankSum=0.166;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:666,0,407 -chr1 147606 . A C 1323.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.20;MQ0=0;QD=29.38;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1352,105,0 -chr1 147628 . C T 1132.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.90;MQ0=0;QD=33.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1161,90,0 -chr1 147635 . A G 947.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;QD=28.17;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:976,78,0 -chr1 147636 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.792;DP=26;Dels=0.00;FS=1.796;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.40;MQ0=0;MQRankSum=-2.081;QD=23.18;ReadPosRankSum=1.272;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,19:26:99:631,0,203 -chr1 147641 . T A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.241;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=0;MQRankSum=-1.623;QD=24.39;ReadPosRankSum=1.241;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,19:25:99:638,0,170 -chr1 147653 . T G 1125.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.44;MQ0=0;QD=36.65;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1154,93,0 -chr1 147665 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.781;DP=31;Dels=0.00;FS=11.051;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.68;MQ0=0;MQRankSum=2.182;QD=11.86;ReadPosRankSum=-1.741;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:396,0,590 -chr1 147671 . C T 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=30;Dels=0.00;FS=8.496;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-1.517;QD=15.93;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:506,0,416 -chr1 147698 . T C 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=29;Dels=0.00;FS=11.831;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.240;QD=15.47;ReadPosRankSum=-2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:477,0,517 -chr1 147700 . A G 1091.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1120,84,0 -chr1 147730 . T C 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=24.449;HaplotypeScore=2.5770;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.345;QD=13.02;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:523,0,753 -chr1 147779 . C T 1482.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1511,111,0 -chr1 147815 . G A 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.116;DP=38;Dels=0.00;FS=5.625;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.779;QD=10.52;ReadPosRankSum=1.129;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S6N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:428,0,860 -chr1 147816 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=38;Dels=0.00;FS=5.221;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.154;QD=10.44;ReadPosRankSum=1.292;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S6|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:425,0,850 -chr1 147861 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-2.322;QD=18.06;ReadPosRankSum=-0.782;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S21|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:823,0,602 -chr1 147863 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.540;QD=18.84;ReadPosRankSum=-0.782;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S22T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:857,0,597 -chr1 147893 . A C 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=28;Dels=0.00;FS=12.411;HaplotypeScore=17.4716;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.534;QD=13.31;ReadPosRankSum=1.694;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y32S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:401,0,517 -chr1 147940 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992;DP=60;Dels=0.00;FS=5.651;HaplotypeScore=4.9890;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=1;MQRankSum=2.013;QD=2.28;ReadPosRankSum=0.601;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E48K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,9:60:99:165,0,1548 -chr1 147974 . G T 2172.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.02;MQ0=1;QD=32.90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W59L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2201,172,0 -chr1 147980 . T C 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=60;Dels=0.00;FS=2.594;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=1;MQRankSum=-5.013;QD=5.68;ReadPosRankSum=2.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L61S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:369,0,1413 -chr1 148008 . T G 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.047;DP=70;Dels=0.00;FS=5.868;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-4.821;QD=6.14;ReadPosRankSum=0.000;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T70|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:458,0,1746 -chr1 148023 . G A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=65;Dels=0.00;FS=8.565;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-4.083;QD=6.41;ReadPosRankSum=0.082;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V75|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:445,0,1615 -chr1 148028 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=60;Dels=0.00;FS=14.560;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.07;MQ0=0;MQRankSum=-4.165;QD=5.43;ReadPosRankSum=0.768;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S77L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,15:60:99:354,0,1522 -chr1 148029 . G A 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=57;Dels=0.00;FS=9.963;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-2.445;QD=5.21;ReadPosRankSum=1.708;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S77|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:43,13:57:99:325,0,1421 -chr1 148050 . T C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=2.073;QD=10.00;ReadPosRankSum=-0.265;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I84|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:678,0,1415 -chr1 148062 . G A 2262.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=26.81;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R88|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2291,178,0 -chr1 148077 . T G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.434;DP=53;Dels=0.00;FS=12.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-4.267;QD=7.07;ReadPosRankSum=0.313;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H93Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,14:53:99:403,0,1389 -chr1 148078 . C A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.438;DP=54;Dels=0.00;FS=12.716;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=-4.017;QD=6.61;ReadPosRankSum=0.365;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P94T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,14:54:99:385,0,1444 -chr1 148095 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=44;Dels=0.00;FS=14.379;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.117;QD=6.61;ReadPosRankSum=1.003;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A99|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:319,0,1163 -chr1 148104 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=48;Dels=0.00;FS=16.904;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-4.176;QD=7.10;ReadPosRankSum=-0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A102|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,13:48:99:369,0,1201 -chr1 148117 . T C 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=50;Dels=0.00;FS=18.397;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=-3.965;QD=4.16;ReadPosRankSum=1.152;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S107P|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,10:50:99:236,0,1399 -chr1 148124 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=49;Dels=0.00;FS=20.451;HaplotypeScore=1.8499;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.155;QD=3.73;ReadPosRankSum=0.409;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T109I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:211,0,1394 -chr1 148128 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=48;Dels=0.00;FS=20.451;HaplotypeScore=45.3427;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-4.649;QD=3.72;ReadPosRankSum=0.608;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A110|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,9:48:99:207,0,1389 -chr1 148133 . A G 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=46;Dels=0.00;FS=20.653;HaplotypeScore=118.8295;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-4.624;QD=3.82;ReadPosRankSum=-0.194;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D112G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,9:46:99:204,0,1210 -chr1 148165 . C G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=43;Dels=0.00;FS=1.213;HaplotypeScore=4.9810;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.859;QD=11.99;ReadPosRankSum=-1.096;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P123A|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:544,0,806 -chr1 148184 . A G 1381.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.9827;MLEAC=2;MLEAF=1.00;MQ=56.12;MQ0=0;QD=29.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K129R|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1410,111,0 -chr1 148218 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.156;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=0.826;QD=13.38;ReadPosRankSum=0.216;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S140|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:590,0,747 -chr1 148366 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=46;Dels=0.00;FS=2.594;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=1;MQRankSum=0.742;QD=18.06;ReadPosRankSum=0.811;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:859,0,635 -chr1 148435 . A C 1097.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=54;Dels=0.00;FS=9.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.801;QD=20.33;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,32:54:99:1126,0,692 -chr1 148463 . A G 1201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268;DP=54;Dels=0.00;FS=1.155;HaplotypeScore=28.9952;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.199;QD=22.25;ReadPosRankSum=0.507;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,35:54:99:1230,0,586 -chr1 148468 . A G 1266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.651;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=15.2316;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.761;QD=23.46;ReadPosRankSum=0.615;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,36:54:99:1295,0,544 -chr1 148595 . C T 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.094;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.341;QD=12.88;ReadPosRankSum=-0.048;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:685,0,1002 -chr1 148617 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.242;DP=50;Dels=0.00;FS=1.142;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.203;QD=15.00;ReadPosRankSum=-1.901;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:778,0,841 -chr1 148704 . G C 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.330;QD=17.33;ReadPosRankSum=-0.481;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,798 -chr1 148761 . A T 1165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.413;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.244;QD=17.66;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1194,0,997 -chr1 148794 . T C 1570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.757;DP=84;Dels=0.00;FS=0.829;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.198;QD=18.70;ReadPosRankSum=-0.117;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,47:84:99:1599,0,1205 -chr1 148795 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=81;Dels=0.00;FS=0.833;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.043;QD=14.77;ReadPosRankSum=-0.327;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:44,37:81:99:1225,0,1499 -chr1 148840 . T A 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.283;DP=67;Dels=0.00;FS=6.538;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.018;QD=15.13;ReadPosRankSum=0.094;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1042,0,1215 -chr1 148975 . A T 1278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=70;Dels=0.00;FS=2.050;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.446;QD=18.27;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1307,0,1024 -chr1 148997 . T C 2678.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.02;MQ0=0;QD=25.77;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2707,205,0 -chr1 149029 . T C 1230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=64;Dels=0.00;FS=7.922;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=4;MQRankSum=-3.991;QD=19.23;ReadPosRankSum=0.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,40:64:99:1259,0,799 -chr1 149049 . C T 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=53;Dels=0.00;FS=4.125;HaplotypeScore=3.9326;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.050;QD=15.88;ReadPosRankSum=0.650;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:870,0,827 -chr1 149054 . T A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.693;DP=53;Dels=0.00;FS=1.097;HaplotypeScore=2.9329;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.556;QD=14.32;ReadPosRankSum=1.012;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:787,0,898 -chr1 149065 . C T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.38;MQ0=4;MQRankSum=3.705;QD=16.74;ReadPosRankSum=-1.056;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:748,0,583 -chr1 149079 . T A 1585.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.50;MQ0=0;QD=35.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1614,120,0 -chr1 149083 . G A 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=1.535;QD=16.43;ReadPosRankSum=1.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:636,0,597 -chr1 149099 . C T 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.884;DP=40;Dels=0.00;FS=2.794;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-0.095;QD=14.47;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,754 -chr1 149136 . A C 1526.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=32.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1555,117,0 -chr1 149156 . G A 46.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;DP=52;Dels=0.00;FS=6.760;HaplotypeScore=3.3564;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.965;QD=0.90;ReadPosRankSum=-3.566;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R158|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,7:52:75:75,0,1569 -chr1 149170 . A G 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.215;DP=58;Dels=0.00;FS=6.984;HaplotypeScore=11.3843;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.167;QD=0.36;ReadPosRankSum=-0.215;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E163G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,7:58:49:49,0,1750 -chr1 149174 . A G 793.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.409;DP=60;Dels=0.00;FS=14.447;HaplotypeScore=10.5956;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.030;QD=13.23;ReadPosRankSum=0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P164|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:822,0,1037 -chr1 149224 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=47;Dels=0.00;FS=19.146;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.421;QD=14.51;ReadPosRankSum=-0.769;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I181T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,21:47:99:710,0,673 -chr1 149225 . C G 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=47;Dels=0.00;FS=6.565;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.526;QD=1.55;ReadPosRankSum=1.164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I181M|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:101,0,1493 -chr1 149237 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=43;Dels=0.00;FS=4.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.284;QD=0.81;ReadPosRankSum=1.118;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L185|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:38,5:43:63:63,0,1390 -chr1 149253 . C T 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P191S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,105,0 -chr1 149279 . G A 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.121;DP=34;Dels=0.00;FS=8.198;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;QD=14.85;ReadPosRankSum=0.155;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S199|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:533,0,627 -chr1 149379 . T C 993.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.329;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=2.8936;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.187;QD=20.28;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:1022,0,551 -chr1 149421 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.477;DP=43;Dels=0.00;FS=1.218;HaplotypeScore=3.8299;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.086;QD=13.09;ReadPosRankSum=0.037;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,836 -chr1 149472 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.074;QD=12.76;ReadPosRankSum=-0.015;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:513,0,690 -chr1 149514 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.243;QD=12.10;ReadPosRankSum=1.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:464,0,734 -chr1 149653 . G T 579.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.40;MQ0=1;QD=28.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,16:16:45:608,45,0 -chr1 149713 . T G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=42;Dels=0.00;FS=1.480;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.750;QD=12.83;ReadPosRankSum=0.496;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:567,0,822 -chr1 149716 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.591;DP=44;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.177;QD=14.22;ReadPosRankSum=-0.365;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,836 -chr1 149737 . A G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.238;QD=16.15;ReadPosRankSum=1.192;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:755,0,792 -chr1 149745 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.697;QD=13.88;ReadPosRankSum=1.519;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:653,0,850 -chr1 149746 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.247;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.420;QD=13.21;ReadPosRankSum=1.732;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:649,0,910 -chr1 149780 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=33;Dels=0.00;FS=3.967;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.998;QD=11.84;ReadPosRankSum=-1.803;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,13:33:99:419,0,669 -chr1 149946 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.827;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=-1.482;QD=12.69;ReadPosRankSum=0.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:701,0,1128 -chr1 149947 . G A 2084.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=27.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2113,157,0 -chr1 149959 . T G 1968.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.79;MQ0=0;QD=31.52;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1997,150,0 -chr1 149962 . T C 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=50;Dels=0.00;FS=1.172;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.553;QD=10.14;ReadPosRankSum=-0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:535,0,1193 -chr1 150069 . A G 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-1.083;QD=17.49;ReadPosRankSum=0.217;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I248V|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:19,21:40:99:728,0,642 -chr1 150083 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=42;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=2.679;QD=14.76;ReadPosRankSum=0.859;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,802 -chr1 150232 . C T 2061.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=24.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2090,159,0 -chr1 150236 . G A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.696;DP=55;Dels=0.00;FS=5.672;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.713;QD=12.12;ReadPosRankSum=0.850;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:695,0,1131 -chr1 150249 . C G 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.844;QD=13.76;ReadPosRankSum=2.150;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,24:55:99:785,0,958 -chr1 150265 . C T 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=57;Dels=0.00;FS=2.302;HaplotypeScore=2.8318;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.049;QD=11.47;ReadPosRankSum=2.072;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,22:57:99:682,0,1070 -chr1 150297 . T C 2289.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=28.40;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2318,175,0 -chr1 150375 . T G 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.134;DP=48;Dels=0.00;FS=14.013;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.610;QD=14.87;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,881 -chr1 150494 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.680;DP=38;Dels=0.00;FS=1.849;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.182;QD=25.63;ReadPosRankSum=1.541;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,28:38:99:1002,0,268 -chr1 150499 . C A 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.340;DP=37;Dels=0.00;FS=1.885;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=1;MQRankSum=-0.698;QD=5.89;ReadPosRankSum=-1.378;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,10:37:99:246,0,955 -chr1 150581 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.334;DP=28;Dels=0.00;FS=7.346;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.220;QD=6.46;ReadPosRankSum=-0.318;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:209,0,766 -chr1 150588 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.05;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1302,96,0 -chr1 150606 . C T 1237.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1266,93,0 -chr1 150717 . T A,G 1153.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.04;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,16,20:36:99:1346,748,699,599,0,539 -chr1 150752 . G A 1457.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1486,114,0 -chr1 150838 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.568;DP=52;Dels=0.00;FS=6.106;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.029;QD=10.65;ReadPosRankSum=1.741;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:582,0,1173 -chr1 150929 . G A 2230.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.19;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2259,172,0 -chr1 150953 . C A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.538;DP=60;Dels=0.00;FS=31.975;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.044;QD=16.33;ReadPosRankSum=-0.680;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1008,0,1004 -chr1 150957 . T C 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.859;DP=61;Dels=0.00;FS=31.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.888;QD=17.03;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1067,0,979 -chr1 151031 . T A 2189.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=33.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2218,166,0 -chr1 151074 . A T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=1.9853;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.650;QD=16.10;ReadPosRankSum=-0.550;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:817,0,821 -chr1 151153 . T A 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=58;Dels=0.00;FS=7.584;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.355;QD=13.15;ReadPosRankSum=-0.087;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:791,0,1148 -chr1 151277 . G C 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.054;DP=35;Dels=0.00;FS=8.547;HaplotypeScore=3.9810;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.126;QD=9.39;ReadPosRankSum=0.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P284|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_151216_151324) GT:AD:DP:GQ:PL 0/1:22,12:35:99:357,0,750 -chr1 151351 . A G 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.257;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=5.9768;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.771;QD=21.17;ReadPosRankSum=-0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:1150,0,663 -chr1 151361 . A G,T 1601.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,26,24:50:99:1836,882,804,954,0,882 -chr1 151391 . T A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.522;DP=43;Dels=0.00;FS=1.286;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.140;QD=10.46;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,15:43:99:478,0,965 -chr1 151489 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=1.065;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.773;QD=17.41;ReadPosRankSum=-0.401;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:951,0,823 -chr1 151542 . C T 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.309;DP=63;Dels=0.00;FS=30.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.313;QD=17.04;ReadPosRankSum=-0.351;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1102,0,1065 -chr1 151610 . C A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.325;DP=59;Dels=0.00;FS=9.684;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.218;QD=14.40;ReadPosRankSum=1.356;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:878,0,1066 -chr1 151618 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=61;Dels=0.00;FS=5.239;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.094;QD=16.44;ReadPosRankSum=0.815;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,31:61:99:1031,0,1031 -chr1 151695 . T G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.206;DP=51;Dels=0.00;FS=1.161;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.688;QD=20.33;ReadPosRankSum=2.209;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1065,0,641 -chr1 151785 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2478,184,0 -chr1 151923 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=42;Dels=0.00;FS=6.816;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.225;QD=12.64;ReadPosRankSum=-0.225;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,17:42:99:559,0,782 -chr1 151972 . A G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.562;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.876;QD=17.48;ReadPosRankSum=-0.614;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:745,0,597 -chr1 152191 . C G 1805.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=30.22;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1834,147,0 -chr1 152290 . A G 1160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=72;Dels=0.00;FS=4.729;HaplotypeScore=2.7880;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.788;QD=16.12;ReadPosRankSum=1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,35:72:99:1189,0,1208 -chr1 152381 . C A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.235;QD=10.50;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:595,0,1229 -chr1 152382 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.305;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.873;QD=10.07;ReadPosRankSum=-0.009;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:562,0,1258 -chr1 152486 . A G 2355.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2384,181,0 -chr1 152515 . T A 2726.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2755,208,0 -chr1 152581 . C A 2660.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2689,202,0 -chr1 152658 . A T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=65;Dels=0.00;FS=3.385;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.165;QD=14.69;ReadPosRankSum=-0.574;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:983,0,1258 -chr1 152684 . C G 2666.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2695,202,0 -chr1 152720 . A G 1186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.563;QD=18.84;ReadPosRankSum=0.826;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1215,0,861 -chr1 152741 . G T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=61;Dels=0.00;FS=3.616;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=0.365;QD=13.05;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:824,0,1171 -chr1 152749 . T C 1986.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.667;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.72;MQ0=1;MQRankSum=-0.360;QD=25.29;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,53:54:99:2015,153,0 -chr1 152752 . G C 2005.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.46;MQ0=1;QD=30.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2034,153,0 -chr1 152755 . T C 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=55;Dels=0.00;FS=3.860;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=1;MQRankSum=2.481;QD=17.30;ReadPosRankSum=1.370;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:980,0,789 -chr1 152892 . T C 96.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.44;MQ0=4;QD=10.70;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:9:124,9,0 -chr1 152911 . G A 137.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.54;MQ0=4;QD=12.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:165,12,0 -chr1 152938 . C T 136.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.683;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.60;MQ0=4;MQRankSum=1.683;QD=10.46;ReadPosRankSum=1.001;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:6,7:13:12:164,12,0 -chr1 153166 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=5.7547;MLEAC=1;MLEAF=0.500;MQ=18.57;MQ0=5;MQRankSum=1.137;QD=2.93;ReadPosRankSum=1.137;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,10:30:92:116,0,92 -chr1 153200 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=33;Dels=0.00;FS=3.979;HaplotypeScore=1.7046;MLEAC=1;MLEAF=0.500;MQ=15.76;MQ0=8;MQRankSum=0.670;QD=1.11;ReadPosRankSum=1.136;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,10:33:65:65,0,140 -chr1 153324 . A G 148.31 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.081;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.9300;MLEAC=1;MLEAF=0.500;MQ=13.59;MQ0=11;MQRankSum=2.944;QD=4.24;ReadPosRankSum=2.348;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:9,25:35:21:200,21,0 -chr1 153381 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=68;Dels=0.00;FS=15.911;HaplotypeScore=21.0001;MLEAC=1;MLEAF=0.500;MQ=12.66;MQ0=25;MQRankSum=0.041;QD=0.61;ReadPosRankSum=0.528;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,13:68:70:70,0,248 -chr1 153430 . T C 161.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.369;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.7356;MLEAC=2;MLEAF=1.00;MQ=10.12;MQ0=25;MQRankSum=0.822;QD=3.68;ReadPosRankSum=-1.734;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,34:44:24:190,24,0 -chr1 153445 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=-0.451;QD=0.83;ReadPosRankSum=0.239;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,12:67:84:84,0,310 -chr1 153446 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.512;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=1.877;QD=0.65;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:59,8:67:72:72,0,323 -chr1 153476 . C T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=14.6632;MLEAC=1;MLEAF=0.500;MQ=16.01;MQ0=39;MQRankSum=1.279;QD=5.89;ReadPosRankSum=0.316;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,35:76:79:476,0,79 -chr1 153481 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=79;Dels=0.00;FS=2.335;HaplotypeScore=14.5114;MLEAC=1;MLEAF=0.500;MQ=15.99;MQ0=39;MQRankSum=0.178;QD=0.62;ReadPosRankSum=-0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:67,12:79:77:77,0,497 -chr1 153516 . G T 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.961;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=40;MQRankSum=1.294;QD=0.37;ReadPosRankSum=0.222;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,8:86:60:60,0,573 -chr1 153518 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=17.03;MQ0=39;MQRankSum=1.715;QD=0.41;ReadPosRankSum=-1.174;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,12:84:63:63,0,569 -chr1 153554 . T C 71.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.458;DP=51;Dels=0.00;FS=5.129;HaplotypeScore=5.7732;MLEAC=1;MLEAF=0.500;MQ=14.69;MQ0=20;MQRankSum=0.275;QD=1.41;ReadPosRankSum=-1.078;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,19:51:99:100,0,209 -chr1 153590 . T C 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=7.8158;MLEAC=1;MLEAF=0.500;MQ=13.34;MQ0=22;MQRankSum=0.750;QD=1.69;ReadPosRankSum=0.824;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,41:74:99:153,0,172 -chr1 153593 . T A 267.79 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=73;Dels=0.00;FS=12.430;HaplotypeScore=16.3870;MLEAC=1;MLEAF=0.500;MQ=13.50;MQ0=20;MQRankSum=-2.002;QD=3.67;ReadPosRankSum=0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,65:73:23:296,0,23 -chr1 153603 . C T 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.475;DP=131;Dels=0.00;FS=1.943;HaplotypeScore=7.3720;MLEAC=1;MLEAF=0.500;MQ=19.19;MQ0=28;MQRankSum=1.316;QD=3.97;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:83,47:131:99:548,0,748 -chr1 153634 . C T 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.160;DP=250;Dels=0.00;FS=8.821;HaplotypeScore=55.7961;MLEAC=1;MLEAF=0.500;MQ=21.90;MQ0=51;MQRankSum=-0.113;QD=0.76;ReadPosRankSum=2.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:217,33:250:99:218,0,3652 -chr1 153635 . A T 2861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.523;DP=250;Dels=0.00;FS=76.787;HaplotypeScore=57.8078;MLEAC=1;MLEAF=0.500;MQ=22.51;MQ0=49;MQRankSum=3.056;QD=11.45;ReadPosRankSum=2.693;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:101,149:250:99:2890,0,1044 -chr1 153682 . C T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=249;Dels=0.00;FS=4.305;HaplotypeScore=56.1815;MLEAC=1;MLEAF=0.500;MQ=24.41;MQ0=45;MQRankSum=2.445;QD=0.69;ReadPosRankSum=1.423;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,20:249:99:200,0,3583 -chr1 153721 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=246;Dels=0.00;FS=1.847;HaplotypeScore=63.1880;MLEAC=1;MLEAF=0.500;MQ=23.87;MQ0=46;MQRankSum=3.002;QD=0.06;ReadPosRankSum=-2.172;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,14:246:42:42,0,3329 -chr1 153722 . G A 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=245;Dels=0.00;FS=1.279;HaplotypeScore=60.2739;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=46;MQRankSum=2.339;QD=0.86;ReadPosRankSum=1.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:218,26:245:99:239,0,3144 -chr1 153752 . T C 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.489;DP=115;Dels=0.00;FS=5.126;HaplotypeScore=12.2854;MLEAC=1;MLEAF=0.500;MQ=17.73;MQ0=25;MQRankSum=-2.081;QD=0.17;ReadPosRankSum=-1.203;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,40:115:48:48,0,900 -chr1 153768 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=106;Dels=0.00;FS=2.104;HaplotypeScore=3.8507;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=30;MQRankSum=-0.643;QD=1.08;ReadPosRankSum=0.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,30:106:99:143,0,668 -chr1 153796 . G A 1945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=209;Dels=0.00;FS=0.000;HaplotypeScore=23.0694;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=44;MQRankSum=4.401;QD=9.31;ReadPosRankSum=0.585;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:85,120:209:99:1974,0,350 -chr1 153918 . G A 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=231;Dels=0.00;FS=102.092;HaplotypeScore=38.2429;MLEAC=1;MLEAF=0.500;MQ=21.52;MQ0=56;MQRankSum=1.367;QD=0.09;ReadPosRankSum=2.636;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:212,19:231:49:49,0,2890 -chr1 153928 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=177;Dels=0.00;FS=70.822;HaplotypeScore=49.5301;MLEAC=1;MLEAF=0.500;MQ=19.80;MQ0=52;MQRankSum=2.469;QD=0.32;ReadPosRankSum=1.151;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:165,11:177:84:84,0,1870 -chr1 153931 . G C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.672;DP=171;Dels=0.00;FS=63.103;HaplotypeScore=41.3083;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=50;MQRankSum=3.349;QD=7.01;ReadPosRankSum=-0.504;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:103,67:171:99:1227,0,745 -chr1 153947 . A G 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=117;Dels=0.00;FS=16.425;HaplotypeScore=22.7832;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=38;MQRankSum=2.093;QD=2.57;ReadPosRankSum=-1.715;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:97,20:117:99:329,0,946 -chr1 153962 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.029;DP=76;Dels=0.00;FS=28.843;HaplotypeScore=13.6296;MLEAC=1;MLEAF=0.500;MQ=17.52;MQ0=25;MQRankSum=3.039;QD=5.14;ReadPosRankSum=-2.479;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,22:76:99:419,0,279 -chr1 153982 . C G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=27;Dels=0.00;FS=10.000;HaplotypeScore=2.6670;MLEAC=1;MLEAF=0.500;MQ=11.06;MQ0=11;MQRankSum=2.285;QD=1.36;ReadPosRankSum=2.415;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,5:27:29:65,0,29 -chr1 154000 . A C 52.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.44;MQ0=1;QD=8.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:80,9,0 -chr1 154002 . G A 52.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.74;MQ0=1;QD=10.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:80,9,0 -chr1 154038 . G A 30.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.736;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.18;MQ0=1;MQRankSum=0.736;QD=7.69;ReadPosRankSum=-0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,3:4:6:58,6,0 -chr1 154066 . G A 262.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=23.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,10:11:27:291,27,0 -chr1 154073 . A T 236.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=21.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:265,24,0 -chr1 154089 . C T 246.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.061;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9468;MLEAC=1;MLEAF=0.500;MQ=27.14;MQ0=4;MQRankSum=2.003;QD=16.41;ReadPosRankSum=2.003;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,10:15:11:274,0,11 -chr1 154114 . T C 272.41 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.778;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=25.10;MQ0=4;MQRankSum=2.024;QD=15.13;ReadPosRankSum=0.934;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,13:18:8:300,8,0 -chr1 154133 . C T 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.115;DP=35;Dels=0.00;FS=9.558;HaplotypeScore=3.5584;MLEAC=1;MLEAF=0.500;MQ=18.65;MQ0=14;MQRankSum=2.353;QD=3.25;ReadPosRankSum=1.445;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:142,0,207 -chr1 154140 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.372;QD=0.88;ReadPosRankSum=0.501;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,368 -chr1 154141 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.501;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.238;QD=0.88;ReadPosRankSum=0.167;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,372 -chr1 154150 . C T 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;DP=52;Dels=0.00;FS=11.840;HaplotypeScore=12.4214;MLEAC=1;MLEAF=0.500;MQ=19.66;MQ0=15;MQRankSum=1.795;QD=3.11;ReadPosRankSum=-1.146;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,11:52:99:190,0,332 -chr1 154162 . G A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.044;DP=55;Dels=0.00;FS=11.710;HaplotypeScore=10.1969;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=15;MQRankSum=2.642;QD=4.32;ReadPosRankSum=-0.664;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:43,12:55:99:266,0,265 -chr1 154178 . A T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=57;Dels=0.00;FS=12.518;HaplotypeScore=35.4325;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=14;MQRankSum=0.047;QD=0.65;ReadPosRankSum=0.421;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:49,8:57:65:65,0,554 -chr1 154185 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=32.5155;MLEAC=1;MLEAF=0.500;MQ=19.28;MQ0=13;MQRankSum=-1.073;QD=0.29;ReadPosRankSum=-0.593;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:47,8:55:44:44,0,542 -chr1 154186 . C T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;DP=56;Dels=0.00;FS=6.576;HaplotypeScore=25.1706;MLEAC=1;MLEAF=0.500;MQ=19.31;MQ0=13;MQRankSum=2.199;QD=5.50;ReadPosRankSum=1.671;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,16:56:99:336,0,269 -chr1 154211 . G T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=20.8680;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=-1.269;QD=0.41;ReadPosRankSum=1.843;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,10:58:52:52,0,633 -chr1 154212 . G A 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=58;Dels=0.00;FS=23.517;HaplotypeScore=19.0376;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=0.000;QD=0.77;ReadPosRankSum=-1.855;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:48,10:58:73:73,0,611 -chr1 154215 . A G 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=11.7095;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=12;MQRankSum=-0.934;QD=0.60;ReadPosRankSum=2.084;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:45,10:55:61:61,0,555 -chr1 154233 . T A 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.328;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=4.6866;MLEAC=1;MLEAF=0.500;MQ=22.49;MQ0=0;MQRankSum=-1.708;QD=3.52;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:148,0,338 -chr1 154250 . A G 353.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=2.8562;MLEAC=2;MLEAF=1.00;MQ=21.26;MQ0=0;QD=20.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:382,45,0 -chr1 154253 . T G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=0;MQRankSum=0.174;QD=6.85;ReadPosRankSum=0.637;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,7:15:99:131,0,128 -chr1 154292 . T C 33.74 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.69;MQ0=3;QD=4.82;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,5:7:6:61,6,0 -chr1 154334 . G A 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=29;Dels=0.00;FS=9.558;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=23.50;MQ0=4;MQRankSum=-0.028;QD=4.34;ReadPosRankSum=-1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:154,0,227 -chr1 154358 . C A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.756;DP=47;Dels=0.00;FS=6.284;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.42;MQ0=3;MQRankSum=-1.018;QD=0.26;ReadPosRankSum=-0.844;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,9:47:40:40,0,642 -chr1 154359 . T G 544.14 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.915;DP=45;Dels=0.00;FS=12.648;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=3;MQRankSum=0.678;QD=12.09;ReadPosRankSum=0.265;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,34:45:24:632,24,0 -chr1 154370 . C A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=51;Dels=0.00;FS=8.661;HaplotypeScore=31.0665;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=4;MQRankSum=-2.073;QD=0.43;ReadPosRankSum=1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,13:51:50:50,0,714 -chr1 154426 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=49;Dels=0.00;FS=2.566;HaplotypeScore=5.9227;MLEAC=1;MLEAF=0.500;MQ=20.19;MQ0=9;MQRankSum=-0.765;QD=0.85;ReadPosRankSum=-0.359;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,10:49:70:70,0,505 -chr1 154501 . C T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=30;Dels=0.00;FS=2.793;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=20.43;MQ0=7;MQRankSum=2.328;QD=1.86;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,3:30:84:84,0,237 -chr1 154559 . G A 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.761;DP=30;Dels=0.00;FS=8.741;HaplotypeScore=6.7678;MLEAC=1;MLEAF=0.500;MQ=21.74;MQ0=1;MQRankSum=1.761;QD=2.36;ReadPosRankSum=0.953;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,5:30:99:99,0,279 -chr1 154589 . G A 67.03 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.06;MQ0=1;QD=7.45;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:12:95,12,0 -chr1 154697 . A G 47.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=20.50;MQ0=0;QD=15.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr1 154715 . A G 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.988;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=24.23;MQ0=0;MQRankSum=0.406;QD=2.27;ReadPosRankSum=-0.406;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:7:44:44,0,65 -chr1 154731 . T A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=3.8976;MLEAC=1;MLEAF=0.500;MQ=22.58;MQ0=0;MQRankSum=1.214;QD=3.78;ReadPosRankSum=-1.214;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,3:10:66:66,0,111 -chr1 154741 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.309;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=-1.309;QD=1.82;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:50:50,0,124 -chr1 154746 . C T 193.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=2;MLEAF=1.00;MQ=21.34;MQ0=0;QD=16.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:222,24,0 -chr1 154748 . G C 40.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.185;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=1.664;QD=3.40;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,3:12:69:69,0,77 -chr1 154754 . C T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=7.8245;MLEAC=1;MLEAF=0.500;MQ=21.59;MQ0=0;MQRankSum=1.246;QD=2.34;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,3:14:61:61,0,161 -chr1 154802 . G A 95.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.831;DP=13;Dels=0.00;FS=2.533;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=17.54;MQ0=1;MQRankSum=2.367;QD=7.38;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,7:13:5:123,0,5 -chr1 154809 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=18.22;MQ0=1;MQRankSum=1.296;QD=1.24;ReadPosRankSum=-1.532;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,2:12:43:43,0,89 -chr1 154987 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.751;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=2;MLEAF=1.00;MQ=9.62;MQ0=4;MQRankSum=0.751;QD=1.67;ReadPosRankSum=0.751;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,12:13:6:49,6,0 -chr1 155087 . G A 13.97 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=8.76;MQ0=18;MQRankSum=-0.736;QD=0.67;ReadPosRankSum=0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,18:21:23:42,0,23 -chr1 155148 . C T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=98;Dels=0.00;FS=2.718;HaplotypeScore=13.7215;MLEAC=1;MLEAF=0.500;MQ=23.52;MQ0=36;MQRankSum=0.569;QD=0.13;ReadPosRankSum=-1.756;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:89,8:98:41:41,0,1299 -chr1 155229 . G A 480.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.42;MQ0=12;QD=10.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:51:509,51,0 -chr1 155280 . G A 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=11.9766;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=12;MQRankSum=3.514;QD=1.38;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:118,13:131:99:209,0,2278 -chr1 155283 . G A 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=138;Dels=0.00;FS=1.657;HaplotypeScore=13.9302;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=13;MQRankSum=-1.295;QD=0.08;ReadPosRankSum=-0.289;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:125,13:138:39:39,0,2616 -chr1 155314 . T C 2942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=180;Dels=0.00;FS=0.919;HaplotypeScore=9.2358;MLEAC=1;MLEAF=0.500;MQ=31.00;MQ0=20;MQRankSum=-4.581;QD=16.35;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,153:180:99:2971,0,552 -chr1 155368 . C T 1195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=116;Dels=0.00;FS=10.244;HaplotypeScore=19.2230;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=28;MQRankSum=-3.527;QD=10.31;ReadPosRankSum=-0.904;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,89:116:99:1224,0,527 -chr1 155372 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=110;Dels=0.00;FS=21.794;HaplotypeScore=22.7736;MLEAC=1;MLEAF=0.500;MQ=26.51;MQ0=28;MQRankSum=-2.154;QD=5.63;ReadPosRankSum=-1.004;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,56:110:99:648,0,967 -chr1 155396 . T C 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=11.0107;MLEAC=1;MLEAF=0.500;MQ=20.74;MQ0=18;MQRankSum=0.787;QD=6.88;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,42:60:99:441,0,159 -chr1 155402 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.238;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=14.3324;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=15;MQRankSum=0.120;QD=0.70;ReadPosRankSum=1.919;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,7:51:64:64,0,412 -chr1 155404 . G A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.763;DP=50;Dels=0.00;FS=2.315;HaplotypeScore=14.9975;MLEAC=1;MLEAF=0.500;MQ=18.26;MQ0=14;MQRankSum=-0.535;QD=2.86;ReadPosRankSum=0.049;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:171,0,293 -chr1 155489 . G A 2696.77 . AC=2;AF=1.00;AN=2;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=54.3672;MLEAC=2;MLEAF=1.00;MQ=28.17;MQ0=15;QD=18.60;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,143:145:99:2725,270,0 -chr1 155496 . C T 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.978;DP=159;Dels=0.00;FS=16.800;HaplotypeScore=104.1353;MLEAC=1;MLEAF=0.500;MQ=28.15;MQ0=19;MQRankSum=4.281;QD=1.63;ReadPosRankSum=-1.263;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:142,17:159:99:287,0,2754 -chr1 155542 . G A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=109;Dels=0.00;FS=13.436;HaplotypeScore=10.2277;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=23;MQRankSum=3.323;QD=2.63;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:93,16:109:99:315,0,1464 -chr1 155548 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.467;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=19.0733;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=22;MQRankSum=1.496;QD=0.18;ReadPosRankSum=0.594;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:92,9:104:47:47,0,1624 -chr1 155558 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=83;Dels=0.00;FS=2.807;HaplotypeScore=16.4098;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=22;MQRankSum=-3.424;QD=6.50;ReadPosRankSum=-1.063;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,48:83:99:568,0,598 -chr1 155561 . G A 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.883;DP=74;Dels=0.00;FS=6.505;HaplotypeScore=10.4277;MLEAC=1;MLEAF=0.500;MQ=24.10;MQ0=19;MQRankSum=3.377;QD=3.31;ReadPosRankSum=0.558;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:273,0,780 -chr1 155586 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.592;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.4598;MLEAC=1;MLEAF=0.500;MQ=17.41;MQ0=15;MQRankSum=1.659;QD=0.72;ReadPosRankSum=-0.829;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,3:33:52:52,0,180 -chr1 155593 . G A 101.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.635;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=2;MLEAF=1.00;MQ=13.93;MQ0=11;MQRankSum=0.529;QD=4.39;ReadPosRankSum=-1.134;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,13:23:12:129,12,0 -chr1 155655 . A G 941.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.704;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=3.7914;MLEAC=2;MLEAF=1.00;MQ=23.15;MQ0=4;MQRankSum=1.320;QD=18.11;ReadPosRankSum=-1.065;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,48:52:74:970,74,0 -chr1 155704 . T C 886.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=23.78;MQ0=5;QD=18.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,48:48:87:915,87,0 -chr1 155711 . T C 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006;DP=48;Dels=0.00;FS=10.017;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=5;MQRankSum=-2.049;QD=6.66;ReadPosRankSum=2.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:348,0,395 -chr1 155748 . G T 107.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.97;MQ0=2;QD=6.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:136,15,0 -chr1 155814 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.84;MQ0=1;QD=6.21;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:65,9,0 -chr1 155851 . A T 60.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=11.42;MQ0=4;QD=5.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:88,12,0 -chr1 155852 . C T 60.03 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.93;MQ0=5;QD=5.00;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:88,12,0 -chr1 155921 . C T 563.77 . AC=2;AF=1.00;AN=2;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=40;QD=6.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,81:81:69:592,69,0 -chr1 156028 . T C 2144.77 . AC=2;AF=1.00;AN=2;DP=128;Dels=0.00;FS=0.000;HaplotypeScore=3.6927;MLEAC=2;MLEAF=1.00;MQ=20.13;MQ0=19;QD=16.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,124:128:99:2173,231,0 -chr1 156056 . G A 1257.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.469;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=18.35;MQ0=26;MQRankSum=0.191;QD=12.97;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:12,85:97:99:1286,109,0 -chr1 156246 . G A 1190.77 . AC=2;AF=1.00;AN=2;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=20.38;MQ0=6;QD=15.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,77:78:99:1219,129,0 -chr1 156279 . C A 10.9 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=4;QD=1.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:3:37,3,0 -chr1 156526 . A G 48.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr1 156547 . A G 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=56;Dels=0.00;FS=5.379;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.83;MQ0=1;MQRankSum=0.887;QD=14.50;ReadPosRankSum=1.631;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,999 -chr1 156554 . T G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.004;DP=67;Dels=0.00;FS=4.974;HaplotypeScore=1.7313;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=1;MQRankSum=-1.187;QD=13.74;ReadPosRankSum=2.549;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1225 -chr1 156595 . T C 2518.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;QD=29.54;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2547,190,0 -chr1 156606 . A C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.388;QD=20.16;ReadPosRankSum=2.689;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,39:67:99:1379,0,939 -chr1 156782 . C T 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=67;Dels=0.00;FS=3.401;HaplotypeScore=3.7879;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.087;QD=13.65;ReadPosRankSum=-1.036;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:943,0,1345 -chr1 156846 . T A 1011.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=63;Dels=0.00;FS=3.924;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=2;MQRankSum=0.166;QD=16.06;ReadPosRankSum=2.460;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1040,0,959 -chr1 156855 . T C 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.634;DP=65;Dels=0.00;FS=9.722;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=2;MQRankSum=-0.848;QD=17.73;ReadPosRankSum=1.937;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1181,0,930 -chr1 156873 . C A 440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.088;DP=54;Dels=0.00;FS=4.462;HaplotypeScore=1.7781;MLEAC=1;MLEAF=0.500;MQ=57.51;MQ0=2;MQRankSum=-0.709;QD=8.16;ReadPosRankSum=0.210;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:54:99:469,0,1228 -chr1 156909 . G C 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.429;DP=59;Dels=0.00;FS=5.572;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=4;MQRankSum=0.042;QD=13.79;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:842,0,823 -chr1 156944 . G A 1215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=65;Dels=0.00;FS=0.962;HaplotypeScore=1.8316;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=2;MQRankSum=-0.243;QD=18.70;ReadPosRankSum=1.160;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,37:65:99:1244,0,895 -chr1 157008 . C T 1261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=79;Dels=0.00;FS=7.743;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.24;MQ0=0;MQRankSum=1.211;QD=15.97;ReadPosRankSum=-0.240;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,39:79:99:1290,0,1323 -chr1 157051 . C T 2830.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=28.67;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I320|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2859,217,0 -chr1 157058 . G A 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=69;Dels=0.00;FS=2.053;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.597;QD=14.53;ReadPosRankSum=0.814;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E323K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 0/1:38,31:69:99:1031,0,1223 -chr1 157169 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=58;Dels=0.00;FS=2.379;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.173;QD=13.27;ReadPosRankSum=0.973;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:798,0,1053 -chr1 157239 . C T 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.399;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=14.77;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:885,0,1106 -chr1 157240 . T A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.086;QD=14.63;ReadPosRankSum=1.196;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:877,0,1125 -chr1 157275 . G A 1900.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.20;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1929,147,0 -chr1 157331 . G A 1541.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1570,117,0 -chr1 157449 . C G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.059;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=0.040;QD=18.19;ReadPosRankSum=-0.929;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1065,0,774 -chr1 157515 . T A 1070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.511;DP=64;Dels=0.00;FS=5.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.17;MQ0=0;MQRankSum=-0.839;QD=16.73;ReadPosRankSum=0.879;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1099,0,1080 -chr1 157636 . T G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.591;QD=13.12;ReadPosRankSum=0.988;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,29:71:99:960,0,1393 -chr1 157678 . C T 2841.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.8273;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=30.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2870,214,0 -chr1 157733 . T G 2546.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=1;QD=32.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2575,190,0 -chr1 157895 . A G 2244.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.96;MQ0=2;QD=30.24;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2273,169,0 -chr1 157961 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.614;DP=56;Dels=0.00;FS=2.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.124;QD=14.01;ReadPosRankSum=0.654;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:813,0,1117 -chr1 158098 . C T 10.9 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.00;MQ0=0;QD=10.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 -chr1 158261 . T A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=23.67;MQ0=3;MQRankSum=1.231;QD=5.72;ReadPosRankSum=-1.231;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,2:8:28:74,0,28 -chr1 158283 . C T 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.77;ReadPosRankSum=-1.733;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:62:62,0,105 -chr1 158288 . C T 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.898;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.3135;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.81;ReadPosRankSum=-0.898;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:64:64,0,104 -chr1 158368 . A G 424.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.21;MQ0=0;QD=32.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:453,36,0 -chr1 158427 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.660;DP=16;Dels=0.00;FS=17.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQ0=1;MQRankSum=0.505;QD=1.36;ReadPosRankSum=2.093;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,3:16:50:50,0,292 -chr1 158461 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=16;Dels=0.00;FS=11.139;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=39.10;MQ0=1;MQRankSum=-1.083;QD=0.87;ReadPosRankSum=-0.505;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,4:16:42:42,0,369 -chr1 158596 . T C 606.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.058;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.36;MQ0=5;MQRankSum=1.809;QD=18.96;ReadPosRankSum=0.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,28:32:32:635,32,0 -chr1 158745 . A G 347.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.00;MQ0=3;QD=21.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:376,33,0 -chr1 159147 . A G 38.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr1 159238 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=60.21;MQ0=0;QD=32.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2085,157,0 -chr1 159252 . G A 1542.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.28;MQ0=0;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1571,117,0 -chr1 159421 . C A 2132.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=26.0957;MLEAC=2;MLEAF=1.00;MQ=60.29;MQ0=0;QD=24.99;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2161,163,0 -chr1 159489 . A C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=35;Dels=0.00;FS=5.503;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.782;QD=9.99;ReadPosRankSum=0.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:378,0,778 -chr1 159490 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.923;DP=36;Dels=0.00;FS=5.305;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.017;QD=8.80;ReadPosRankSum=0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:345,0,811 -chr1 159582 . A C 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.531;QD=16.89;ReadPosRankSum=0.155;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,34:64:99:1109,0,986 -chr1 159628 . G A 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.490;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.246;QD=12.01;ReadPosRankSum=1.624;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:689,0,1123 -chr1 159661 . T C 1693.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1722,132,0 -chr1 159721 . T G 1542.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=1;QD=30.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1571,120,0 -chr1 159818 . G C 2039.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=58.07;MQ0=1;QD=29.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2068,157,0 -chr1 159860 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=31;Dels=0.00;FS=1.455;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=1;MQRankSum=1.161;QD=15.99;ReadPosRankSum=-0.581;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:524,0,479 -chr1 159991 . T A 2027.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2056,154,0 -chr1 160001 . G A 1962.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1991,147,0 -chr1 160043 . A G 1679.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1708,126,0 -chr1 160064 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=44;Dels=0.00;FS=4.575;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.662;QD=13.65;ReadPosRankSum=2.440;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:629,0,815 -chr1 160171 . C A 1993.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.78;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A363D|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160110_160217) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2022,156,0 -chr1 160220 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.049;DP=63;Dels=0.00;FS=8.766;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=1;MQRankSum=0.585;QD=15.46;ReadPosRankSum=0.275;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1002,0,1082 -chr1 160223 . T C 2397.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=1;QD=28.87;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,62:63:99:2426,184,0 -chr1 160312 . T C 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=0.460;QD=18.96;ReadPosRankSum=0.700;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,32:51:99:995,0,618 -chr1 160344 . G T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=1;MQRankSum=-0.844;QD=17.19;ReadPosRankSum=-1.600;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1025,0,815 -chr1 160346 . C T 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.698;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=1;MQRankSum=-1.756;QD=18.01;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1109,0,813 -chr1 160403 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=47;Dels=0.00;FS=2.597;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=0.187;QD=15.87;ReadPosRankSum=1.792;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:774,0,801 -chr1 160457 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.631;DP=50;Dels=0.00;FS=6.171;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=-1.072;QD=15.06;ReadPosRankSum=-0.691;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:781,0,825 -chr1 160628 . A G 1125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.790;DP=56;Dels=0.00;FS=3.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.486;QD=20.10;ReadPosRankSum=0.964;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1154,0,734 -chr1 160653 . T C 936.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.121;DP=49;Dels=0.00;FS=2.547;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;QD=19.12;ReadPosRankSum=1.337;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:965,0,743 -chr1 160771 . A G 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=0.483;QD=11.82;ReadPosRankSum=0.983;EFF=SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R393|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160727_160819) GT:AD:DP:GQ:PL 0/1:20,15:35:99:442,0,684 -chr1 160830 . T C 1740.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=32.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1769,129,0 -chr1 160855 . T G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.510;QD=16.59;ReadPosRankSum=0.790;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:841,0,789 -chr1 160924 . A T 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.068;DP=45;Dels=0.00;FS=4.461;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=1;MQRankSum=0.305;QD=15.66;ReadPosRankSum=2.608;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:733,0,738 -chr1 161085 . T C 995.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=50;Dels=0.00;FS=4.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.708;QD=19.92;ReadPosRankSum=0.314;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1024,0,658 -chr1 161127 . C T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.700;DP=43;Dels=0.00;FS=2.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.281;QD=14.51;ReadPosRankSum=0.159;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:652,0,837 -chr1 161227 . G A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=54;Dels=0.00;FS=1.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.588;QD=17.01;ReadPosRankSum=1.522;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M421I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161192_161296) GT:AD:DP:GQ:PL 0/1:27,27:54:99:947,0,859 -chr1 161350 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.657;DP=58;Dels=0.00;FS=2.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=1;MQRankSum=-1.366;QD=13.12;ReadPosRankSum=0.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:789,0,1101 -chr1 161518 . G T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.065;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.343;QD=20.21;ReadPosRankSum=0.639;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1079,0,713 -chr1 161550 . T G 2153.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2182,163,0 -chr1 161583 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=48;Dels=0.00;FS=1.275;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.066;QD=17.70;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:878,0,744 -chr1 161598 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.505;QD=16.36;ReadPosRankSum=-0.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:748,0,762 -chr1 161607 . G A 761.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.527;QD=16.56;ReadPosRankSum=0.154;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:790,0,787 -chr1 161743 . A C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.492;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=57.06;MQ0=1;MQRankSum=0.379;QD=15.60;ReadPosRankSum=-1.327;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K479Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,22:41:99:668,0,538 -chr1 161769 . A T 896.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=46;Dels=0.00;FS=9.187;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=1;MQRankSum=0.471;QD=19.49;ReadPosRankSum=0.172;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K487N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,27:46:99:925,0,511 -chr1 161794 . A C 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.236;DP=52;Dels=0.00;FS=10.280;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.58;MQ0=1;MQRankSum=-0.009;QD=11.69;ReadPosRankSum=-2.236;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I496L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,25:52:99:636,0,971 -chr1 161795 . T A 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.758;DP=53;Dels=0.00;FS=10.399;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=-0.513;QD=12.26;ReadPosRankSum=-2.363;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I496K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,26:53:99:678,0,963 -chr1 161822 . C T 899.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.364;DP=66;Dels=0.00;FS=11.007;HaplotypeScore=3.5506;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=1;MQRankSum=-1.119;QD=13.63;ReadPosRankSum=1.484;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P505L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:35,30:66:99:928,0,1200 -chr1 161928 . A G 1788.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.37;MQ0=0;QD=29.28;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1817,138,0 -chr1 162022 . A G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.438;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.169;QD=11.01;ReadPosRankSum=1.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:744,0,1397 -chr1 162207 . G A 2798.77 . AC=2;AF=1.00;AN=2;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.29;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,71:71:99:2827,214,0 -chr1 162353 . G C 1411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.839;QD=20.46;ReadPosRankSum=0.322;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,42:69:99:1440,0,796 -chr1 162433 . T G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.759;DP=62;Dels=0.00;FS=3.875;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.175;QD=11.56;ReadPosRankSum=0.455;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:745,0,1353 -chr1 162531 . C T 1811.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1840,141,0 -chr1 162535 . G T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=48;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.094;QD=13.18;ReadPosRankSum=0.596;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:661,0,948 -chr1 162542 . A C,T 1553.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.36;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,28,20:48:99:1782,749,665,1033,0,973 -chr1 162739 . G T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=6;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.406;QD=11.29;ReadPosRankSum=-1.537;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:6:45:96,0,45 -chr1 162750 . G T 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=8;Dels=0.00;FS=7.068;HaplotypeScore=2.9939;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.517;QD=14.97;ReadPosRankSum=-1.920;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,5:8:77:148,0,77 -chr1 162805 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.349;DP=24;Dels=0.00;FS=6.214;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.920;QD=0.91;ReadPosRankSum=0.611;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,3:24:50:50,0,779 -chr1 162820 . T C 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=28;Dels=0.00;FS=7.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.539;QD=5.78;ReadPosRankSum=-2.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:190,0,773 -chr1 162833 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.944;DP=31;Dels=0.00;FS=12.129;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.218;QD=26.80;ReadPosRankSum=0.130;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,24:31:99:859,0,157 -chr1 163107 . T C 1577.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.40;MQ0=1;QD=30.33;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1606,117,0 -chr1 163152 . G C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=54;Dels=0.00;FS=5.807;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.98;MQ0=0;MQRankSum=0.996;QD=10.96;ReadPosRankSum=-0.127;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1162 -chr1 163218 . T G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.806;QD=15.84;ReadPosRankSum=-0.456;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:820,0,917 -chr1 163281 . T A 1020.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=49;Dels=0.00;FS=5.959;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.365;QD=20.83;ReadPosRankSum=-0.133;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1049,0,617 -chr1 163602 . A T 1204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=60;Dels=0.00;FS=1.004;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.135;QD=20.08;ReadPosRankSum=-1.080;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1233,0,823 -chr1 163615 . A C 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=61;Dels=0.00;FS=0.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.905;QD=15.06;ReadPosRankSum=0.485;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:947,0,1113 -chr1 163628 . T C 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=65;Dels=0.00;FS=0.942;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.992;QD=16.09;ReadPosRankSum=0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:1074,0,1122 -chr1 163725 . C T 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=1.996;QD=17.52;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1027,0,891 -chr1 163736 . G C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-0.360;QD=17.74;ReadPosRankSum=-0.280;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1057,0,874 -chr1 163748 . T G 2436.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.15;MQ0=1;QD=33.58;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:1,62:63:99:2465,187,0 -chr1 163777 . C A 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.340;DP=58;Dels=0.00;FS=2.434;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=2;MQRankSum=0.445;QD=18.15;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1081,0,777 -chr1 163806 . C T 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=52;Dels=0.00;FS=4.176;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=0.386;QD=15.90;ReadPosRankSum=0.763;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:855,0,885 -chr1 163808 . A G 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;DP=49;Dels=0.00;FS=2.654;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=1;MQRankSum=-2.064;QD=17.10;ReadPosRankSum=0.186;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:866,0,770 -chr1 163854 . A G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-1.274;QD=13.14;ReadPosRankSum=0.742;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:646,0,892 -chr1 163894 . A C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.626;QD=14.66;ReadPosRankSum=0.011;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:688,0,813 -chr1 163957 . T A 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.596;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.570;QD=15.70;ReadPosRankSum=-1.105;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,29:61:99:986,0,1103 -chr1 163980 . A G 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=63;Dels=0.00;FS=3.778;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.763;QD=16.33;ReadPosRankSum=-1.010;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1057,0,1126 -chr1 164145 . A T 2835.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.01;MQ0=0;QD=32.13;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2864,220,0 -chr1 164203 . T G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.489;DP=77;Dels=0.00;FS=0.917;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.110;QD=13.15;ReadPosRankSum=1.352;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:44,33:77:99:1041,0,1470 -chr1 164252 . A C 1239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.049;DP=65;Dels=0.00;FS=3.361;HaplotypeScore=3.6644;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.297;QD=19.07;ReadPosRankSum=-0.284;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1268,0,967 -chr1 164282 . T G 1111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=64;Dels=0.00;FS=8.767;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.443;QD=17.37;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1140,0,1007 -chr1 164379 . G A 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.789;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.7845;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.487;QD=17.46;ReadPosRankSum=0.834;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1285,0,1107 -chr1 164466 . A T 2375.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.56;MQ0=0;QD=28.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2404,181,0 -chr1 164494 . T C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.288;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.082;QD=11.78;ReadPosRankSum=2.323;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:641,0,1102 -chr1 164861 . T C 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=68;Dels=0.00;FS=4.986;HaplotypeScore=1.9732;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.679;QD=18.48;ReadPosRankSum=-1.576;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,40:68:99:1285,0,918 -chr1 164906 . A G 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.84;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2139,163,0 -chr1 164958 . A G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.907;DP=50;Dels=0.00;FS=1.129;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.295;QD=12.86;ReadPosRankSum=-1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:671,0,981 -chr1 165095 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.531;QD=16.03;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,944 -chr1 165389 . T G 915.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=62;Dels=0.00;FS=5.213;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-2.850;QD=14.77;ReadPosRankSum=-1.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,29:62:99:944,0,1149 -chr1 165407 . C A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.847;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.97;MQ0=0;MQRankSum=-5.528;QD=13.62;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1192 -chr1 165447 . A G 873.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=5.913;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=4.271;QD=17.83;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:902,0,692 -chr1 165482 . G T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-0.596;QD=13.47;ReadPosRankSum=0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:42:99:594,0,720 -chr1 165483 . G T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.222;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-1.082;QD=15.12;ReadPosRankSum=0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,21:41:99:648,0,635 -chr1 165526 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.764;QD=21.70;ReadPosRankSum=0.631;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,30:47:99:1048,0,485 -chr1 165678 . C T 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;DP=56;Dels=0.00;FS=5.297;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.10;MQ0=0;MQRankSum=-3.048;QD=17.67;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1018,0,833 -chr1 165701 . T A 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.17;MQ0=0;MQRankSum=-1.305;QD=19.86;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1061,0,610 -chr1 165957 . G A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=42;Dels=0.00;FS=6.343;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.657;QD=17.66;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:770,0,629 -chr1 165982 . T G 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.314;DP=35;Dels=0.00;FS=1.320;HaplotypeScore=2.6981;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.007;QD=15.28;ReadPosRankSum=-0.677;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:563,0,552 -chr1 166129 . A T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.425;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.719;QD=14.24;ReadPosRankSum=2.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:612,0,716 -chr1 166135 . T G 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=40;Dels=0.00;FS=4.837;HaplotypeScore=2.7214;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.300;QD=15.12;ReadPosRankSum=1.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,714 -chr1 166157 . C T 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.204;DP=19;Dels=0.00;FS=17.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=1.592;QD=16.30;ReadPosRankSum=-0.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:9,10:19:99:338,0,285 -chr1 166165 . G A 819.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;QD=35.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:848,66,0 -chr1 166187 . T C 745.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.71;MQ0=0;QD=23.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:774,60,0 -chr1 166200 . C T 1299.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=13.5158;MLEAC=2;MLEAF=1.00;MQ=55.26;MQ0=0;QD=30.02;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1328,99,0 -chr1 166214 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.550;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.69;MQ0=0;MQRankSum=-5.017;QD=10.28;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:388,0,673 -chr1 166219 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-5.166;QD=12.70;ReadPosRankSum=-0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:498,0,722 -chr1 166226 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=35;Dels=0.00;FS=1.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-5.050;QD=14.16;ReadPosRankSum=1.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:524,0,649 -chr1 166233 . G A 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=-4.961;QD=13.89;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:556,0,691 -chr1 166248 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=-3.398;QD=13.51;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,645 -chr1 166255 . A C 437.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=13.4643;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-3.919;QD=12.88;ReadPosRankSum=2.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:466,0,539 -chr1 166256 . C T 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=35;Dels=0.00;FS=2.984;HaplotypeScore=14.4309;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-3.394;QD=13.59;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:504,0,583 -chr1 166297 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=52;Dels=0.00;FS=1.203;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-0.194;QD=19.76;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1056,0,614 -chr1 166322 . T A 1149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=19.16;ReadPosRankSum=0.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1178,0,786 -chr1 166453 . A G 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.040;DP=55;Dels=0.00;FS=9.665;HaplotypeScore=2.6999;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.583;QD=17.09;ReadPosRankSum=-2.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:968,0,816 -chr1 166585 . G A 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;DP=56;Dels=0.00;FS=2.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.945;QD=13.09;ReadPosRankSum=0.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:761,0,1060 -chr1 166654 . A T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=46;Dels=0.00;FS=4.286;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=-1.445;QD=16.45;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:785,0,700 -chr1 166658 . T G 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.864;DP=44;Dels=0.00;FS=9.040;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=-2.277;QD=15.95;ReadPosRankSum=0.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:730,0,641 -chr1 166669 . G C 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=42;Dels=0.00;FS=15.562;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=1;MQRankSum=-0.595;QD=17.68;ReadPosRankSum=-0.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:771,0,549 -chr1 166716 . A G 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.762;DP=46;Dels=0.00;FS=4.124;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=2;MQRankSum=-1.715;QD=15.93;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:761,0,715 -chr1 166733 . T G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.886;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=1.7337;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=2;MQRankSum=-1.925;QD=13.15;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:712,0,936 -chr1 166734 . G T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.213;DP=54;Dels=0.00;FS=5.816;HaplotypeScore=3.7324;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=2;MQRankSum=-2.232;QD=12.46;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:701,0,1010 -chr1 166737 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=56;Dels=0.00;FS=5.681;HaplotypeScore=4.7320;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=2;MQRankSum=-1.928;QD=11.89;ReadPosRankSum=1.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:694,0,1084 -chr1 166751 . A C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=57;Dels=0.00;FS=2.274;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=1;MQRankSum=-0.813;QD=14.42;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:850,0,1009 -chr1 166834 . G A 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=38;Dels=0.00;FS=25.349;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=0.410;QD=15.34;ReadPosRankSum=0.167;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:611,0,646 -chr1 166877 . T A 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=32;Dels=0.00;FS=21.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.083;QD=13.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:468,0,592 -chr1 166961 . T C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=32;Dels=0.00;FS=15.187;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.468;QD=8.99;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:316,0,780 -chr1 167041 . T A 743.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.8441;MLEAC=2;MLEAF=1.00;MQ=57.88;MQ0=0;QD=34.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:772,63,0 -chr1 167090 . C T 1469.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;QD=28.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1498,114,0 -chr1 167165 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1604,120,0 -chr1 167170 . A C 1602.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1631,123,0 -chr1 167208 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.357;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.870;QD=12.28;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:593,0,944 -chr1 167228 . C G 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=45;Dels=0.00;FS=2.529;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.633;QD=18.57;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:864,0,666 -chr1 167283 . A G 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.416;DP=47;Dels=0.00;FS=13.823;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.906;QD=17.55;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:853,0,735 -chr1 167363 . T A 1954.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1983,153,0 -chr1 167371 . G A 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.387;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.897;QD=17.33;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,760 -chr1 167399 . G T 890.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.694;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.632;QD=16.20;ReadPosRankSum=-0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:919,0,873 -chr1 167568 . C T 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.926;QD=14.91;ReadPosRankSum=-1.266;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:729,0,770 -chr1 167574 . G T 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.580;QD=14.26;ReadPosRankSum=-1.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:670,0,813 -chr1 167656 . G A 1543.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.41;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1572,123,0 -chr1 167672 . C G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.527;QD=11.41;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:496,0,851 -chr1 167681 . A T 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-0.635;QD=12.42;ReadPosRankSum=-1.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:649,0,985 -chr1 168087 . G A 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7985;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.503;QD=14.59;ReadPosRankSum=0.781;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:714,0,900 -chr1 168095 . G C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.150;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.112;QD=17.61;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:891,0,777 -chr1 168096 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.232;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.551;QD=14.46;ReadPosRankSum=-0.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:737,0,907 -chr1 168153 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=44;Dels=0.00;FS=6.747;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=1.608;QD=15.79;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,22:44:99:723,0,628 -chr1 168196 . G A 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=34;Dels=0.00;FS=3.353;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=0.659;QD=13.11;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:474,0,581 -chr1 168202 . G T 1401.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=39.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1430,108,0 -chr1 168341 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=58;Dels=0.00;FS=1.012;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.993;QD=13.50;ReadPosRankSum=-0.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:811,0,1056 -chr1 168360 . G T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648;DP=55;Dels=0.00;FS=2.266;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.955;QD=12.69;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:726,0,991 -chr1 168533 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=0.230;QD=11.62;ReadPosRankSum=-1.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P42L|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:21,16:37:99:458,0,718 -chr1 168548 . A T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=0.239;QD=11.20;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y47F|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:23,15:38:99:454,0,793 -chr1 168693 . T C 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.458;DP=42;Dels=0.00;FS=4.987;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=2;MQRankSum=-0.505;QD=10.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S95|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:26,15:42:99:483,0,823 -chr1 168747 . A T 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=48;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=1;MQRankSum=0.649;QD=14.06;ReadPosRankSum=-0.309;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G113|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:25,23:48:99:703,0,783 -chr1 168840 . T C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.320;DP=52;Dels=0.00;FS=5.785;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=1.858;QD=15.55;ReadPosRankSum=0.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:837,0,857 -chr1 168897 . T C 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.871;DP=57;Dels=0.00;FS=5.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.07;MQ0=0;MQRankSum=0.583;QD=14.80;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:872,0,987 -chr1 168928 . C T 2404.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=62.12;MQ0=0;QD=31.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2433,184,0 -chr1 168963 . A C 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.126;DP=70;Dels=0.00;FS=0.909;HaplotypeScore=4.3674;MLEAC=1;MLEAF=0.500;MQ=61.66;MQ0=1;MQRankSum=1.602;QD=15.61;ReadPosRankSum=0.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,35:70:99:1121,0,1161 -chr1 168974 . T C 245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=49;Dels=0.00;FS=5.429;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-4.252;QD=5.02;ReadPosRankSum=2.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:274,0,1377 -chr1 168984 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=50;Dels=0.00;FS=1.222;HaplotypeScore=2.6583;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-3.464;QD=8.06;ReadPosRankSum=1.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:431,0,1261 -chr1 169015 . C G 1930.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=1;QD=24.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1959,147,0 -chr1 169059 . T C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=48;Dels=0.00;FS=1.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=9.25;ReadPosRankSum=2.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:472,0,1188 -chr1 169061 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.503;QD=10.74;ReadPosRankSum=0.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,18:51:99:576,0,1182 -chr1 169185 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=50;Dels=0.00;FS=4.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.980;QD=11.94;ReadPosRankSum=-1.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:625,0,1008 -chr1 169348 . G T 2385.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2414,181,0 -chr1 169423 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.535;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.324;QD=14.74;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:618,0,620 -chr1 169424 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.169;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.690;QD=14.42;ReadPosRankSum=0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:605,0,616 -chr1 169456 . C G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.543;DP=47;Dels=0.00;FS=13.725;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=-1.163;QD=13.68;ReadPosRankSum=0.388;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:671,0,799 -chr1 169607 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.477;DP=58;Dels=0.00;FS=3.625;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.227;QD=14.24;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:854,0,1075 -chr1 169642 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.356;DP=58;Dels=0.00;FS=3.717;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.639;QD=14.27;ReadPosRankSum=-0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:856,0,1091 -chr1 169648 . A G 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=59;Dels=0.00;FS=5.223;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.312;QD=14.28;ReadPosRankSum=-0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:871,0,1059 -chr1 169705 . C T 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=63;Dels=0.00;FS=0.971;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.354;QD=12.92;ReadPosRankSum=0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:842,0,1216 -chr1 169719 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.216;DP=60;Dels=0.00;FS=0.971;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.529;QD=13.80;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1191 -chr1 169815 . T C 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.744;DP=85;Dels=0.00;FS=5.036;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=1;MQRankSum=-0.413;QD=6.71;ReadPosRankSum=-0.785;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:63,22:85:99:599,0,2148 -chr1 169830 . T G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;DP=82;Dels=0.00;FS=5.065;HaplotypeScore=4.3793;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=1;MQRankSum=0.781;QD=7.48;ReadPosRankSum=-0.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:58,24:82:99:642,0,1903 -chr1 169867 . A T 1602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.283;DP=92;Dels=0.00;FS=3.988;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=57.78;MQ0=0;MQRankSum=0.596;QD=17.42;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,51:92:99:1631,0,1086 -chr1 169896 . A G 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=92;Dels=0.00;FS=1.896;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-1.080;QD=8.30;ReadPosRankSum=0.557;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:792,0,2212 -chr1 169909 . A G 1909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=89;Dels=0.00;FS=2.916;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.306;QD=21.46;ReadPosRankSum=-1.499;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,54:89:99:1938,0,1053 -chr1 169968 . C T 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.404;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.734;QD=6.51;ReadPosRankSum=1.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,23:95:99:647,0,2530 -chr1 169972 . T C 2032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.409;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.407;QD=20.53;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,62:99:99:2061,0,1189 -chr1 169997 . G T 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.396;DP=92;Dels=0.00;FS=3.217;HaplotypeScore=46.8443;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=1.054;QD=7.27;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:68,24:92:99:697,0,2342 -chr1 170001 . A C 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.420;DP=93;Dels=0.00;FS=3.202;HaplotypeScore=65.8412;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.583;QD=6.35;ReadPosRankSum=-0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:619,0,2321 -chr1 170005 . T A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=62.8400;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=0.339;QD=9.09;ReadPosRankSum=1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:60,31:91:99:855,0,2167 -chr1 170011 . T A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.010;DP=90;Dels=0.00;FS=3.403;HaplotypeScore=40.8458;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.801;QD=6.26;ReadPosRankSum=0.496;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,21:90:99:592,0,2430 -chr1 170043 . G T 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=92;Dels=0.00;FS=6.914;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.005;QD=5.60;ReadPosRankSum=0.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,20:92:99:543,0,2449 -chr1 170079 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=84;Dels=0.00;FS=36.316;HaplotypeScore=155.6412;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.479;QD=3.88;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:354,0,2529 -chr1 170134 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.806;DP=84;Dels=0.00;FS=25.920;HaplotypeScore=2.3987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.915;QD=2.15;ReadPosRankSum=1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:71,13:84:99:209,0,2556 -chr1 170169 . T A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=75;Dels=0.00;FS=22.598;HaplotypeScore=2.7329;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.239;QD=2.08;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,10:75:99:184,0,2327 -chr1 170210 . A C 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=80;Dels=0.00;FS=12.034;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=-0.591;QD=11.07;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:914,0,1744 -chr1 170224 . G A 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=77;Dels=0.00;FS=12.005;HaplotypeScore=3.7332;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=1;MQRankSum=-0.353;QD=11.24;ReadPosRankSum=-0.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,29:77:99:894,0,1620 -chr1 170239 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.912;DP=71;Dels=0.00;FS=8.610;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=1;MQRankSum=-0.098;QD=11.11;ReadPosRankSum=1.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:45,26:71:99:817,0,1578 -chr1 170266 . C T 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.026;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=4.0879;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.051;QD=9.33;ReadPosRankSum=0.076;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:709,0,1696 -chr1 170289 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=2.006;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.339;QD=9.96;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:51,26:77:99:795,0,1734 -chr1 170303 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=63;Dels=0.00;FS=33.610;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.166;QD=5.60;ReadPosRankSum=2.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:381,0,1693 -chr1 170304 . A G 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=63;Dels=0.00;FS=8.306;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.545;QD=6.76;ReadPosRankSum=0.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:454,0,1606 -chr1 170360 . C T 818.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.394;DP=63;Dels=0.00;FS=0.955;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.256;QD=13.00;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:847,0,1189 -chr1 170364 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=59;Dels=0.00;FS=2.175;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=0.510;QD=14.08;ReadPosRankSum=0.936;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:859,0,1076 -chr1 170366 . C T 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=59;Dels=0.00;FS=1.010;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.234;QD=14.39;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:877,0,1076 -chr1 170381 . C T 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=59;Dels=0.00;FS=9.493;HaplotypeScore=9.7866;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.356;QD=11.00;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:677,0,1290 -chr1 170382 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=59;Dels=0.00;FS=7.433;HaplotypeScore=10.7863;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.341;QD=3.44;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:231,0,1765 -chr1 170393 . T A 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=67;Dels=0.00;FS=1.050;HaplotypeScore=21.7756;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.059;QD=12.73;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,26:67:99:881,0,961 -chr1 170403 . C A 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=68;Dels=0.00;FS=2.482;HaplotypeScore=25.9777;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.799;QD=5.08;ReadPosRankSum=0.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:374,0,1880 -chr1 170482 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=57;Dels=0.00;FS=11.052;HaplotypeScore=19.8261;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=-0.166;QD=8.54;ReadPosRankSum=0.166;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:515,0,1440 -chr1 170483 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.764;DP=54;Dels=0.00;FS=14.133;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.397;QD=9.20;ReadPosRankSum=-0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:525,0,1294 -chr1 170487 . A G 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.892;QD=3.05;ReadPosRankSum=-0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,9:56:99:199,0,1721 -chr1 170502 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=57;Dels=0.00;FS=1.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.354;QD=4.54;ReadPosRankSum=-1.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,11:57:99:287,0,1595 -chr1 170515 . G C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.903;DP=63;Dels=0.00;FS=10.967;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.124;QD=6.27;ReadPosRankSum=1.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:423,0,1617 -chr1 170578 . C G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.493;QD=8.29;ReadPosRankSum=-0.627;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,19:65:99:567,0,1665 -chr1 170582 . C T 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=65;Dels=0.00;FS=12.918;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.097;QD=7.18;ReadPosRankSum=2.829;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:495,0,1695 -chr1 170584 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=66;Dels=0.00;FS=3.389;HaplotypeScore=31.9744;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.899;QD=17.30;ReadPosRankSum=2.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1170,0,1057 -chr1 170628 . C T 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.299;DP=67;Dels=0.00;FS=2.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=0.483;QD=13.62;ReadPosRankSum=0.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:941,0,1173 -chr1 170648 . G A 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=67;Dels=0.00;FS=6.632;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=0;MQRankSum=-1.055;QD=1.77;ReadPosRankSum=1.823;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:55,12:67:99:147,0,1992 -chr1 170807 . C G 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.270;DP=63;Dels=0.00;FS=8.737;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.906;QD=13.71;ReadPosRankSum=-0.546;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:892,0,1101 -chr1 170817 . G A 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=59;Dels=0.00;FS=3.720;HaplotypeScore=21.9878;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.618;QD=13.42;ReadPosRankSum=0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,26:59:99:820,0,1062 -chr1 170849 . A T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=51;Dels=0.00;FS=13.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.123;QD=15.02;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,925 -chr1 170873 . A T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.666;DP=58;Dels=0.00;FS=17.770;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.826;QD=17.91;ReadPosRankSum=-1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1067,0,865 -chr1 170879 . G A 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.614;DP=59;Dels=0.00;FS=14.005;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.493;QD=16.74;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1016,0,929 -chr1 170937 . C G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.022;DP=60;Dels=0.00;FS=5.062;HaplotypeScore=3.7392;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=1.504;QD=15.53;ReadPosRankSum=-1.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:960,0,1076 -chr1 170995 . G T 921.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.784;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=-1.752;QD=18.44;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:950,0,694 -chr1 171012 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.147;DP=55;Dels=0.00;FS=2.354;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-2.330;QD=21.27;ReadPosRankSum=1.308;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1198,0,645 -chr1 171029 . C T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.183;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.183;QD=20.21;ReadPosRankSum=2.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,34:52:99:1079,0,514 -chr1 171034 . A G 1294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-1.803;QD=23.54;ReadPosRankSum=1.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1323,0,554 -chr1 171062 . A G 1228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=52;Dels=0.00;FS=2.506;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.024;QD=23.63;ReadPosRankSum=-0.527;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,35:52:99:1257,0,545 -chr1 171065 . C A 1210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.009;DP=51;Dels=0.00;FS=2.449;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.908;QD=23.74;ReadPosRankSum=-0.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1239,0,544 -chr1 171068 . G T 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.744;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.725;QD=23.96;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1298,0,506 -chr1 171215 . C T 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;DP=66;Dels=0.00;FS=2.128;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.155;QD=18.66;ReadPosRankSum=1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,37:66:99:1260,0,877 -chr1 171376 . A G 2221.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2250,169,0 -chr1 171546 . A T 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=52;Dels=0.00;FS=1.174;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.350;QD=17.88;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,29:52:99:958,0,752 -chr1 171611 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.465;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=15.99;ReadPosRankSum=-0.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:748,0,784 -chr1 171683 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1707,132,0 -chr1 171685 . A G 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.679;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.182;QD=15.73;ReadPosRankSum=1.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:689,0,730 -chr1 171706 . C G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=45;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.351;QD=15.73;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:736,0,753 -chr1 171990 . G T 2282.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2311,172,0 -chr1 172009 . G A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.720;DP=61;Dels=0.00;FS=11.177;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.109;QD=12.93;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:817,0,1209 -chr1 172061 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.707;DP=51;Dels=0.00;FS=18.810;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.159;QD=15.94;ReadPosRankSum=1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:841,0,812 -chr1 172078 . G A 1642.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.98;MQ0=0;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1671,129,0 -chr1 172093 . C T 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=35;Dels=0.00;FS=3.303;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=0.728;QD=22.02;ReadPosRankSum=0.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:799,0,305 -chr1 172108 . C T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.397;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=32.9713;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-1.397;QD=2.10;ReadPosRankSum=-0.826;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,7:27:85:85,0,539 -chr1 172146 . G C 1035.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aGg|T826R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1064,84,0 -chr1 172150 . T C 1050.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=25.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I825V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1079,87,0 -chr1 172178 . T C 1336.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P815|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1365,114,0 -chr1 172179 . G C 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.716;QD=12.55;ReadPosRankSum=1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P815R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:505,0,656 -chr1 172203 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.094;DP=46;Dels=0.00;FS=11.390;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-2.028;QD=12.73;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S807L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:614,0,792 -chr1 172283 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.164;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-0.747;QD=9.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G780|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,14:33:99:332,0,598 -chr1 172319 . A G 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=1;MQRankSum=0.833;QD=22.99;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S768|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,23:33:99:787,0,281 -chr1 172364 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=0.201;QD=23.02;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P753|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,26:36:99:857,0,295 -chr1 172459 . T C 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=43;Dels=0.00;FS=14.539;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=1;MQRankSum=0.000;QD=20.90;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I722V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:16,27:43:99:927,0,470 -chr1 172499 . A G 1675.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L708|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1704,129,0 -chr1 172613 . G C 2055.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=57.02;MQ0=0;QD=34.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L670|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2084,162,0 -chr1 172721 . A G 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=52;Dels=0.00;FS=10.166;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.276;QD=14.23;ReadPosRankSum=-0.958;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D634|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,23:52:99:768,0,1005 -chr1 172810 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.584;DP=54;Dels=0.00;FS=5.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=0.733;QD=10.96;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S605G|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1125 -chr1 173004 . G A 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.007;QD=16.90;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T540I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,22:41:99:721,0,631 -chr1 173180 . C T 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.132;QD=14.91;ReadPosRankSum=1.155;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S481|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:595,0,656 -chr1 173273 . A C 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.237;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.026;QD=19.10;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgG|R450|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1079,0,685 -chr1 173338 . C G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=53;Dels=0.00;FS=1.043;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.759;QD=14.54;ReadPosRankSum=-1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V429L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,24:53:99:799,0,968 -chr1 173346 . C T 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.210;QD=13.37;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G426E|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,23:54:99:750,0,981 -chr1 173348 . A G 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=12.61;ReadPosRankSum=-0.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N425|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:32,22:54:99:709,0,1099 -chr1 173405 . A G 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=42;Dels=0.00;FS=9.292;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.162;QD=12.76;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L406|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,19:42:99:564,0,777 -chr1 173410 . C T 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.566;DP=46;Dels=0.00;FS=8.606;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.794;QD=17.91;ReadPosRankSum=0.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V405I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,607 -chr1 173421 . C A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=45;Dels=0.00;FS=11.272;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.582;QD=13.37;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W401L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,20:45:99:630,0,843 -chr1 173444 . G A 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.970;QD=10.77;ReadPosRankSum=0.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I393|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,19:48:99:545,0,1014 -chr1 173446 . T C 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.885;DP=49;Dels=0.00;FS=2.535;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-1.190;QD=11.95;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I393V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,20:49:99:614,0,949 -chr1 173456 . G C 1836.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.90;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L389|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1865,141,0 -chr1 173462 . A G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=52;Dels=0.00;FS=5.860;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.951;QD=11.80;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N387|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,21:52:99:642,0,1078 -chr1 173510 . C T 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000;DP=53;Dels=0.00;FS=1.110;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=2;MQRankSum=-0.086;QD=9.45;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P371|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,23:53:99:529,0,994 -chr1 173561 . T C 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=55;Dels=0.00;FS=1.072;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=2;MQRankSum=0.864;QD=14.30;ReadPosRankSum=0.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K354|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:28,27:55:99:815,0,864 -chr1 173585 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=52;Dels=0.00;FS=2.386;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-1.379;QD=11.82;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I346|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,22:52:99:643,0,934 -chr1 173596 . C A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.149;DP=52;Dels=0.00;FS=1.065;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-0.331;QD=17.67;ReadPosRankSum=0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A343S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:947,0,721 -chr1 173627 . A G 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=52;Dels=0.00;FS=1.082;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=0.180;QD=16.84;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L332|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:904,0,775 -chr1 173642 . A T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.002;DP=46;Dels=0.00;FS=6.250;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.935;QD=13.82;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A327|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:24,22:46:99:664,0,819 -chr1 173687 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.658;QD=14.97;ReadPosRankSum=0.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G312|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,21:44:99:687,0,788 -chr1 173717 . A G 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=4.925;HaplotypeScore=1.7323;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.982;QD=17.52;ReadPosRankSum=0.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D302|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:17,19:36:99:659,0,518 -chr1 173759 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=6.309;HaplotypeScore=1.8237;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.154;QD=15.46;ReadPosRankSum=-0.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E288|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:22,21:43:99:693,0,696 -chr1 173818 . C A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.603;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-1.032;QD=15.94;ReadPosRankSum=-1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A269S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,27:50:99:825,0,741 -chr1 173846 . G A 1783.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S259|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1812,141,0 -chr1 173921 . G A 1387.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L234|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1416,105,0 -chr1 173942 . C T 1229.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=37.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S227|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1258,93,0 -chr1 173991 . T A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.550;QD=13.08;ReadPosRankSum=0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q211L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,15:35:99:486,0,659 -chr1 174026 . G T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.138;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.579;QD=14.71;ReadPosRankSum=1.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S199R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,21:42:99:646,0,703 -chr1 174172 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.056;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.622;QD=1.68;ReadPosRankSum=-3.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S151C|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:43,7:50:99:112,0,1507 -chr1 174192 . G A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-1.855;QD=3.51;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T144M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,8:45:99:186,0,1296 -chr1 174204 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.410;DP=46;Dels=0.00;FS=1.159;HaplotypeScore=5.9821;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=1.606;QD=12.86;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H140R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:620,0,865 -chr1 174214 . T G 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DP=37;Dels=0.00;FS=1.982;HaplotypeScore=7.7151;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.595;QD=1.37;ReadPosRankSum=2.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K137Q|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,5:37:79:79,0,1105 -chr1 174232 . C T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.406;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.789;QD=3.93;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G131S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,7:34:99:162,0,947 -chr1 174240 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.038;DP=32;Dels=0.00;FS=1.814;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-2.100;QD=2.99;ReadPosRankSum=0.941;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P128L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,6:32:99:124,0,917 -chr1 174248 . G A 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.044;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.194;QD=1.13;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G125|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,4:29:61:61,0,891 -chr1 174251 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-3.203;QD=0.99;ReadPosRankSum=0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q124|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,4:30:58:58,0,916 -chr1 174253 . G T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-3.037;QD=1.88;ReadPosRankSum=0.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q124K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:79:79,0,826 -chr1 174257 . G A 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-3.037;QD=1.77;ReadPosRankSum=1.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H122|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:76:76,0,816 -chr1 174272 . G A 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.316;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-3.196;QD=2.54;ReadPosRankSum=1.370;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D117|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:107,0,934 -chr1 174280 . G T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.297;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-3.218;QD=2.37;ReadPosRankSum=1.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L115M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,5:32:99:104,0,957 -chr1 174286 . G C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.671;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-3.303;QD=2.44;ReadPosRankSum=0.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L113V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:104,0,936 -chr1 174310 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.07;MQ0=0;MQRankSum=-2.399;QD=19.31;ReadPosRankSum=-1.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A105T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:11,24:35:99:704,0,322 -chr1 174313 . G C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.59;ReadPosRankSum=-0.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L104V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:50:50,0,1107 -chr1 174316 . C T 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.660;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.9900;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.56;ReadPosRankSum=-0.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V103I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:49:49,0,1123 -chr1 174328 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-2.863;QD=0.42;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V99I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:36,4:40:45:45,0,1148 -chr1 174343 . C T 49.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=0;MQRankSum=-3.088;QD=1.11;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D94N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:40,5:45:78:78,0,1238 -chr1 174344 . A C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.079;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=0;MQRankSum=3.308;QD=9.99;ReadPosRankSum=-2.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T93|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,16:45:99:478,0,949 -chr1 174366 . A G 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.432;QD=2.63;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L86P|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:178,0,1581 -chr1 174384 . G A 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=12.0923;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-4.975;QD=3.53;ReadPosRankSum=0.848;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P80L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,11:62:99:247,0,1745 -chr1 174411 . C T 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.738;QD=2.14;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C71Y|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:150,0,1746 -chr1 174419 . C T 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-4.754;QD=1.78;ReadPosRankSum=1.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R68|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:50,9:59:99:133,0,1748 -chr1 174420 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.019;DP=60;Dels=0.00;FS=1.030;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=2.493;QD=11.21;ReadPosRankSum=-0.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R68K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,23:60:99:701,0,1219 -chr1 174440 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=60;Dels=0.00;FS=3.855;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-4.283;QD=0.50;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S61|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:53,7:60:58:58,0,1883 -chr1 174476 . C T 1633.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.230;DP=51;Dels=0.00;FS=10.504;HaplotypeScore=2.3300;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=2.857;QD=32.03;ReadPosRankSum=-0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S49|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:3,48:51:40:1662,40,0 -chr1 174490 . C T 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=53;Dels=0.00;FS=8.491;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-3.764;QD=2.13;ReadPosRankSum=-0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D45N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:45,8:53:99:141,0,1535 -chr1 174501 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=50;Dels=0.00;FS=5.507;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-3.283;QD=3.02;ReadPosRankSum=-0.808;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R41H|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:41,9:50:99:179,0,1448 -chr1 174533 . C G 2385.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=25.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L30|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2414,184,0 -chr1 174565 . T C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;DP=66;Dels=0.00;FS=2.875;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=57.27;MQ0=0;MQRankSum=-1.776;QD=3.19;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T20A|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:54,11:66:99:239,0,1827 -chr1 174590 . C A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=58;Dels=0.00;FS=6.430;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.01;MQ0=0;MQRankSum=-2.077;QD=1.20;ReadPosRankSum=-0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L11F|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,7:58:98:98,0,1786 -chr1 174616 . C T 904.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.4534;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-0.293;QD=18.46;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A3T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,28:49:99:933,0,662 -chr1 174675 . G A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=42;Dels=0.00;FS=11.439;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.088;QD=15.57;ReadPosRankSum=0.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:682,0,737 -chr1 174689 . G A 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=47;Dels=0.00;FS=8.283;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-0.221;QD=14.08;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,21:47:99:690,0,836 -chr1 174766 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=2.107;QD=3.74;ReadPosRankSum=-1.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:193,0,1204 -chr1 174767 . G A 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-1.576;QD=3.65;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:189,0,1253 -chr1 174776 . G T 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=30;Dels=0.00;FS=12.809;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=1;MQRankSum=-0.811;QD=17.13;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:542,0,441 -chr1 174825 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.264;DP=30;Dels=0.00;FS=5.710;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.260;QD=18.79;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:592,0,412 -chr1 174849 . C T 503.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=9.9864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:532,39,0 -chr1 174856 . T C 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=9.9864;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=-3.069;QD=13.77;ReadPosRankSum=-2.821;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:455,0,505 -chr1 174866 . G T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=1;MQRankSum=-2.467;QD=18.28;ReadPosRankSum=-2.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:668,0,443 -chr1 174893 . G C 1410.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=27.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1439,108,0 -chr1 174896 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.059;DP=36;Dels=0.00;FS=7.563;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-1.893;QD=18.63;ReadPosRankSum=2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:699,0,483 -chr1 174908 . G A 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.143;DP=36;Dels=0.00;FS=7.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.525;QD=14.19;ReadPosRankSum=-1.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:539,0,683 -chr1 174931 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;DP=33;Dels=0.00;FS=7.712;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.630;QD=15.27;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,16:33:99:532,0,597 -chr1 174937 . T C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=33;Dels=0.00;FS=7.702;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.284;QD=14.39;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:503,0,630 -chr1 174940 . C A 1210.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1239,93,0 -chr1 174946 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.250;DP=35;Dels=0.00;FS=10.992;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.150;QD=13.19;ReadPosRankSum=0.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:490,0,676 -chr1 174949 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=37;Dels=0.00;FS=16.331;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.751;QD=13.40;ReadPosRankSum=-0.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:524,0,731 -chr1 174959 . A C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.957;DP=36;Dels=0.00;FS=23.979;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.535;QD=11.58;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:445,0,733 -chr1 174960 . G C 1421.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1450,108,0 -chr1 174965 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.564;DP=38;Dels=0.00;FS=25.258;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.777;QD=15.76;ReadPosRankSum=1.173;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:38:99:627,0,565 -chr1 175000 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=31;Dels=0.00;FS=19.167;HaplotypeScore=3.5778;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.048;QD=16.86;ReadPosRankSum=0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:551,0,513 -chr1 175050 . C T 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.635;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=-3.633;QD=11.15;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:307,0,488 -chr1 175051 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.191;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-4.077;QD=10.91;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:301,0,523 -chr1 175057 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.016;DP=23;Dels=0.00;FS=1.713;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-3.752;QD=12.08;ReadPosRankSum=1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:306,0,446 -chr1 175058 . T C 814.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:843,63,0 -chr1 175059 . A G 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;DP=24;Dels=0.00;FS=3.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.91;MQ0=0;MQRankSum=3.766;QD=15.28;ReadPosRankSum=-1.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:395,0,347 -chr1 175061 . C T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=26;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-3.944;QD=10.22;ReadPosRankSum=1.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:294,0,532 -chr1 175067 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=4.465;QD=14.78;ReadPosRankSum=1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:516,0,577 -chr1 175070 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.850;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=-4.501;QD=17.05;ReadPosRankSum=-1.284;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:591,0,501 -chr1 175078 . G T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.051;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.709;QD=17.24;ReadPosRankSum=-1.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:666,0,570 -chr1 175079 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.800;QD=17.35;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:670,0,560 -chr1 175082 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.533;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=4.587;QD=14.75;ReadPosRankSum=1.082;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:574,0,663 -chr1 175088 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.728;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.931;QD=16.17;ReadPosRankSum=-0.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:659,0,646 -chr1 175118 . A G 626.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.220;DP=33;Dels=0.00;FS=1.402;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.45;MQ0=0;MQRankSum=4.681;QD=18.99;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:655,0,376 -chr1 175131 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=32;Dels=0.00;FS=1.440;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-4.457;QD=11.06;ReadPosRankSum=1.226;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:382,0,689 -chr1 175148 . T G 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.711;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=55.44;MQ0=0;MQRankSum=-2.725;QD=1.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,3:18:50:50,0,556 -chr1 175149 . T C 617.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=34.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,17:18:48:646,48,0 -chr1 175157 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.94;ReadPosRankSum=-1.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:46:46,0,572 -chr1 175160 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.509;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.78;ReadPosRankSum=-1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:43:43,0,598 -chr1 175191 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.635;DP=24;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.412;QD=1.41;ReadPosRankSum=-1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,5:24:62:62,0,696 -chr1 175195 . A G 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=24;Dels=0.00;FS=2.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=3.341;QD=27.91;ReadPosRankSum=0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:5,19:24:71:698,0,71 -chr1 175196 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.932;DP=23;Dels=0.00;FS=2.671;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.391;QD=1.90;ReadPosRankSum=-0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,5:23:72:72,0,661 -chr1 175215 . A C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=15.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-4.028;QD=6.64;ReadPosRankSum=-0.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:201,0,652 -chr1 175251 . C T 1564.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.50;MQ0=0;QD=35.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1593,117,0 -chr1 175255 . C A 1746.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.74;MQ0=0;QD=28.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1775,132,0 -chr1 175270 . T G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.924;DP=54;Dels=0.00;FS=2.436;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-5.061;QD=12.94;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:727,0,1094 -chr1 175316 . G A 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=-3.991;QD=13.74;ReadPosRankSum=1.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:674,0,909 -chr1 175333 . A G 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=41;Dels=0.00;FS=1.298;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=-4.353;QD=11.17;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:486,0,819 -chr1 175342 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.626;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-4.498;QD=9.69;ReadPosRankSum=0.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:416,0,840 -chr1 175343 . A G 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.450;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=-4.561;QD=9.21;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:406,0,870 -chr1 175351 . C T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.893;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-4.553;QD=8.76;ReadPosRankSum=-0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:370,0,874 -chr1 175354 . T A 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.347;QD=8.35;ReadPosRankSum=-0.626;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:329,0,790 -chr1 175364 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=34;Dels=0.00;FS=1.879;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=0;MQRankSum=-4.021;QD=4.35;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:176,0,882 -chr1 175395 . C T 1069.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.59;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1098,81,0 -chr1 175462 . C T 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.111;DP=54;Dels=0.00;FS=9.949;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-4.141;QD=7.07;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:410,0,1172 -chr1 175465 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;DP=52;Dels=0.00;FS=7.479;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=50.66;MQ0=2;MQRankSum=-4.022;QD=7.53;ReadPosRankSum=-0.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,15:52:99:420,0,1104 -chr1 175476 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.975;DP=49;Dels=0.00;FS=9.035;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-4.277;QD=8.16;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:428,0,984 -chr1 175478 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.647;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-5.820;QD=8.67;ReadPosRankSum=4.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:453,0,901 -chr1 175489 . G A 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;DP=42;Dels=0.00;FS=4.393;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.18;MQ0=2;MQRankSum=-3.213;QD=10.16;ReadPosRankSum=4.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:455,0,695 -chr1 175502 . C T 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=37;Dels=0.00;FS=3.650;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=1;MQRankSum=-5.014;QD=10.10;ReadPosRankSum=3.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:402,0,770 -chr1 175510 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.695;DP=29;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=-4.339;QD=8.82;ReadPosRankSum=1.942;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:284,0,642 -chr1 175518 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.414;DP=29;Dels=0.00;FS=2.032;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=4.291;QD=21.16;ReadPosRankSum=-0.791;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:642,0,280 -chr1 175519 . T C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.728;DP=26;Dels=0.00;FS=1.927;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.53;MQ0=1;MQRankSum=-3.990;QD=6.95;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:209,0,614 -chr1 175550 . T C 868.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=0;QD=29.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:897,69,0 -chr1 175583 . C G 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.905;DP=43;Dels=0.00;FS=3.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.67;MQ0=0;MQRankSum=-4.384;QD=4.32;ReadPosRankSum=-4.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:214,0,1136 -chr1 175588 . A T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=44;Dels=0.00;FS=1.379;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-4.418;QD=4.88;ReadPosRankSum=-2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:243,0,1139 -chr1 175611 . A C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=48;Dels=0.00;FS=1.311;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-4.679;QD=4.64;ReadPosRankSum=1.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:251,0,1281 -chr1 175625 . A C 1275.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1304,99,0 -chr1 175674 . T C 812.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.22;MQ0=0;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:841,63,0 -chr1 175724 . C T 657.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.67;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:686,54,0 -chr1 175730 . G A 621.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=31.41;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:650,51,0 -chr1 175731 . A G 612.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=26.71;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:641,51,0 -chr1 175771 . A G 825.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=25.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,21:22:63:854,63,0 -chr1 175776 . G A 814.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=27.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:843,66,0 -chr1 175784 . T C 738.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.94;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:767,57,0 -chr1 175787 . G A 702.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;QD=30.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:731,54,0 -chr1 175809 . C T 591.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:620,45,0 -chr1 175815 . G T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.594;QD=0.74;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,2:15:39:39,0,491 -chr1 175833 . C A 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.203;QD=19.75;ReadPosRankSum=-1.203;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:3,6:9:88:206,0,88 -chr1 175887 . T A 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=31;Dels=0.00;FS=11.982;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=-0.104;QD=15.86;ReadPosRankSum=0.894;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:520,0,468 -chr1 175892 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=30;Dels=0.00;FS=11.831;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.240;QD=15.53;ReadPosRankSum=2.859;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:494,0,466 -chr1 175895 . T A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=30;Dels=0.00;FS=8.557;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=-0.982;QD=14.76;ReadPosRankSum=2.990;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,475 -chr1 175993 . C A 385.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.200;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=0;MQRankSum=-0.646;QD=16.77;ReadPosRankSum=0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:414,0,304 -chr1 176009 . T C 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=0.380;QD=16.09;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:350,0,229 -chr1 176036 . A T 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=21;Dels=0.00;FS=4.419;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=0.187;QD=19.32;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:7,14:21:99:434,0,213 -chr1 176049 . C T 718.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.65;MQ0=0;QD=21.77;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:747,60,0 -chr1 176097 . T G 339.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:368,30,0 -chr1 176139 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.97;MQ0=0;QD=32.45;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:912,69,0 -chr1 176158 . C G 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=26;Dels=0.00;FS=24.095;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=1.397;QD=10.95;ReadPosRankSum=-0.079;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:313,0,559 -chr1 176165 . T C 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=27;Dels=0.00;FS=25.156;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=0.979;QD=10.81;ReadPosRankSum=-0.226;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:320,0,588 -chr1 176174 . T C 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=23.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-0.381;QD=7.07;ReadPosRankSum=-0.064;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:198,0,602 -chr1 176177 . G A 905.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.96;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:934,69,0 -chr1 176195 . C T 1025.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.45;MQ0=0;QD=32.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1054,78,0 -chr1 176207 . C T 870.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=26.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:899,66,0 -chr1 176233 . C T 725.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=26.02;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:754,57,0 -chr1 176286 . G A 535.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=31.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:564,45,0 -chr1 176290 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=32.99;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:589,48,0 -chr1 176293 . G A 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=17;Dels=0.00;FS=6.117;HaplotypeScore=12.9225;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=1.642;QD=21.99;ReadPosRankSum=2.774;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:4,13:17:99:402,0,106 -chr1 176307 . T A 463.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.868;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=0;MQRankSum=-1.519;QD=28.96;ReadPosRankSum=1.519;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,15:16:9:491,9,0 -chr1 176308 . T A 420.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.556;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-2.302;QD=26.30;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:2,14:16:32:449,0,32 -chr1 176309 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=16;Dels=0.00;FS=6.317;HaplotypeScore=14.9199;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-1.637;QD=5.24;ReadPosRankSum=0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,4:16:99:112,0,330 -chr1 176346 . T A 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.960;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.11;MQ0=0;MQRankSum=-1.920;QD=5.44;ReadPosRankSum=-0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:137,0,516 -chr1 176350 . T C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440;DP=21;Dels=0.00;FS=7.501;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.68;MQ0=0;MQRankSum=0.662;QD=22.85;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:6,15:21:99:508,0,178 -chr1 176353 . T C 739.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=5.9978;MLEAC=2;MLEAF=1.00;MQ=49.68;MQ0=0;QD=24.14;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:21:60:768,60,0 -chr1 176364 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.154;DP=30;Dels=0.00;FS=6.914;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-0.110;QD=9.29;ReadPosRankSum=-0.374;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:307,0,694 -chr1 176371 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.936;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=0.363;QD=9.24;ReadPosRankSum=-0.325;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:333,0,777 -chr1 176377 . G A 1335.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.86;MQ0=0;QD=32.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1364,102,0 -chr1 176389 . G C 1302.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=55.23;MQ0=0;QD=22.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1331,99,0 -chr1 176391 . A G 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.646;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.568;QD=8.05;ReadPosRankSum=-1.273;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:294,0,820 -chr1 176394 . G A 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.255;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.333;QD=8.39;ReadPosRankSum=-0.842;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:305,0,820 -chr1 176397 . C T 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338;DP=32;Dels=0.00;FS=9.755;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=0.427;QD=8.12;ReadPosRankSum=-1.037;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:288,0,782 -chr1 176400 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=56.80;MQ0=0;QD=27.50;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1146,87,0 -chr1 176402 . T A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.647;DP=34;Dels=0.00;FS=11.168;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=0.472;QD=19.23;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,20:34:99:682,0,440 -chr1 176422 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=43;Dels=0.00;FS=10.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.013;QD=10.02;ReadPosRankSum=0.716;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:459,0,874 -chr1 176432 . G T 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=44;Dels=0.00;FS=10.793;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.275;QD=19.24;ReadPosRankSum=-0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:875,0,599 -chr1 176471 . G C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;DP=39;Dels=0.00;FS=2.886;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.520;QD=15.99;ReadPosRankSum=-0.239;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:652,0,620 -chr1 176483 . T G 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.208;DP=46;Dels=0.00;FS=2.660;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.714;QD=16.23;ReadPosRankSum=-0.022;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:775,0,731 -chr1 176494 . G A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.467;DP=44;Dels=0.00;FS=4.658;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.705;QD=17.68;ReadPosRankSum=1.292;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:806,0,667 -chr1 176561 . T C 1205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=45;Dels=0.00;FS=7.565;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=26.79;ReadPosRankSum=-1.424;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,33:45:99:1234,0,358 -chr1 176568 . G C 285.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=44;Dels=0.00;FS=5.029;HaplotypeScore=20.3301;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;QD=6.49;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:314,0,1180 -chr1 176599 . G C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.076;QD=0.94;ReadPosRankSum=-0.227;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,4:37:63:63,0,1130 -chr1 176618 . C T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=49;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.553;QD=14.46;ReadPosRankSum=-2.864;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:737,0,944 -chr1 176635 . C T 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.787;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.075;QD=13.67;ReadPosRankSum=1.784;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:657,0,863 -chr1 176661 . A T 1847.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1876,141,0 -chr1 176688 . T C 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.618;DP=44;Dels=0.00;FS=5.897;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=1;MQRankSum=-0.962;QD=18.13;ReadPosRankSum=0.110;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:826,0,625 -chr1 176698 . C T 1695.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=1;QD=32.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1724,129,0 -chr1 176733 . G A 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=32.93;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0 -chr1 176761 . A T 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=1;MQRankSum=1.449;QD=2.15;ReadPosRankSum=-2.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,3:18:67:67,0,485 -chr1 176800 . G A 390.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.42;MQ0=0;QD=30.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:419,33,0 -chr1 176848 . G T 11.83 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.90;MQ0=0;MQRankSum=0.804;QD=5.91;ReadPosRankSum=0.804;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,1:2:3:38,3,0 -chr1 177059 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.067;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.03;MQ0=24;MQRankSum=-1.333;QD=1.47;ReadPosRankSum=2.933;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,11:38:84:84,0,91 -chr1 177070 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=11.58;MQ0=27;MQRankSum=-0.689;QD=1.43;ReadPosRankSum=-2.793;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,9:39:84:84,0,91 -chr1 177088 . A C 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.599;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.40;MQ0=30;MQRankSum=0.825;QD=0.71;ReadPosRankSum=-0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,6:42:58:58,0,94 -chr1 177252 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.667;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=10.59;MQ0=35;MQRankSum=-1.333;QD=1.14;ReadPosRankSum=-1.867;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,13:49:84:84,0,91 -chr1 177401 . A C 299.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=18.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:24:328,24,0 -chr1 177522 . A C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=0;MQRankSum=-1.692;QD=19.39;ReadPosRankSum=-0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,15:25:99:513,0,327 -chr1 177533 . A C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.661;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-1.713;QD=17.07;ReadPosRankSum=-0.415;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:472,0,360 -chr1 177599 . C T 1453.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1482,111,0 -chr1 177668 . A G 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.893;QD=10.57;ReadPosRankSum=0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:430,0,785 -chr1 177672 . C G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.827;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.730;QD=11.08;ReadPosRankSum=0.438;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:427,0,755 -chr1 177673 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.730;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.990;QD=11.33;ReadPosRankSum=0.406;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:436,0,759 -chr1 177685 . C T 1270.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=40.5933;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=0;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1299,96,0 -chr1 177713 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.12;MQ0=0;MQRankSum=4.183;QD=19.34;ReadPosRankSum=0.383;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:705,0,508 -chr1 177736 . T G 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-4.078;QD=12.81;ReadPosRankSum=0.906;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:438,0,601 -chr1 177753 . T A 1468.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.25;MQ0=0;QD=28.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1497,114,0 -chr1 177771 . C T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-4.477;QD=16.37;ReadPosRankSum=0.663;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:683,0,691 -chr1 177787 . T C 1629.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=33.13;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1658,123,0 -chr1 177789 . A G 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.25;MQ0=0;MQRankSum=4.009;QD=13.47;ReadPosRankSum=1.245;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,20:46:99:648,0,869 -chr1 177795 . G T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.622;DP=44;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-1.983;QD=16.77;ReadPosRankSum=-0.270;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:766,0,709 -chr1 177797 . C T 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-2.636;QD=17.06;ReadPosRankSum=-0.595;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:762,0,706 -chr1 177814 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-2.138;QD=16.18;ReadPosRankSum=-0.047;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:740,0,797 -chr1 177863 . C A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.327;DP=44;Dels=0.00;FS=2.649;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.900;QD=18.79;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:855,0,637 -chr1 177874 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=46;Dels=0.00;FS=2.569;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.816;QD=14.93;ReadPosRankSum=-0.860;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:715,0,849 -chr1 177924 . T G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.175;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.467;QD=14.22;ReadPosRankSum=0.014;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:583,0,741 -chr1 177937 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.402;QD=13.92;ReadPosRankSum=-1.034;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:571,0,787 -chr1 177938 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.869;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.327;QD=14.73;ReadPosRankSum=-1.556;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:632,0,783 -chr1 177940 . C T 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-1.786;QD=17.81;ReadPosRankSum=1.645;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:812,0,687 -chr1 177955 . T C 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.014;QD=20.06;ReadPosRankSum=0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,28:48:99:991,0,659 -chr1 177959 . T G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=49;Dels=0.00;FS=1.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.359;QD=12.16;ReadPosRankSum=0.544;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:624,0,1063 -chr1 177983 . A G 1899.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.4892;MLEAC=2;MLEAF=1.00;MQ=59.77;MQ0=0;QD=26.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1928,144,0 -chr1 177992 . G A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.388;QD=17.00;ReadPosRankSum=0.466;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:878,0,780 -chr1 178064 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.137;QD=14.80;ReadPosRankSum=-0.229;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:576,0,654 -chr1 178089 . G C 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.777;DP=34;Dels=0.00;FS=3.270;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=1;MQRankSum=-0.777;QD=17.73;ReadPosRankSum=0.235;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:631,0,457 -chr1 178121 . C A 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=41;Dels=0.00;FS=1.294;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=-1.035;QD=19.46;ReadPosRankSum=0.676;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:826,0,488 -chr1 178255 . T C 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.918;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.153;QD=11.21;ReadPosRankSum=1.458;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:387,0,613 -chr1 178259 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.469;DP=29;Dels=0.00;FS=1.449;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.329;QD=13.89;ReadPosRankSum=1.206;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:431,0,537 -chr1 178261 . T A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.066;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.460;QD=12.41;ReadPosRankSum=1.250;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:388,0,533 -chr1 178263 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.963;DP=30;Dels=0.00;FS=1.484;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.879;QD=13.29;ReadPosRankSum=1.549;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,13:30:99:427,0,582 -chr1 178287 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.465;QD=12.47;ReadPosRankSum=-0.575;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:340,0,480 -chr1 178289 . G C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.205;QD=11.87;ReadPosRankSum=-0.263;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,481 -chr1 178299 . A T 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=23;Dels=0.00;FS=1.674;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.403;QD=11.42;ReadPosRankSum=-0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:291,0,437 -chr1 178322 . G A 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.414;DP=26;Dels=0.00;FS=5.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.723;QD=14.53;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:406,0,467 -chr1 178360 . A G 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=39;Dels=0.00;FS=9.536;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.169;QD=13.33;ReadPosRankSum=0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:548,0,674 -chr1 178364 . T A 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=42;Dels=0.00;FS=6.822;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.639;QD=13.02;ReadPosRankSum=0.928;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:575,0,786 -chr1 178390 . A G 1140.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=43.1047;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.62;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1169,87,0 -chr1 178393 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=32.4731;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.88;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1204,90,0 -chr1 178400 . G A 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;QD=26.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1209,93,0 -chr1 178402 . A C 1294.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=58.02;MQ0=0;QD=27.35;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1323,99,0 -chr1 178406 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=3.905;QD=16.45;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:637,0,616 -chr1 178418 . C T 1535.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.98;MQ0=0;QD=29.23;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1564,117,0 -chr1 178431 . A G 1627.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.75;MQ0=0;QD=31.86;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1656,123,0 -chr1 178470 . C T 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=34;Dels=0.00;FS=2.928;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-2.467;QD=17.46;ReadPosRankSum=-1.570;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:622,0,545 -chr1 178476 . G T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.884;QD=8.63;ReadPosRankSum=1.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,611 -chr1 178477 . A G 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.269;DP=26;Dels=0.00;FS=1.596;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.910;QD=9.80;ReadPosRankSum=0.701;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:283,0,607 -chr1 178478 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.466;QD=8.11;ReadPosRankSum=1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:231,0,607 -chr1 178481 . A G 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.408;QD=8.63;ReadPosRankSum=1.486;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,606 -chr1 178485 . T C 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.141;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.540;QD=11.53;ReadPosRankSum=0.329;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:351,0,575 -chr1 178493 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-2.900;QD=12.23;ReadPosRankSum=1.207;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,593 -chr1 178499 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.953;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.630;QD=12.23;ReadPosRankSum=1.503;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,603 -chr1 178504 . A G 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=28;Dels=0.00;FS=1.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.019;QD=13.17;ReadPosRankSum=0.998;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:397,0,533 -chr1 178548 . T C 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.026;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.451;QD=11.14;ReadPosRankSum=-0.975;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:318,0,550 -chr1 178628 . A G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.831;DP=38;Dels=0.00;FS=1.378;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-1.015;QD=9.68;ReadPosRankSum=0.708;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:396,0,801 -chr1 178641 . T C 1162.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.07;MQ0=0;QD=31.81;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1191,93,0 -chr1 178645 . G T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=31;Dels=0.00;FS=1.525;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.35;MQ0=0;MQRankSum=-0.152;QD=7.54;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:262,0,672 -chr1 178672 . T C 271.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=27.18;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:300,24,0 -chr1 178673 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=26.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:298,24,0 -chr1 178709 . G A 304.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.04;MQ0=3;QD=19.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:333,30,0 -chr1 178719 . T C 176.84 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.41;MQ0=3;QD=14.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,12:12:18:205,18,0 -chr1 178740 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.796;DP=26;Dels=0.00;FS=6.166;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.19;MQ0=11;MQRankSum=-1.408;QD=1.41;ReadPosRankSum=-0.674;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,8:26:65:65,0,324 -chr1 178796 . T C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.153;DP=25;Dels=0.00;FS=6.726;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.15;MQ0=9;MQRankSum=0.404;QD=2.11;ReadPosRankSum=2.153;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,10:25:81:81,0,383 -chr1 178979 . T C 232.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.041;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.286;QD=12.25;ReadPosRankSum=-0.041;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,9:19:99:261,0,334 -chr1 179063 . T A 690.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:719,54,0 -chr1 179198 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.885;DP=40;Dels=0.00;FS=9.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=3;MQRankSum=4.522;QD=12.94;ReadPosRankSum=2.437;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:546,0,642 -chr1 179200 . A T 1439.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.25;MQ0=3;QD=28.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1468,108,0 -chr1 179320 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=4.336;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-0.475;QD=15.77;ReadPosRankSum=0.578;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:785,0,835 -chr1 179364 . T G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.428;DP=58;Dels=0.00;FS=7.156;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.284;QD=17.29;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1031,0,933 -chr1 179397 . G T 2003.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.90;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2032,147,0 -chr1 179511 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=55;Dels=0.00;FS=1.064;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=1.179;QD=14.23;ReadPosRankSum=1.655;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:811,0,1053 -chr1 179518 . C T 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.855;QD=5.68;ReadPosRankSum=-0.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:318,0,1406 -chr1 179542 . C T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.582;DP=59;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.05;MQ0=0;MQRankSum=2.112;QD=5.64;ReadPosRankSum=-0.814;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:361,0,1612 -chr1 179564 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=67;Dels=0.00;FS=6.477;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.831;QD=16.70;ReadPosRankSum=-0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,34:67:99:1147,0,1135 -chr1 179583 . T C 2571.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=0;QD=33.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2600,193,0 -chr1 179617 . A T 2299.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.562;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;MQRankSum=1.392;QD=28.69;ReadPosRankSum=0.085;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,60:61:99:2328,144,0 -chr1 179762 . G A 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=51;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.21;MQ0=0;MQRankSum=-1.618;QD=18.31;ReadPosRankSum=-0.407;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:962,0,770 -chr1 179884 . G C 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=28;Dels=0.00;FS=4.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.47;MQ0=0;MQRankSum=-1.658;QD=11.03;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:337,0,516 -chr1 179951 . C T 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.506;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=61.42;MQ0=0;MQRankSum=-2.488;QD=11.47;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:579,0,987 -chr1 180063 . G T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.238;QD=18.63;ReadPosRankSum=-0.015;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1146,0,891 -chr1 180136 . T A 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.350;QD=16.88;ReadPosRankSum=-0.012;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:754,0,646 -chr1 180164 . C T 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.143;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.075;QD=14.02;ReadPosRankSum=1.546;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:687,0,853 -chr1 180372 . A C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.314;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=-1.285;QD=16.26;ReadPosRankSum=0.671;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:646,0,633 -chr1 180419 . G T 1311.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=8.9974;MLEAC=2;MLEAF=1.00;MQ=58.26;MQ0=0;QD=32.14;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1340,102,0 -chr1 180460 . G A 1379.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=1;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1408,105,0 -chr1 180463 . T A 537.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.550;DP=35;Dels=0.00;FS=1.423;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=1;MQRankSum=2.273;QD=15.36;ReadPosRankSum=-0.517;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:566,0,578 -chr1 180470 . G C 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=36;Dels=0.00;FS=1.373;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=3.571;QD=16.24;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,18:36:99:613,0,506 -chr1 180531 . A C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=1;MQRankSum=0.486;QD=16.20;ReadPosRankSum=-0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:579,0,522 -chr1 180557 . C G 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=1;QD=32.27;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1209,90,0 -chr1 180708 . G A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=24;Dels=0.00;FS=4.269;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.223;QD=24.12;ReadPosRankSum=0.953;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S43N|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:7,17:24:99:607,0,206 -chr1 180728 . A G 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.774;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.437;QD=9.58;ReadPosRankSum=-0.489;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R50G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:18,9:27:99:287,0,626 -chr1 180746 . C T 1097.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P56S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1126,90,0 -chr1 180749 . T C 1103.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=26.57;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C57R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1132,87,0 -chr1 180758 . C T 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=25;Dels=0.00;FS=13.757;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.027;QD=12.87;ReadPosRankSum=1.068;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L60F|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:14,11:25:99:350,0,458 -chr1 181012 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.249;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.6617;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.626;QD=23.03;ReadPosRankSum=-0.542;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,20:29:99:696,0,216 -chr1 181024 . C A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.742;QD=20.41;ReadPosRankSum=1.506;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:620,0,319 -chr1 181102 . T G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=33;Dels=0.00;FS=3.837;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.862;QD=17.27;ReadPosRankSum=0.560;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:598,0,487 -chr1 181156 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.560;QD=12.49;ReadPosRankSum=-0.429;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,10:22:99:303,0,376 -chr1 181173 . A C 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=15;Dels=0.00;FS=3.256;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.59;MQ0=0;MQRankSum=0.884;QD=11.45;ReadPosRankSum=-0.648;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:200,0,268 -chr1 181194 . A G 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=19;Dels=0.00;FS=2.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=2.149;QD=7.51;ReadPosRankSum=-2.850;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:171,0,426 -chr1 181230 . T A 1286.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=31.97;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1315,96,0 -chr1 181244 . G T 1304.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.89;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1333,99,0 -chr1 181276 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=-0.905;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,13:36:99:431,0,793 -chr1 181325 . G C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=2.299;HaplotypeScore=1.8279;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=-1.711;QD=9.16;ReadPosRankSum=0.678;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:239,0,509 -chr1 181330 . A G 904.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.8279;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:933,72,0 -chr1 181337 . A G 906.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=56.47;MQ0=0;QD=29.13;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:935,72,0 -chr1 181340 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.025;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=56.31;MQ0=0;MQRankSum=-1.259;QD=11.87;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,471 -chr1 181363 . C T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.002;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.743;QD=9.21;ReadPosRankSum=0.936;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:240,0,515 -chr1 181373 . C G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.033;DP=23;Dels=0.00;FS=3.982;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.033;QD=8.99;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:235,0,521 -chr1 181378 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.646;DP=23;Dels=0.00;FS=4.200;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=3.647;QD=19.64;ReadPosRankSum=-1.130;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:480,0,235 -chr1 181389 . T G 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.52;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:682,54,0 -chr1 181394 . T C 708.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=29.42;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:737,57,0 -chr1 181400 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=29.72;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:715,54,0 -chr1 181432 . C T 663.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.63;MQ0=0;QD=28.65;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:692,51,0 -chr1 181520 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.692;DP=35;Dels=0.00;FS=3.290;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=2;MQRankSum=-3.125;QD=7.62;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:295,0,721 -chr1 181569 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.437;DP=41;Dels=0.00;FS=11.992;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.50;MQ0=0;MQRankSum=-0.807;QD=11.26;ReadPosRankSum=0.463;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:490,0,840 -chr1 181583 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=39;Dels=0.00;FS=8.484;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-1.317;QD=12.25;ReadPosRankSum=1.827;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:506,0,762 -chr1 181595 . G A 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=37;Dels=0.00;FS=9.049;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-1.322;QD=14.13;ReadPosRankSum=0.319;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:551,0,655 -chr1 181616 . A G 1243.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.37;MQ0=0;QD=26.17;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1272,96,0 -chr1 181649 . A G 871.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.28;MQ0=0;QD=28.35;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:900,72,0 -chr1 181678 . C A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.180;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=11.4067;MLEAC=1;MLEAF=0.500;MQ=54.06;MQ0=0;MQRankSum=-0.467;QD=4.27;ReadPosRankSum=2.335;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,3:14:88:88,0,315 -chr1 181750 . T C 1735.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=2;MLEAF=1.00;MQ=61.04;MQ0=0;QD=29.40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L98S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1764,132,0 -chr1 181932 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.890;DP=42;Dels=0.00;FS=2.883;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=0;MQRankSum=-0.630;QD=20.26;ReadPosRankSum=0.577;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C159R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:15,27:42:99:879,0,440 -chr1 182026 . T G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=1.966;QD=13.51;ReadPosRankSum=0.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L190R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,608 -chr1 182058 . G C 1193.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=29.48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V201L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1222,93,0 -chr1 182100 . A G 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.141;DP=37;Dels=0.00;FS=16.118;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=2.302;QD=20.29;ReadPosRankSum=-0.955;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R215G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:14,23:37:99:779,0,366 -chr1 182108 . G A 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=39;Dels=0.00;FS=10.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.794;QD=9.92;ReadPosRankSum=0.188;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S217|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:24,15:39:99:415,0,775 -chr1 182195 . C A 1439.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=30.91;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I246|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1468,111,0 -chr1 182198 . G A 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.182;QD=17.62;ReadPosRankSum=0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L247|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:16,19:35:99:645,0,523 -chr1 182199 . A T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.475;QD=17.35;ReadPosRankSum=0.792;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M248L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:17,19:36:99:653,0,531 -chr1 182231 . G A 1226.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;QD=29.57;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A258|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:96:1255,96,0 -chr1 182291 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.930;DP=43;Dels=0.00;FS=26.079;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.032;QD=9.86;ReadPosRankSum=-0.828;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V278|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:28,15:43:99:452,0,940 -chr1 182317 . C T 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=43;Dels=0.00;FS=22.687;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-0.239;QD=11.09;ReadPosRankSum=1.018;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:505,0,912 -chr1 182395 . C T 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.875;DP=36;Dels=0.00;FS=3.014;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.462;QD=13.88;ReadPosRankSum=-2.786;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:528,0,655 -chr1 182404 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=42;Dels=0.00;FS=1.218;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=0.834;QD=17.09;ReadPosRankSum=0.430;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),SPLICE_SITE_ACCEPTOR(HIGH||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:746,0,627 -chr1 182424 . G A 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.760;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.738;QD=17.82;ReadPosRankSum=0.952;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A287|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:21,26:47:99:866,0,703 -chr1 182545 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.911;DP=38;Dels=0.00;FS=1.257;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.986;QD=11.26;ReadPosRankSum=-1.015;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V328I|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:23,15:38:99:456,0,764 -chr1 182610 . A G 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-2.012;QD=10.40;ReadPosRankSum=1.873;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:382,0,506 -chr1 182637 . T C 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.289;DP=36;Dels=0.00;FS=8.730;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=-2.372;QD=17.99;ReadPosRankSum=1.735;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:676,0,448 -chr1 182641 . T C 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=38;Dels=0.00;FS=13.898;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=-2.511;QD=14.86;ReadPosRankSum=2.365;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:593,0,579 -chr1 182646 . A G,T 974.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.03;MQ0=0;QD=27.06;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/2:0,18,18:36:99:1162,642,594,520,0,465 -chr1 182648 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.525;DP=35;Dels=0.00;FS=17.460;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.723;QD=15.34;ReadPosRankSum=2.228;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:565,0,436 -chr1 182657 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=46;Dels=0.00;FS=7.638;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.778;QD=18.06;ReadPosRankSum=-1.934;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:859,0,438 -chr1 182668 . T C 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.640;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=5.9516;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.805;QD=14.92;ReadPosRankSum=-0.685;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:774,0,262 -chr1 182674 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=30.8083;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=-4.923;QD=15.46;ReadPosRankSum=-1.147;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,27:47:99:755,0,282 -chr1 182714 . G A 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=56.43;MQ0=0;QD=25.68;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,172,0 -chr1 182756 . A G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=40;Dels=0.00;FS=6.474;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.783;QD=5.17;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,9:40:99:235,0,1016 -chr1 182758 . G A 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.359;DP=40;Dels=0.00;FS=9.072;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-1.078;QD=5.67;ReadPosRankSum=0.672;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:255,0,986 -chr1 182775 . T G 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=44;Dels=0.00;FS=3.185;HaplotypeScore=2.9961;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.227;QD=11.61;ReadPosRankSum=-2.232;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:539,0,817 -chr1 182800 . A T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=41;Dels=0.00;FS=1.435;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.552;QD=14.73;ReadPosRankSum=0.039;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:632,0,657 -chr1 182818 . G T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.464;QD=16.27;ReadPosRankSum=1.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A353S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:565,0,472 -chr1 182821 . T G 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4440;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.284;QD=15.90;ReadPosRankSum=1.392;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S354A|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:553,0,504 -chr1 182977 . A G 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=61;Dels=0.00;FS=1.012;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.470;QD=13.67;ReadPosRankSum=1.411;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I406V|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:33,28:61:99:862,0,1096 -chr1 183001 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.024;DP=56;Dels=0.00;FS=2.198;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=1.958;QD=15.73;ReadPosRankSum=0.156;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L414|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:28,28:56:99:909,0,927 -chr1 183099 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.462;QD=15.10;ReadPosRankSum=-1.154;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L446|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:723,0,679 -chr1 183112 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-1.631;QD=13.93;ReadPosRankSum=-1.738;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S451C|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:683,0,847 -chr1 183122 . A G 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.754;DP=49;Dels=0.00;FS=6.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.010;QD=14.34;ReadPosRankSum=-1.538;EFF=SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*454|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:731,0,933 -chr1 183134 . G C 1853.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=19.9966;MLEAC=2;MLEAF=1.00;MQ=59.84;MQ0=0;QD=28.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1882,141,0 -chr1 183164 . G A 1985.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=23.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2014,153,0 -chr1 183180 . A T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=53;Dels=0.00;FS=2.623;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=-0.670;QD=13.92;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:766,0,944 -chr1 183192 . C T 1829.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=4.4532;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=33.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1858,150,0 -chr1 183206 . C T 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=47;Dels=0.00;FS=2.919;HaplotypeScore=3.7882;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.613;QD=12.29;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:606,0,947 -chr1 183210 . C A 1916.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1945,147,0 -chr1 183264 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=38;Dels=0.00;FS=1.237;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-2.646;QD=15.47;ReadPosRankSum=0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:616,0,690 -chr1 183410 . C A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.9453;MLEAC=1;MLEAF=0.500;MQ=55.82;MQ0=0;MQRankSum=-1.739;QD=4.72;ReadPosRankSum=-2.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:184,0,765 -chr1 183443 . G A 1009.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=0;QD=27.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1038,81,0 -chr1 183460 . C T 838.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:867,69,0 -chr1 183464 . G A 858.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=29.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:887,69,0 -chr1 183493 . C A 473.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.39;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:502,39,0 -chr1 183509 . A G 339.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.00;MQ0=1;QD=28.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:368,30,0 -chr1 183531 . G A 267.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.51;MQ0=1;QD=26.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:296,24,0 -chr1 183542 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=6.6549;MLEAC=2;MLEAF=1.00;MQ=39.61;MQ0=1;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:266,21,0 -chr1 183564 . G A 265.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:294,24,0 -chr1 183568 . A G 273.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:302,24,0 -chr1 183569 . C T 272.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:301,24,0 -chr1 183580 . G T 378.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.45;MQ0=1;QD=23.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:407,33,0 -chr1 183601 . C T 413.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:442,36,0 -chr1 183602 . G C 414.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:443,36,0 -chr1 183606 . C T 458.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.57;MQ0=0;QD=25.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:39:487,39,0 -chr1 183618 . C T 490.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.82;MQ0=0;QD=25.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:519,42,0 -chr1 183623 . A G 484.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.91;MQ0=1;QD=24.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:42:513,42,0 -chr1 183645 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=1;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,21:21:48:589,48,0 -chr1 183881 . T C 84.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.25;MQ0=1;QD=14.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:112,12,0 -chr1 184039 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=17;Dels=0.00;FS=11.761;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=14.06;MQ0=10;MQRankSum=1.300;QD=3.87;ReadPosRankSum=1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:12,5:17:39:94,0,39 -chr1 184048 . G A 68.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;DP=14;Dels=0.00;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.98;MQ0=8;MQRankSum=0.000;QD=4.91;ReadPosRankSum=1.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,6:14:25:97,0,25 -chr1 184262 . G A 35.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.39;MQ0=0;QD=17.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:63,6,0 -chr1 184325 . T A 368.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:397,30,0 -chr1 184366 . G T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.495;DP=7;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=-1.495;QD=2.41;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,2:7:45:45,0,172 -chr1 184384 . T A 250.8 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.83;MQ0=0;QD=27.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,9:9:21:279,21,0 -chr1 184401 . T C 297.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:326,24,0 -chr1 184419 . C T 459.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.09;MQ0=0;QD=32.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,14:14:36:488,36,0 -chr1 184437 . A C 589.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:618,45,0 -chr1 184457 . T A 615.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=57.14;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:644,48,0 -chr1 184511 . A G 177.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:206,15,0 -chr1 184520 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:154,12,0 -chr1 184712 . A G 14.68 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.76;MQ0=5;MQRankSum=0.804;QD=2.10;ReadPosRankSum=0.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:6,1:7:3:41,3,0 -chr1 184812 . C T 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.740;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=1.849;QD=22.60;ReadPosRankSum=-2.589;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,9:13:24:322,24,0 -chr1 184813 . G A 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.382;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-2.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,8:13:24:322,24,0 -chr1 184816 . T C 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.106;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-0.978;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:3,8:13:24:322,24,0 -chr1 184870 . C G 77.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:105,9,0 -chr1 184877 . A C 110.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.51;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:138,12,0 -chr1 184924 . T C 381.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.07;MQ0=0;QD=34.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:410,33,0 -chr1 184928 . A G 414.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.28;MQ0=0;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:443,36,0 -chr1 184947 . T C 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.40;MQ0=0;QD=29.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0 -chr1 184967 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.750;DP=26;Dels=0.00;FS=4.435;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.68;MQ0=0;MQRankSum=-3.139;QD=6.91;ReadPosRankSum=-2.639;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:208,0,643 -chr1 184971 . G C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=27;Dels=0.00;FS=6.965;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.77;MQ0=0;MQRankSum=-3.060;QD=8.84;ReadPosRankSum=-1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,9:27:99:267,0,627 -chr1 184992 . C A 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=30;Dels=0.00;FS=3.779;HaplotypeScore=7.2988;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=0;MQRankSum=-3.443;QD=10.59;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:346,0,566 -chr1 184999 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.172;DP=36;Dels=0.00;FS=2.798;HaplotypeScore=2.3001;MLEAC=1;MLEAF=0.500;MQ=57.43;MQ0=0;MQRankSum=-2.789;QD=16.38;ReadPosRankSum=-2.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:618,0,532 -chr1 185038 . A T 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=37;Dels=0.00;FS=5.015;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-0.820;QD=19.32;ReadPosRankSum=2.088;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:743,0,477 -chr1 185039 . T A 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=39;Dels=0.00;FS=4.649;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.736;QD=11.46;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:475,0,785 -chr1 185068 . A T 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.341;DP=40;Dels=0.00;FS=6.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=1.559;QD=19.29;ReadPosRankSum=0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:800,0,540 -chr1 185070 . C G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.801;QD=18.68;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:794,0,571 -chr1 185084 . C A 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=41;Dels=0.00;FS=6.934;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.781;QD=18.95;ReadPosRankSum=-0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:805,0,519 -chr1 185087 . G A 1558.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;QD=32.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1587,120,0 -chr1 185096 . A G 492.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=37;Dels=0.00;FS=5.209;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.383;QD=13.32;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:521,0,697 -chr1 185113 . T C 1279.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=28.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1308,99,0 -chr1 185114 . G A 1207.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1236,93,0 -chr1 185129 . C A 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.123;DP=36;Dels=0.00;FS=2.788;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.459;QD=15.88;ReadPosRankSum=0.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:600,0,584 -chr1 185138 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656;DP=37;Dels=0.00;FS=1.289;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=1.595;QD=14.70;ReadPosRankSum=-0.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:572,0,645 -chr1 185141 . G A 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-1.139;QD=15.31;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:564,0,590 -chr1 185145 . G T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.115;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.139;QD=14.36;ReadPosRankSum=0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:502,0,598 -chr1 185186 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.484;DP=37;Dels=0.00;FS=1.280;HaplotypeScore=19.3302;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.960;QD=16.40;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:635,0,578 -chr1 185222 . T A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.397;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.101;QD=16.48;ReadPosRankSum=1.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:770,0,755 -chr1 185241 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.103;QD=15.31;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:763,0,865 -chr1 185245 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.619;QD=15.29;ReadPosRankSum=-0.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:762,0,868 -chr1 185259 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=49;Dels=0.00;FS=2.460;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.136;QD=13.95;ReadPosRankSum=-0.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:712,0,900 -chr1 185264 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.367;DP=52;Dels=0.00;FS=1.072;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-1.606;QD=14.51;ReadPosRankSum=-1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:783,0,962 -chr1 185289 . C T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-1.022;QD=12.65;ReadPosRankSum=-0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:623,0,933 -chr1 185299 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=16.4921;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=-2.184;QD=11.52;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:535,0,917 -chr1 185346 . C T 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=33;Dels=0.00;FS=8.695;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-3.050;QD=9.45;ReadPosRankSum=1.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:340,0,747 -chr1 185347 . A G 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=33;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.826;QD=10.57;ReadPosRankSum=1.890;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:377,0,759 -chr1 185372 . T C 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=29;Dels=0.00;FS=17.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-4.382;QD=8.51;ReadPosRankSum=0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:275,0,692 -chr1 185376 . C G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.478;DP=28;Dels=0.00;FS=21.622;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=5.49;ReadPosRankSum=1.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:182,0,778 -chr1 185383 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=28;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.24;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:147,0,783 -chr1 185387 . A G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.478;DP=28;Dels=0.00;FS=19.859;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.81;ReadPosRankSum=0.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:163,0,736 -chr1 185394 . A C 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=27;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-3.703;QD=4.25;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:143,0,783 -chr1 185401 . T A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.242;DP=29;Dels=0.00;FS=15.529;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-3.742;QD=3.85;ReadPosRankSum=-0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,6:29:99:140,0,846 -chr1 185407 . C T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=23;Dels=0.00;FS=6.628;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-2.784;QD=0.86;ReadPosRankSum=-2.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,3:23:48:48,0,737 -chr1 185480 . G A 732.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:761,57,0 -chr1 185486 . C T 684.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=29.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:713,54,0 -chr1 185509 . T C 606.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.65;MQ0=0;QD=28.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:635,48,0 -chr1 185547 . C T 637.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.964;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=-1.156;QD=24.50;ReadPosRankSum=1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,17:18:14:666,14,0 -chr1 185642 . A T 574.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.69;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:603,45,0 -chr1 185689 . A C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.167;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.58;MQ0=1;MQRankSum=-2.906;QD=7.24;ReadPosRankSum=-1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,8:24:99:202,0,578 -chr1 185691 . T G 889.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=1;QD=27.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:918,69,0 -chr1 185717 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=33;Dels=0.00;FS=3.365;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=1;MQRankSum=-1.880;QD=10.51;ReadPosRankSum=0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:375,0,665 -chr1 185726 . G C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=39;Dels=0.00;FS=4.887;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=-2.190;QD=15.22;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:622,0,634 -chr1 185747 . A T 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-1.881;QD=20.81;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:923,0,453 -chr1 185776 . A G 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.350;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=1;MQRankSum=-1.287;QD=22.38;ReadPosRankSum=2.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,28:39:99:901,0,314 -chr1 185800 . C T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.468;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.9825;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=1;MQRankSum=-0.406;QD=25.35;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,23:28:89:738,0,89 -chr1 185804 . T G 590.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=28;Dels=0.00;FS=8.073;HaplotypeScore=5.6476;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=1;MQRankSum=1.135;QD=21.10;ReadPosRankSum=0.436;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:3,22:28:16:690,0,16 -chr1 185818 . T G 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=24;Dels=0.00;FS=2.570;HaplotypeScore=2.9824;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=1;MQRankSum=1.176;QD=24.03;ReadPosRankSum=-0.852;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:4,20:24:53:605,0,53 -chr1 186025 . A C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9066;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=4.46;ReadPosRankSum=1.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,2:4:46:46,0,47 -chr1 186043 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=38;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.26;MQ0=5;MQRankSum=-1.963;QD=15.02;ReadPosRankSum=-2.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:599,0,549 -chr1 186058 . T A 1383.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.62;MQ0=5;QD=34.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1412,105,0 -chr1 186081 . A G 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-0.474;QD=15.86;ReadPosRankSum=2.879;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:710,0,742 -chr1 186083 . T A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=2.928;QD=16.48;ReadPosRankSum=-2.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:737,0,714 -chr1 186128 . C G 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=19.8272;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.043;QD=12.22;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,16:39:99:505,0,805 -chr1 186204 . A T 1634.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=52.86;MQ0=7;QD=30.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1663,126,0 -chr1 186205 . G C 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=52;Dels=0.00;FS=2.716;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=7;MQRankSum=0.198;QD=8.55;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,19:52:99:473,0,903 -chr1 186248 . C T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=39;Dels=0.00;FS=2.991;HaplotypeScore=12.5646;MLEAC=1;MLEAF=0.500;MQ=51.44;MQ0=4;MQRankSum=-0.750;QD=13.92;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:571,0,491 -chr1 186252 . T C 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=38;Dels=0.00;FS=1.412;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=52.11;MQ0=3;MQRankSum=-1.250;QD=14.41;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:576,0,472 -chr1 186263 . T C 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=45;Dels=0.00;FS=1.264;HaplotypeScore=23.4286;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=2.794;QD=10.37;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:495,0,824 -chr1 186273 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=50;Dels=0.00;FS=8.671;HaplotypeScore=22.6968;MLEAC=1;MLEAF=0.500;MQ=55.43;MQ0=1;MQRankSum=3.184;QD=12.62;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:659,0,894 -chr1 186302 . T C 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=49;Dels=0.00;FS=5.993;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.254;QD=19.63;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:990,0,585 -chr1 186305 . G A 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;DP=45;Dels=0.00;FS=2.751;HaplotypeScore=2.8649;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.332;QD=18.73;ReadPosRankSum=-0.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:871,0,521 -chr1 186318 . T C 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=2.087;QD=10.03;ReadPosRankSum=-0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:560,0,1118 -chr1 186366 . G A 683.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.40;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:712,54,0 -chr1 186382 . G A 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.17;MQ0=0;QD=28.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr1 186396 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.37;MQ0=0;MQRankSum=-1.756;QD=22.10;ReadPosRankSum=-2.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,16:18:34:426,0,34 -chr1 186407 . T C 557.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.691;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.89;MQ0=0;MQRankSum=-1.909;QD=24.25;ReadPosRankSum=-2.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,21:23:20:586,0,20 -chr1 186440 . C A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;DP=31;Dels=0.00;FS=19.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.71;MQ0=0;MQRankSum=3.153;QD=1.48;ReadPosRankSum=-2.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,4:31:74:74,0,835 -chr1 186449 . C A 1104.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.29;MQ0=0;QD=28.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1133,90,0 -chr1 186454 . C T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.649;DP=34;Dels=0.00;FS=22.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-3.817;QD=27.05;ReadPosRankSum=2.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,28:34:99:948,0,144 -chr1 186460 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=32;Dels=0.00;FS=17.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.19;MQ0=0;MQRankSum=-3.790;QD=26.90;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,26:32:99:889,0,146 -chr1 186464 . T C 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=34;Dels=0.00;FS=19.762;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.63;MQ0=0;MQRankSum=-4.046;QD=25.85;ReadPosRankSum=1.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:7,27:34:99:907,0,182 -chr1 186478 . T C 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=-3.990;QD=21.03;ReadPosRankSum=-0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,17:25:99:554,0,243 -chr1 186480 . A C 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=3.932;QD=8.51;ReadPosRankSum=1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:241,0,553 -chr1 186483 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:912,72,0 -chr1 186485 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.47;ReadPosRankSum=-1.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:499,0,249 -chr1 186488 . C T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=19.60;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:479,0,255 -chr1 186496 . G T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.613;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.16;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:492,0,235 -chr1 186499 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.12;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:491,0,247 -chr1 186500 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.08;ReadPosRankSum=-0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:490,0,245 -chr1 186522 . A G 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.47;MQ0=0;MQRankSum=3.201;QD=8.57;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:191,0,365 -chr1 186527 . T A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.452;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.08;MQ0=0;MQRankSum=-3.138;QD=14.60;ReadPosRankSum=0.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,12:18:99:291,0,198 -chr1 186553 . C T 134.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=0;QD=33.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:162,12,0 -chr1 186562 . C T 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=12;Dels=0.00;FS=6.818;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=0;MQRankSum=2.637;QD=8.15;ReadPosRankSum=0.825;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,4:12:99:126,0,256 -chr1 186565 . C T 383.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.26;MQ0=0;QD=34.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:412,33,0 -chr1 186581 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=11;Dels=0.00;FS=3.310;HaplotypeScore=1.7987;MLEAC=1;MLEAF=0.500;MQ=42.26;MQ0=0;MQRankSum=2.003;QD=2.25;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:9,2:11:53:53,0,266 -chr1 186587 . A G 52.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=17.58;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,2:3:6:80,6,0 -chr1 186588 . T C 53.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;QD=17.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:81,6,0 -chr1 186590 . T C 44.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=14.93;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26 -chr1 186605 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=28;Dels=0.00;FS=12.091;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=3.575;QD=20.53;ReadPosRankSum=-3.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,17:28:99:603,0,347 -chr1 186611 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.843;QD=11.44;ReadPosRankSum=2.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:360,0,648 -chr1 186614 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.798;QD=11.72;ReadPosRankSum=2.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:368,0,655 -chr1 186624 . C T 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.559;DP=34;Dels=0.00;FS=11.031;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.146;QD=11.32;ReadPosRankSum=2.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:413,0,758 -chr1 186629 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.439;DP=38;Dels=0.00;FS=8.924;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=4.390;QD=20.20;ReadPosRankSum=-0.695;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:796,0,505 -chr1 186638 . G A 1706.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=24.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1735,129,0 -chr1 186658 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=53;Dels=0.00;FS=6.435;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-3.592;QD=11.94;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:661,0,1102 -chr1 186661 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.611;DP=54;Dels=0.00;FS=6.487;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=0;MQRankSum=-3.283;QD=12.29;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:692,0,1121 -chr1 186663 . C T 1074.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=57;Dels=0.00;FS=8.033;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=3.964;QD=18.86;ReadPosRankSum=1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1103,0,821 -chr1 186666 . G A 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=56;Dels=0.00;FS=6.180;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=3.767;QD=19.30;ReadPosRankSum=0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1109,0,798 -chr1 186683 . A C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=53;Dels=0.00;FS=1.158;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-3.312;QD=12.86;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:710,0,1078 -chr1 186694 . T C 1666.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=30.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1695,126,0 -chr1 186695 . C T 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=4.002;QD=16.74;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:765,0,705 -chr1 186696 . C T 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=3.924;QD=17.18;ReadPosRankSum=0.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:767,0,660 -chr1 186702 . C T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.286;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.080;QD=13.35;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:629,0,825 -chr1 186707 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.738;QD=15.75;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:737,0,782 -chr1 186723 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.815;DP=40;Dels=0.00;FS=2.843;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.650;QD=16.19;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:676,0,656 -chr1 186725 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.588;QD=16.65;ReadPosRankSum=-1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:711,0,635 -chr1 186730 . C T 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=6.398;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.477;QD=2.81;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:36,7:43:99:149,0,1300 -chr1 186735 . T C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.621;DP=43;Dels=0.00;FS=4.425;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.278;QD=14.62;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:657,0,661 -chr1 186738 . C T 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.029;DP=43;Dels=0.00;FS=1.242;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.109;QD=14.95;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:671,0,692 -chr1 186794 . C A 2054.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=32.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2083,157,0 -chr1 186799 . A C 2004.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2033,154,0 -chr1 186800 . T C 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.519;QD=17.51;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:921,0,810 -chr1 186804 . C T 2108.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2137,166,0 -chr1 186814 . G A 2540.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=29.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2569,196,0 -chr1 186823 . T C 2655.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=27.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2684,202,0 -chr1 186853 . A G 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.007;DP=60;Dels=0.00;FS=1.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.037;QD=13.25;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:823,0,1142 -chr1 186856 . A G 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.735;QD=17.49;ReadPosRankSum=1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1095,0,816 -chr1 186871 . C T 2064.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=34.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2093,160,0 -chr1 186897 . A G 1641.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1670,129,0 -chr1 186922 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=39;Dels=0.00;FS=10.184;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.363;QD=15.74;ReadPosRankSum=0.576;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:642,0,675 -chr1 186958 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=38;Dels=0.00;FS=9.513;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.015;QD=15.89;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:632,0,693 -chr1 186977 . T C 1690.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=33.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1719,129,0 -chr1 186990 . T A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.733;DP=43;Dels=0.00;FS=1.194;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=1.494;QD=16.67;ReadPosRankSum=-0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:745,0,730 -chr1 186991 . G A 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.624;DP=42;Dels=0.00;FS=1.170;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-2.632;QD=15.64;ReadPosRankSum=0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:685,0,742 -chr1 186992 . C T 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.654;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.503;QD=15.31;ReadPosRankSum=0.980;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:656,0,735 -chr1 187055 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.270;DP=49;Dels=0.00;FS=6.133;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.990;QD=15.77;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:801,0,876 -chr1 187064 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=47;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.075;QD=16.42;ReadPosRankSum=-0.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:800,0,846 -chr1 187065 . G A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=46;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.923;QD=16.71;ReadPosRankSum=-1.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:797,0,815 -chr1 187147 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=1.192;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.400;QD=15.06;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:676,0,759 -chr1 187173 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=1.128;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.970;QD=15.78;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:833,0,844 -chr1 187185 . A T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.328;DP=59;Dels=0.00;FS=1.046;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.148;QD=15.59;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:948,0,1051 -chr1 187200 . T C 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286;DP=70;Dels=0.00;FS=12.081;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=0;MQRankSum=-5.431;QD=3.13;ReadPosRankSum=-3.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:58,12:70:99:247,0,2146 -chr1 187208 . T G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=73;Dels=0.00;FS=9.609;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=-5.455;QD=2.83;ReadPosRankSum=-2.746;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:61,12:73:99:235,0,2122 -chr1 187209 . A C 990.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=73;Dels=0.00;FS=1.959;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=2.896;QD=13.57;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:42,31:73:99:1019,0,1427 -chr1 187247 . G A 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.510;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.33;MQ0=0;MQRankSum=-1.357;QD=19.20;ReadPosRankSum=-1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1084,0,781 -chr1 187248 . G T 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.193;DP=53;Dels=0.00;FS=3.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-1.911;QD=18.18;ReadPosRankSum=-0.763;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:992,0,786 -chr1 187270 . C G 518.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=38;Dels=0.00;FS=2.937;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-5.255;QD=13.65;ReadPosRankSum=3.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:547,0,742 -chr1 187298 . C T 1101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=0;MQRankSum=0.258;QD=21.60;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,36:51:99:1130,0,459 -chr1 187302 . A G 1787.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1816,135,0 -chr1 187346 . C T 972.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.918;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.31;MQ0=3;MQRankSum=2.275;QD=31.38;ReadPosRankSum=1.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:5,26:31:78:1001,78,0 -chr1 187362 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=38;Dels=0.00;FS=1.434;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=4;MQRankSum=-2.189;QD=9.18;ReadPosRankSum=0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:377,0,655 -chr1 187385 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=54.34;MQ0=3;QD=34.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,35:37:99:1290,99,0 -chr1 187414 . C A 1254.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.94;MQ0=0;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1283,99,0 -chr1 187461 . C A 765.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=29.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:794,60,0 -chr1 187503 . G A 696.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=0;QD=34.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:725,54,0 -chr1 187522 . A T 1152.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.33;MQ0=0;QD=31.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1181,90,0 -chr1 187574 . T A 1364.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.88;MQ0=2;QD=28.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,36:38:99:1393,108,0 -chr1 187614 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.29;MQ0=2;QD=33.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,25:26:69:901,69,0 -chr1 187714 . G C 1203.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.78;MQ0=2;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,42:42:96:1232,96,0 -chr1 187753 . T C 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.068;DP=59;Dels=0.00;FS=1.104;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=0.555;QD=14.44;ReadPosRankSum=-5.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:880,0,1099 -chr1 187793 . T C 1189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=15.7240;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.945;QD=19.83;ReadPosRankSum=3.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1218,0,816 -chr1 187844 . T C 876.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.394;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.259;QD=21.38;ReadPosRankSum=-0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,26:41:99:905,0,488 -chr1 187894 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=46;Dels=0.00;FS=4.031;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.055;QD=15.97;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:763,0,746 -chr1 187903 . C T 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=46;Dels=0.00;FS=6.439;HaplotypeScore=4.0994;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=0.791;QD=16.86;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:804,0,717 -chr1 188013 . T A 834.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.291;QD=16.37;ReadPosRankSum=0.725;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:863,0,808 -chr1 188103 . G A 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073;DP=55;Dels=0.00;FS=4.032;HaplotypeScore=2.6641;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.347;QD=14.07;ReadPosRankSum=0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:30,25:55:99:802,0,993 -chr1 188173 . G A 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=42;Dels=0.00;FS=2.786;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=16.61;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:20,22:42:99:726,0,669 -chr1 188266 . A G 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:28,27:56:99:907,0,965 -chr1 188270 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,27:54:99:879,0,898 -chr1 188311 . T G 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,28:53:99:930,0,831 -chr1 188357 . C T 1327.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1356,105,0 -chr1 188364 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,770 -chr1 188393 . T C 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:24,18:42:99:544,0,828 -chr1 188395 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:23,18:41:99:572,0,791 -chr1 188416 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,14:39:99:426,0,821 -chr1 188438 . C A 930.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:21,29:50:99:959,0,659 -chr1 188621 . G A 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,22:49:99:733,0,926
--- a/VCFToolFilter/vcfToolsFilter.sh Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) - -filein=$1 -fileout_label=$2 -fileout=$3 -filelog=$4 -export=$5 -frequency=$6 -max_freq=$7 -allow_missing=$8 -nb_alleles_min=$9 -nb_alleles_max=${10} -type=${11} -bound_start=${12} -bound_end=${13} - - -if [ "${14}" != "None" ] -then samples="--samples ${14}" -fi - -if [ "${15}" != "None" ] -then chromosomes="--chromosomes ${15}" -fi - -if [ "$bound_start" -gt "$bound_end" ] -then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2 -fi - -if [ "$nb_alleles_min" -gt "$nb_alleles_max" ] -then tmp=$nb_alleles_min ; nb_alleles_min=$nb_alleles_max ; nb_alleles_max=$tmp ; echo "Warning : Minimum number of alleles must be lower than maximum number of allele!" >&2 -fi - -perl $tool_path/VCFToolsFilter.pl --input $filein --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --nb_alleles $nb_alleles_min','$nb_alleles_max --type $type --bounds $bound_start','$bound_end $samples $chromosomes - -if [ "$export" = "VCF" ] -then cp $fileout_label.recode.vcf $fileout ; rm $fileout_label.recode.vcf -elif [ "$export" = "freq" ] -then cp $fileout_label.frq $fileout ; rm $fileout_label.frq -else cp $fileout_label.ped $fileout; cp $fileout_label.map ${16} ; rm $fileout_label.ped $fileout_label.map -fi - -cp vcftools.log $filelog -rm vcftools.log
--- a/VCFToolFilter/vcfToolsFilter.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,268 +0,0 @@ -<tool id="sniplay_vcftoolsfilter" name="VCF tools filter" version="1.1.1"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Filter VCF using VCFtools</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - <requirement type="package" version="0.1.12b">VCFtools</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="perl"> - vcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end - #if str( $samples ) == "": - 'None' - #else - $samples - #end if - #if str( $chromosomes ) == "": - 'None' - #else - $chromosomes - #end if - #if str( $export ) == "plink": - $fileout_map - #else - '' - #end if - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> - <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/> - <param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list"> - <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> - </param> - <param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list"> - <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> - </param> - <param name="export" type="select" label="Output format" > - <option value="VCF" selected="true">VCF</option> - <option value="freq">freq</option> - <option value="plink">plink</option> - </param> - <param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." /> - <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." /> - <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." /> - <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" /> - <param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" /> - <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." > - <option value="ALL" selected="true">All</option> - <option value="SNP">SNP</option> - <option value="INDEL">Indel</option> - </param> - <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." /> - <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout" format="vcf" label="${fileout_label}.#if str($export)=='plink' then 'ped' else '' # #if str($export)=='freq' then 'frq' else '' # #if str($export)=='VCF' then 'vcf' else '' #" > - <change_format> - <when input="export" value="freq" format="tabular" /> - <when input="export" value="plink" format="txt" /> - </change_format> - </data> - <data name="fileout_map" format="txt" label="${fileout_label}.map"> - <filter>(export == 'plink')</filter> - </data> - <data name="filelog" format="txt" label="${fileout_label}.log" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> - <param name="filein" value="sample.vcf" /> - <param name="chromosomes" value="chr1" /> - <param name="export" value="VCF" /> - <param name="frequency" value="0.001" /> - <param name="max_freq" value="0.5" /> - <param name="allow_missing" value="0" /> - <param name="nb_alleles_min" value="2" /> - <param name="nb_alleles_max" value="4" /> - <param name="type_p" value="ALL" /> - <param name="bound_start" value="1" /> - <param name="bound_end" value="100000000" /> - <output name="fileout" file="result.vcf" /> - <output name="filelog" file="result.log" /> - </test> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** - ---------------------------------------------------- - -.. class:: infomark - -**Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep. - ---------------------------------------------------- - -================ -VCF tools filter -================ - ------------ -Description ------------ - - Filter VCF file - ------------------ -Workflow position ------------------ - -**Upstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= - - -**Downstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= - - ----------- -Input file ----------- - -VCF file - VCF file with all SNPs - ----------- -Parameters ----------- - -Output file basename - Prefix for the output VCF file - -Samples - Samples to be analyzed. Comma separated list - -Chromosomes - Chromosomes to be analyzed. Comma separated list - -Output format - VCF/freq/plink - -Minimum MAF - Minimum frequency - -Maximum MAF - Maximum frequency - -Missing data proportion - Allowed missing data proportion per site. Must be comprised between 0 and 1. - -Number of alleles - Accepted number of alleles min and max. - -Polymorphisms - Type of polymorphisms to keep (ALL/SNP/INDEL). -Bounds - Lower bound and upper bound for a range of sites to be processed. - ------------- -Output files ------------- - -VCF file - VCF file filtered - -Log file - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -VCF file ---------- - -:: - - #fileformat=VCFv4.1 - #FILTER=<ID=LowQual,Description="Low quality"> - #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> - [...] - CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 - chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 - - -Parameters -========== - -Output name -> filtered_chr1 - -Chromosomes -> chr1 - -Output format -> VCF - -Minimum MAF -> 0.001 - -Maximum MAF -> 0.5 - -Missing data proportion -> 1 - -Number of alleles min -> 2 - -Number of alleles max -> 4 - -Polymorphisms -> All - -Lower bound -> 1 - -Upper bound -> 100000000 - - -Output files -============ - -filtered_genelist_intron.vcf ---------- - -:: - - #fileformat=VCFv4.1 - #FILTER=<ID=LowQual,Description="Low quality"> - #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> - [...] - CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 - chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0 - - - </help> - -</tool>
--- a/VCFToolsStats/VCFToolsStats.pl Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ - -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $usage = qq~Usage:$0 <args> [<opts>] - -where <args> are: - - -i, --input <VCF input> - -o, --out <output basename> -~; -$usage .= "\n"; - -my ($input,$out); - -GetOptions( - "input=s" => \$input, - "out=s" => \$out -); - - -die $usage - if ( !$input); - - - -my $nb_gene = `grep -c mRNA $input`; -$nb_gene =~s/\n//g; -my $nb_intergenic = `grep -c INTERGENIC $input`; -$nb_intergenic =~s/\n//g; - -my $nb_intron = `grep -c INTRON $input`; -$nb_intron =~s/\n//g; -my $nb_UTR = `grep -c UTR $input`; -$nb_UTR =~s/\n//g; -my $nb_exon = $nb_gene - $nb_intron - $nb_UTR; - -my $nb_ns = `grep -c NON_SYNONYMOUS_CODING $input`; -$nb_ns =~s/\n//g; -my $nb_s = $nb_exon - $nb_ns; - - - - -#system("$VCFTOOLS_EXE --vcf $input --remove-filtered-all --out $out --hardy >>vcftools.log 2>&1"); -system("vcftools --vcf $input --remove-filtered-all --out $out --het >>vcftools.log 2>&1"); -system("vcftools --vcf $input --remove-filtered-all --out $out --TsTv-summary >>vcftools.log 2>&1"); -system("vcftools --vcf $input --remove-filtered-all --out $out --missing-indv >>vcftools.log 2>&1"); - -open(my $G,">$out.annotation"); -print $G "Genic $nb_gene\n"; -print $G "Intergenic $nb_intergenic\n"; -print $G "========\n"; -print $G "Intron $nb_intron\n"; -print $G "Exon $nb_exon\n"; -print $G "UTR $nb_UTR\n"; -print $G "========\n"; -print $G "Non-syn $nb_ns\n"; -print $G "Synonym $nb_s\n"; -close($G); - - - - - - -
--- a/VCFToolsStats/test-data/result.TsTv.summary Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -MODEL COUNT -AC 371 -AG 1467 -AT 562 -CG 330 -CT 1659 -GT 397 -Ts 3126 -Tv 1660
--- a/VCFToolsStats/test-data/result.annotation Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -Genic 4489 -Intergenic 466 -======== -Intron 960 -Exon 3248 -UTR 281 -======== -Non-syn 226 -Synonym 3022
--- a/VCFToolsStats/test-data/result.het Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -INDV O(HOM) E(HOM) N_SITES F -CATB1 0 0.0 3616 0.00000
--- a/VCFToolsStats/test-data/result.imiss Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS -CATB1 4813 0 0 0
--- a/VCFToolsStats/test-data/result.log Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --het - --out vcf_stats - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Individual Heterozygosity - Individual Heterozygosity: Only using biallelic SNPs. -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --out vcf_stats - --TsTv-summary - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Ts/Tv summary -Ts/Tv ratio: 1.883 -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds - -VCFtools - v0.1.12b -(C) Adam Auton and Anthony Marcketta 2009 - -Parameters as interpreted: - --vcf /w/galaxy/galaxy4gwen/galaxy-dist/database/files/000/dataset_21.dat - --missing-indv - --out vcf_stats - --remove-filtered-all - -After filtering, kept 1 out of 1 Individuals -Outputting Individual Missingness -After filtering, kept 4813 out of a possible 4955 Sites -Run Time = 0.00 seconds
--- a/VCFToolsStats/test-data/sample.vcf Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5000 +0,0 @@ -##fileformat=VCFv4.1 -##FILTER=<ID=LowQual,Description="Low quality"> -##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> -##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false"> -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> -##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> -##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> -##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> -##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> -##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> -##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> -##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> -##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> -##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> -##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> -##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> -##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> -##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> -##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> -##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> -##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> -##contig=<ID=chr1,length=38193400> -##contig=<ID=chr10,length=27624748> -##contig=<ID=chr11,length=33540656> -##contig=<ID=chr2,length=54522928> -##contig=<ID=chr3,length=32030951> -##contig=<ID=chr4,length=28191985> -##contig=<ID=chr5,length=29137935> -##contig=<ID=chr6,length=37293965> -##contig=<ID=chr7,length=29833120> -##contig=<ID=chr8,length=31585744> -##contig=<ID=chr9,length=22352177> -##contig=<ID=chr0,length=205603396> -##reference=file:///data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta -##SnpEffVersion="2.0.5d (build 2012-01-19), by Pablo Cingolani" -##SnpEffCmd="SnpEff eff coffea /apps/www/sniplay.cirad.fr/data/Coffee/Argemo_genomic.nonannotated.vcf.2 -i VCF -o VCF -c snpEff.config " -##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effefct_Impact | Functional_Class | Codon_Change | Amino_Acid_change | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' "> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 -chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 -chr1 2232 . A C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;QD=11.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr1 2264 . C T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=5;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=0.358;QD=13.75;ReadPosRankSum=-1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:2,3:5:53:97,0,53 -chr1 2353 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.5027;MLEAC=1;MLEAF=0.500;MQ=31.07;MQ0=3;MQRankSum=0.261;QD=1.18;ReadPosRankSum=-1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:19,7:26:59:59,0,409 -chr1 2482 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.294;DP=19;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=26.95;MQ0=7;MQRankSum=0.370;QD=10.94;ReadPosRankSum=-1.109;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:5,14:19:83:236,0,83 -chr1 2558 . A T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=45;Dels=0.00;FS=4.170;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=28.40;MQ0=13;MQRankSum=0.121;QD=17.55;ReadPosRankSum=-0.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,32:45:99:818,0,101 -chr1 2925 . A T 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.619;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=5.7776;MLEAC=1;MLEAF=0.500;MQ=38.24;MQ0=1;MQRankSum=0.372;QD=17.59;ReadPosRankSum=-1.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:380,0,275 -chr1 2941 . A G 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.63;MQ0=1;MQRankSum=1.524;QD=14.78;ReadPosRankSum=0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:7,8:15:99:250,0,227 -chr1 2985 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.19;MQ0=8;QD=6.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:7,4:11:9:101,9,0 -chr1 3705 . G T 103.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.32;MQ0=0;QD=14.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:131,12,0 -chr1 3745 . A T 180.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.44;MQ0=0;QD=22.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:209,18,0 -chr1 3864 . C T 33.74 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.81;MQ0=4;QD=3.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,9:9:6:61,6,0 -chr1 3887 . G C 131.9 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.03;MQ0=5;QD=6.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,22:22:15:160,15,0 -chr1 3944 . G T 182.84 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.63;MQ0=5;QD=7.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,25:25:18:211,18,0 -chr1 4109 . C T 151.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.59;MQ0=0;QD=21.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:180,15,0 -chr1 4438 . T C 90.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.849;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.69;MQ0=2;MQRankSum=2.700;QD=6.00;ReadPosRankSum=-2.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:10,5:15:12:118,12,0 -chr1 4555 . G A 51.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.51;MQ0=0;QD=17.25;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:79,6,0 -chr1 4733 . C G 135.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.22;MQ0=0;QD=22.51;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:163,12,0 -chr1 4879 . T C 114.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.81;MQ0=0;QD=19.01;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:142,12,0 -chr1 4945 . G A 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=29;Dels=0.00;FS=3.123;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.25;MQ0=1;MQRankSum=3.132;QD=11.10;ReadPosRankSum=3.363;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,15:29:43:350,0,43 -chr1 4947 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.742;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.38;MQ0=1;MQRankSum=3.401;QD=11.64;ReadPosRankSum=3.360;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:16,15:31:40:389,0,40 -chr1 4961 . C T 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.427;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.65;MQ0=1;MQRankSum=-3.749;QD=0.99;ReadPosRankSum=-0.165;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,25:43:71:71,0,437 -chr1 4967 . T C 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.980;DP=41;Dels=0.00;FS=1.219;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=26.25;MQ0=1;MQRankSum=4.072;QD=10.09;ReadPosRankSum=-0.897;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,16:41:70:442,0,70 -chr1 4981 . A C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=6.8693;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=3.500;QD=6.80;ReadPosRankSum=-1.759;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,11:36:88:273,0,88 -chr1 4987 . T G 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.583;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=13.8254;MLEAC=1;MLEAF=0.500;MQ=24.42;MQ0=1;MQRankSum=-2.450;QD=1.66;ReadPosRankSum=1.983;EFF=UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|),UTR_3_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,15:36:88:88,0,296 -chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0 -chr1 5110 . A G 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.328;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.75;MQ0=3;MQRankSum=-0.421;QD=4.51;ReadPosRankSum=-1.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:123,0,278 -chr1 5170 . A G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=25.23;MQ0=2;MQRankSum=0.212;QD=3.65;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,7:15:83:83,0,127 -chr1 5171 . T G 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=26.11;MQ0=1;MQRankSum=0.212;QD=3.91;ReadPosRankSum=0.533;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,6:14:83:83,0,122 -chr1 5284 . A C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.9827;MLEAC=1;MLEAF=0.500;MQ=34.72;MQ0=1;MQRankSum=-0.784;QD=3.49;ReadPosRankSum=-1.445;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:105,0,410 -chr1 5324 . C T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.780;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=3;MQRankSum=1.491;QD=10.44;ReadPosRankSum=-0.818;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:10,10:20:99:237,0,166 -chr1 5361 . A G 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=24.40;MQ0=2;MQRankSum=1.412;QD=11.41;ReadPosRankSum=0.688;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:9,14:24:44:302,0,44 -chr1 5557 . A G 298.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.74;MQ0=5;QD=18.67;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:327,30,0 -chr1 5648 . T C 59.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.66;MQ0=3;QD=6.59;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:1,8:9:9:87,9,0 -chr1 5834 . G T 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.3843;MLEAC=1;MLEAF=0.500;MQ=27.17;MQ0=1;MQRankSum=1.191;QD=0.93;ReadPosRankSum=0.714;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,2:17:44:44,0,279 -chr1 5889 . T G 147.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=21.23;MQ0=4;MQRankSum=-0.248;QD=8.17;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:4,14:18:11:175,0,11 -chr1 5890 . T G 229.78 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=2;MLEAF=1.00;MQ=21.11;MQ0=4;QD=12.09;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,19:19:24:258,24,0 -chr1 5938 . C G 64.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.520;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.73;MQ0=10;MQRankSum=1.034;QD=3.08;ReadPosRankSum=0.597;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:15,6:21:69:93,0,69 -chr1 5968 . A T 115.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.07;MQ0=8;QD=7.24;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:144,15,0 -chr1 5974 . A G 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.818;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=18.51;MQ0=8;MQRankSum=0.296;QD=1.88;ReadPosRankSum=1.580;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:14,4:18:62:62,0,114 -chr1 6010 . A T 490.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.66;MQ0=2;QD=21.34;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,23:23:45:519,45,0 -chr1 6041 . T A 311.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=28.89;MQ0=0;QD=14.85;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,21:21:33:340,33,0 -chr1 6209 . A G 273.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.61;MQ0=6;QD=13.04;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,20:21:30:302,30,0 -chr1 6350 . T G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=16.20;MQ0=21;MQRankSum=1.670;QD=2.93;ReadPosRankSum=-0.085;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:163,0,206 -chr1 6426 . T C 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=25.78;MQ0=2;MQRankSum=-1.099;QD=5.25;ReadPosRankSum=0.859;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:301,0,677 -chr1 6486 . A G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=16;MQRankSum=-0.330;QD=8.00;ReadPosRankSum=0.268;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:39,25:64:99:540,0,604 -chr1 6532 . C T 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=53;Dels=0.00;FS=4.619;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=17.32;MQ0=28;MQRankSum=0.087;QD=2.22;ReadPosRankSum=-0.379;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:146,0,419 -chr1 6577 . G A 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.35;MQ0=17;MQRankSum=-1.883;QD=6.11;ReadPosRankSum=0.269;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:8,25:33:28:230,0,28 -chr1 6607 . T C 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=-1.702;QD=2.28;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:117,0,385 -chr1 6609 . G T 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=5.9778;MLEAC=1;MLEAF=0.500;MQ=18.87;MQ0=12;MQRankSum=0.904;QD=2.30;ReadPosRankSum=-0.204;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:32,7:39:99:118,0,377 -chr1 6675 . G A 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=52;Dels=0.00;FS=8.076;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.45;MQ0=15;MQRankSum=-1.788;QD=1.13;ReadPosRankSum=-0.973;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,16:52:87:87,0,729 -chr1 6691 . G T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=49;Dels=0.00;FS=8.321;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=17;MQRankSum=-0.467;QD=0.71;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:36,13:49:63:63,0,703 -chr1 6725 . G A 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=26;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=22.03;MQ0=9;MQRankSum=-0.927;QD=7.45;ReadPosRankSum=-0.146;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 0/1:13,13:26:99:222,0,183 -chr1 6752 . T C 113.9 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.88;MQ0=6;QD=10.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,11:11:15:142,15,0 -chr1 6942 . G C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.400;DP=21;Dels=0.00;FS=13.222;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.08;MQ0=7;MQRankSum=0.267;QD=2.66;ReadPosRankSum=-1.067;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:14,7:21:84:84,0,137 -chr1 7107 . C T 262.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.283;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.07;MQ0=9;MQRankSum=1.189;QD=10.11;ReadPosRankSum=-1.302;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:7,19:26:6:290,6,0 -chr1 7384 . T G 58.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.259;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.91;MQ0=30;MQRankSum=0.259;QD=1.40;ReadPosRankSum=0.583;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,16:42:87:87,0,93 -chr1 8682 . T G 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.57;MQ0=23;MQRankSum=-1.898;QD=7.02;ReadPosRankSum=0.429;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:8,30:38:99:295,0,141 -chr1 8738 . A G 850.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.36;MQ0=29;QD=15.75;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:72:879,72,0 -chr1 8785 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.453;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.27;MQ0=40;MQRankSum=-2.450;QD=1.48;ReadPosRankSum=1.668;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:102,0,173 -chr1 8936 . C T 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.372;DP=47;Dels=0.00;FS=11.458;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.37;MQ0=14;MQRankSum=2.448;QD=5.61;ReadPosRankSum=1.430;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,12:47:99:292,0,700 -chr1 8946 . A G 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.028;DP=39;Dels=0.00;FS=15.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=13;MQRankSum=1.417;QD=5.94;ReadPosRankSum=0.472;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:260,0,533 -chr1 9013 . A T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=33;Dels=0.00;FS=3.522;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.84;MQ0=24;MQRankSum=0.729;QD=2.05;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,9:33:96:96,0,100 -chr1 9080 . C T 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=17.47;MQ0=24;MQRankSum=-1.866;QD=1.82;ReadPosRankSum=0.633;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,13:34:90:90,0,190 -chr1 10305 . A G 786.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.23;MQ0=10;QD=23.84;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:6,27:33:63:815,63,0 -chr1 10540 . G C 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.965;DP=45;Dels=0.00;FS=17.175;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.78;MQ0=1;MQRankSum=-1.779;QD=6.82;ReadPosRankSum=2.279;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:335,0,1095 -chr1 10565 . T C 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.695;DP=49;Dels=0.00;FS=38.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.02;MQ0=2;MQRankSum=0.662;QD=20.57;ReadPosRankSum=-2.211;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,31:49:99:1036,0,420 -chr1 10997 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=59;Dels=0.00;FS=1.096;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=27.99;MQ0=9;MQRankSum=0.204;QD=10.11;ReadPosRankSum=-0.961;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:625,0,593 -chr1 11025 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.654;QD=4.94;ReadPosRankSum=1.721;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:310,0,779 -chr1 11026 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.001;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.25;MQ0=15;MQRankSum=-0.814;QD=4.84;ReadPosRankSum=1.694;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,20:57:99:304,0,778 -chr1 11155 . G T 882.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.9841;MLEAC=2;MLEAF=1.00;MQ=25.38;MQ0=8;QD=22.07;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:84:911,84,0 -chr1 11199 . G A 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.053;DP=54;Dels=0.00;FS=15.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.97;MQ0=5;MQRankSum=-2.335;QD=4.79;ReadPosRankSum=2.164;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:287,0,1004 -chr1 11255 . A G 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=45;Dels=0.00;FS=8.137;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=44.39;MQ0=0;MQRankSum=-1.761;QD=1.79;ReadPosRankSum=-2.826;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,10:45:99:109,0,1164 -chr1 11591 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.305;DP=31;Dels=0.00;FS=8.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.119;QD=4.96;ReadPosRankSum=-1.665;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:182,0,762 -chr1 11716 . T C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.463;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-0.962;QD=0.60;ReadPosRankSum=-2.049;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:43:43,0,741 -chr1 11719 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=25;Dels=0.00;FS=10.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.67;MQ0=0;MQRankSum=-1.213;QD=0.48;ReadPosRankSum=-2.132;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,3:25:40:40,0,773 -chr1 11750 . A T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.197;DP=39;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.68;MQ0=1;MQRankSum=-4.052;QD=2.58;ReadPosRankSum=-2.335;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,10:39:99:129,0,976 -chr1 11773 . T C 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=49;Dels=0.00;FS=8.883;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.29;MQ0=1;MQRankSum=-5.316;QD=5.40;ReadPosRankSum=-0.400;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:293,0,1185 -chr1 11891 . A T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.82;MQ0=0;MQRankSum=-3.709;QD=8.61;ReadPosRankSum=-0.055;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:433,0,1013 -chr1 11902 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.656;DP=42;Dels=0.00;FS=1.270;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=46.98;MQ0=0;MQRankSum=-3.019;QD=7.21;ReadPosRankSum=-0.525;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:331,0,973 -chr1 11906 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.095;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.51;MQ0=0;MQRankSum=-2.883;QD=7.41;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:332,0,920 -chr1 11911 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.998;DP=38;Dels=0.00;FS=3.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.65;MQ0=0;MQRankSum=-2.124;QD=4.81;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:211,0,908 -chr1 11921 . A T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.641;DP=38;Dels=0.00;FS=5.870;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-1.608;QD=3.52;ReadPosRankSum=0.348;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,10:38:99:162,0,926 -chr1 11929 . A G 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.970;DP=36;Dels=0.00;FS=9.839;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.95;MQ0=0;MQRankSum=-1.465;QD=3.13;ReadPosRankSum=-0.171;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,8:36:99:141,0,932 -chr1 11994 . G A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.393;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=38.03;MQ0=3;MQRankSum=-1.960;QD=1.98;ReadPosRankSum=0.635;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:127,0,1191 -chr1 12008 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=38.65;MQ0=3;MQRankSum=-3.004;QD=4.01;ReadPosRankSum=0.628;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:265,0,1308 -chr1 12023 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=68;Dels=0.00;FS=3.645;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=41.63;MQ0=3;MQRankSum=-1.795;QD=7.56;ReadPosRankSum=-1.088;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:43,25:68:99:542,0,1441 -chr1 12050 . G C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=68;Dels=0.00;FS=5.033;HaplotypeScore=2.9268;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=3;MQRankSum=-1.538;QD=11.88;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:836,0,1326 -chr1 12090 . A G 888.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=57;Dels=0.00;FS=2.245;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=0;MQRankSum=-4.892;QD=15.59;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:917,0,995 -chr1 12162 . A T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.98;MQ0=2;MQRankSum=-4.602;QD=6.88;ReadPosRankSum=-0.119;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:21,13:34:99:262,0,708 -chr1 12186 . G C 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=38;Dels=0.00;FS=3.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.59;MQ0=2;MQRankSum=-3.949;QD=6.10;ReadPosRankSum=-1.854;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:25,13:38:99:260,0,884 -chr1 12195 . C G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.111;DP=39;Dels=0.00;FS=1.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=2;MQRankSum=-3.882;QD=4.64;ReadPosRankSum=-1.898;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:209,0,927 -chr1 12249 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.999;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.19;MQ0=0;MQRankSum=-5.596;QD=11.75;ReadPosRankSum=2.865;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:686,0,1109 -chr1 12250 . C A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.017;DP=56;Dels=0.00;FS=2.386;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=-5.563;QD=11.66;ReadPosRankSum=2.848;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:33,23:56:99:681,0,1094 -chr1 12252 . T C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.084;DP=55;Dels=0.00;FS=2.426;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.486;QD=12.00;ReadPosRankSum=2.722;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:688,0,1075 -chr1 12271 . A G 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.19;ReadPosRankSum=0.908;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,18:47:99:507,0,1022 -chr1 12273 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=47;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.00;MQ0=0;MQRankSum=-5.395;QD=10.00;ReadPosRankSum=0.711;EFF=START_GAINED(LOW||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,18:47:99:498,0,1029 -chr1 12283 . T G 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=45;Dels=0.00;FS=6.601;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.612;QD=8.97;ReadPosRankSum=-0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:29,16:45:99:432,0,953 -chr1 12293 . G C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.726;DP=43;Dels=0.00;FS=13.073;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=-4.370;QD=9.81;ReadPosRankSum=-2.000;EFF=UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|Exon_chr1_12138_12431) GT:AD:DP:GQ:PL 0/1:28,15:43:99:450,0,932 -chr1 12432 . C T 860.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.21;MQ0=0;QD=31.88;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:889,72,0 -chr1 12461 . A T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=31;Dels=0.00;FS=6.929;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=43.06;MQ0=0;MQRankSum=-3.047;QD=3.44;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:135,0,662 -chr1 12610 . A C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=16;Dels=0.00;FS=2.796;HaplotypeScore=10.5708;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=1.371;QD=2.99;ReadPosRankSum=-2.526;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:13,3:16:76:76,0,324 -chr1 12640 . T G 605.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=1;QD=30.29;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:51:634,51,0 -chr1 12680 . A T 555.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.13;MQ0=1;QD=32.69;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,17:17:42:584,42,0 -chr1 12768 . A C 859.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=32.48;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:888,69,0 -chr1 12883 . G A 787.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=29.11;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:816,60,0 -chr1 12886 . G A 784.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.75;MQ0=0;QD=27.81;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:813,60,0 -chr1 12926 . T C 761.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.31;MQ0=0;QD=28.06;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:790,60,0 -chr1 12964 . G C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=38;Dels=0.00;FS=15.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-3.703;QD=1.41;ReadPosRankSum=1.421;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,6:38:82:82,0,1161 -chr1 12993 . G T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=43;Dels=0.00;FS=25.224;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.523;QD=5.20;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:252,0,1151 -chr1 12994 . A T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=43;Dels=0.00;FS=21.598;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.59;MQ0=0;MQRankSum=-4.528;QD=4.25;ReadPosRankSum=-1.193;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:211,0,1187 -chr1 13041 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=33;Dels=0.00;FS=12.234;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-3.337;QD=2.66;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,6:33:99:116,0,945 -chr1 13045 . G A 88.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=32;Dels=0.00;FS=12.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=0;MQRankSum=-3.307;QD=2.77;ReadPosRankSum=2.148;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,6:32:99:117,0,908 -chr1 13074 . C T 821.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.270;DP=27;Dels=0.00;FS=3.388;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;MQRankSum=2.122;QD=30.44;ReadPosRankSum=0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:3,24:27:32:850,32,0 -chr1 13123 . T A 1348.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.40;MQ0=0;QD=34.58;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1377,102,0 -chr1 13136 . C T 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=41;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.46;MQ0=0;MQRankSum=-1.074;QD=4.43;ReadPosRankSum=3.016;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,11:41:99:210,0,1033 -chr1 13137 . C T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=42;Dels=0.00;FS=14.892;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.95;MQ0=0;MQRankSum=0.715;QD=24.21;ReadPosRankSum=-3.118;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:11,31:42:99:1045,0,215 -chr1 13270 . G A 1048.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=3;QD=34.96;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,30:30:81:1077,81,0 -chr1 13273 . A T 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=30;Dels=0.00;FS=2.876;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.55;MQ0=3;MQRankSum=-3.741;QD=9.36;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:309,0,598 -chr1 13280 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.606;DP=28;Dels=0.00;FS=2.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.14;MQ0=2;MQRankSum=-3.610;QD=8.85;ReadPosRankSum=-1.080;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:276,0,564 -chr1 13292 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=29;Dels=0.00;FS=5.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.02;MQ0=2;MQRankSum=-3.138;QD=10.03;ReadPosRankSum=-0.276;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:319,0,601 -chr1 13308 . T G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=29;Dels=0.00;FS=2.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=-3.380;QD=9.68;ReadPosRankSum=3.332;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,644 -chr1 13344 . T C 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=19;Dels=0.00;FS=23.096;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=1;MQRankSum=-0.592;QD=1.94;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,3:19:65:65,0,546 -chr1 13347 . A T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.846;DP=21;Dels=0.00;FS=37.433;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=1;MQRankSum=1.196;QD=5.47;ReadPosRankSum=-2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:143,0,499 -chr1 13363 . G A 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=17;Dels=0.00;FS=33.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.13;MQ0=0;MQRankSum=0.818;QD=13.87;ReadPosRankSum=0.337;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:264,0,308 -chr1 13378 . C G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=13;Dels=0.00;FS=19.956;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=0.529;QD=15.29;ReadPosRankSum=1.461;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,7:13:99:227,0,159 -chr1 13390 . T C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=13;Dels=0.00;FS=21.553;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.47;MQ0=0;MQRankSum=-0.212;QD=17.52;ReadPosRankSum=2.927;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:5,8:13:99:256,0,126 -chr1 13403 . G A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-1.580;QD=21.18;ReadPosRankSum=2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,7:10:88:240,0,88 -chr1 13404 . T A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=0.895;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,217 -chr1 13405 . A G 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=10;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.78;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:86:86,0,244 -chr1 13407 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=10;Dels=0.00;FS=19.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=1.580;QD=5.48;ReadPosRankSum=-2.166;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,3:10:83:83,0,214 -chr1 13424 . C A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.550;DP=7;Dels=0.00;FS=15.441;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=54.99;MQ0=0;MQRankSum=-1.754;QD=13.25;ReadPosRankSum=-0.550;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:3,4:7:90:121,0,90 -chr1 13484 . T A 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=11;Dels=0.00;FS=6.264;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=0;MQRankSum=-2.228;QD=9.07;ReadPosRankSum=-1.398;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,4:11:99:128,0,245 -chr1 13514 . C T 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.849;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.67;ReadPosRankSum=1.312;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:128,0,321 -chr1 13526 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.91;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:131,0,293 -chr1 13529 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.700;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=0.077;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,261 -chr1 13533 . A C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-2.546;QD=7.60;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:9,4:13:99:127,0,316 -chr1 13543 . G T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=13;Dels=0.00;FS=16.782;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=0.377;QD=13.06;ReadPosRankSum=-2.777;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:7,6:13:99:198,0,209 -chr1 13601 . C T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.355;DP=33;Dels=0.00;FS=6.893;HaplotypeScore=2.5316;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-0.954;QD=18.30;ReadPosRankSum=1.732;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:12,20:33:99:632,0,392 -chr1 13654 . T G 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.876;DP=32;Dels=0.00;FS=2.000;HaplotypeScore=17.2143;MLEAC=1;MLEAF=0.500;MQ=44.78;MQ0=0;MQRankSum=-3.367;QD=6.71;ReadPosRankSum=0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:243,0,696 -chr1 13805 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=1.000;QD=13.95;ReadPosRankSum=1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:712,0,955 -chr1 13962 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=56;Dels=0.00;FS=1.048;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.041;QD=15.07;ReadPosRankSum=0.567;EFF=UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:872,0,1029 -chr1 14025 . A G 1167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=4.5620;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.490;QD=19.14;ReadPosRankSum=0.702;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,36:61:99:1196,0,669 -chr1 14039 . C T 781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.305;DP=61;Dels=0.00;FS=1.002;HaplotypeScore=2.6609;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.839;QD=12.82;ReadPosRankSum=-1.116;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:810,0,1140 -chr1 14053 . A G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.152;DP=61;Dels=0.00;FS=3.495;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.107;QD=16.44;ReadPosRankSum=1.469;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1031,0,874 -chr1 14525 . C T 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=57;Dels=0.00;FS=7.529;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.041;QD=20.52;ReadPosRankSum=0.447;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1198,0,732 -chr1 14531 . A G 1030.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=54;Dels=0.00;FS=7.625;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.153;QD=19.09;ReadPosRankSum=0.045;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:22,31:54:99:1059,0,726 -chr1 14540 . C T 1109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.716;DP=56;Dels=0.00;FS=9.774;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=-0.899;QD=19.82;ReadPosRankSum=-0.716;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1138,0,754 -chr1 14569 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.646;QD=16.28;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:956,0,955 -chr1 14614 . T G 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.395;QD=17.88;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:958,0,770 -chr1 14674 . G T 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.419;QD=17.11;ReadPosRankSum=1.228;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:952,0,875 -chr1 14720 . C A 2453.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2482,187,0 -chr1 14957 . C T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=43;Dels=0.00;FS=2.756;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=1;MQRankSum=-0.253;QD=16.99;ReadPosRankSum=-0.758;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:759,0,646 -chr1 15110 . T A 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=65;Dels=0.00;FS=0.970;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.569;QD=12.66;ReadPosRankSum=0.261;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:39,26:65:99:851,0,1349 -chr1 15135 . A G 1010.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.364;QD=16.04;ReadPosRankSum=-1.767;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1039,0,1093 -chr1 15338 . C T 1812.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.74;MQ0=1;QD=24.29;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1841,138,0 -chr1 15597 . C A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=47;Dels=0.00;FS=6.639;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.617;QD=9.89;ReadPosRankSum=-0.797;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:493,0,1065 -chr1 15875 . A C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=42;Dels=0.00;FS=1.222;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=1;MQRankSum=-0.066;QD=12.90;ReadPosRankSum=1.064;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:570,0,798 -chr1 15977 . A T 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.672;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=53.37;MQ0=3;MQRankSum=-3.958;QD=12.64;ReadPosRankSum=-1.385;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:736,0,832 -chr1 16014 . C G 2424.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=10.8438;MLEAC=2;MLEAF=1.00;MQ=52.58;MQ0=3;QD=33.68;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,69:72:99:2453,187,0 -chr1 16017 . T G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=72;Dels=0.00;FS=1.018;HaplotypeScore=11.7597;MLEAC=1;MLEAF=0.500;MQ=52.21;MQ0=3;MQRankSum=-3.104;QD=11.80;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,28:72:99:878,0,1143 -chr1 16621 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=65;Dels=0.00;FS=3.448;HaplotypeScore=2.7337;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.323;QD=18.41;ReadPosRankSum=-1.247;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1225,0,946 -chr1 16671 . C T 1029.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=52;Dels=0.00;FS=2.477;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.746;QD=19.80;ReadPosRankSum=0.075;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1058,0,684 -chr1 16700 . C G 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.439;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=1.092;QD=18.80;ReadPosRankSum=-0.912;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:893,0,570 -chr1 16782 . C T 1114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9279;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=1.342;QD=17.69;ReadPosRankSum=-0.791;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1143,0,988 -chr1 16844 . C A 2131.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.55;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2160,160,0 -chr1 16871 . T C 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=59;Dels=0.00;FS=5.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.494;QD=14.76;ReadPosRankSum=-0.373;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:899,0,1075 -chr1 16912 . T A 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.631;DP=51;Dels=0.00;FS=7.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.556;QD=15.86;ReadPosRankSum=-1.724;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:837,0,878 -chr1 16926 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.660;DP=48;Dels=0.00;FS=6.044;HaplotypeScore=2.7745;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=0.042;QD=14.35;ReadPosRankSum=-0.249;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:717,0,884 -chr1 17027 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=65;Dels=0.00;FS=4.856;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.944;QD=14.46;ReadPosRankSum=-0.495;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:968,0,1247 -chr1 17241 . C G 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.811;QD=17.86;ReadPosRankSum=-0.258;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S190C|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_17170_17247),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:975,0,797 -chr1 17324 . T G 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.562;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.432;QD=18.63;ReadPosRankSum=0.875;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,675 -chr1 17567 . C T 1999.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.64;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2028,153,0 -chr1 17672 . A G 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.381;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.326;QD=14.24;ReadPosRankSum=1.143;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:555,0,636 -chr1 17713 . A T 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.481;DP=51;Dels=0.00;FS=2.418;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=15.64;ReadPosRankSum=-0.519;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:826,0,870 -chr1 17738 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=56;Dels=0.00;FS=2.356;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=12.19;ReadPosRankSum=0.820;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:711,0,1047 -chr1 17873 . G C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.910;QD=21.06;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:997,0,530 -chr1 17905 . A G 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=57;Dels=0.00;FS=2.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.659;QD=19.52;ReadPosRankSum=0.773;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,34:57:99:1141,0,733 -chr1 18041 . A G 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=57;Dels=0.00;FS=2.316;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.610;QD=18.47;ReadPosRankSum=-0.569;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I221V|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18036_18114) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1081,0,804 -chr1 18164 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.433;QD=11.99;ReadPosRankSum=-0.972;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:568,0,952 -chr1 18166 . T C 1777.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.02;MQ0=0;QD=28.69;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1806,135,0 -chr1 18454 . C T 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=45;Dels=0.00;FS=1.130;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=0.329;QD=16.22;ReadPosRankSum=0.102;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T314M|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:22,23:45:99:758,0,703 -chr1 18478 . T C 502.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=1.364;QD=13.59;ReadPosRankSum=1.242;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTa/cCa|L322P|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_18248_18565) GT:AD:DP:GQ:PL 0/1:21,16:37:99:531,0,711 -chr1 18624 . T A 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=47;Dels=0.00;FS=4.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.140;QD=13.06;ReadPosRankSum=1.194;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:642,0,913 -chr1 19081 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.091;QD=22.92;ReadPosRankSum=-0.051;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A390|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:16,35:51:99:1197,0,486 -chr1 19138 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.496;DP=58;Dels=0.00;FS=5.223;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.717;QD=14.88;ReadPosRankSum=-0.655;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y409|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_19027_19309) GT:AD:DP:GQ:PL 0/1:31,27:58:99:891,0,1083 -chr1 19465 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=16.00;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:924,0,944 -chr1 19863 . T G 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.194;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.2772;MLEAC=1;MLEAF=0.500;MQ=60.50;MQ0=0;MQRankSum=-0.350;QD=8.83;ReadPosRankSum=-0.868;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,14:43:99:408,0,1042 -chr1 20158 . T C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.686;QD=16.39;ReadPosRankSum=-0.668;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:897,0,842 -chr1 20454 . T C 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-1.324;QD=15.62;ReadPosRankSum=0.255;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:700,0,709 -chr1 20566 . G T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=35;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-1.275;QD=14.34;ReadPosRankSum=-2.633;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:530,0,669 -chr1 20614 . T C 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.266;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.223;QD=15.59;ReadPosRankSum=1.394;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:761,0,807 -chr1 20629 . A G 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.400;DP=45;Dels=0.00;FS=1.143;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=15.64;ReadPosRankSum=2.446;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:732,0,822 -chr1 20630 . A C 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.984;QD=16.60;ReadPosRankSum=1.956;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:742,0,712 -chr1 20726 . T G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.220;DP=40;Dels=0.00;FS=1.408;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.190;QD=10.77;ReadPosRankSum=0.512;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:459,0,906 -chr1 20954 . G T 1159.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.566;QD=14.14;ReadPosRankSum=1.500;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1188,0,1568 -chr1 21221 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.356;QD=18.35;ReadPosRankSum=0.853;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L545|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_20985_21233) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1056,0,780 -chr1 21683 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=0.586;QD=14.07;ReadPosRankSum=-0.823;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:802,0,1087 -chr1 21687 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.157;DP=55;Dels=0.00;FS=1.070;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.182;QD=20.14;ReadPosRankSum=-0.026;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1136,0,682 -chr1 21744 . A G 953.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.008;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.188;QD=16.73;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,28:57:99:982,0,944 -chr1 21947 . T G 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.907;QD=12.46;ReadPosRankSum=-0.326;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:701,0,1131 -chr1 22299 . T C 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=48;Dels=0.00;FS=6.116;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.826;QD=19.77;ReadPosRankSum=0.324;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A649|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:20,28:48:99:977,0,660 -chr1 22327 . T G 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=45;Dels=0.00;FS=4.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.767;QD=21.53;ReadPosRankSum=-0.059;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S659A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:17,28:45:99:997,0,550 -chr1 23334 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=39;Dels=0.00;FS=2.875;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=0;MQRankSum=0.928;QD=12.87;ReadPosRankSum=-0.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A994|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_22000_23367) GT:AD:DP:GQ:PL 0/1:23,16:39:99:530,0,737 -chr1 23394 . A T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=52;Dels=0.00;FS=2.388;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.410;QD=16.90;ReadPosRankSum=0.531;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,27:52:99:907,0,841 -chr1 23447 . T A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=47;Dels=0.00;FS=1.119;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.054;QD=16.36;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:797,0,690 -chr1 23455 . T G 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.768;DP=47;Dels=0.00;FS=2.552;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=0.646;QD=18.46;ReadPosRankSum=-0.821;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:896,0,614 -chr1 23515 . G A,T 1409.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.35;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/2:0,23,21:44:99:1623,749,680,874,0,814 -chr1 23725 . G A 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=42;Dels=0.00;FS=6.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.428;QD=16.80;ReadPosRankSum=1.384;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:734,0,720 -chr1 23982 . C T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=55;Dels=0.00;FS=2.640;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-1.005;QD=19.45;ReadPosRankSum=0.885;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,33:55:99:1098,0,682 -chr1 24069 . T A 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.713;DP=48;Dels=0.00;FS=8.862;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=1;MQRankSum=0.330;QD=15.50;ReadPosRankSum=0.713;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:772,0,789 -chr1 24151 . A G 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.694;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.785;QD=17.06;ReadPosRankSum=1.854;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1021|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24104_24302) GT:AD:DP:GQ:PL 0/1:21,25:46:99:813,0,677 -chr1 24389 . C A 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=48;Dels=0.00;FS=6.267;HaplotypeScore=27.9952;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=1;MQRankSum=0.567;QD=17.52;ReadPosRankSum=-0.546;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:869,0,711 -chr1 24436 . T C 934.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.691;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=-1.964;QD=18.33;ReadPosRankSum=-0.577;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S1080|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_24411_24543) GT:AD:DP:GQ:PL 0/1:23,28:51:99:963,0,687 -chr1 24548 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=46;Dels=0.00;FS=6.474;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.411;QD=21.39;ReadPosRankSum=1.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:1012,0,541 -chr1 24661 . C G 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-1.176;QD=13.44;ReadPosRankSum=1.960;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:687,0,875 -chr1 24708 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.037;DP=43;Dels=0.00;FS=1.164;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-1.588;QD=11.79;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:535,0,872 -chr1 24751 . C T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=50;Dels=0.00;FS=8.018;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.278;QD=12.94;ReadPosRankSum=-1.022;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:675,0,1009 -chr1 24820 . T A 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.600;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.461;QD=18.66;ReadPosRankSum=1.129;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1148,0,824 -chr1 24862 . T C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.409;DP=51;Dels=0.00;FS=13.641;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.789;QD=13.52;ReadPosRankSum=-0.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:718,0,995 -chr1 24930 . T C 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.762;DP=52;Dels=0.00;FS=27.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.560;QD=15.23;ReadPosRankSum=0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:820,0,960 -chr1 25113 . T A 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=40;Dels=0.00;FS=16.130;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.639;QD=18.64;ReadPosRankSum=1.998;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:774,0,623 -chr1 25137 . G A 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=0.665;QD=17.66;ReadPosRankSum=-0.317;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:664,0,574 -chr1 25267 . A G 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.616;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.877;QD=18.93;ReadPosRankSum=-2.014;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:861,0,649 -chr1 25375 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.084;QD=16.13;ReadPosRankSum=0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:980,0,985 -chr1 25379 . A G 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.8311;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.716;QD=17.74;ReadPosRankSum=0.093;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1004,0,818 -chr1 25601 . A G 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.979;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=16.39;ReadPosRankSum=1.281;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:995,0,972 -chr1 25654 . G T 2337.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.57;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2366,175,0 -chr1 25678 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=47;Dels=0.00;FS=2.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.653;QD=11.34;ReadPosRankSum=0.875;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T1175|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:30,17:47:99:561,0,1005 -chr1 25747 . G A 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.324;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=0.246;QD=9.48;ReadPosRankSum=1.361;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1198|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:29,14:43:99:436,0,1051 -chr1 25763 . G C 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.339;DP=44;Dels=0.00;FS=9.359;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.817;QD=10.97;ReadPosRankSum=-1.570;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V1204L|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_25668_25963) GT:AD:DP:GQ:PL 0/1:27,16:44:99:511,0,956 -chr1 26086 . G T 2202.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=3.4093;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.67;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2231,169,0 -chr1 26087 . A G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=54;Dels=0.00;FS=1.059;HaplotypeScore=2.6207;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.099;QD=17.55;ReadPosRankSum=1.238;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:976,0,871 -chr1 26119 . G T 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=55;Dels=0.00;FS=2.268;HaplotypeScore=2.9962;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.557;QD=16.52;ReadPosRankSum=-1.540;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:937,0,919 -chr1 26334 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.965;DP=50;Dels=0.00;FS=1.280;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-0.080;QD=6.24;ReadPosRankSum=3.146;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:340,0,1268 -chr1 26660 . T C 1722.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=38.42;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1751,129,0 -chr1 26702 . A T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.942;DP=54;Dels=0.00;FS=10.090;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.192;QD=12.53;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:705,0,1095 -chr1 26910 . T G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.210;DP=49;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.332;QD=17.36;ReadPosRankSum=-0.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S1297A|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:23,26:49:99:879,0,760 -chr1 27095 . A T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.581;DP=41;Dels=0.00;FS=4.926;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.784;QD=21.90;ReadPosRankSum=-0.151;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P1358|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:14,27:41:99:926,0,391 -chr1 27394 . A G 928.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=53;Dels=0.00;FS=5.960;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.100;QD=17.52;ReadPosRankSum=-0.809;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N1458S|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_26832_27933) GT:AD:DP:GQ:PL 0/1:21,32:53:99:957,0,694 -chr1 27940 . G T 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.545;QD=15.06;ReadPosRankSum=-0.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:781,0,874 -chr1 28249 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=41;Dels=0.00;FS=1.216;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.088;QD=19.41;ReadPosRankSum=0.696;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:824,0,613 -chr1 28269 . C T 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.609;QD=18.99;ReadPosRankSum=-1.031;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:845,0,552 -chr1 28430 . T C 718.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.035;QD=14.09;ReadPosRankSum=-0.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:747,0,985 -chr1 28468 . T C 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=55;Dels=0.00;FS=3.953;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=1;MQRankSum=0.650;QD=15.50;ReadPosRankSum=0.419;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:881,0,955 -chr1 28487 . T G 2391.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=1;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2420,178,0 -chr1 28990 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.224;DP=58;Dels=0.00;FS=16.948;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.031;QD=17.39;ReadPosRankSum=0.202;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:1037,0,1003 -chr1 29042 . A C 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=57;Dels=0.00;FS=5.341;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.937;QD=18.98;ReadPosRankSum=1.049;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1110,0,905 -chr1 29090 . G T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.457;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.506;QD=23.46;ReadPosRankSum=-0.248;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:16,36:52:99:1248,0,498 -chr1 29155 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.513;QD=18.08;ReadPosRankSum=-0.050;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:914,0,699 -chr1 29212 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=59;Dels=0.00;FS=2.209;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.359;QD=15.64;ReadPosRankSum=-2.011;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:951,0,1091 -chr1 29443 . T C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.937;DP=47;Dels=0.00;FS=7.013;HaplotypeScore=2.8089;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.184;QD=8.40;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:423,0,970 -chr1 29543 . G C 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=52;Dels=0.00;FS=2.441;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=2;MQRankSum=-0.700;QD=11.09;ReadPosRankSum=0.260;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:605,0,1005 -chr1 29549 . T A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=50;Dels=0.00;FS=4.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=2;MQRankSum=0.096;QD=11.00;ReadPosRankSum=0.607;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:578,0,972 -chr1 29794 . C G 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.493;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.447;QD=14.07;ReadPosRankSum=-0.865;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:746,0,926 -chr1 30062 . C G 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.890;DP=56;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.330;QD=18.85;ReadPosRankSum=0.725;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1084,0,794 -chr1 30283 . A G 1779.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.20;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1808,135,0 -chr1 30505 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.057;DP=59;Dels=0.00;FS=3.878;HaplotypeScore=2.5980;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.388;QD=14.98;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T1668|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:32,27:59:99:912,0,1076 -chr1 30578 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.114;DP=59;Dels=0.00;FS=5.208;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.220;QD=16.66;ReadPosRankSum=0.523;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S1693G|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1011,0,918 -chr1 30610 . G A 853.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.888;DP=63;Dels=0.00;FS=2.122;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.012;QD=13.55;ReadPosRankSum=0.709;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S1703|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_30414_30776) GT:AD:DP:GQ:PL 0/1:33,30:63:99:882,0,1106 -chr1 30810 . T G 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=52;Dels=0.00;FS=1.095;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.743;QD=12.21;ReadPosRankSum=-0.141;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:663,0,1056 -chr1 30850 . G A 1094.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.596;DP=56;Dels=0.00;FS=1.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.864;QD=19.55;ReadPosRankSum=1.099;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1123,0,720 -chr1 30887 . A C 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.277;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.841;QD=16.93;ReadPosRankSum=0.720;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1027,0,969 -chr1 30927 . C G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.191;DP=49;Dels=0.00;FS=8.536;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.040;QD=18.49;ReadPosRankSum=1.296;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:934,0,707 -chr1 31004 . G T 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.387;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.766;QD=15.64;ReadPosRankSum=1.054;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:951,0,1000 -chr1 31025 . A C 964.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=59;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.371;QD=16.35;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:993,0,950 -chr1 31036 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.630;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.81;MQ0=0;MQRankSum=0.950;QD=16.34;ReadPosRankSum=-0.770;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:829,0,810 -chr1 31213 . A G 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=51;Dels=0.00;FS=3.933;HaplotypeScore=24.9899;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.293;QD=17.62;ReadPosRankSum=-0.311;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:927,0,826 -chr1 31497 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.007;DP=35;Dels=0.00;FS=4.982;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.347;QD=16.14;ReadPosRankSum=-0.479;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:593,0,535 -chr1 31537 . T A 1517.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.76;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1546,114,0 -chr1 31710 . G T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.314;DP=41;Dels=0.00;FS=6.637;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=13.19;ReadPosRankSum=0.876;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:569,0,741 -chr1 31712 . G A 1534.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=32.25;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1563,120,0 -chr1 31714 . A G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.219;DP=40;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.163;QD=15.17;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:635,0,705 -chr1 31754 . A T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=45;Dels=0.00;FS=1.145;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.058;QD=14.73;ReadPosRankSum=0.102;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:691,0,823 -chr1 31917 . G A 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=60;Dels=0.00;FS=3.613;HaplotypeScore=1.9981;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.430;QD=20.53;ReadPosRankSum=0.174;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1260,0,770 -chr1 31921 . G A 1051.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.128;DP=55;Dels=0.00;FS=1.022;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.561;QD=19.12;ReadPosRankSum=0.691;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1080,0,742 -chr1 32111 . A G 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=49;Dels=0.00;FS=2.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.156;QD=18.44;ReadPosRankSum=0.211;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:932,0,729 -chr1 32214 . G A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.166;DP=48;Dels=0.00;FS=6.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=1;MQRankSum=-0.118;QD=14.31;ReadPosRankSum=1.123;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:715,0,905 -chr1 32230 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.182;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=2;MQRankSum=-0.176;QD=15.49;ReadPosRankSum=-1.233;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:710,0,732 -chr1 32312 . A T 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.306;DP=57;Dels=0.00;FS=7.278;HaplotypeScore=0.9159;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.485;QD=16.08;ReadPosRankSum=-0.978;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:945,0,894 -chr1 32410 . A G 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.180;DP=58;Dels=0.00;FS=7.306;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.539;QD=13.43;ReadPosRankSum=-1.008;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:807,0,1109 -chr1 32760 . G T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.396;QD=15.74;ReadPosRankSum=0.648;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:894,0,892 -chr1 32761 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.076;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=1.577;QD=15.01;ReadPosRankSum=1.274;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,925 -chr1 32762 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.506;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.151;QD=14.77;ReadPosRankSum=1.078;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:811,0,950 -chr1 32810 . T A 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.129;DP=44;Dels=0.00;FS=1.278;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.481;QD=15.63;ReadPosRankSum=0.246;EFF=INTRON(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:716,0,594 -chr1 32950 . A G 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=2.4536;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.302;QD=20.89;ReadPosRankSum=-0.427;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V1779|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:1010,0,566 -chr1 33016 . T G 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.707;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=-0.787;QD=2.54;ReadPosRankSum=-1.826;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P1801|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,11:48:99:150,0,1307 -chr1 33031 . G A 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=10.1485;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=3;MQRankSum=0.261;QD=2.75;ReadPosRankSum=0.239;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q1806|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,13:56:99:182,0,1518 -chr1 33037 . T C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.294;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=22.7136;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=1.518;QD=11.25;ReadPosRankSum=0.008;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P1808|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,22:59:99:692,0,1127 -chr1 33046 . T A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.993;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=13.5584;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=3;MQRankSum=-1.164;QD=4.86;ReadPosRankSum=0.237;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L1811|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,17:59:99:315,0,1459 -chr1 33129 . A T 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.555;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=2.016;QD=6.77;ReadPosRankSum=-0.990;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aTa|K1839I|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,18:65:99:468,0,1588 -chr1 33136 . T A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=61;Dels=0.00;FS=16.845;HaplotypeScore=2.3893;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=2.025;QD=6.85;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtA|V1841|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,16:61:99:446,0,1486 -chr1 33139 . G T 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=57;Dels=0.00;FS=11.731;HaplotypeScore=5.2554;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=1.441;QD=6.50;ReadPosRankSum=-1.169;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P1842|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:57:99:399,0,1431 -chr1 33146 . A C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.634;DP=65;Dels=0.00;FS=13.675;HaplotypeScore=4.3887;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=0.261;QD=6.46;ReadPosRankSum=-1.112;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R1845|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:448,0,1646 -chr1 33199 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.004;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.694;QD=8.54;ReadPosRankSum=0.743;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V1862|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,21:72:99:643,0,1752 -chr1 33262 . G A 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=78;Dels=0.00;FS=3.343;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-1.196;QD=7.68;ReadPosRankSum=-0.514;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G1883|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,24:78:99:627,0,1895 -chr1 33289 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=77;Dels=0.00;FS=6.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.605;QD=8.93;ReadPosRankSum=2.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S1892|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:716,0,1845 -chr1 33320 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-0.494;QD=8.34;ReadPosRankSum=0.778;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,24:75:99:654,0,1810 -chr1 33322 . A G 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.707;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.160;QD=7.88;ReadPosRankSum=0.267;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctA/ctG|L1903|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,23:74:99:611,0,1773 -chr1 33328 . C T 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=0.608;QD=8.90;ReadPosRankSum=-0.662;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L1905|Cc01g00030|mRNA||GSCOCT00012437001|Exon_chr1_32889_33973),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,26:76:99:705,0,1756 -chr1 33511 . T C 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.801;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=28.0954;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.180;QD=7.78;ReadPosRankSum=-0.255;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:63,27:90:99:728,0,2042 -chr1 33518 . T A 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.325;DP=89;Dels=0.00;FS=0.876;HaplotypeScore=29.8838;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.272;QD=8.12;ReadPosRankSum=-1.798;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:751,0,2141 -chr1 33534 . A T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=82;Dels=0.00;FS=1.081;HaplotypeScore=4.6992;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.708;QD=3.67;ReadPosRankSum=0.006;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,16:82:99:329,0,2363 -chr1 33542 . A G 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=84;Dels=0.00;FS=2.421;HaplotypeScore=3.3981;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.159;QD=3.43;ReadPosRankSum=-0.427;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,16:84:99:316,0,2385 -chr1 33544 . T C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.216;DP=85;Dels=0.00;FS=5.901;HaplotypeScore=2.3989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-2.519;QD=2.62;ReadPosRankSum=0.156;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:70,15:85:99:251,0,2424 -chr1 33549 . T C 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.895;DP=85;Dels=0.00;FS=5.608;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.928;QD=3.20;ReadPosRankSum=-0.983;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:300,0,2403 -chr1 33583 . A G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=0.183;QD=6.04;ReadPosRankSum=-0.048;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,25:100:99:632,0,2624 -chr1 33591 . T G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.576;QD=6.44;ReadPosRankSum=0.766;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:75,27:102:99:685,0,2559 -chr1 33634 . G T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=92;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.309;QD=10.87;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,33:92:99:1028,0,2053 -chr1 33635 . T A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=93;Dels=0.00;FS=2.888;HaplotypeScore=4.3078;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.261;QD=10.54;ReadPosRankSum=0.285;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:60,33:93:99:1008,0,2023 -chr1 33648 . T C 1214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.582;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.076;QD=12.40;ReadPosRankSum=-1.008;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,40:98:99:1243,0,1959 -chr1 33649 . T C 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.519;DP=97;Dels=0.00;FS=0.836;HaplotypeScore=29.5675;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-0.096;QD=8.31;ReadPosRankSum=3.319;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:67,29:97:99:834,0,2354 -chr1 33669 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.973;DP=93;Dels=0.00;FS=2.768;HaplotypeScore=17.9952;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.606;QD=12.58;ReadPosRankSum=0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1198,0,1907 -chr1 33692 . G A 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.680;DP=95;Dels=0.00;FS=8.628;HaplotypeScore=1.7719;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.994;QD=11.82;ReadPosRankSum=1.470;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,38:95:99:1151,0,1994 -chr1 33756 . T A 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.209;DP=101;Dels=0.00;FS=21.595;HaplotypeScore=25.9789;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.917;QD=10.34;ReadPosRankSum=-0.467;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:1073,0,2323 -chr1 33765 . T C 2096.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.987;DP=97;Dels=0.00;FS=2.797;HaplotypeScore=26.9788;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.109;QD=21.62;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:35,62:97:99:2125,0,1120 -chr1 33783 . C A 3600.77 . AC=2;AF=1.00;AN=2;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,91:91:99:3629,274,0 -chr1 33800 . T C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=84;Dels=0.00;FS=1.935;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-2.651;QD=8.32;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,25:84:99:727,0,2083 -chr1 33805 . A G 2115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.718;DP=85;Dels=0.00;FS=0.901;HaplotypeScore=2.8243;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=4.074;QD=24.89;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,60:85:99:2144,0,700 -chr1 33816 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=74;Dels=0.00;FS=2.126;HaplotypeScore=26.8598;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-5.767;QD=8.16;ReadPosRankSum=0.084;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:632,0,1874 -chr1 33817 . C T 1791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.176;DP=75;Dels=0.00;FS=2.086;HaplotypeScore=25.9931;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-1.936;QD=23.89;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,51:75:99:1820,0,743 -chr1 33825 . C G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.639;DP=73;Dels=0.00;FS=2.189;HaplotypeScore=66.4539;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.355;QD=8.34;ReadPosRankSum=-0.152;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:637,0,1756 -chr1 33827 . A G 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.248;DP=73;Dels=0.00;FS=3.559;HaplotypeScore=65.4541;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=0;MQRankSum=-6.574;QD=8.26;ReadPosRankSum=-0.262;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,21:73:99:631,0,1850 -chr1 33850 . G A 967.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=85;Dels=0.00;FS=5.848;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-4.789;QD=11.39;ReadPosRankSum=-1.730;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:996,0,1874 -chr1 33851 . C T 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=85;Dels=0.00;FS=5.930;HaplotypeScore=20.9875;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-5.199;QD=11.44;ReadPosRankSum=-1.593;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:54,31:85:99:1001,0,1842 -chr1 33860 . A T 1131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=94;Dels=0.00;FS=0.798;HaplotypeScore=46.8065;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=2.315;QD=12.04;ReadPosRankSum=-0.705;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,38:94:99:1160,0,1948 -chr1 33863 . A G 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.497;DP=93;Dels=0.00;FS=0.897;HaplotypeScore=49.5927;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=2.899;QD=7.59;ReadPosRankSum=-0.568;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:68,25:93:99:734,0,2127 -chr1 33867 . T C 877.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=88;Dels=0.00;FS=5.938;HaplotypeScore=51.2136;MLEAC=1;MLEAF=0.500;MQ=58.15;MQ0=0;MQRankSum=-2.770;QD=9.97;ReadPosRankSum=1.358;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:59,29:88:99:906,0,2073 -chr1 33870 . A T 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.369;DP=86;Dels=0.00;FS=6.242;HaplotypeScore=47.2312;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.848;QD=9.56;ReadPosRankSum=2.170;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:850,0,1959 -chr1 33871 . G C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=86;Dels=0.00;FS=7.832;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-3.203;QD=10.01;ReadPosRankSum=2.382;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:58,28:86:99:889,0,1966 -chr1 33872 . A T 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=86;Dels=0.00;FS=5.975;HaplotypeScore=48.2298;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.211;QD=10.02;ReadPosRankSum=2.503;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:57,29:86:99:890,0,1958 -chr1 33881 . T C 2424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.386;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=26.4025;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-0.490;QD=25.80;ReadPosRankSum=1.236;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:24,70:94:99:2453,0,686 -chr1 33890 . C T 1338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.822;DP=97;Dels=0.00;FS=16.850;HaplotypeScore=21.9948;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-2.421;QD=13.80;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,41:97:99:1367,0,1887 -chr1 33916 . A T 1213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.196;DP=82;Dels=0.00;FS=19.829;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.075;QD=14.80;ReadPosRankSum=1.230;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:45,37:82:99:1242,0,1531 -chr1 33954 . T A 3289.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=2;MLEAF=1.00;MQ=59.22;MQ0=0;QD=34.54;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:3318,250,0 -chr1 33959 . A T 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.821;DP=80;Dels=0.00;FS=8.032;HaplotypeScore=19.9908;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-1.205;QD=10.91;ReadPosRankSum=-0.277;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:52,28:80:99:901,0,1837 -chr1 33967 . G T 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=83;Dels=0.00;FS=3.410;HaplotypeScore=22.8560;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.531;QD=6.85;ReadPosRankSum=0.160;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:597,0,2149 -chr1 33970 . T C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.516;DP=83;Dels=0.00;FS=4.648;HaplotypeScore=21.8565;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.792;QD=9.15;ReadPosRankSum=-1.739;EFF=UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|),UTR_3_PRIME(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|) GT:AD:DP:GQ:PL 0/1:56,26:83:99:788,0,1880 -chr1 33978 . T C 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.032;QD=8.11;ReadPosRankSum=-1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,23:81:99:685,0,2028 -chr1 33982 . G T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.029;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-3.048;QD=7.57;ReadPosRankSum=-1.195;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,21:77:99:611,0,1932 -chr1 34048 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=83;Dels=0.00;FS=3.608;HaplotypeScore=36.7760;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=1;MQRankSum=2.374;QD=5.44;ReadPosRankSum=1.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:480,0,2239 -chr1 34056 . A T 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.173;DP=83;Dels=0.00;FS=11.444;HaplotypeScore=20.9499;MLEAC=1;MLEAF=0.500;MQ=55.66;MQ0=1;MQRankSum=-5.405;QD=13.89;ReadPosRankSum=-2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,36:83:99:1181,0,1566 -chr1 34066 . T C 1342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.343;DP=87;Dels=0.00;FS=8.990;HaplotypeScore=6.9949;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=2;MQRankSum=-5.146;QD=15.43;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1371,0,1526 -chr1 34080 . G A 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=97;Dels=0.00;FS=6.820;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-2.713;QD=2.35;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,13:97:99:256,0,2928 -chr1 34081 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.776;DP=97;Dels=0.00;FS=1.486;HaplotypeScore=18.9960;MLEAC=1;MLEAF=0.500;MQ=55.90;MQ0=2;MQRankSum=-3.102;QD=0.20;ReadPosRankSum=1.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,8:97:48:48,0,3121 -chr1 34096 . C A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.605;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=1;MQRankSum=0.463;QD=5.36;ReadPosRankSum=3.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,22:104:99:586,0,2872 -chr1 34098 . A G 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-3.070;QD=8.59;ReadPosRankSum=3.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,31:103:99:913,0,2440 -chr1 34099 . T A 3974.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=13.7725;MLEAC=2;MLEAF=1.00;MQ=56.44;MQ0=1;QD=32.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:4003,298,0 -chr1 34115 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=117;Dels=0.00;FS=2.007;HaplotypeScore=38.4977;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=0.701;QD=4.35;ReadPosRankSum=0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,22:117:99:537,0,3369 -chr1 34126 . A G 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=133;Dels=0.00;FS=3.779;HaplotypeScore=3.5158;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=1;MQRankSum=4.108;QD=6.87;ReadPosRankSum=-0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,34:133:99:942,0,3399 -chr1 34143 . T C 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.256;DP=120;Dels=0.00;FS=6.188;HaplotypeScore=2.5772;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=1.550;QD=10.02;ReadPosRankSum=-0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,40:120:99:1231,0,2753 -chr1 34161 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.244;DP=113;Dels=0.00;FS=0.978;HaplotypeScore=2.7868;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=1;MQRankSum=-0.596;QD=3.30;ReadPosRankSum=1.772;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,18:113:99:401,0,3276 -chr1 34191 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=45;Dels=0.00;FS=9.532;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=0.990;QD=18.35;ReadPosRankSum=1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:854,0,672 -chr1 34210 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.402;DP=49;Dels=0.00;FS=6.502;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.291;QD=18.63;ReadPosRankSum=0.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:941,0,668 -chr1 34256 . A T 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.236;DP=36;Dels=0.00;FS=2.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.317;QD=15.52;ReadPosRankSum=1.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:587,0,649 -chr1 34258 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.991;QD=16.78;ReadPosRankSum=1.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:582,0,541 -chr1 34267 . C T 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=43;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.832;QD=12.16;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:551,0,893 -chr1 34273 . T C 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.491;DP=50;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.867;QD=19.76;ReadPosRankSum=0.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1016,0,658 -chr1 34278 . G C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.618;DP=51;Dels=0.00;FS=4.059;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.998;QD=12.47;ReadPosRankSum=-1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:664,0,1003 -chr1 34304 . G A 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=62;Dels=0.00;FS=23.390;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.136;QD=19.01;ReadPosRankSum=0.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1207,0,837 -chr1 34343 . C T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=52;Dels=0.00;FS=19.687;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.695;QD=19.98;ReadPosRankSum=-1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1067,0,693 -chr1 34344 . A G 2050.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2079,154,0 -chr1 34345 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;DP=53;Dels=0.00;FS=19.902;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.803;QD=12.77;ReadPosRankSum=1.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:705,0,1098 -chr1 34354 . G A 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=50;Dels=0.00;FS=11.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-1.241;QD=19.06;ReadPosRankSum=-1.182;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:981,0,660 -chr1 34385 . T G 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.698;DP=63;Dels=0.00;FS=57.702;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-5.740;QD=12.35;ReadPosRankSum=-2.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:806,0,989 -chr1 34399 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=48;Dels=0.00;FS=35.938;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.904;QD=7.72;ReadPosRankSum=0.742;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:48:99:399,0,977 -chr1 34401 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=47;Dels=0.00;FS=33.249;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.64;MQ0=0;MQRankSum=-4.904;QD=7.87;ReadPosRankSum=3.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,17:47:99:398,0,951 -chr1 34402 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=48;Dels=0.00;FS=36.487;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=0;MQRankSum=-4.958;QD=7.66;ReadPosRankSum=2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,17:48:99:396,0,1008 -chr1 34406 . A C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.650;DP=49;Dels=0.00;FS=17.048;HaplotypeScore=11.6760;MLEAC=1;MLEAF=0.500;MQ=51.77;MQ0=0;MQRankSum=-4.478;QD=1.51;ReadPosRankSum=2.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:102,0,1316 -chr1 34420 . C A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.268;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.57;ReadPosRankSum=4.621;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:279,0,1055 -chr1 34423 . G C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.758;DP=45;Dels=0.00;FS=27.476;HaplotypeScore=2.6635;MLEAC=1;MLEAF=0.500;MQ=52.05;MQ0=0;MQRankSum=-4.989;QD=5.55;ReadPosRankSum=4.989;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:278,0,1050 -chr1 34434 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=29;Dels=0.00;FS=1.455;HaplotypeScore=1.6637;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.196;QD=12.99;ReadPosRankSum=0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:405,0,509 -chr1 34498 . G A 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.733;DP=43;Dels=0.00;FS=5.601;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.273;QD=5.44;ReadPosRankSum=-0.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:262,0,1179 -chr1 34554 . A G 1556.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1585,120,0 -chr1 34561 . G A 1507.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;QD=28.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1536,123,0 -chr1 34587 . A G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=1.339;QD=18.49;ReadPosRankSum=-1.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:583,0,433 -chr1 34649 . C T 1118.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.34;MQ0=0;QD=36.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1147,84,0 -chr1 34723 . C T 1680.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.32;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1709,132,0 -chr1 34750 . C T 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=43;Dels=0.00;FS=6.795;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=0.628;QD=19.09;ReadPosRankSum=-1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:849,0,524 -chr1 34774 . C A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=4;MQRankSum=-2.557;QD=0.57;ReadPosRankSum=-2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,5:47:55:55,0,1310 -chr1 34784 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.92;MQ0=4;MQRankSum=-2.318;QD=1.69;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,6:46:99:106,0,1235 -chr1 34787 . C T 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=47.62;MQ0=4;MQRankSum=-2.195;QD=1.88;ReadPosRankSum=-0.682;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,6:45:99:113,0,1162 -chr1 34789 . C G 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=49;Dels=0.00;FS=1.637;HaplotypeScore=3.7163;MLEAC=1;MLEAF=0.500;MQ=47.34;MQ0=4;MQRankSum=-2.928;QD=2.06;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:129,0,1309 -chr1 34798 . A G 471.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.7158;MLEAC=1;MLEAF=0.500;MQ=43.82;MQ0=4;MQRankSum=-3.693;QD=7.86;ReadPosRankSum=-1.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:500,0,1302 -chr1 34809 . A C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=57;Dels=0.00;FS=2.399;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-4.370;QD=11.56;ReadPosRankSum=-0.063;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:687,0,973 -chr1 34810 . A T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.662;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=9.9935;MLEAC=1;MLEAF=0.500;MQ=43.70;MQ0=4;MQRankSum=-3.916;QD=8.31;ReadPosRankSum=1.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:502,0,1179 -chr1 34837 . G A 96.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.873;DP=54;Dels=0.00;FS=3.624;HaplotypeScore=73.4163;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=4;MQRankSum=-0.811;QD=1.79;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:125,0,1456 -chr1 34841 . G A 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.447;DP=52;Dels=0.00;FS=1.656;HaplotypeScore=90.4049;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=4;MQRankSum=-0.555;QD=2.05;ReadPosRankSum=2.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,10:52:99:135,0,1269 -chr1 34842 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.032;DP=49;Dels=0.00;FS=4.664;HaplotypeScore=91.4038;MLEAC=1;MLEAF=0.500;MQ=45.63;MQ0=4;MQRankSum=1.770;QD=0.55;ReadPosRankSum=-3.277;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,6:49:55:55,0,1172 -chr1 34864 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=48;Dels=0.00;FS=9.092;HaplotypeScore=49.3566;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-4.082;QD=7.35;ReadPosRankSum=3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,14:48:99:381,0,1135 -chr1 34865 . A G 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=48;Dels=0.00;FS=19.848;HaplotypeScore=56.3327;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=1;MQRankSum=-2.525;QD=1.75;ReadPosRankSum=3.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,7:48:99:112,0,1393 -chr1 34879 . G C 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=71;Dels=0.04;FS=44.625;HaplotypeScore=41.5658;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=4;MQRankSum=-6.053;QD=8.41;ReadPosRankSum=-2.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,27:68:99:625,0,1412 -chr1 34886 . A T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=74;Dels=0.00;FS=13.029;HaplotypeScore=24.3736;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=4;MQRankSum=-3.738;QD=0.75;ReadPosRankSum=-2.040;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:84:84,0,2145 -chr1 34898 . G A 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.605;DP=77;Dels=0.00;FS=42.789;HaplotypeScore=2.7797;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=4;MQRankSum=-5.924;QD=7.45;ReadPosRankSum=0.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,27:77:99:602,0,1708 -chr1 34918 . G A 1463.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.14;MQ0=1;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1492,114,0 -chr1 34936 . A C 1246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.631;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.68;MQ0=0;MQRankSum=-1.529;QD=26.64;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,33:34:78:1275,78,0 -chr1 34944 . G T 1292.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1321,99,0 -chr1 34949 . A T 1277.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.41;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1306,99,0 -chr1 34958 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7321;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=0;QD=28.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1146,87,0 -chr1 34980 . A C 287.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.76;MQ0=0;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:316,24,0 -chr1 34983 . A T 363.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.46;MQ0=0;QD=30.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:392,30,0 -chr1 34999 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=46;Dels=0.00;FS=5.844;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=-2.426;QD=3.97;ReadPosRankSum=-3.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,9:46:99:211,0,1278 -chr1 35001 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.443;DP=47;Dels=0.00;FS=8.113;HaplotypeScore=1.8318;MLEAC=1;MLEAF=0.500;MQ=50.71;MQ0=0;MQRankSum=-2.404;QD=4.29;ReadPosRankSum=-3.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,10:47:99:230,0,1358 -chr1 35012 . C T 3813.77 . AC=2;AF=1.00;AN=2;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=43.12;MQ0=18;QD=31.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:121:99:3842,307,0 -chr1 35021 . C A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.012;DP=128;Dels=0.00;FS=17.106;HaplotypeScore=9.9826;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=18;MQRankSum=-0.515;QD=0.24;ReadPosRankSum=2.376;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:118,10:128:59:59,0,3327 -chr1 35026 . C T 1359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.350;DP=127;Dels=0.00;FS=27.172;HaplotypeScore=10.7166;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=18;MQRankSum=-7.635;QD=10.71;ReadPosRankSum=-3.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,50:127:99:1388,0,1991 -chr1 35045 . T C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=133;Dels=0.00;FS=0.000;HaplotypeScore=40.6483;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=16;MQRankSum=3.328;QD=1.80;ReadPosRankSum=-0.988;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,16:133:99:267,0,3398 -chr1 35046 . A G 1154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.005;DP=127;Dels=0.00;FS=27.280;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=47.31;MQ0=14;MQRankSum=-8.458;QD=9.09;ReadPosRankSum=4.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,44:127:99:1183,0,2391 -chr1 35047 . T C 1481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.640;DP=126;Dels=0.00;FS=10.732;HaplotypeScore=40.9141;MLEAC=1;MLEAF=0.500;MQ=47.97;MQ0=14;MQRankSum=-8.951;QD=11.76;ReadPosRankSum=7.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,51:126:99:1510,0,2115 -chr1 35052 . A T 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=120;Dels=0.00;FS=2.223;HaplotypeScore=77.1059;MLEAC=1;MLEAF=0.500;MQ=49.27;MQ0=9;MQRankSum=2.565;QD=2.49;ReadPosRankSum=-2.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,16:120:99:327,0,3293 -chr1 35056 . C T 4286.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=62.1757;MLEAC=2;MLEAF=1.00;MQ=50.09;MQ0=7;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4315,337,0 -chr1 35058 . C T 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.351;DP=119;Dels=0.00;FS=4.666;HaplotypeScore=52.1779;MLEAC=1;MLEAF=0.500;MQ=50.70;MQ0=5;MQRankSum=-5.373;QD=3.75;ReadPosRankSum=2.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,23:119:99:475,0,3197 -chr1 35060 . G A 79.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.055;DP=117;Dels=0.00;FS=17.881;HaplotypeScore=51.1782;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=4;MQRankSum=-5.477;QD=0.68;ReadPosRankSum=3.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:103,14:117:99:108,0,3463 -chr1 35062 . G A 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.950;DP=113;Dels=0.00;FS=18.470;HaplotypeScore=57.1737;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-8.371;QD=7.89;ReadPosRankSum=5.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,36:113:99:920,0,2624 -chr1 35075 . G C 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.602;DP=107;Dels=0.00;FS=5.257;HaplotypeScore=32.3401;MLEAC=1;MLEAF=0.500;MQ=53.81;MQ0=0;MQRankSum=-8.219;QD=7.81;ReadPosRankSum=1.447;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,33:107:99:864,0,2509 -chr1 35077 . C G 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=33.3400;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=-5.857;QD=2.21;ReadPosRankSum=0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,14:107:99:265,0,2739 -chr1 35087 . C T 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=97;Dels=0.00;FS=2.025;HaplotypeScore=16.1548;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=0;MQRankSum=-7.328;QD=5.34;ReadPosRankSum=-2.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:546,0,2468 -chr1 35095 . C T 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=88;Dels=0.00;FS=1.246;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=0;MQRankSum=-5.345;QD=0.66;ReadPosRankSum=-2.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,11:88:86:86,0,2675 -chr1 35096 . A G 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=88;Dels=0.00;FS=1.393;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=-5.134;QD=0.32;ReadPosRankSum=-2.860;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,10:88:56:56,0,2777 -chr1 35164 . T G 3737.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=115.8992;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=26.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,95:95:99:3766,283,0 -chr1 35172 . A C 1478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.986;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=29.8173;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=2;MQRankSum=2.017;QD=14.64;ReadPosRankSum=1.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1507,0,1792 -chr1 35184 . C G 3588.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.10;MQ0=2;QD=33.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3617,277,0 -chr1 35205 . G A 2760.77 . AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=50.07;MQ0=2;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,80:80:99:2789,217,0 -chr1 35248 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.610;DP=59;Dels=0.00;FS=5.425;HaplotypeScore=11.8817;MLEAC=1;MLEAF=0.500;MQ=36.39;MQ0=4;MQRankSum=1.904;QD=4.39;ReadPosRankSum=-1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:287,0,1045 -chr1 35251 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=57;Dels=0.00;FS=6.294;HaplotypeScore=10.9876;MLEAC=1;MLEAF=0.500;MQ=36.08;MQ0=4;MQRankSum=-1.563;QD=8.49;ReadPosRankSum=2.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:512,0,755 -chr1 35260 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=49;Dels=0.00;FS=2.866;HaplotypeScore=5.9548;MLEAC=1;MLEAF=0.500;MQ=32.62;MQ0=4;MQRankSum=-1.252;QD=6.97;ReadPosRankSum=2.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:370,0,613 -chr1 35264 . G A 863.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=29.67;MQ0=4;QD=21.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:892,75,0 -chr1 35265 . C A 872.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=5.9548;MLEAC=2;MLEAF=1.00;MQ=30.23;MQ0=4;QD=20.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:75:901,75,0 -chr1 35283 . A G 1303.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.9990;MLEAC=2;MLEAF=1.00;MQ=35.84;MQ0=2;QD=24.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:1332,111,0 -chr1 35288 . G T 267.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=6.9868;MLEAC=1;MLEAF=0.500;MQ=37.11;MQ0=2;MQRankSum=-1.073;QD=4.96;ReadPosRankSum=2.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:296,0,926 -chr1 35292 . T C 1507.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.062;DP=60;Dels=0.00;FS=4.130;HaplotypeScore=6.9868;MLEAC=2;MLEAF=1.00;MQ=40.07;MQ0=2;MQRankSum=-0.557;QD=25.13;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,57:60:92:1536,92,0 -chr1 35316 . G A 2080.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=43.24;MQ0=1;QD=31.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2109,165,0 -chr1 35396 . A G 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.266;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.6626;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=3.180;QD=22.13;ReadPosRankSum=0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,29:43:99:980,0,405 -chr1 35403 . C T 1648.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.6634;MLEAC=2;MLEAF=1.00;MQ=54.38;MQ0=0;QD=35.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1677,126,0 -chr1 35406 . T G 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.6632;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=0;MQRankSum=-2.541;QD=9.24;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:398,0,951 -chr1 35445 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.615;DP=32;Dels=0.00;FS=3.211;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=0;MQRankSum=2.394;QD=21.12;ReadPosRankSum=-0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:704,0,324 -chr1 35483 . T A 221.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.021;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-1.247;QD=7.15;ReadPosRankSum=-1.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:250,0,750 -chr1 35491 . G T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.408;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=1;MLEAF=0.500;MQ=48.70;MQ0=0;MQRankSum=1.222;QD=19.59;ReadPosRankSum=1.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:753,0,428 -chr1 35497 . G A 1437.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=20.9946;MLEAC=2;MLEAF=1.00;MQ=48.93;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1466,111,0 -chr1 35499 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=21.8612;MLEAC=1;MLEAF=0.500;MQ=48.22;MQ0=1;MQRankSum=-1.459;QD=11.77;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:499,0,781 -chr1 35561 . A T 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;QD=35.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0 -chr1 35564 . T A 470.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:499,36,0 -chr1 35576 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.516;DP=32;Dels=0.00;FS=3.734;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.149;QD=7.84;ReadPosRankSum=-4.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:279,0,688 -chr1 35588 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=38;Dels=0.00;FS=5.225;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.261;QD=9.02;ReadPosRankSum=-2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,819 -chr1 35633 . G A 1506.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=53.32;MQ0=1;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1535,117,0 -chr1 35691 . T C 1735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.139;DP=81;Dels=0.00;FS=0.889;HaplotypeScore=1.7319;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.513;QD=21.43;ReadPosRankSum=0.601;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,51:81:99:1764,0,836 -chr1 35707 . C A 3162.77 . AC=2;AF=1.00;AN=2;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=32.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,82:82:99:3191,238,0 -chr1 35739 . G A 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=74;Dels=0.00;FS=17.134;HaplotypeScore=1.6483;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=0;MQRankSum=-0.689;QD=4.63;ReadPosRankSum=-2.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,16:74:99:371,0,2031 -chr1 35804 . T C 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.427;DP=109;Dels=0.00;FS=5.672;HaplotypeScore=3.9987;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=1;MQRankSum=-6.467;QD=6.13;ReadPosRankSum=0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,28:109:99:696,0,2821 -chr1 35807 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.906;DP=108;Dels=0.00;FS=7.240;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=2;MQRankSum=-6.417;QD=6.27;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,28:108:99:705,0,2709 -chr1 35843 . A T 2756.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=30.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2785,214,0 -chr1 35857 . C A 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=53.9074;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-0.442;QD=2.19;ReadPosRankSum=-1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,10:68:99:177,0,1820 -chr1 35860 . A C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.173;DP=74;Dels=0.00;FS=3.561;HaplotypeScore=73.8862;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=0;MQRankSum=0.722;QD=6.77;ReadPosRankSum=3.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,20:74:99:529,0,1811 -chr1 35870 . A T 2448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.943;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=27.0091;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=1;MQRankSum=2.228;QD=26.05;ReadPosRankSum=-0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,72:94:99:2477,0,566 -chr1 35900 . T C 3238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355;DP=119;Dels=0.00;FS=8.381;HaplotypeScore=194.4919;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=3;MQRankSum=-1.040;QD=27.22;ReadPosRankSum=1.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,96:119:99:3267,0,489 -chr1 35951 . T A 1015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=127;Dels=0.00;FS=0.000;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=2;MQRankSum=-0.149;QD=8.00;ReadPosRankSum=0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,37:127:99:1044,0,2832 -chr1 35968 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=50.3624;MLEAC=2;MLEAF=1.00;MQ=56.18;MQ0=0;QD=29.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2085,162,0 -chr1 35979 . G A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.196;DP=96;Dels=0.00;FS=17.564;HaplotypeScore=12.6997;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=2;MQRankSum=-1.392;QD=0.89;ReadPosRankSum=3.011;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,10:96:99:114,0,2869 -chr1 36004 . G A 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=72;Dels=0.00;FS=9.104;HaplotypeScore=76.6328;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-1.369;QD=0.25;ReadPosRankSum=-1.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,7:72:46:46,0,2207 -chr1 36045 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=132;Dels=0.00;FS=0.896;HaplotypeScore=43.4929;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.565;QD=3.33;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:110,22:132:99:468,0,3861 -chr1 36103 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=141;Dels=0.00;FS=41.173;HaplotypeScore=7.9970;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.254;QD=0.83;ReadPosRankSum=2.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:126,15:141:99:145,0,4391 -chr1 36153 . G C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=89;Dels=0.00;FS=7.730;HaplotypeScore=3.8273;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.014;QD=6.33;ReadPosRankSum=1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,21:89:99:592,0,2434 -chr1 36180 . T A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=100;Dels=0.00;FS=0.858;HaplotypeScore=3.7118;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.137;QD=7.78;ReadPosRankSum=0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,29:100:99:806,0,2559 -chr1 36205 . C T 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.427;DP=124;Dels=0.00;FS=0.755;HaplotypeScore=17.7034;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.466;QD=7.79;ReadPosRankSum=-0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,35:124:99:994,0,3181 -chr1 36213 . T C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.280;DP=132;Dels=0.00;FS=2.347;HaplotypeScore=19.5352;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-0.237;QD=1.48;ReadPosRankSum=0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,15:132:99:223,0,4265 -chr1 36259 . T C 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.248;DP=134;Dels=0.00;FS=3.770;HaplotypeScore=89.4890;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.222;QD=6.63;ReadPosRankSum=-1.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,33:134:99:916,0,3559 -chr1 36261 . A G 780.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.776;DP=132;Dels=0.00;FS=2.746;HaplotypeScore=86.5740;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.433;QD=5.91;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,32:132:99:809,0,3579 -chr1 36273 . T C 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.181;DP=118;Dels=0.00;FS=1.774;HaplotypeScore=117.6849;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.361;QD=5.75;ReadPosRankSum=-0.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,28:118:99:707,0,3229 -chr1 36286 . A T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=98;Dels=0.00;FS=0.915;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=2.210;QD=5.89;ReadPosRankSum=0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:605,0,2724 -chr1 36287 . A T 2373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.322;DP=96;Dels=0.00;FS=1.851;HaplotypeScore=132.2089;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=1;MQRankSum=0.853;QD=24.73;ReadPosRankSum=1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,68:96:99:2402,0,835 -chr1 36289 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.239;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=83.8835;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=1;MQRankSum=2.678;QD=5.48;ReadPosRankSum=1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,22:99:99:571,0,2798 -chr1 36290 . A T 2719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=84.8831;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=1;MQRankSum=-1.327;QD=27.20;ReadPosRankSum=-0.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,76:100:99:2748,0,648 -chr1 36320 . T A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=92;Dels=0.00;FS=0.939;HaplotypeScore=45.5348;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-3.017;QD=6.49;ReadPosRankSum=0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,23:92:99:625,0,2459 -chr1 36333 . G A 2428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.737;DP=96;Dels=0.00;FS=12.492;HaplotypeScore=24.9952;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=1;MQRankSum=-3.960;QD=25.30;ReadPosRankSum=0.841;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,71:96:99:2457,0,747 -chr1 36341 . T C 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=100;Dels=0.00;FS=14.157;HaplotypeScore=25.7839;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=1;MQRankSum=-3.263;QD=8.96;ReadPosRankSum=0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,30:100:99:924,0,2374 -chr1 36361 . G A 2302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=91;Dels=0.00;FS=2.218;HaplotypeScore=4.6978;MLEAC=1;MLEAF=0.500;MQ=55.09;MQ0=1;MQRankSum=-4.586;QD=25.31;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,69:91:99:2331,0,612 -chr1 36362 . T G 3325.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=3.9091;MLEAC=2;MLEAF=1.00;MQ=54.92;MQ0=1;QD=32.06;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3354,250,0 -chr1 36377 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=102;Dels=0.00;FS=10.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-5.406;QD=9.55;ReadPosRankSum=-0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,34:102:99:1002,0,2367 -chr1 36383 . T C 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.211;DP=103;Dels=0.00;FS=9.011;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-6.104;QD=9.69;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,36:103:99:1026,0,2320 -chr1 36393 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.454;DP=108;Dels=0.00;FS=2.766;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-6.108;QD=8.56;ReadPosRankSum=-0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,38:108:99:953,0,2423 -chr1 36408 . C T 2376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=104;Dels=0.00;FS=4.359;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=0;MQRankSum=-0.816;QD=22.85;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,77:104:99:2405,0,763 -chr1 36427 . A T 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.872;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=3.8148;MLEAC=1;MLEAF=0.500;MQ=51.50;MQ0=0;MQRankSum=-6.246;QD=6.56;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,28:94:99:645,0,2385 -chr1 36447 . A T 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.515;DP=107;Dels=0.00;FS=0.770;HaplotypeScore=3.5157;MLEAC=1;MLEAF=0.500;MQ=51.35;MQ0=0;MQRankSum=-6.584;QD=7.45;ReadPosRankSum=-0.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,35:107:99:825,0,2544 -chr1 36455 . A C 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.393;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=26.1134;MLEAC=1;MLEAF=0.500;MQ=51.36;MQ0=0;MQRankSum=-6.423;QD=7.65;ReadPosRankSum=-1.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:832,0,2482 -chr1 36464 . A C 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.836;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=48.2350;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-2.154;QD=5.85;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:602,0,2428 -chr1 36466 . C T 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.251;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=27.3765;MLEAC=1;MLEAF=0.500;MQ=51.39;MQ0=0;MQRankSum=-7.882;QD=17.75;ReadPosRankSum=-0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,59:96:99:1732,0,1115 -chr1 36483 . A G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-3.339;QD=5.65;ReadPosRankSum=0.429;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,21:91:99:542,0,2305 -chr1 36503 . T C 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.33;MQ0=0;MQRankSum=-0.635;QD=0.59;ReadPosRankSum=3.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,9:86:79:79,0,2347 -chr1 36504 . T C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.112;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=80.4897;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.130;QD=5.11;ReadPosRankSum=5.608;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,19:88:99:478,0,2018 -chr1 36505 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=79.0748;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=0;MQRankSum=-2.029;QD=4.27;ReadPosRankSum=5.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,17:88:99:404,0,2137 -chr1 36518 . A G 895.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.366;DP=101;Dels=0.00;FS=5.616;HaplotypeScore=12.9006;MLEAC=1;MLEAF=0.500;MQ=47.84;MQ0=0;MQRankSum=-1.467;QD=8.87;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,35:101:99:924,0,1480 -chr1 36532 . C G 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=115;Dels=0.00;FS=1.129;HaplotypeScore=33.9847;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=0;MQRankSum=2.072;QD=2.35;ReadPosRankSum=-1.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,15:115:99:298,0,2777 -chr1 36538 . C T 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=114;Dels=0.00;FS=3.778;HaplotypeScore=31.9878;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-8.542;QD=10.94;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,62:114:99:1275,0,1800 -chr1 36561 . C T 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=91;Dels=0.00;FS=7.684;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-6.542;QD=10.96;ReadPosRankSum=0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,33:91:99:1026,0,2069 -chr1 36566 . G A 965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=95;Dels=0.00;FS=7.431;HaplotypeScore=17.9938;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-6.234;QD=10.17;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,33:95:99:994,0,2189 -chr1 36574 . G A 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.133;DP=93;Dels=0.00;FS=3.666;HaplotypeScore=36.9659;MLEAC=1;MLEAF=0.500;MQ=54.28;MQ0=0;MQRankSum=-1.444;QD=4.45;ReadPosRankSum=1.036;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,18:93:99:442,0,2629 -chr1 36578 . G A 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=3.342;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=54.25;MQ0=0;MQRankSum=-5.365;QD=8.58;ReadPosRankSum=0.452;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,25:83:99:740,0,2021 -chr1 36581 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=24.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2478,187,0 -chr1 36582 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.643;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=35.9664;MLEAC=1;MLEAF=0.500;MQ=53.95;MQ0=0;MQRankSum=-1.757;QD=7.39;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,17:63:99:494,0,1649 -chr1 36587 . G A 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.268;DP=64;Dels=0.00;FS=1.061;HaplotypeScore=19.9719;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-4.946;QD=8.75;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,20:64:99:588,0,1587 -chr1 36594 . C T 1517.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1546,117,0 -chr1 36595 . A C 1513.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=24.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1542,120,0 -chr1 36601 . T C 1588.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=28.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1617,120,0 -chr1 36605 . C T 1541.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1570,117,0 -chr1 36616 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.18;MQ0=0;MQRankSum=-5.166;QD=11.34;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,15:38:99:459,0,805 -chr1 36621 . T C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.251;DP=36;Dels=0.00;FS=1.421;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=56.02;MQ0=0;MQRankSum=-4.460;QD=12.77;ReadPosRankSum=-1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,751 -chr1 36626 . C T 362.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=67;Dels=0.00;FS=6.207;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=53.11;MQ0=0;MQRankSum=-2.986;QD=5.41;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,15:67:99:391,0,1838 -chr1 36630 . T C 2560.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=1.9985;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=32.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2589,196,0 -chr1 36644 . A G 2044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.378;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=14.7297;MLEAC=1;MLEAF=0.500;MQ=53.58;MQ0=0;MQRankSum=-4.784;QD=26.56;ReadPosRankSum=-3.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,59:77:99:2073,0,508 -chr1 36651 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.907;DP=75;Dels=0.00;FS=2.457;HaplotypeScore=29.6893;MLEAC=1;MLEAF=0.500;MQ=53.83;MQ0=0;MQRankSum=-2.272;QD=4.60;ReadPosRankSum=-2.563;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:373,0,2131 -chr1 36656 . T C 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.462;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=16.6941;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-3.172;QD=3.11;ReadPosRankSum=2.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:277,0,2375 -chr1 36662 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=33.6895;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-1.103;QD=5.30;ReadPosRankSum=-1.807;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,17:80:99:452,0,2194 -chr1 36667 . A G 1572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.127;DP=88;Dels=0.00;FS=6.014;HaplotypeScore=19.7292;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=-3.331;QD=17.87;ReadPosRankSum=3.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,48:88:99:1601,0,1351 -chr1 36673 . G T 1522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.190;DP=87;Dels=0.00;FS=6.027;HaplotypeScore=50.6295;MLEAC=1;MLEAF=0.500;MQ=55.85;MQ0=0;MQRankSum=-3.286;QD=17.50;ReadPosRankSum=4.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,46:87:99:1551,0,1404 -chr1 36679 . G A,C 994.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.028;DP=83;Dels=0.00;FS=6.491;HaplotypeScore=3.6668;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.79;MQ0=0;MQRankSum=-3.906;QD=11.98;ReadPosRankSum=3.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:18,20,45:83:99:1681,965,1561,114,0,635 -chr1 36680 . G T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.401;DP=83;Dels=0.00;FS=1.073;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=0.921;QD=6.54;ReadPosRankSum=1.102;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:571,0,2139 -chr1 36681 . C A 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.220;DP=83;Dels=0.00;FS=2.291;HaplotypeScore=37.6485;MLEAC=1;MLEAF=0.500;MQ=55.95;MQ0=0;MQRankSum=0.648;QD=6.82;ReadPosRankSum=0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,21:83:99:594,0,2067 -chr1 36692 . C T 2055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.272;DP=84;Dels=0.00;FS=1.085;HaplotypeScore=21.9809;MLEAC=1;MLEAF=0.500;MQ=56.56;MQ0=0;MQRankSum=-2.422;QD=24.47;ReadPosRankSum=2.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,63:83:99:2084,0,534 -chr1 36698 . C A 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=83;Dels=0.00;FS=8.813;HaplotypeScore=18.7747;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=0;MQRankSum=0.221;QD=9.43;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,26:83:99:811,0,1969 -chr1 36713 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.135;DP=86;Dels=0.00;FS=1.174;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-5.106;QD=3.24;ReadPosRankSum=1.351;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:307,0,2592 -chr1 36714 . G A 1263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=86;Dels=0.00;FS=13.988;HaplotypeScore=17.5182;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=0;MQRankSum=-2.103;QD=14.69;ReadPosRankSum=-0.913;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,39:86:99:1292,0,1579 -chr1 36726 . G A 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=93;Dels=0.00;FS=12.102;HaplotypeScore=22.7149;MLEAC=1;MLEAF=0.500;MQ=57.37;MQ0=0;MQRankSum=2.213;QD=7.48;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,26:93:99:724,0,2287 -chr1 36731 . A G 2521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.037;DP=95;Dels=0.00;FS=2.183;HaplotypeScore=22.5037;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-1.447;QD=26.54;ReadPosRankSum=-2.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,76:95:99:2550,0,452 -chr1 36745 . C G 1591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.959;DP=97;Dels=0.00;FS=21.761;HaplotypeScore=2.1877;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=0;MQRankSum=-3.929;QD=16.41;ReadPosRankSum=1.490;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,49:97:99:1620,0,1518 -chr1 36764 . T C 1128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.112;DP=75;Dels=0.00;FS=17.360;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-2.794;QD=15.05;ReadPosRankSum=4.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,34:75:99:1157,0,1382 -chr1 36765 . T G 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.179;DP=75;Dels=0.00;FS=14.729;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-2.439;QD=14.36;ReadPosRankSum=4.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,33:75:99:1105,0,1430 -chr1 36767 . T C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.723;DP=76;Dels=0.00;FS=14.305;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.429;QD=15.77;ReadPosRankSum=3.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,36:76:99:1227,0,1335 -chr1 36796 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.162;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.8300;MLEAC=1;MLEAF=0.500;MQ=55.32;MQ0=0;MQRankSum=-6.512;QD=3.92;ReadPosRankSum=0.721;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:420,0,2683 -chr1 36817 . A G 1277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.149;DP=101;Dels=0.00;FS=1.617;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-2.941;QD=12.65;ReadPosRankSum=0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,45:101:99:1306,0,1931 -chr1 36850 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=113;Dels=0.00;FS=1.797;HaplotypeScore=42.9345;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=2.503;QD=6.50;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,28:113:99:763,0,2839 -chr1 36857 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=112;Dels=0.00;FS=6.385;HaplotypeScore=44.9514;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=-0.969;QD=4.13;ReadPosRankSum=-0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,21:112:99:491,0,3074 -chr1 36860 . T A 1910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.351;DP=112;Dels=0.00;FS=10.516;HaplotypeScore=64.8364;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=0;MQRankSum=0.143;QD=17.06;ReadPosRankSum=-0.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,60:112:99:1939,0,1715 -chr1 36867 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=115;Dels=0.00;FS=2.674;HaplotypeScore=43.9466;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.637;QD=7.66;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:115:99:909,0,2706 -chr1 36869 . A G 1776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.227;DP=112;Dels=0.00;FS=8.872;HaplotypeScore=21.9682;MLEAC=1;MLEAF=0.500;MQ=57.28;MQ0=1;MQRankSum=0.192;QD=15.86;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,55:112:99:1805,0,1829 -chr1 36898 . T G 3694.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=58.61;MQ0=1;QD=33.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3723,283,0 -chr1 36921 . G A 1095.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.776;DP=105;Dels=0.00;FS=1.642;HaplotypeScore=58.3901;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=0.967;QD=10.44;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,37:105:99:1124,0,2298 -chr1 36924 . T C 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=104;Dels=0.01;FS=11.095;HaplotypeScore=64.0672;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=1;MQRankSum=-0.152;QD=6.57;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,27:103:99:711,0,2625 -chr1 36928 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.431;DP=101;Dels=0.01;FS=13.977;HaplotypeScore=62.9043;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=1;MQRankSum=-0.447;QD=6.57;ReadPosRankSum=0.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,26:100:99:692,0,2509 -chr1 36933 . A G 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.768;DP=98;Dels=0.00;FS=1.634;HaplotypeScore=39.9143;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=3.401;QD=17.77;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,53:98:99:1770,0,1349 -chr1 36937 . C T 1282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.506;DP=96;Dels=0.00;FS=1.678;HaplotypeScore=21.5624;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-2.005;QD=13.36;ReadPosRankSum=-0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,42:96:99:1311,0,1753 -chr1 36951 . A G 3101.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.536;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=4.9494;MLEAC=2;MLEAF=1.00;MQ=54.16;MQ0=2;MQRankSum=1.691;QD=31.53;ReadPosRankSum=-1.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,85:86:99:3130,247,0 -chr1 36957 . A G 3098.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.648;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=3.2851;MLEAC=2;MLEAF=1.00;MQ=53.34;MQ0=2;MQRankSum=1.690;QD=28.09;ReadPosRankSum=-1.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,83:84:99:3127,241,0 -chr1 36980 . G C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=87;Dels=0.00;FS=5.532;HaplotypeScore=19.2784;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=1;MQRankSum=-2.668;QD=4.49;ReadPosRankSum=1.236;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UPSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,17:87:99:419,0,2324 -chr1 36986 . G A,T 2608.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.692;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=1.6385;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.63;MQ0=1;MQRankSum=-0.418;QD=29.64;ReadPosRankSum=-1.015;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:1,37,50:88:99:2946,1693,1587,1253,0,1106 -chr1 36990 . C T 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=88;Dels=0.00;FS=11.050;HaplotypeScore=16.5790;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=-2.013;QD=12.11;ReadPosRankSum=-0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:50,38:88:99:1094,0,1532 -chr1 37033 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=97;Dels=0.00;FS=29.507;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.66;MQ0=1;MQRankSum=1.751;QD=5.93;ReadPosRankSum=-1.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:74,23:97:99:603,0,2295 -chr1 37035 . G A 1683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=95;Dels=0.00;FS=32.836;HaplotypeScore=60.3467;MLEAC=1;MLEAF=0.500;MQ=44.62;MQ0=1;MQRankSum=-1.237;QD=17.72;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:39,56:95:99:1712,0,1110 -chr1 37086 . T C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=83;Dels=0.00;FS=8.748;HaplotypeScore=15.4050;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=1;MQRankSum=0.495;QD=6.67;ReadPosRankSum=-0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:60,23:83:99:582,0,1632 -chr1 37098 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.373;DP=78;Dels=0.00;FS=22.975;HaplotypeScore=17.1337;MLEAC=1;MLEAF=0.500;MQ=38.80;MQ0=1;MQRankSum=2.695;QD=3.33;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,15:78:99:288,0,1577 -chr1 37106 . A C 1959.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.633;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=9.8922;MLEAC=2;MLEAF=1.00;MQ=38.34;MQ0=1;MQRankSum=-0.247;QD=27.60;ReadPosRankSum=0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:1,70:71:99:1988,143,0 -chr1 37110 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=70;Dels=0.00;FS=20.054;HaplotypeScore=6.6058;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=1;MQRankSum=2.417;QD=3.65;ReadPosRankSum=-0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:57,13:70:99:284,0,1351 -chr1 37144 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.027;DP=75;Dels=0.01;FS=19.781;HaplotypeScore=21.1656;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=0.880;QD=7.64;ReadPosRankSum=0.119;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:49,25:74:99:601,0,1238 -chr1 37145 . G C 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=74;Dels=0.00;FS=1.342;HaplotypeScore=17.3626;MLEAC=1;MLEAF=0.500;MQ=33.28;MQ0=5;MQRankSum=-1.467;QD=1.58;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),START_GAINED(LOW||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:63,11:74:99:145,0,1687 -chr1 37146 . T C 1981.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.057;DP=73;Dels=0.00;FS=1.906;HaplotypeScore=17.3626;MLEAC=2;MLEAF=1.00;MQ=33.50;MQ0=5;MQRankSum=0.070;QD=27.15;ReadPosRankSum=-0.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:8,65:73:96:2010,96,0 -chr1 37167 . A G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.120;DP=75;Dels=0.00;FS=11.212;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=30.73;MQ0=5;MQRankSum=-0.123;QD=11.62;ReadPosRankSum=0.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),UTR_5_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:37,38:75:99:900,0,875 -chr1 37195 . A C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.498;DP=63;Dels=0.00;FS=34.326;HaplotypeScore=4.2993;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=6;MQRankSum=0.788;QD=4.57;ReadPosRankSum=1.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acC|T7|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,16:63:99:316,0,1127 -chr1 37208 . A C 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.181;DP=59;Dels=0.00;FS=17.669;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=30.82;MQ0=6;MQRankSum=0.988;QD=3.18;ReadPosRankSum=-1.371;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R12|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:47,12:59:99:216,0,1075 -chr1 37234 . A G 585.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.20;MQ0=5;QD=18.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P20|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,31:31:66:614,66,0 -chr1 37263 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.279;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=28.54;MQ0=4;MQRankSum=-0.748;QD=15.24;ReadPosRankSum=-0.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R30L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:10,26:36:99:577,0,117 -chr1 37277 . G A 105.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=37;Dels=0.00;FS=1.773;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=34.79;MQ0=3;MQRankSum=-0.596;QD=2.86;ReadPosRankSum=0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D35N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:27,10:37:99:134,0,662 -chr1 37288 . G T 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7802;MLEAC=1;MLEAF=0.500;MQ=39.98;MQ0=2;MQRankSum=-1.717;QD=2.72;ReadPosRankSum=0.610;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E38D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:36,11:47:99:156,0,970 -chr1 37303 . G A,T 1674.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.9926;MLEAC=1,1;MLEAF=0.500,0.500;MQ=46.60;MQ0=1;QD=26.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q43H|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q43|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/2:0,54,10:64:99:1936,347,200,1589,0,1559 -chr1 37305 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.346;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=23.7316;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-3.229;QD=1.45;ReadPosRankSum=2.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTc/gCc|V44A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:58,11:69:99:128,0,1781 -chr1 37314 . T C 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.448;DP=80;Dels=0.00;FS=1.179;HaplotypeScore=13.7857;MLEAC=1;MLEAF=0.500;MQ=48.12;MQ0=1;MQRankSum=1.805;QD=2.56;ReadPosRankSum=-1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I47T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:67,13:80:99:233,0,1973 -chr1 37336 . T C 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=2.6540;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=2.094;QD=8.05;ReadPosRankSum=0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D54|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:68,31:99:99:825,0,2213 -chr1 37361 . C A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.201;DP=104;Dels=0.00;FS=2.268;HaplotypeScore=5.3893;MLEAC=1;MLEAF=0.500;MQ=47.39;MQ0=6;MQRankSum=-1.098;QD=2.63;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Acc|P63T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:85,19:104:99:302,0,2484 -chr1 37404 . C T 1818.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=7;QD=27.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S77F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1847,159,0 -chr1 37414 . C A 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=53;Dels=0.00;FS=5.282;HaplotypeScore=6.9624;MLEAC=1;MLEAF=0.500;MQ=36.19;MQ0=7;MQRankSum=0.103;QD=3.94;ReadPosRankSum=-1.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccA|P80|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:40,13:53:99:237,0,933 -chr1 37420 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.384;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=5.8162;MLEAC=1;MLEAF=0.500;MQ=30.80;MQ0=7;MQRankSum=-0.141;QD=2.92;ReadPosRankSum=-0.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A82|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:30,10:40:99:145,0,591 -chr1 37458 . C T 161.8 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.06;MQ0=0;QD=12.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCa/gTa|A95V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,13:13:21:190,21,0 -chr1 37459 . A G 199.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.74;MQ0=0;QD=14.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A95|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,14:14:24:228,24,0 -chr1 37480 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=6.5977;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=1;MQRankSum=-3.019;QD=0.74;ReadPosRankSum=-1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V102|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:24,11:35:54:54,0,540 -chr1 37528 . A T 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.145;DP=99;Dels=0.00;FS=1.426;HaplotypeScore=2.0463;MLEAC=1;MLEAF=0.500;MQ=31.63;MQ0=3;MQRankSum=-2.642;QD=0.76;ReadPosRankSum=1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E118D|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:80,19:99:99:103,0,1690 -chr1 37553 . C T 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.618;DP=101;Dels=0.00;FS=0.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=32.94;MQ0=5;MQRankSum=-4.815;QD=2.51;ReadPosRankSum=1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L127|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:66,35:101:99:282,0,1683 -chr1 37602 . C G 2282.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=37.45;MQ0=5;QD=30.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S143C|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2311,186,0 -chr1 37607 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=74;Dels=0.00;FS=8.462;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=38.66;MQ0=5;MQRankSum=0.654;QD=9.08;ReadPosRankSum=1.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Gta|L145V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_36982_37621) GT:AD:DP:GQ:PL 0/1:43,31:74:99:700,0,1242 -chr1 37632 . T A 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.285;DP=70;Dels=0.00;FS=1.067;HaplotypeScore=165.3085;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=2;MQRankSum=-0.738;QD=5.55;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:417,0,1466 -chr1 37654 . T C 334.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.313;DP=79;Dels=0.00;FS=1.038;HaplotypeScore=60.4783;MLEAC=1;MLEAF=0.500;MQ=40.53;MQ0=0;MQRankSum=-1.554;QD=4.24;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,19:79:99:363,0,1794 -chr1 37679 . T C 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=69;Dels=0.01;FS=3.415;HaplotypeScore=131.3512;MLEAC=1;MLEAF=0.500;MQ=36.89;MQ0=2;MQRankSum=0.051;QD=0.20;ReadPosRankSum=-0.256;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,7:68:42:42,0,1556 -chr1 37687 . A G 1378.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=69.8232;MLEAC=2;MLEAF=1.00;MQ=34.79;MQ0=2;QD=20.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,65:66:99:1407,129,0 -chr1 37807 . C T 3962.77 . AC=2;AF=1.00;AN=2;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.64;MQ0=1;QD=33.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,105:105:99:3991,313,0 -chr1 37815 . A C 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.480;DP=107;Dels=0.00;FS=2.466;HaplotypeScore=2.4531;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=2.701;QD=2.40;ReadPosRankSum=1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,15:107:99:285,0,3245 -chr1 37819 . A G 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=106;Dels=0.00;FS=2.428;HaplotypeScore=49.4245;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=2;MQRankSum=3.086;QD=2.82;ReadPosRankSum=0.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:327,0,3127 -chr1 37827 . T C 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.964;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=281.8552;MLEAC=1;MLEAF=0.500;MQ=52.18;MQ0=2;MQRankSum=-1.196;QD=9.12;ReadPosRankSum=1.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,36:105:99:986,0,2427 -chr1 37829 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.186;DP=103;Dels=0.00;FS=1.099;HaplotypeScore=280.8554;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=2;MQRankSum=-5.390;QD=2.67;ReadPosRankSum=-1.865;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,16:103:99:303,0,3052 -chr1 37845 . C G 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.010;DP=105;Dels=0.00;FS=1.721;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.33;MQ0=2;MQRankSum=-0.287;QD=12.40;ReadPosRankSum=0.867;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,43:105:99:1330,0,2039 -chr1 37852 . A T 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=114;Dels=0.00;FS=7.406;HaplotypeScore=34.8876;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=2;MQRankSum=1.342;QD=6.74;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,29:114:99:797,0,2971 -chr1 37858 . G T 4069.77 . AC=2;AF=1.00;AN=2;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=23.1962;MLEAC=2;MLEAF=1.00;MQ=55.35;MQ0=2;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,106:106:99:4098,313,0 -chr1 37891 . A G 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.450;DP=105;Dels=0.00;FS=3.911;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=1;MQRankSum=1.160;QD=3.39;ReadPosRankSum=-1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,17:105:99:384,0,3122 -chr1 37931 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.853;DP=94;Dels=0.00;FS=6.552;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=3.443;QD=5.77;ReadPosRankSum=-0.138;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,22:94:99:571,0,2560 -chr1 37938 . T G 3392.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:3421,259,0 -chr1 37969 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=52;Dels=0.00;FS=4.310;HaplotypeScore=2.3113;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-4.200;QD=11.26;ReadPosRankSum=1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:614,0,1176 -chr1 37972 . A G 2052.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=3.3111;MLEAC=2;MLEAF=1.00;MQ=57.23;MQ0=0;QD=26.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:53:99:2081,154,0 -chr1 37991 . G C 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.39;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,153,0 -chr1 37996 . T C 1956.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=28.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1985,147,0 -chr1 37999 . A T 1924.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.53;MQ0=0;QD=43.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1953,144,0 -chr1 38000 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=50;Dels=0.00;FS=9.868;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=-4.276;QD=8.80;ReadPosRankSum=-0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:468,0,1240 -chr1 38009 . A C 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=62;Dels=0.00;FS=21.281;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.304;QD=13.03;ReadPosRankSum=-3.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:836,0,1230 -chr1 38043 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=22.795;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.05;MQ0=0;MQRankSum=1.867;QD=15.45;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1048,0,1191 -chr1 38145 . C A 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.426;DP=22;Dels=0.00;FS=4.506;HaplotypeScore=20.3295;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=1.195;QD=18.67;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,13:22:99:439,0,169 -chr1 38190 . A C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=20;Dels=0.00;FS=37.992;HaplotypeScore=15.6751;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-3.279;QD=16.94;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:8,12:20:99:367,0,253 -chr1 38209 . G T 1079.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=11.5981;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1108,84,0 -chr1 38232 . G A 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.397;DP=26;Dels=0.00;FS=45.405;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-4.243;QD=19.84;ReadPosRankSum=-2.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:544,0,277 -chr1 38259 . T A 394.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.43;MQ0=0;QD=32.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:33:423,33,0 -chr1 38267 . C T 397.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=23.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:426,33,0 -chr1 38269 . G C 393.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=28.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:422,33,0 -chr1 38272 . G A 407.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.95;MQ0=0;QD=24.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:436,33,0 -chr1 38282 . G A 562.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:591,45,0 -chr1 38290 . T G 1662.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.33;MQ0=0;QD=30.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1691,132,0 -chr1 38305 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.174;DP=54;Dels=0.00;FS=1.164;HaplotypeScore=26.0834;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-0.232;QD=7.13;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:413,0,1363 -chr1 38320 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.621;DP=61;Dels=0.00;FS=5.712;HaplotypeScore=186.2137;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=2.727;QD=8.73;ReadPosRankSum=0.530;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:561,0,1414 -chr1 38327 . A G 2319.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=146.9227;MLEAC=2;MLEAF=1.00;MQ=53.56;MQ0=0;QD=29.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,61:63:99:2348,184,0 -chr1 38332 . G C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.367;DP=64;Dels=0.00;FS=1.052;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=3.453;QD=7.42;ReadPosRankSum=-2.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,19:64:99:503,0,1580 -chr1 38333 . G A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.193;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=20.8715;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=-3.324;QD=11.43;ReadPosRankSum=2.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:771,0,1350 -chr1 38335 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.608;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=19.8719;MLEAC=1;MLEAF=0.500;MQ=53.87;MQ0=0;MQRankSum=-3.117;QD=12.89;ReadPosRankSum=1.435;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,27:66:99:879,0,1194 -chr1 38344 . C T 2874.77 . AC=2;AF=1.00;AN=2;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=36.8803;MLEAC=2;MLEAF=1.00;MQ=54.82;MQ0=0;QD=32.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,73:73:99:2903,220,0 -chr1 38350 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=2.904;QD=7.78;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,26:91:99:736,0,2251 -chr1 38352 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.858;DP=91;Dels=0.00;FS=0.951;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=0;MQRankSum=3.445;QD=5.45;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:91:99:524,0,2399 -chr1 38354 . A G 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=92;Dels=0.00;FS=1.151;HaplotypeScore=33.7387;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=0.796;QD=1.80;ReadPosRankSum=-3.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,13:92:99:194,0,2761 -chr1 38356 . C T 3570.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.7339;MLEAC=2;MLEAF=1.00;MQ=55.21;MQ0=0;QD=30.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3599,268,0 -chr1 38380 . G C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=103;Dels=0.00;FS=1.016;HaplotypeScore=5.5532;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=0.452;QD=3.40;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,18:103:99:378,0,2986 -chr1 38386 . A G 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.945;DP=101;Dels=0.00;FS=2.163;HaplotypeScore=5.8191;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=1.265;QD=4.05;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,18:101:99:437,0,2897 -chr1 38406 . A G 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.994;DP=110;Dels=0.00;FS=0.886;HaplotypeScore=38.9762;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=2.927;QD=5.29;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,24:110:99:610,0,2961 -chr1 38410 . G C 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.160;DP=107;Dels=0.00;FS=5.387;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=1.092;QD=8.61;ReadPosRankSum=-0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,32:107:99:949,0,2628 -chr1 38412 . A G 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=107;Dels=0.00;FS=1.876;HaplotypeScore=39.9755;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.410;QD=5.99;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),INTRON(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,26:107:99:669,0,2864 -chr1 38514 . A G 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=93;Dels=0.00;FS=5.348;HaplotypeScore=43.8521;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-1.505;QD=3.79;ReadPosRankSum=1.100;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I168V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:73,19:93:99:381,0,2418 -chr1 38516 . T G 3066.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.284;DP=85;Dels=0.00;FS=3.166;HaplotypeScore=43.8875;MLEAC=2;MLEAF=1.00;MQ=49.63;MQ0=0;MQRankSum=-0.509;QD=31.58;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I168M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:1,84:85:99:3095,218,0 -chr1 38519 . A C 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.706;DP=83;Dels=0.00;FS=18.028;HaplotypeScore=44.8742;MLEAC=1;MLEAF=0.500;MQ=49.02;MQ0=0;MQRankSum=-2.301;QD=15.17;ReadPosRankSum=1.618;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcA/gcC|A169|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:40,43:83:99:1287,0,1261 -chr1 38524 . G T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=87;Dels=0.00;FS=8.398;HaplotypeScore=47.8556;MLEAC=1;MLEAF=0.500;MQ=48.63;MQ0=0;MQRankSum=0.082;QD=6.37;ReadPosRankSum=1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gTt|G171V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:64,23:87:99:582,0,2000 -chr1 38580 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.789;DP=83;Dels=0.00;FS=10.079;HaplotypeScore=4.2557;MLEAC=1;MLEAF=0.500;MQ=42.00;MQ0=0;MQRankSum=1.229;QD=9.35;ReadPosRankSum=-1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A190T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:49,33:83:99:804,0,1512 -chr1 38614 . G T 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=88;Dels=0.00;FS=8.617;HaplotypeScore=41.5773;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=-1.852;QD=7.99;ReadPosRankSum=-1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R201L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:62,26:88:99:731,0,1964 -chr1 38616 . C T 1299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.710;DP=88;Dels=0.00;FS=3.034;HaplotypeScore=74.9440;MLEAC=1;MLEAF=0.500;MQ=46.09;MQ0=0;MQRankSum=2.195;QD=14.77;ReadPosRankSum=0.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L202|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:45,43:88:99:1328,0,1423 -chr1 38621 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=92;Dels=0.00;FS=8.548;HaplotypeScore=74.6108;MLEAC=1;MLEAF=0.500;MQ=45.88;MQ0=0;MQRankSum=-2.005;QD=6.60;ReadPosRankSum=-1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N203|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:68,24:92:99:635,0,2194 -chr1 38624 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.167;DP=92;Dels=0.00;FS=18.358;HaplotypeScore=71.5984;MLEAC=1;MLEAF=0.500;MQ=45.57;MQ0=0;MQRankSum=-0.682;QD=4.52;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A204|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:70,22:92:99:444,0,2305 -chr1 38633 . G A 1358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.729;DP=93;Dels=0.00;FS=4.284;HaplotypeScore=20.6300;MLEAC=1;MLEAF=0.500;MQ=46.35;MQ0=0;MQRankSum=1.841;QD=14.61;ReadPosRankSum=0.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P207|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,51:93:99:1387,0,1217 -chr1 38643 . A G 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.552;DP=96;Dels=0.00;FS=1.832;HaplotypeScore=4.1979;MLEAC=1;MLEAF=0.500;MQ=45.75;MQ0=0;MQRankSum=1.806;QD=17.82;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T211A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,54:96:99:1739,0,1020 -chr1 38657 . C T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.378;DP=85;Dels=0.00;FS=2.540;HaplotypeScore=14.1583;MLEAC=1;MLEAF=0.500;MQ=45.85;MQ0=1;MQRankSum=1.974;QD=26.04;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H215|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,70:85:99:2242,0,177 -chr1 38659 . A C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.241;DP=83;Dels=0.00;FS=9.582;HaplotypeScore=13.1589;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=1.020;QD=5.08;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E216A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:63,20:83:99:450,0,1930 -chr1 38708 . T C 1093.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.976;DP=42;Dels=0.00;FS=2.564;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=2;MQRankSum=1.592;QD=26.04;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D232|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:3,39:42:29:1122,29,0 -chr1 38723 . C T 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=4.5678;MLEAC=1;MLEAF=0.500;MQ=34.19;MQ0=2;MQRankSum=1.958;QD=16.83;ReadPosRankSum=-0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S237|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,22:30:76:533,0,76 -chr1 38732 . C T 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.472;DP=25;Dels=0.00;FS=2.077;HaplotypeScore=8.5290;MLEAC=1;MLEAF=0.500;MQ=28.41;MQ0=2;MQRankSum=1.921;QD=7.63;ReadPosRankSum=-1.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F240|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,9:25:99:219,0,204 -chr1 38739 . A G 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.986;DP=21;Dels=0.00;FS=14.564;HaplotypeScore=7.2577;MLEAC=1;MLEAF=0.500;MQ=26.73;MQ0=2;MQRankSum=1.056;QD=11.42;ReadPosRankSum=-1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T243A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:7,14:21:61:268,0,61 -chr1 38754 . C T 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.922;DP=27;Dels=0.00;FS=23.314;HaplotypeScore=3.4383;MLEAC=1;MLEAF=0.500;MQ=24.11;MQ0=1;MQRankSum=1.291;QD=6.03;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L248|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:17,10:27:99:191,0,164 -chr1 38813 . G A 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=45;Dels=0.00;FS=10.745;HaplotypeScore=6.7165;MLEAC=1;MLEAF=0.500;MQ=23.36;MQ0=6;MQRankSum=0.418;QD=3.44;ReadPosRankSum=-0.933;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T267|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,14:45:99:183,0,334 -chr1 38818 . G A 239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.899;DP=44;Dels=0.00;FS=36.491;HaplotypeScore=10.4483;MLEAC=1;MLEAF=0.500;MQ=23.61;MQ0=6;MQRankSum=2.543;QD=5.45;ReadPosRankSum=-1.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C269Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,12:44:99:268,0,339 -chr1 38827 . G T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.662;DP=48;Dels=0.00;FS=16.528;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.16;MQ0=7;MQRankSum=0.544;QD=3.04;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cTc|R272L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,14:48:99:174,0,437 -chr1 38828 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.199;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=14.4027;MLEAC=1;MLEAF=0.500;MQ=23.63;MQ0=7;MQRankSum=1.593;QD=10.36;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgT|R272|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:16,33:49:99:536,0,103 -chr1 38834 . G A 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.131;DP=50;Dels=0.00;FS=1.394;HaplotypeScore=10.1537;MLEAC=1;MLEAF=0.500;MQ=24.71;MQ0=8;MQRankSum=0.472;QD=5.02;ReadPosRankSum=0.341;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgA|R274|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,18:50:99:279,0,381 -chr1 38874 . G A 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.215;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=9.5155;MLEAC=1;MLEAF=0.500;MQ=24.48;MQ0=8;MQRankSum=-0.446;QD=6.30;ReadPosRankSum=0.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V288M|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:22,21:43:99:299,0,317 -chr1 38881 . G A 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=41;Dels=0.00;FS=18.266;HaplotypeScore=21.0278;MLEAC=1;MLEAF=0.500;MQ=26.69;MQ0=6;MQRankSum=0.334;QD=1.80;ReadPosRankSum=-1.159;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGc/tAc|C290Y|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:30,11:41:99:102,0,593 -chr1 38886 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=42;Dels=0.00;FS=1.336;HaplotypeScore=14.7997;MLEAC=1;MLEAF=0.500;MQ=27.24;MQ0=6;MQRankSum=0.652;QD=4.83;ReadPosRankSum=2.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V292I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:31,11:42:99:231,0,490 -chr1 38927 . G A 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.113;DP=30;Dels=0.00;FS=1.455;HaplotypeScore=5.5545;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=1;MQRankSum=-0.895;QD=9.99;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G305|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:15,15:30:99:328,0,330 -chr1 38933 . C T 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.620;DP=28;Dels=0.00;FS=4.494;HaplotypeScore=6.2885;MLEAC=1;MLEAF=0.500;MQ=33.72;MQ0=0;MQRankSum=-1.020;QD=1.35;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y307|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:23,5:28:66:66,0,561 -chr1 38942 . G C 697.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=10.5944;MLEAC=2;MLEAF=1.00;MQ=34.49;MQ0=0;QD=26.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggC|G310|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,26:26:63:726,63,0 -chr1 38949 . T C 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.480;DP=23;Dels=0.00;FS=6.415;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=34.90;MQ0=0;MQRankSum=1.291;QD=14.51;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Ctt|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,14:23:99:362,0,165 -chr1 38951 . T G 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=21;Dels=0.00;FS=2.884;HaplotypeScore=5.1982;MLEAC=1;MLEAF=0.500;MQ=36.04;MQ0=0;MQRankSum=0.151;QD=1.18;ReadPosRankSum=-2.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F313L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,3:21:53:53,0,465 -chr1 38954 . A G 534.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=2;MLEAF=1.00;MQ=36.30;MQ0=0;QD=28.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00030|mRNA||GSCOCT00012437001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P314|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,19:19:48:563,48,0 -chr1 38996 . T G 345.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=32.02;MQ0=1;QD=19.21;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctG|L328|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,13:18:30:374,30,0 -chr1 38998 . G A 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=22;Dels=0.00;FS=3.358;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=30.79;MQ0=1;MQRankSum=2.426;QD=14.94;ReadPosRankSum=2.499;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gAa|G329E|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:9,13:22:30:357,0,30 -chr1 39012 . C T 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.081;DP=31;Dels=0.00;FS=6.864;HaplotypeScore=3.8698;MLEAC=1;MLEAF=0.500;MQ=29.64;MQ0=2;MQRankSum=0.242;QD=0.99;ReadPosRankSum=1.534;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L334|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:25,6:31:59:59,0,466 -chr1 39047 . T C 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.226;DP=43;Dels=0.00;FS=8.463;HaplotypeScore=12.3919;MLEAC=1;MLEAF=0.500;MQ=26.75;MQ0=5;MQRankSum=0.113;QD=2.27;ReadPosRankSum=-0.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D345|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:36,7:43:99:126,0,608 -chr1 39056 . A T 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.448;DP=51;Dels=0.00;FS=13.801;HaplotypeScore=11.9705;MLEAC=1;MLEAF=0.500;MQ=26.54;MQ0=6;MQRankSum=1.911;QD=6.82;ReadPosRankSum=-0.405;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K348N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:32,19:51:99:376,0,461 -chr1 39103 . C T 1400.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=3.9611;MLEAC=2;MLEAF=1.00;MQ=29.47;MQ0=10;QD=21.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gTg|A364V|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,66:66:99:1429,129,0 -chr1 39113 . C T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.057;DP=67;Dels=0.00;FS=2.370;HaplotypeScore=12.4314;MLEAC=1;MLEAF=0.500;MQ=30.14;MQ0=9;MQRankSum=-3.266;QD=8.16;ReadPosRankSum=1.680;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T367|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,41:67:99:575,0,677 -chr1 39116 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.016;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.93;MQ0=9;MQRankSum=3.100;QD=8.41;ReadPosRankSum=-0.858;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y368|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,24:67:99:592,0,634 -chr1 39117 . G C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.149;DP=67;Dels=0.00;FS=1.309;HaplotypeScore=10.4367;MLEAC=1;MLEAF=0.500;MQ=29.61;MQ0=9;MQRankSum=1.678;QD=16.32;ReadPosRankSum=-0.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V369L|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:18,49:67:99:1122,0,102 -chr1 39150 . G A 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.147;DP=74;Dels=0.00;FS=5.772;HaplotypeScore=13.8080;MLEAC=1;MLEAF=0.500;MQ=28.74;MQ0=6;MQRankSum=2.238;QD=5.12;ReadPosRankSum=1.855;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E380K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:57,17:74:99:407,0,823 -chr1 39172 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.714;DP=58;Dels=0.00;FS=4.464;HaplotypeScore=6.4651;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=1;MQRankSum=2.790;QD=5.15;ReadPosRankSum=0.121;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R387K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:44,14:58:99:327,0,622 -chr1 39178 . A C 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.108;DP=53;Dels=0.00;FS=7.365;HaplotypeScore=8.0329;MLEAC=1;MLEAF=0.500;MQ=27.39;MQ0=0;MQRankSum=2.138;QD=3.96;ReadPosRankSum=0.384;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gCg|E389A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:42,11:53:99:238,0,621 -chr1 39240 . C A 821.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.94;MQ0=0;QD=21.07;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P410T|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:78:850,78,0 -chr1 39253 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.96;MQ0=2;QD=20.64;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R414K|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,39:39:75:833,75,0 -chr1 39271 . G T 806.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.780;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=5.3949;MLEAC=2;MLEAF=1.00;MQ=26.69;MQ0=8;MQRankSum=2.441;QD=18.34;ReadPosRankSum=1.535;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aTa|R420I|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:9,35:44:50:835,50,0 -chr1 39276 . G T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.189;DP=48;Dels=0.00;FS=2.414;HaplotypeScore=5.3949;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=9;MQRankSum=0.777;QD=1.14;ReadPosRankSum=-0.609;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ttt|V422F|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:43,5:48:83:83,0,754 -chr1 39306 . G A 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.574;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.9525;MLEAC=1;MLEAF=0.500;MQ=26.06;MQ0=10;MQRankSum=0.296;QD=2.81;ReadPosRankSum=1.235;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D432N|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:41,8:49:99:166,0,570 -chr1 39324 . C T 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=8.4793;MLEAC=1;MLEAF=0.500;MQ=22.99;MQ0=11;MQRankSum=0.420;QD=3.08;ReadPosRankSum=-0.128;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L438|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:34,12:46:99:170,0,488 -chr1 39353 . C T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=9;MQRankSum=-0.726;QD=3.15;ReadPosRankSum=-0.286;EFF=SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H447|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:26,13:39:99:151,0,416 -chr1 39356 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=24.07;MQ0=9;MQRankSum=-0.636;QD=1.55;ReadPosRankSum=0.194;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S448|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:27,9:36:84:84,0,463 -chr1 39366 . C G 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.6622;MLEAC=1;MLEAF=0.500;MQ=24.65;MQ0=7;MQRankSum=1.387;QD=13.05;ReadPosRankSum=0.000;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgc/Ggc|R452G|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 0/1:8,25:33:68:459,0,68 -chr1 39388 . T C 309.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.36;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V459A|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:338,36,0 -chr1 39389 . T C 316.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.02;MQ0=2;QD=19.80;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V459|Cc01g00040|mRNA||GSCOCT00012436001|Exon_chr1_38460_39766) GT:AD:DP:GQ:PL 1/1:0,16:16:36:345,36,0 -chr1 39403 . T C 290.98 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.255;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.86;MQ0=2;MQRankSum=1.104;QD=17.12;ReadPosRankSum=-0.255;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:3,14:17:13:319,13,0 -chr1 39422 . T C 231.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.16;MQ0=1;QD=19.32;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:260,24,0 -chr1 39447 . T C 117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.212;DP=26;Dels=0.00;FS=9.558;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=4;MQRankSum=2.899;QD=4.53;ReadPosRankSum=-0.862;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,5:26:99:146,0,489 -chr1 39484 . T C 611.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8320;MLEAC=2;MLEAF=1.00;MQ=30.77;MQ0=3;QD=26.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:640,51,0 -chr1 39510 . G A 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=20;Dels=0.00;FS=2.963;HaplotypeScore=7.6395;MLEAC=1;MLEAF=0.500;MQ=30.59;MQ0=3;MQRankSum=2.583;QD=6.49;ReadPosRankSum=-0.053;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:158,0,271 -chr1 39526 . A G 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.749;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.8216;MLEAC=1;MLEAF=0.500;MQ=28.66;MQ0=3;MQRankSum=-1.408;QD=6.20;ReadPosRankSum=1.749;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,8:14:99:115,0,155 -chr1 39567 . G C 371.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.10;MQ0=1;QD=15.49;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:42:400,42,0 -chr1 39584 . T C 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.136;DP=38;Dels=0.03;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.96;MQ0=1;MQRankSum=0.330;QD=14.99;ReadPosRankSum=0.330;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:74:598,0,74 -chr1 39587 . T C 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=40;Dels=0.03;FS=7.160;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.64;MQ0=1;MQRankSum=-0.714;QD=1.07;ReadPosRankSum=-0.165;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,7:39:71:71,0,649 -chr1 39596 . A T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.479;DP=52;Dels=0.00;FS=9.385;HaplotypeScore=3.4616;MLEAC=1;MLEAF=0.500;MQ=33.54;MQ0=1;MQRankSum=-1.360;QD=0.76;ReadPosRankSum=0.065;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,8:52:68:68,0,1009 -chr1 39631 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=77;Dels=0.00;FS=1.669;HaplotypeScore=7.9697;MLEAC=1;MLEAF=0.500;MQ=33.50;MQ0=1;MQRankSum=-0.513;QD=0.63;ReadPosRankSum=1.240;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:77:77:77,0,1546 -chr1 39643 . C A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.541;QD=1.37;ReadPosRankSum=-1.004;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:116,0,1373 -chr1 39644 . T C 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.657;DP=64;Dels=0.00;FS=1.508;HaplotypeScore=19.0317;MLEAC=1;MLEAF=0.500;MQ=34.92;MQ0=0;MQRankSum=0.599;QD=1.54;ReadPosRankSum=-0.966;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,9:64:99:127,0,1357 -chr1 39648 . G C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=58.2273;MLEAC=1;MLEAF=0.500;MQ=35.15;MQ0=0;MQRankSum=3.645;QD=21.79;ReadPosRankSum=-1.153;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,48:62:58:1379,0,58 -chr1 39651 . C G 1622.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=56.2590;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=0;QD=27.98;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:1651,138,0 -chr1 39652 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=58;Dels=0.00;FS=1.714;HaplotypeScore=66.4027;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-1.217;QD=0.34;ReadPosRankSum=0.263;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,7:58:48:48,0,1327 -chr1 39656 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=58;Dels=0.00;FS=17.787;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.14;MQ0=0;MQRankSum=-3.172;QD=6.93;ReadPosRankSum=1.492;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:430,0,880 -chr1 39657 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.197;DP=57;Dels=0.00;FS=10.567;HaplotypeScore=76.5466;MLEAC=1;MLEAF=0.500;MQ=36.40;MQ0=0;MQRankSum=-2.652;QD=3.77;ReadPosRankSum=1.846;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:243,0,1124 -chr1 39659 . C T 63.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.644;DP=56;Dels=0.00;FS=3.377;HaplotypeScore=37.1251;MLEAC=1;MLEAF=0.500;MQ=36.35;MQ0=0;MQRankSum=0.246;QD=1.14;ReadPosRankSum=0.199;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,8:56:92:92,0,1236 -chr1 39662 . A G 1224.79 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=54.7091;MLEAC=1;MLEAF=0.500;MQ=36.36;MQ0=0;QD=22.68;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:54:99:1385,118,0 -chr1 39664 . A C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.270;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=53.7676;MLEAC=1;MLEAF=0.500;MQ=36.29;MQ0=0;MQRankSum=-3.301;QD=0.21;ReadPosRankSum=1.393;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,11:53:39:39,0,1193 -chr1 39669 . G A 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.015;DP=50;Dels=0.00;FS=1.659;HaplotypeScore=69.6890;MLEAC=1;MLEAF=0.500;MQ=35.68;MQ0=0;MQRankSum=-0.075;QD=0.30;ReadPosRankSum=1.955;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,6:50:43:43,0,1137 -chr1 39670 . C T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=44;Dels=0.00;FS=2.860;HaplotypeScore=65.0263;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=1.698;QD=6.43;ReadPosRankSum=0.000;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:311,0,662 -chr1 39671 . C A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=69.6870;MLEAC=1;MLEAF=0.500;MQ=33.34;MQ0=0;MQRankSum=-2.765;QD=0.86;ReadPosRankSum=-0.217;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,11:44:66:66,0,915 -chr1 39673 . C A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.953;DP=42;Dels=0.00;FS=4.360;HaplotypeScore=59.5432;MLEAC=1;MLEAF=0.500;MQ=33.27;MQ0=0;MQRankSum=1.563;QD=9.57;ReadPosRankSum=0.902;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:430,0,510 -chr1 39676 . G A 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=41;Dels=0.00;FS=5.757;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=-0.931;QD=13.90;ReadPosRankSum=-0.215;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:12,29:41:99:598,0,311 -chr1 39678 . G A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=41;Dels=0.00;FS=6.236;HaplotypeScore=49.3994;MLEAC=1;MLEAF=0.500;MQ=33.35;MQ0=0;MQRankSum=1.091;QD=2.77;ReadPosRankSum=1.923;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,7:41:99:142,0,757 -chr1 39681 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=40;Dels=0.00;FS=1.360;HaplotypeScore=29.6132;MLEAC=1;MLEAF=0.500;MQ=33.13;MQ0=0;MQRankSum=1.431;QD=6.37;ReadPosRankSum=-0.635;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:283,0,590 -chr1 39685 . T C 820.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=10.9898;MLEAC=2;MLEAF=1.00;MQ=34.61;MQ0=0;QD=24.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:75:849,75,0 -chr1 39710 . A G 29.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.30;MQ0=0;MQRankSum=-0.736;QD=9.93;ReadPosRankSum=0.736;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:1,2:3:29:58,0,29 -chr1 39718 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr1 39719 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=19.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:67,6,0 -chr1 39722 . C A 37.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.27;MQ0=0;QD=18.87;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 -chr1 39725 . A G 39.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.42;MQ0=0;QD=13.25;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:67,6,0 -chr1 39728 . T C 39.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.26;MQ0=0;QD=9.94;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,4:4:6:67,6,0 -chr1 39736 . C T 237.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.78;MQ0=0;QD=19.82;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:266,24,0 -chr1 39751 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.930;QD=14.14;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:212,0,40 -chr1 39756 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=0;MQRankSum=0.761;QD=14.60;ReadPosRankSum=-0.085;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:3,10:13:40:218,0,40 -chr1 39758 . A G 241.78 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=30.63;MQ0=0;QD=18.60;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,12:13:24:270,24,0 -chr1 39777 . T A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=21.2570;MLEAC=1;MLEAF=0.500;MQ=36.27;MQ0=0;MQRankSum=1.668;QD=22.67;ReadPosRankSum=-0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,21:25:29:595,0,29 -chr1 39810 . T C 2246.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.769;DP=69;Dels=0.00;FS=2.663;HaplotypeScore=6.9006;MLEAC=2;MLEAF=1.00;MQ=41.37;MQ0=0;MQRankSum=1.949;QD=32.56;ReadPosRankSum=0.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,67:69:99:2275,144,0 -chr1 39820 . T G 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=75;Dels=0.00;FS=0.967;HaplotypeScore=5.9128;MLEAC=1;MLEAF=0.500;MQ=40.90;MQ0=0;MQRankSum=2.599;QD=10.33;ReadPosRankSum=1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:803,0,1331 -chr1 39826 . A C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.234;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=2.9758;MLEAC=1;MLEAF=0.500;MQ=40.59;MQ0=0;MQRankSum=2.470;QD=10.80;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:892,0,1425 -chr1 39866 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-3.071;DP=50;Dels=0.04;FS=1.930;HaplotypeScore=58.2750;MLEAC=1;MLEAF=0.500;MQ=43.17;MQ0=0;MQRankSum=0.945;QD=0.48;ReadPosRankSum=-3.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,5:48:52:52,0,1435 -chr1 39890 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.405;DP=34;Dels=0.00;FS=6.017;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.76;MQ0=0;MQRankSum=-2.459;QD=5.43;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:213,0,772 -chr1 39891 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=43;Dels=0.00;FS=1.596;HaplotypeScore=26.6204;MLEAC=1;MLEAF=0.500;MQ=40.93;MQ0=1;MQRankSum=-2.575;QD=3.44;ReadPosRankSum=2.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:176,0,1067 -chr1 39914 . A T 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=23.4102;MLEAC=1;MLEAF=0.500;MQ=40.57;MQ0=4;MQRankSum=0.588;QD=15.15;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:710,0,508 -chr1 39960 . C A,T 1177.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=42.42;MQ0=3;QD=25.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,22,25:47:99:1385,655,589,730,0,673 -chr1 39961 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.209;DP=47;Dels=0.00;FS=1.512;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=42.42;MQ0=3;MQRankSum=1.537;QD=14.12;ReadPosRankSum=-0.645;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:692,0,570 -chr1 39965 . A G 1518.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.4258;MLEAC=2;MLEAF=1.00;MQ=42.93;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,43:47:99:1547,126,0 -chr1 39976 . A G 1421.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.63;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1450,117,0 -chr1 39993 . A G 1637.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.2512;MLEAC=2;MLEAF=1.00;MQ=43.23;MQ0=0;QD=34.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1666,135,0 -chr1 40003 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.65;MQ0=0;MQRankSum=-3.665;QD=10.36;ReadPosRankSum=-2.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:453,0,706 -chr1 40005 . G A 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.023;DP=42;Dels=0.00;FS=12.410;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=0.221;QD=5.64;ReadPosRankSum=-2.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:265,0,940 -chr1 40007 . T A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=42;Dels=0.00;FS=4.327;HaplotypeScore=36.9270;MLEAC=1;MLEAF=0.500;MQ=41.54;MQ0=0;MQRankSum=3.748;QD=16.04;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:702,0,465 -chr1 40020 . C T 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=42;Dels=0.00;FS=15.124;HaplotypeScore=19.7971;MLEAC=1;MLEAF=0.500;MQ=41.55;MQ0=0;MQRankSum=1.991;QD=3.33;ReadPosRankSum=-2.632;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:99:168,0,1045 -chr1 40026 . A G 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.995;DP=44;Dels=0.00;FS=1.981;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1169 -chr1 40027 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.961;DP=44;Dels=0.00;FS=4.177;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=43.37;MQ0=0;MQRankSum=-1.590;QD=0.59;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,5:44:54:54,0,1200 -chr1 40029 . T C 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=38;Dels=0.00;FS=1.939;HaplotypeScore=27.1716;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=1.977;QD=25.73;ReadPosRankSum=0.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:5,32:38:68:1006,0,68 -chr1 40032 . T C 1048.85 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=0;MQRankSum=4.052;QD=28.35;ReadPosRankSum=-2.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,30:37:17:1077,0,17 -chr1 40037 . G T 1253.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=12.1898;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=0;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1282,108,0 -chr1 40050 . T C 1369.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.02;MQ0=0;QD=33.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1398,117,0 -chr1 40053 . C G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=5.5950;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=0;MQRankSum=1.442;QD=5.73;ReadPosRankSum=-0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,11:46:99:292,0,1057 -chr1 40084 . T A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=0.136;QD=13.27;ReadPosRankSum=-0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:665,0,943 -chr1 40096 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=0.374;QD=13.50;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:676,0,875 -chr1 40115 . G A 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.138;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=21.9178;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.379;QD=19.83;ReadPosRankSum=-1.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:980,0,633 -chr1 40186 . A G 2354.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=55.52;MQ0=0;QD=25.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2383,181,0 -chr1 40187 . T C 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=65;Dels=0.00;FS=14.460;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-3.656;QD=0.92;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,9:65:88:88,0,1926 -chr1 40200 . A G 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=16.7520;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=0.152;QD=1.71;ReadPosRankSum=-1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:153,0,2048 -chr1 40205 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=74;Dels=0.00;FS=1.321;HaplotypeScore=20.7504;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-4.008;QD=0.46;ReadPosRankSum=2.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:62:62,0,1934 -chr1 40212 . G A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=73;Dels=0.00;FS=1.331;HaplotypeScore=32.7378;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-0.609;QD=2.30;ReadPosRankSum=1.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,11:73:99:196,0,1961 -chr1 40216 . C T 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=77;Dels=0.00;FS=3.483;HaplotypeScore=23.9149;MLEAC=1;MLEAF=0.500;MQ=53.72;MQ0=0;MQRankSum=2.932;QD=7.82;ReadPosRankSum=-1.909;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,25:77:99:630,0,1637 -chr1 40235 . A G 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.661;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=35.5558;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-0.751;QD=9.86;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,29:80:99:817,0,1701 -chr1 40238 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.173;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=31.6873;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-3.462;QD=5.38;ReadPosRankSum=-2.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:475,0,2185 -chr1 40257 . G A 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.159;DP=89;Dels=0.00;FS=1.765;HaplotypeScore=39.6559;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-4.194;QD=14.62;ReadPosRankSum=-0.491;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,40:89:99:1329,0,1466 -chr1 40262 . T C 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.662;DP=90;Dels=0.00;FS=12.546;HaplotypeScore=41.5222;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.449;QD=14.11;ReadPosRankSum=-0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,40:90:99:1298,0,1623 -chr1 40276 . G A 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.940;DP=99;Dels=0.00;FS=2.892;HaplotypeScore=39.6083;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=4.526;QD=8.99;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,30:99:99:918,0,2233 -chr1 40279 . A C,G 2850.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=22.6138;MLEAC=1,1;MLEAF=0.500,0.500;MQ=54.31;MQ0=0;QD=28.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,73,17:100:99:3203,624,407,2579,0,2528 -chr1 40299 . T C 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=94;Dels=0.00;FS=4.739;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.77;MQ0=0;MQRankSum=1.944;QD=0.97;ReadPosRankSum=1.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,10:94:99:119,0,2786 -chr1 40300 . A G 1244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=96;Dels=0.00;FS=2.677;HaplotypeScore=9.9774;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.317;QD=12.97;ReadPosRankSum=1.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,43:96:99:1273,0,1762 -chr1 40316 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=100;Dels=0.00;FS=6.354;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.47;MQ0=0;MQRankSum=-6.856;QD=4.66;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,23:100:99:494,0,2754 -chr1 40317 . G A 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.745;DP=98;Dels=0.00;FS=6.790;HaplotypeScore=64.5095;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=0.824;QD=4.58;ReadPosRankSum=-0.313;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:477,0,2577 -chr1 40321 . T A 3751.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=68.1412;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3780,292,0 -chr1 40326 . T C 1103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=102;Dels=0.00;FS=8.509;HaplotypeScore=104.4492;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=5.492;QD=10.82;ReadPosRankSum=1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:65,37:102:99:1132,0,2119 -chr1 40331 . C T 611.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.325;DP=93;Dels=0.00;FS=0.000;HaplotypeScore=42.7177;MLEAC=1;MLEAF=0.500;MQ=54.62;MQ0=0;MQRankSum=3.620;QD=6.58;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:640,0,2316 -chr1 40336 . C T 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.612;DP=89;Dels=0.00;FS=7.137;HaplotypeScore=40.7185;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=4.995;QD=12.21;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,34:89:99:1115,0,1717 -chr1 40340 . T C 1638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=87;Dels=0.00;FS=8.927;HaplotypeScore=60.7684;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.839;QD=18.84;ReadPosRankSum=-0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,52:87:99:1667,0,1091 -chr1 40350 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.570;DP=100;Dels=0.00;FS=2.227;HaplotypeScore=42.2843;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=0;MQRankSum=-3.916;QD=2.79;ReadPosRankSum=-0.327;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:307,0,2907 -chr1 40357 . A G 1180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=101;Dels=0.00;FS=8.331;HaplotypeScore=60.4654;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-3.892;QD=11.69;ReadPosRankSum=-1.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,40:100:99:1209,0,1863 -chr1 40359 . T C 3820.77 . AC=2;AF=1.00;AN=2;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=60.4654;MLEAC=2;MLEAF=1.00;MQ=56.15;MQ0=0;QD=29.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:101:99:3849,295,0 -chr1 40367 . G A 1455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.630;DP=100;Dels=0.00;FS=2.623;HaplotypeScore=40.4721;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=3.679;QD=14.56;ReadPosRankSum=-0.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,45:100:99:1484,0,1789 -chr1 40385 . A T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.211;DP=99;Dels=0.00;FS=2.269;HaplotypeScore=13.6606;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=0;MQRankSum=-2.742;QD=3.11;ReadPosRankSum=-0.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,17:99:99:336,0,2801 -chr1 40386 . T C 3699.77 . AC=2;AF=1.00;AN=2;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=13.6606;MLEAC=2;MLEAF=1.00;MQ=57.21;MQ0=0;QD=26.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,100:100:99:3728,298,0 -chr1 40390 . C A 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=102;Dels=0.00;FS=10.470;HaplotypeScore=47.4671;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=0;MQRankSum=-0.627;QD=2.08;ReadPosRankSum=-1.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,14:102:99:240,0,3128 -chr1 40397 . T C 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=99;Dels=0.00;FS=2.447;HaplotypeScore=91.1211;MLEAC=1;MLEAF=0.500;MQ=57.63;MQ0=0;MQRankSum=-2.184;QD=2.04;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:230,0,3009 -chr1 40398 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=98;Dels=0.00;FS=0.959;HaplotypeScore=91.9098;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-0.904;QD=4.41;ReadPosRankSum=1.820;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,20:98:99:460,0,2711 -chr1 40401 . C A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.162;DP=96;Dels=0.00;FS=2.289;HaplotypeScore=54.1136;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-1.696;QD=3.29;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,16:96:99:344,0,2884 -chr1 40405 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.881;DP=97;Dels=0.00;FS=4.295;HaplotypeScore=68.8441;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=0;MQRankSum=1.976;QD=7.68;ReadPosRankSum=-0.753;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,27:97:99:773,0,2466 -chr1 40415 . A G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.202;DP=95;Dels=0.00;FS=4.129;HaplotypeScore=16.3079;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.121;QD=2.67;ReadPosRankSum=1.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:282,0,2906 -chr1 40423 . G A 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=14.9944;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-0.719;QD=7.61;ReadPosRankSum=-0.969;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,27:94:99:744,0,2306 -chr1 40444 . C T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=25.1958;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=1.888;QD=4.66;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,18:91:99:452,0,2590 -chr1 40450 . C T 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=86;Dels=0.00;FS=10.543;HaplotypeScore=36.1917;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=-0.407;QD=1.33;ReadPosRankSum=0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,10:86:99:143,0,2614 -chr1 40451 . C T 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.552;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=37.1784;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=0;MQRankSum=2.698;QD=1.68;ReadPosRankSum=0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,12:86:99:173,0,2633 -chr1 40454 . T C 3335.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=37.1746;MLEAC=2;MLEAF=1.00;MQ=54.30;MQ0=0;QD=34.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:88:99:3364,259,0 -chr1 40455 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=89;Dels=0.00;FS=5.908;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=0.165;QD=8.65;ReadPosRankSum=0.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,27:89:99:798,0,2174 -chr1 40458 . G A 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.752;DP=90;Dels=0.00;FS=1.024;HaplotypeScore=37.1645;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=1.062;QD=3.88;ReadPosRankSum=0.175;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,17:90:99:377,0,2596 -chr1 40468 . C T 3532.77 . AC=2;AF=1.00;AN=2;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=32.9796;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:94:99:3561,277,0 -chr1 40469 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.779;DP=94;Dels=0.00;FS=5.381;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-1.186;QD=0.15;ReadPosRankSum=2.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,8:94:42:42,0,3030 -chr1 40480 . C A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=106;Dels=0.00;FS=4.744;HaplotypeScore=40.7109;MLEAC=1;MLEAF=0.500;MQ=53.17;MQ0=0;MQRankSum=-0.111;QD=4.04;ReadPosRankSum=0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,21:106:99:456,0,3043 -chr1 40490 . T C 2948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.616;DP=107;Dels=0.00;FS=9.034;HaplotypeScore=71.4806;MLEAC=1;MLEAF=0.500;MQ=52.29;MQ0=0;MQRankSum=1.008;QD=27.56;ReadPosRankSum=2.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,85:107:99:2977,0,405 -chr1 40495 . C G 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.391;DP=114;Dels=0.00;FS=1.985;HaplotypeScore=71.4457;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-0.918;QD=5.58;ReadPosRankSum=1.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,23:114:99:664,0,2502 -chr1 40497 . G C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=69.4473;MLEAC=1;MLEAF=0.500;MQ=51.94;MQ0=0;MQRankSum=-0.543;QD=2.38;ReadPosRankSum=-0.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,17:112:99:295,0,3323 -chr1 40511 . A G 3183.76 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=116;Dels=0.00;FS=0.000;HaplotypeScore=39.7486;MLEAC=1;MLEAF=0.500;MQ=52.34;MQ0=0;MQRankSum=0.371;QD=27.45;ReadPosRankSum=0.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,92:116:99:3212,0,569 -chr1 40524 . G A 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.064;DP=123;Dels=0.00;FS=2.035;HaplotypeScore=26.4109;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=0;MQRankSum=-2.672;QD=2.92;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,21:123:99:387,0,3524 -chr1 40526 . G A 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=123;Dels=0.00;FS=2.894;HaplotypeScore=26.2780;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-0.204;QD=5.13;ReadPosRankSum=1.764;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:123:99:659,0,3056 -chr1 40541 . G T 4628.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=54.46;MQ0=0;QD=34.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,120:120:99:4657,346,0 -chr1 40559 . T A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.703;DP=122;Dels=0.00;FS=1.745;HaplotypeScore=75.4361;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=3.818;QD=5.47;ReadPosRankSum=1.838;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,27:122:99:695,0,3342 -chr1 40562 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=119;Dels=0.00;FS=6.618;HaplotypeScore=120.3506;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-3.315;QD=3.02;ReadPosRankSum=-1.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,20:119:99:388,0,3464 -chr1 40565 . G A 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=115;Dels=0.00;FS=3.367;HaplotypeScore=128.0268;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-0.666;QD=3.55;ReadPosRankSum=-1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,19:115:99:437,0,3355 -chr1 40570 . T A 2544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=116.1873;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.456;QD=20.86;ReadPosRankSum=-3.072;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,76:122:99:2573,0,1468 -chr1 40572 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.050;DP=126;Dels=0.00;FS=16.724;HaplotypeScore=113.1887;MLEAC=1;MLEAF=0.500;MQ=55.48;MQ0=0;MQRankSum=-3.211;QD=2.10;ReadPosRankSum=-0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,19:126:99:293,0,3847 -chr1 40574 . G A 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.747;DP=128;Dels=0.00;FS=3.770;HaplotypeScore=81.5684;MLEAC=1;MLEAF=0.500;MQ=55.49;MQ0=0;MQRankSum=1.064;QD=1.61;ReadPosRankSum=1.108;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,16:128:99:234,0,3817 -chr1 40587 . A G 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=153;Dels=0.00;FS=0.744;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=1;MQRankSum=2.151;QD=5.55;ReadPosRankSum=0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,34:153:99:877,0,4088 -chr1 40598 . A T 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.298;DP=145;Dels=0.00;FS=0.898;HaplotypeScore=3.5220;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=1;MQRankSum=-3.872;QD=2.10;ReadPosRankSum=2.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:124,21:145:99:333,0,4371 -chr1 40601 . T C 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.858;DP=141;Dels=0.00;FS=0.951;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=55.65;MQ0=1;MQRankSum=-4.326;QD=2.24;ReadPosRankSum=3.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:122,19:141:99:344,0,4357 -chr1 40604 . A G 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=140;Dels=0.00;FS=0.952;HaplotypeScore=3.7881;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=-4.123;QD=2.30;ReadPosRankSum=3.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:121,19:140:99:350,0,4326 -chr1 40607 . A T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=138;Dels=0.00;FS=2.058;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=1;MQRankSum=-3.796;QD=2.44;ReadPosRankSum=2.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:119,19:138:99:365,0,4122 -chr1 40613 . T C 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=138;Dels=0.00;FS=0.884;HaplotypeScore=34.9737;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=1;MQRankSum=-4.247;QD=2.75;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:408,0,4053 -chr1 40618 . A G 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=140;Dels=0.00;FS=8.579;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.14;MQ0=1;MQRankSum=1.916;QD=0.23;ReadPosRankSum=3.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:128,12:140:60:60,0,4583 -chr1 40619 . T G 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.123;DP=141;Dels=0.00;FS=6.410;HaplotypeScore=37.4958;MLEAC=1;MLEAF=0.500;MQ=54.05;MQ0=1;MQRankSum=-2.776;QD=2.23;ReadPosRankSum=-0.855;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:120,20:141:99:342,0,4240 -chr1 40629 . A T 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.928;DP=134;Dels=0.00;FS=0.868;HaplotypeScore=126.7357;MLEAC=1;MLEAF=0.500;MQ=53.57;MQ0=1;MQRankSum=-4.720;QD=3.33;ReadPosRankSum=-1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,22:134:99:474,0,3749 -chr1 40630 . C T 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.225;DP=133;Dels=0.00;FS=2.109;HaplotypeScore=106.7571;MLEAC=1;MLEAF=0.500;MQ=53.52;MQ0=1;MQRankSum=-3.232;QD=2.08;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:113,19:133:99:305,0,3912 -chr1 40631 . C T 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.935;DP=134;Dels=0.00;FS=0.896;HaplotypeScore=109.5452;MLEAC=1;MLEAF=0.500;MQ=53.51;MQ0=1;MQRankSum=-4.705;QD=3.01;ReadPosRankSum=-1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:112,21:134:99:432,0,3926 -chr1 40635 . C A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.206;DP=136;Dels=0.00;FS=10.739;HaplotypeScore=148.7017;MLEAC=1;MLEAF=0.500;MQ=53.34;MQ0=1;MQRankSum=5.098;QD=5.45;ReadPosRankSum=-0.010;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,29:136:99:770,0,3047 -chr1 40637 . G T 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.363;DP=138;Dels=0.00;FS=1.925;HaplotypeScore=146.7025;MLEAC=1;MLEAF=0.500;MQ=53.22;MQ0=1;MQRankSum=-4.406;QD=3.06;ReadPosRankSum=-1.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,22:138:99:450,0,4023 -chr1 40643 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=137;Dels=0.00;FS=0.905;HaplotypeScore=80.3353;MLEAC=1;MLEAF=0.500;MQ=53.30;MQ0=1;MQRankSum=-4.704;QD=2.56;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:117,20:137:99:379,0,4082 -chr1 40644 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=136;Dels=0.00;FS=0.917;HaplotypeScore=81.3352;MLEAC=1;MLEAF=0.500;MQ=53.25;MQ0=1;MQRankSum=-4.475;QD=2.54;ReadPosRankSum=-0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:116,20:136:99:373,0,4107 -chr1 40647 . G A 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=143;Dels=0.00;FS=7.049;HaplotypeScore=90.1298;MLEAC=1;MLEAF=0.500;MQ=52.42;MQ0=1;MQRankSum=6.086;QD=4.35;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:115,28:143:99:650,0,3953 -chr1 40653 . C T 5160.77 . AC=2;AF=1.00;AN=2;DP=138;Dels=0.00;FS=0.000;HaplotypeScore=104.2700;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=1;QD=24.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,138:138:99:5189,397,0 -chr1 40656 . C A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=136;Dels=0.00;FS=2.901;HaplotypeScore=65.3188;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=1;MQRankSum=3.870;QD=4.26;ReadPosRankSum=2.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:109,27:136:99:607,0,3691 -chr1 40663 . C T 1219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.892;DP=131;Dels=0.00;FS=1.470;HaplotypeScore=51.1808;MLEAC=1;MLEAF=0.500;MQ=50.95;MQ0=2;MQRankSum=0.022;QD=9.31;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,44:131:99:1248,0,2916 -chr1 40665 . G A 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.989;DP=129;Dels=0.00;FS=4.193;HaplotypeScore=50.1809;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=2;MQRankSum=3.905;QD=4.50;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:101,28:129:99:609,0,3457 -chr1 40667 . C A 4617.77 . AC=2;AF=1.00;AN=2;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=25.5251;MLEAC=2;MLEAF=1.00;MQ=50.53;MQ0=2;QD=27.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,125:125:99:4646,352,0 -chr1 40679 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=116;Dels=0.00;FS=3.025;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=-6.403;QD=4.21;ReadPosRankSum=0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:517,0,3113 -chr1 40680 . C A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=116;Dels=0.00;FS=5.789;HaplotypeScore=31.7934;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=2;MQRankSum=3.479;QD=5.26;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,27:116:99:638,0,3045 -chr1 40695 . G A 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=109;Dels=0.00;FS=4.432;HaplotypeScore=15.8769;MLEAC=1;MLEAF=0.500;MQ=48.67;MQ0=1;MQRankSum=4.736;QD=1.38;ReadPosRankSum=0.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,12:109:99:179,0,3292 -chr1 40702 . G A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.179;DP=118;Dels=0.00;FS=1.878;HaplotypeScore=12.9449;MLEAC=1;MLEAF=0.500;MQ=49.34;MQ0=1;MQRankSum=3.135;QD=5.11;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,24:118:99:631,0,3094 -chr1 40724 . C T 2276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.371;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=76.4647;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=1;MQRankSum=-4.544;QD=18.51;ReadPosRankSum=0.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,73:123:99:2305,0,1587 -chr1 40726 . A G 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=121;Dels=0.00;FS=0.855;HaplotypeScore=78.4642;MLEAC=1;MLEAF=0.500;MQ=50.50;MQ0=1;MQRankSum=3.987;QD=5.24;ReadPosRankSum=-0.827;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,25:121:99:662,0,3213 -chr1 40730 . T C 2668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.318;DP=119;Dels=0.00;FS=0.742;HaplotypeScore=131.5265;MLEAC=1;MLEAF=0.500;MQ=50.60;MQ0=1;MQRankSum=-1.336;QD=22.43;ReadPosRankSum=1.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,83:119:99:2697,0,1090 -chr1 40731 . T C 163.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=129.2953;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-0.479;QD=1.38;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,14:119:99:192,0,3588 -chr1 40742 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=108;Dels=0.00;FS=0.859;HaplotypeScore=18.6626;MLEAC=1;MLEAF=0.500;MQ=51.05;MQ0=1;MQRankSum=-5.117;QD=4.95;ReadPosRankSum=-1.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,26:108:99:563,0,2912 -chr1 40757 . C T 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=119;Dels=0.00;FS=2.628;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=1;MQRankSum=-5.477;QD=9.18;ReadPosRankSum=-1.588;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:119:99:1121,0,2615 -chr1 40760 . C T 4275.77 . AC=2;AF=1.00;AN=2;DP=117;Dels=0.00;FS=0.000;HaplotypeScore=23.5723;MLEAC=2;MLEAF=1.00;MQ=50.52;MQ0=1;QD=31.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,117:117:99:4304,331,0 -chr1 40769 . C T 3289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=123;Dels=0.00;FS=0.861;HaplotypeScore=41.4575;MLEAC=1;MLEAF=0.500;MQ=50.36;MQ0=1;MQRankSum=-4.495;QD=26.75;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,99:123:99:3318,0,576 -chr1 40773 . G A 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=126;Dels=0.00;FS=2.716;HaplotypeScore=43.4570;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=-2.084;QD=6.91;ReadPosRankSum=2.684;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,32:126:99:899,0,2993 -chr1 40788 . A C 1705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=118;Dels=0.00;FS=2.394;HaplotypeScore=117.6775;MLEAC=1;MLEAF=0.500;MQ=49.33;MQ0=1;MQRankSum=-6.557;QD=14.46;ReadPosRankSum=2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,62:118:99:1734,0,1876 -chr1 40789 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=123;Dels=0.00;FS=11.420;HaplotypeScore=119.6765;MLEAC=1;MLEAF=0.500;MQ=49.20;MQ0=1;MQRankSum=3.191;QD=5.27;ReadPosRankSum=-0.253;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,25:123:99:677,0,3103 -chr1 40791 . A G 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.823;DP=121;Dels=0.00;FS=1.004;HaplotypeScore=70.2853;MLEAC=1;MLEAF=0.500;MQ=49.03;MQ0=1;MQRankSum=-4.589;QD=2.12;ReadPosRankSum=1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,24:121:99:285,0,3412 -chr1 40795 . A T 129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=125;Dels=0.00;FS=0.000;HaplotypeScore=72.2808;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=1;MQRankSum=-2.514;QD=1.04;ReadPosRankSum=2.201;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:108,17:125:99:158,0,3699 -chr1 40803 . C T 2015.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.782;DP=118;Dels=0.00;FS=2.491;HaplotypeScore=47.3955;MLEAC=1;MLEAF=0.500;MQ=47.79;MQ0=1;MQRankSum=-6.205;QD=17.08;ReadPosRankSum=-0.663;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:46,71:118:99:2044,0,1478 -chr1 40809 . C T 2959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.887;DP=111;Dels=0.00;FS=0.920;HaplotypeScore=68.1753;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=1;MQRankSum=0.903;QD=26.66;ReadPosRankSum=-0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,91:111:99:2988,0,335 -chr1 40816 . G A 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.969;DP=113;Dels=0.00;FS=9.418;HaplotypeScore=31.1266;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=1;MQRankSum=-1.806;QD=4.02;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,20:113:99:483,0,2777 -chr1 40819 . T C 4137.77 . AC=2;AF=1.00;AN=2;DP=115;Dels=0.00;FS=0.000;HaplotypeScore=28.2112;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=1;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,115:115:99:4166,316,0 -chr1 40830 . G C 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=19.6261;MLEAC=1;MLEAF=0.500;MQ=46.71;MQ0=1;MQRankSum=-2.358;QD=0.59;ReadPosRankSum=1.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:105,15:120:99:99,0,3552 -chr1 40833 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.298;DP=124;Dels=0.00;FS=3.723;HaplotypeScore=34.4038;MLEAC=1;MLEAF=0.500;MQ=46.84;MQ0=1;MQRankSum=-1.292;QD=2.15;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:104,20:124:99:295,0,3416 -chr1 40839 . T C 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.184;DP=119;Dels=0.00;FS=8.132;HaplotypeScore=32.8812;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=1;MQRankSum=-0.467;QD=1.86;ReadPosRankSum=0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:102,17:119:99:249,0,3382 -chr1 40841 . T A,C 2.14748372629E9 . AC=1,1;AF=0.500,0.500;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=19.0976;MLEAC=1,1;MLEAF=0.500,0.500;MQ=47.51;MQ0=1;QD=27.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:0,17,105:122:99:4117,3653,3614,465,0,164 -chr1 40851 . C G 787.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.730;DP=129;Dels=0.00;FS=22.816;HaplotypeScore=16.7771;MLEAC=1;MLEAF=0.500;MQ=48.66;MQ0=1;MQRankSum=2.703;QD=6.11;ReadPosRankSum=-0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,30:129:99:816,0,3155 -chr1 40863 . T C 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.921;DP=118;Dels=0.00;FS=4.700;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.335;QD=12.98;ReadPosRankSum=0.964;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,57:118:99:1560,0,2100 -chr1 40865 . A G 916.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.140;DP=120;Dels=0.00;FS=2.661;HaplotypeScore=22.9854;MLEAC=1;MLEAF=0.500;MQ=50.52;MQ0=0;MQRankSum=-2.918;QD=7.64;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,36:120:99:945,0,2823 -chr1 40881 . T C 1883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.649;DP=113;Dels=0.00;FS=6.057;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=52.96;MQ0=0;MQRankSum=-3.511;QD=16.67;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,61:113:99:1912,0,1701 -chr1 40884 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.416;DP=112;Dels=0.00;FS=4.487;HaplotypeScore=16.0432;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=0.616;QD=0.92;ReadPosRankSum=1.745;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,12:112:99:131,0,3505 -chr1 40890 . T C 4000.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.376;DP=108;Dels=0.00;FS=3.638;HaplotypeScore=17.6640;MLEAC=2;MLEAF=1.00;MQ=53.47;MQ0=0;MQRankSum=-1.570;QD=32.92;ReadPosRankSum=-0.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,106:108:99:4029,271,0 -chr1 40908 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=-4.713;QD=3.49;ReadPosRankSum=-0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:444,0,3404 -chr1 40913 . A T 4662.77 . AC=2;AF=1.00;AN=2;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=7.8494;MLEAC=2;MLEAF=1.00;MQ=54.87;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,119:120:99:4691,355,0 -chr1 40932 . T C 4651.77 . AC=2;AF=1.00;AN=2;DP=122;Dels=0.00;FS=0.000;HaplotypeScore=29.4883;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,121:122:99:4680,358,0 -chr1 40939 . C T 1562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=122;Dels=0.00;FS=5.633;HaplotypeScore=53.6940;MLEAC=1;MLEAF=0.500;MQ=53.55;MQ0=0;MQRankSum=-6.420;QD=12.81;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,53:122:99:1591,0,2373 -chr1 40942 . G C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=117;Dels=0.00;FS=3.010;HaplotypeScore=52.6941;MLEAC=1;MLEAF=0.500;MQ=53.19;MQ0=0;MQRankSum=2.832;QD=5.14;ReadPosRankSum=2.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,24:117:99:630,0,3142 -chr1 40949 . A T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.841;DP=116;Dels=0.00;FS=1.882;HaplotypeScore=91.2099;MLEAC=1;MLEAF=0.500;MQ=51.71;MQ0=1;MQRankSum=2.660;QD=5.38;ReadPosRankSum=3.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,25:116:99:652,0,3037 -chr1 40953 . G T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=114;Dels=0.00;FS=4.536;HaplotypeScore=90.5131;MLEAC=1;MLEAF=0.500;MQ=51.22;MQ0=1;MQRankSum=-6.362;QD=4.05;ReadPosRankSum=-0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,25:114:99:490,0,2704 -chr1 40963 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.072;DP=115;Dels=0.00;FS=2.488;HaplotypeScore=45.8271;MLEAC=1;MLEAF=0.500;MQ=50.61;MQ0=1;MQRankSum=-6.812;QD=9.88;ReadPosRankSum=1.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,45:115:99:1164,0,2427 -chr1 40965 . A C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=111;Dels=0.00;FS=1.995;HaplotypeScore=24.4867;MLEAC=1;MLEAF=0.500;MQ=50.29;MQ0=1;MQRankSum=-5.421;QD=2.79;ReadPosRankSum=1.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,22:111:99:338,0,3112 -chr1 40977 . A G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.248;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=7.5174;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=1;MQRankSum=3.438;QD=5.38;ReadPosRankSum=0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,25:106:99:598,0,2425 -chr1 40988 . C T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.296;DP=97;Dels=0.00;FS=7.020;HaplotypeScore=26.1924;MLEAC=1;MLEAF=0.500;MQ=46.91;MQ0=1;MQRankSum=1.225;QD=3.47;ReadPosRankSum=-0.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,18:97:99:365,0,2417 -chr1 40989 . T C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.909;DP=94;Dels=0.00;FS=7.233;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=1;MQRankSum=1.405;QD=3.77;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:76,18:94:99:383,0,2284 -chr1 40990 . C T 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=25.1927;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=1;MQRankSum=-4.177;QD=1.04;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,15:92:99:124,0,2472 -chr1 40992 . A T 2915.77 . AC=2;AF=1.00;AN=2;DP=88;Dels=0.00;FS=0.000;HaplotypeScore=105.3192;MLEAC=2;MLEAF=1.00;MQ=45.42;MQ0=1;QD=33.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,88:88:99:2944,235,0 -chr1 41013 . C T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.016;DP=84;Dels=0.00;FS=15.260;HaplotypeScore=153.8354;MLEAC=1;MLEAF=0.500;MQ=39.77;MQ0=1;MQRankSum=0.325;QD=5.07;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:454,0,1750 -chr1 41015 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=85;Dels=0.00;FS=1.324;HaplotypeScore=57.0601;MLEAC=1;MLEAF=0.500;MQ=39.97;MQ0=1;MQRankSum=-2.501;QD=0.41;ReadPosRankSum=0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:85:63:63,0,2037 -chr1 41017 . T C 2590.77 . AC=2;AF=1.00;AN=2;DP=87;Dels=0.00;FS=0.000;HaplotypeScore=57.5017;MLEAC=2;MLEAF=1.00;MQ=39.87;MQ0=1;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,87:87:99:2619,217,0 -chr1 41026 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.073;DP=97;Dels=0.00;FS=3.387;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=40.65;MQ0=1;MQRankSum=1.677;QD=0.36;ReadPosRankSum=-2.910;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,9:97:63:63,0,2499 -chr1 41043 . C T 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=33.8776;MLEAC=1;MLEAF=0.500;MQ=42.40;MQ0=1;MQRankSum=0.065;QD=1.44;ReadPosRankSum=0.698;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,12:92:99:161,0,2256 -chr1 41046 . G A 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.146;DP=89;Dels=0.00;FS=6.728;HaplotypeScore=67.8534;MLEAC=1;MLEAF=0.500;MQ=42.77;MQ0=1;MQRankSum=-2.122;QD=0.77;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:97:97,0,2293 -chr1 41049 . T C 2779.77 . AC=2;AF=1.00;AN=2;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=92.5392;MLEAC=2;MLEAF=1.00;MQ=43.08;MQ0=1;QD=32.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,85:86:99:2808,226,0 -chr1 41054 . G A 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.137;DP=87;Dels=0.00;FS=2.873;HaplotypeScore=97.5277;MLEAC=1;MLEAF=0.500;MQ=43.55;MQ0=0;MQRankSum=-1.875;QD=1.18;ReadPosRankSum=1.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,13:87:99:131,0,2231 -chr1 41056 . G T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.880;DP=86;Dels=0.00;FS=12.658;HaplotypeScore=70.2196;MLEAC=1;MLEAF=0.500;MQ=43.45;MQ0=0;MQRankSum=0.504;QD=8.25;ReadPosRankSum=-0.459;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,31:86:99:738,0,1637 -chr1 41059 . A T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=85;Dels=0.00;FS=1.923;HaplotypeScore=62.5392;MLEAC=1;MLEAF=0.500;MQ=43.72;MQ0=0;MQRankSum=-1.385;QD=7.07;ReadPosRankSum=2.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,28:85:99:629,0,1583 -chr1 41064 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=88;Dels=0.00;FS=1.164;HaplotypeScore=86.8690;MLEAC=1;MLEAF=0.500;MQ=44.00;MQ0=0;MQRankSum=-1.609;QD=1.93;ReadPosRankSum=1.221;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,15:88:99:198,0,2343 -chr1 41084 . T C 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=106;Dels=0.00;FS=1.092;HaplotypeScore=17.4304;MLEAC=1;MLEAF=0.500;MQ=47.41;MQ0=0;MQRankSum=-1.180;QD=1.68;ReadPosRankSum=-2.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,14:106:99:206,0,3074 -chr1 41100 . C A 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.112;DP=116;Dels=0.00;FS=0.765;HaplotypeScore=58.6282;MLEAC=1;MLEAF=0.500;MQ=48.59;MQ0=0;MQRankSum=0.652;QD=7.64;ReadPosRankSum=0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,34:116:99:915,0,2691 -chr1 41103 . C T 572.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.020;DP=114;Dels=0.00;FS=7.549;HaplotypeScore=60.6270;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=0.692;QD=5.02;ReadPosRankSum=-1.089;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,25:114:99:601,0,2970 -chr1 41108 . G A 2256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=104;Dels=0.00;FS=1.668;HaplotypeScore=55.9666;MLEAC=1;MLEAF=0.500;MQ=50.77;MQ0=0;MQRankSum=-3.973;QD=21.70;ReadPosRankSum=0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,68:104:99:2285,0,1135 -chr1 41121 . C T 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=106;Dels=0.00;FS=8.022;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=0;MQRankSum=-4.307;QD=11.10;ReadPosRankSum=1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,39:106:99:1205,0,2309 -chr1 41142 . C A 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.819;DP=93;Dels=0.00;FS=4.344;HaplotypeScore=109.3818;MLEAC=1;MLEAF=0.500;MQ=50.67;MQ0=0;MQRankSum=-3.272;QD=1.78;ReadPosRankSum=-0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,12:93:99:194,0,2886 -chr1 41167 . T A 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.059;DP=80;Dels=0.00;FS=2.024;HaplotypeScore=81.4181;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-5.890;QD=8.08;ReadPosRankSum=2.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,24:80:99:675,0,1872 -chr1 41168 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=85;Dels=0.00;FS=1.308;HaplotypeScore=70.7865;MLEAC=1;MLEAF=0.500;MQ=51.72;MQ0=0;MQRankSum=-3.430;QD=1.28;ReadPosRankSum=1.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,10:85:99:137,0,2676 -chr1 41170 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.253;DP=86;Dels=0.00;FS=2.556;HaplotypeScore=38.2377;MLEAC=1;MLEAF=0.500;MQ=51.83;MQ0=0;MQRankSum=-4.581;QD=2.28;ReadPosRankSum=2.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,13:86:99:224,0,2606 -chr1 41179 . T C 621.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.172;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=18.4473;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-4.595;QD=7.31;ReadPosRankSum=-2.191;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,23:85:99:650,0,2189 -chr1 41195 . C G 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=99;Dels=0.00;FS=3.526;HaplotypeScore=25.2904;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=3.710;QD=4.40;ReadPosRankSum=1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,19:99:99:464,0,2786 -chr1 41199 . C T 552.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.984;DP=96;Dels=0.00;FS=4.808;HaplotypeScore=40.2922;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=2.060;QD=5.76;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,22:96:99:581,0,2606 -chr1 41208 . T C 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.073;DP=95;Dels=0.00;FS=3.709;HaplotypeScore=57.4526;MLEAC=1;MLEAF=0.500;MQ=52.97;MQ0=0;MQRankSum=3.607;QD=4.12;ReadPosRankSum=2.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,17:95:99:420,0,2797 -chr1 41212 . A C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.288;DP=95;Dels=0.00;FS=0.946;HaplotypeScore=22.4583;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-3.985;QD=5.00;ReadPosRankSum=-1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,20:95:99:503,0,2582 -chr1 41218 . T A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=96;Dels=0.00;FS=2.139;HaplotypeScore=56.9737;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=4.681;QD=4.80;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,19:96:99:489,0,2728 -chr1 41224 . C T 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=92;Dels=0.00;FS=8.582;HaplotypeScore=46.8527;MLEAC=1;MLEAF=0.500;MQ=54.51;MQ0=0;MQRankSum=-6.262;QD=11.77;ReadPosRankSum=0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,36:92:99:1111,0,1880 -chr1 41227 . A C 194.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=95;Dels=0.00;FS=1.160;HaplotypeScore=73.8186;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.984;QD=2.05;ReadPosRankSum=1.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,14:95:99:223,0,2919 -chr1 41234 . A T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.452;DP=100;Dels=0.00;FS=2.117;HaplotypeScore=65.6546;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=2.503;QD=4.66;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,20:100:99:494,0,2851 -chr1 41236 . T C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.280;DP=101;Dels=0.00;FS=3.152;HaplotypeScore=35.6864;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.963;QD=0.23;ReadPosRankSum=0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:92,9:101:51:51,0,3322 -chr1 41244 . C G 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.262;DP=106;Dels=0.00;FS=4.109;HaplotypeScore=48.8041;MLEAC=1;MLEAF=0.500;MQ=54.46;MQ0=0;MQRankSum=-2.340;QD=1.59;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,13:106:99:197,0,3333 -chr1 41248 . T C 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=109;Dels=0.00;FS=1.115;HaplotypeScore=41.7628;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-3.636;QD=1.78;ReadPosRankSum=0.974;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,14:109:99:222,0,3400 -chr1 41253 . T A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.602;DP=119;Dels=0.00;FS=6.215;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=1;MQRankSum=0.176;QD=4.21;ReadPosRankSum=1.441;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,22:119:99:529,0,3111 -chr1 41254 . A T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.018;DP=120;Dels=0.00;FS=15.351;HaplotypeScore=39.9312;MLEAC=1;MLEAF=0.500;MQ=53.38;MQ0=1;MQRankSum=-4.673;QD=0.63;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:107,13:120:99:104,0,3713 -chr1 41267 . T A 1376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=124;Dels=0.00;FS=10.609;HaplotypeScore=25.9401;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-7.080;QD=11.10;ReadPosRankSum=0.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,47:124:99:1405,0,2587 -chr1 41268 . T C 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=124;Dels=0.00;FS=4.257;HaplotypeScore=82.8206;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=1;MQRankSum=-0.901;QD=0.91;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:111,13:124:99:141,0,3898 -chr1 41278 . G A 2734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.082;DP=119;Dels=0.00;FS=0.000;HaplotypeScore=36.6252;MLEAC=1;MLEAF=0.500;MQ=52.12;MQ0=1;MQRankSum=1.173;QD=22.98;ReadPosRankSum=0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,80:119:99:2763,0,670 -chr1 41290 . C T 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=114;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=51.25;MQ0=1;MQRankSum=-4.504;QD=5.81;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:86,27:114:99:691,0,2884 -chr1 41305 . C T 1582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.376;DP=107;Dels=0.00;FS=1.558;HaplotypeScore=63.7217;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=1;MQRankSum=-7.979;QD=14.79;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,55:107:99:1611,0,1766 -chr1 41308 . T C 1593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=-8.201;QD=14.90;ReadPosRankSum=0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,56:107:99:1622,0,1675 -chr1 41310 . C G 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.320;DP=105;Dels=0.00;FS=0.974;HaplotypeScore=62.7218;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=1;MQRankSum=-2.583;QD=3.70;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:84,21:105:99:417,0,2941 -chr1 41313 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.319;DP=103;Dels=0.00;FS=0.870;HaplotypeScore=103.1863;MLEAC=1;MLEAF=0.500;MQ=49.22;MQ0=1;MQRankSum=4.857;QD=7.01;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,26:103:99:750,0,2499 -chr1 41314 . G A,T 1081.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-0.513;DP=103;Dels=0.00;FS=0.976;HaplotypeScore=42.1919;MLEAC=1,1;MLEAF=0.500,0.500;MQ=49.10;MQ0=1;MQRankSum=-4.684;QD=10.50;ReadPosRankSum=-0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/2:21,25,57:103:99:1879,1019,1719,147,0,769 -chr1 41322 . G A 1422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=107;Dels=0.00;FS=1.576;HaplotypeScore=70.4344;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=1;MQRankSum=1.616;QD=13.30;ReadPosRankSum=0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,49:107:99:1451,0,1855 -chr1 41331 . C T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.737;DP=103;Dels=0.00;FS=4.657;HaplotypeScore=99.4972;MLEAC=1;MLEAF=0.500;MQ=48.40;MQ0=1;MQRankSum=4.235;QD=5.51;ReadPosRankSum=2.095;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,22:103:99:596,0,2616 -chr1 41334 . A C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.157;DP=101;Dels=0.00;FS=2.142;HaplotypeScore=117.9442;MLEAC=1;MLEAF=0.500;MQ=48.38;MQ0=1;MQRankSum=-2.696;QD=3.51;ReadPosRankSum=0.274;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,19:101:99:383,0,2677 -chr1 41335 . C A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.870;DP=98;Dels=0.00;FS=0.996;HaplotypeScore=118.9429;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=1;MQRankSum=-3.055;QD=4.25;ReadPosRankSum=-0.712;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,20:98:99:445,0,2383 -chr1 41337 . G A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=99;Dels=0.00;FS=3.218;HaplotypeScore=122.9204;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=1;MQRankSum=2.970;QD=6.55;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,24:99:99:677,0,2337 -chr1 41343 . G A 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=74.5936;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=1;MQRankSum=-3.683;QD=5.19;ReadPosRankSum=1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:537,0,2493 -chr1 41365 . G A 298.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=86;Dels=0.00;FS=2.433;HaplotypeScore=14.9634;MLEAC=1;MLEAF=0.500;MQ=47.69;MQ0=0;MQRankSum=1.753;QD=3.47;ReadPosRankSum=1.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,15:86:99:327,0,2341 -chr1 41375 . T C 2374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=87;Dels=0.00;FS=1.026;HaplotypeScore=33.9683;MLEAC=1;MLEAF=0.500;MQ=49.17;MQ0=0;MQRankSum=-1.561;QD=27.30;ReadPosRankSum=-1.912;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,71:87:99:2403,0,364 -chr1 41376 . T G 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.803;DP=87;Dels=0.00;FS=4.036;HaplotypeScore=34.9615;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=0;MQRankSum=-0.455;QD=3.19;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:306,0,2524 -chr1 41377 . T C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.157;DP=88;Dels=0.00;FS=0.884;HaplotypeScore=39.7608;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-0.490;QD=7.20;ReadPosRankSum=3.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,25:88:99:662,0,2148 -chr1 41395 . A G 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.677;DP=84;Dels=0.00;FS=1.101;HaplotypeScore=112.5646;MLEAC=1;MLEAF=0.500;MQ=48.92;MQ0=0;MQRankSum=2.499;QD=3.81;ReadPosRankSum=0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:348,0,2361 -chr1 41396 . A T 1616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.249;DP=79;Dels=0.00;FS=3.137;HaplotypeScore=87.3597;MLEAC=1;MLEAF=0.500;MQ=48.75;MQ0=0;MQRankSum=-0.300;QD=20.47;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,50:79:99:1645,0,823 -chr1 41398 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.022;DP=81;Dels=0.00;FS=3.484;HaplotypeScore=80.5740;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=0;MQRankSum=-1.669;QD=8.63;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,24:81:99:727,0,1467 -chr1 41404 . T C 2294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=97;Dels=0.00;FS=0.832;HaplotypeScore=104.9252;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=4.062;QD=23.66;ReadPosRankSum=2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,68:97:99:2323,0,710 -chr1 41409 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.386;DP=105;Dels=0.00;FS=11.861;HaplotypeScore=51.0534;MLEAC=1;MLEAF=0.500;MQ=48.48;MQ0=0;MQRankSum=-4.669;QD=0.65;ReadPosRankSum=-2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,13:105:96:96,0,3129 -chr1 41415 . G A 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=107;Dels=0.00;FS=11.635;HaplotypeScore=15.7947;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=0;MQRankSum=1.795;QD=3.14;ReadPosRankSum=-0.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,18:107:99:364,0,2936 -chr1 41433 . A G 1679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=111;Dels=0.00;FS=3.563;HaplotypeScore=105.5605;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=-5.707;QD=15.13;ReadPosRankSum=1.023;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,57:111:99:1708,0,1780 -chr1 41435 . A G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.631;DP=109;Dels=0.00;FS=17.321;HaplotypeScore=102.6178;MLEAC=1;MLEAF=0.500;MQ=49.30;MQ0=0;MQRankSum=-4.352;QD=0.94;ReadPosRankSum=2.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,13:109:99:131,0,3341 -chr1 41438 . T G 3087.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.252;DP=111;Dels=0.00;FS=11.712;HaplotypeScore=118.7379;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=0.604;QD=27.82;ReadPosRankSum=0.156;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,93:111:99:3116,0,375 -chr1 41441 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=115;Dels=0.00;FS=6.121;HaplotypeScore=118.1844;MLEAC=1;MLEAF=0.500;MQ=49.65;MQ0=0;MQRankSum=5.083;QD=5.02;ReadPosRankSum=-0.127;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:91,24:115:99:605,0,2982 -chr1 41447 . C T 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.963;DP=113;Dels=0.00;FS=2.061;HaplotypeScore=55.8367;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-4.171;QD=3.53;ReadPosRankSum=-0.765;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,22:113:99:427,0,3162 -chr1 41451 . T C 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.403;DP=114;Dels=0.00;FS=25.914;HaplotypeScore=63.6216;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=0;MQRankSum=-4.658;QD=1.12;ReadPosRankSum=3.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,14:114:99:156,0,3508 -chr1 41458 . T G 2070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.880;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=14.9365;MLEAC=1;MLEAF=0.500;MQ=50.88;MQ0=0;MQRankSum=-8.252;QD=17.55;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,67:118:99:2099,0,1630 -chr1 41472 . G A 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=118;Dels=0.00;FS=4.281;HaplotypeScore=23.8857;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=4.715;QD=5.35;ReadPosRankSum=1.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,25:118:99:660,0,3092 -chr1 41477 . C T 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=116;Dels=0.00;FS=24.979;HaplotypeScore=26.4514;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=-4.819;QD=2.26;ReadPosRankSum=-1.044;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,17:116:99:290,0,3370 -chr1 41490 . C T 1347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=120;Dels=0.00;FS=7.377;HaplotypeScore=103.2713;MLEAC=1;MLEAF=0.500;MQ=51.74;MQ0=0;MQRankSum=-4.581;QD=11.23;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,43:120:99:1376,0,2560 -chr1 41492 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.358;DP=122;Dels=0.00;FS=4.136;HaplotypeScore=109.9755;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-5.075;QD=4.19;ReadPosRankSum=0.670;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,27:122:99:540,0,3167 -chr1 41495 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=120;Dels=0.00;FS=6.076;HaplotypeScore=130.0290;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=0;MQRankSum=-4.101;QD=10.63;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,42:120:99:1304,0,2562 -chr1 41499 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=121;Dels=0.00;FS=8.830;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=4.822;QD=5.84;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,27:121:99:735,0,3300 -chr1 41500 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=123;Dels=0.00;FS=4.152;HaplotypeScore=131.1958;MLEAC=1;MLEAF=0.500;MQ=51.46;MQ0=0;MQRankSum=-4.922;QD=4.27;ReadPosRankSum=2.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,26:123:99:554,0,3500 -chr1 41503 . T C 2252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=119;Dels=0.00;FS=4.440;HaplotypeScore=73.1398;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=-7.475;QD=18.93;ReadPosRankSum=0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,69:119:99:2281,0,1652 -chr1 41543 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=1.422;QD=1.67;ReadPosRankSum=0.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:82,12:94:99:185,0,2657 -chr1 41544 . C A 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=94;Dels=0.00;FS=5.349;HaplotypeScore=33.5509;MLEAC=1;MLEAF=0.500;MQ=45.79;MQ0=0;MQRankSum=0.591;QD=4.56;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,20:94:99:457,0,2138 -chr1 41546 . A G 3381.77 . AC=2;AF=1.00;AN=2;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=27.5019;MLEAC=2;MLEAF=1.00;MQ=45.55;MQ0=0;QD=31.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,94:95:99:3410,268,0 -chr1 41562 . G A 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=90;Dels=0.00;FS=3.007;HaplotypeScore=34.8266;MLEAC=1;MLEAF=0.500;MQ=42.64;MQ0=0;MQRankSum=-0.632;QD=6.88;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,28:90:99:647,0,1945 -chr1 41564 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=55.5562;MLEAC=1;MLEAF=0.500;MQ=41.85;MQ0=0;MQRankSum=1.630;QD=1.23;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:99:130,0,2184 -chr1 41566 . C A 2583.77 . AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=62.4145;MLEAC=2;MLEAF=1.00;MQ=41.29;MQ0=0;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,77:77:99:2612,211,0 -chr1 41569 . T C 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.046;DP=76;Dels=0.00;FS=3.973;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.71;MQ0=0;MQRankSum=1.851;QD=5.79;ReadPosRankSum=0.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,18:76:99:468,0,1633 -chr1 41572 . T C 2032.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.322;DP=75;Dels=0.00;FS=1.682;HaplotypeScore=65.4132;MLEAC=1;MLEAF=0.500;MQ=40.70;MQ0=0;MQRankSum=-0.869;QD=27.11;ReadPosRankSum=-0.537;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,69:75:15:2061,0,15 -chr1 41574 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.327;DP=76;Dels=0.00;FS=3.699;HaplotypeScore=53.4650;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=0;MQRankSum=0.032;QD=9.00;ReadPosRankSum=3.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,25:76:99:712,0,1145 -chr1 41576 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=83;Dels=0.00;FS=1.310;HaplotypeScore=45.4818;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=-1.812;QD=0.39;ReadPosRankSum=-0.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,10:83:61:61,0,2187 -chr1 41587 . C T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=59.1819;MLEAC=1;MLEAF=0.500;MQ=39.01;MQ0=0;MQRankSum=2.270;QD=10.01;ReadPosRankSum=1.892;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:969,0,1542 -chr1 41588 . T A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.902;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=56.1832;MLEAC=1;MLEAF=0.500;MQ=38.88;MQ0=0;MQRankSum=-1.330;QD=3.74;ReadPosRankSum=2.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:71,21:92:99:372,0,2076 -chr1 41593 . A G 2833.77 . AC=2;AF=1.00;AN=2;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=51.2291;MLEAC=2;MLEAF=1.00;MQ=39.22;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,89:89:99:2862,241,0 -chr1 41597 . T A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=93;Dels=0.00;FS=1.013;HaplotypeScore=58.9239;MLEAC=1;MLEAF=0.500;MQ=39.40;MQ0=0;MQRankSum=-1.253;QD=3.26;ReadPosRankSum=-0.777;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,19:93:99:331,0,2049 -chr1 41612 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=94;Dels=0.00;FS=3.843;HaplotypeScore=30.0447;MLEAC=1;MLEAF=0.500;MQ=39.90;MQ0=0;MQRankSum=-1.714;QD=1.66;ReadPosRankSum=-0.857;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:79,15:94:99:184,0,2308 -chr1 41623 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=95;Dels=0.00;FS=1.274;HaplotypeScore=34.4885;MLEAC=1;MLEAF=0.500;MQ=41.23;MQ0=0;MQRankSum=-1.146;QD=0.23;ReadPosRankSum=-2.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,10:95:50:50,0,2553 -chr1 41633 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=97;Dels=0.00;FS=0.962;HaplotypeScore=42.7026;MLEAC=1;MLEAF=0.500;MQ=41.75;MQ0=0;MQRankSum=-1.768;QD=4.76;ReadPosRankSum=1.633;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,23:97:99:490,0,2247 -chr1 41638 . T G 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.578;DP=99;Dels=0.00;FS=11.653;HaplotypeScore=45.8263;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=1.485;QD=4.36;ReadPosRankSum=-0.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:78,21:99:99:460,0,2342 -chr1 41640 . A T 3476.77 . AC=2;AF=1.00;AN=2;DP=102;Dels=0.00;FS=0.000;HaplotypeScore=43.8379;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=34.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,102:102:99:3505,280,0 -chr1 41642 . C T 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.284;DP=102;Dels=0.00;FS=4.287;HaplotypeScore=43.8379;MLEAC=1;MLEAF=0.500;MQ=42.97;MQ0=0;MQRankSum=-1.538;QD=0.99;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:87,12:102:99:129,0,2667 -chr1 41645 . G A 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=106;Dels=0.00;FS=2.304;HaplotypeScore=28.8553;MLEAC=1;MLEAF=0.500;MQ=42.92;MQ0=0;MQRankSum=-1.566;QD=1.82;ReadPosRankSum=-1.328;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,16:106:99:221,0,2816 -chr1 41657 . T C 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.271;DP=113;Dels=0.00;FS=4.518;HaplotypeScore=64.9583;MLEAC=1;MLEAF=0.500;MQ=44.13;MQ0=0;MQRankSum=-2.414;QD=4.06;ReadPosRankSum=1.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:90,23:113:99:487,0,2786 -chr1 41663 . A T 154.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.503;DP=114;Dels=0.00;FS=3.858;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.09;MQ0=0;MQRankSum=-1.442;QD=1.36;ReadPosRankSum=1.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:99,15:114:99:183,0,3367 -chr1 41665 . T A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.927;DP=113;Dels=0.00;FS=3.826;HaplotypeScore=81.6675;MLEAC=1;MLEAF=0.500;MQ=45.28;MQ0=0;MQRankSum=-1.612;QD=1.48;ReadPosRankSum=1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,15:113:99:196,0,3343 -chr1 41669 . A G 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.192;DP=119;Dels=0.00;FS=4.933;HaplotypeScore=68.0952;MLEAC=1;MLEAF=0.500;MQ=45.13;MQ0=0;MQRankSum=-1.839;QD=2.10;ReadPosRankSum=0.185;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:100,19:119:99:278,0,3198 -chr1 41678 . T C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.051;DP=115;Dels=0.00;FS=6.885;HaplotypeScore=79.4081;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=0;MQRankSum=-3.479;QD=3.11;ReadPosRankSum=3.870;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:95,20:115:99:386,0,3047 -chr1 41679 . G A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.748;DP=111;Dels=0.00;FS=3.602;HaplotypeScore=78.4123;MLEAC=1;MLEAF=0.500;MQ=46.33;MQ0=0;MQRankSum=-3.517;QD=2.09;ReadPosRankSum=-0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:94,17:111:99:260,0,3158 -chr1 41680 . A C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=108;Dels=0.00;FS=1.071;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-3.109;QD=1.71;ReadPosRankSum=0.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,15:108:99:213,0,3172 -chr1 41687 . G C 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.837;DP=112;Dels=0.00;FS=2.333;HaplotypeScore=58.7186;MLEAC=1;MLEAF=0.500;MQ=45.86;MQ0=0;MQRankSum=-2.828;QD=1.31;ReadPosRankSum=-0.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:97,15:112:99:175,0,3221 -chr1 41717 . G C 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.104;DP=101;Dels=0.00;FS=10.379;HaplotypeScore=39.1666;MLEAC=1;MLEAF=0.500;MQ=42.12;MQ0=0;MQRankSum=-0.222;QD=1.90;ReadPosRankSum=2.162;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:85,15:101:99:220,0,2653 -chr1 41723 . C T 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.845;DP=104;Dels=0.00;FS=7.631;HaplotypeScore=57.0647;MLEAC=1;MLEAF=0.500;MQ=41.47;MQ0=0;MQRankSum=0.585;QD=7.04;ReadPosRankSum=0.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,30:104:99:760,0,2081 -chr1 41727 . T C 1110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=103;Dels=0.00;FS=25.678;HaplotypeScore=89.0081;MLEAC=1;MLEAF=0.500;MQ=41.42;MQ0=0;MQRankSum=-2.718;QD=10.78;ReadPosRankSum=-0.518;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,43:103:99:1139,0,1804 -chr1 41733 . C T 126.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.025;DP=101;Dels=0.00;FS=8.661;HaplotypeScore=68.3374;MLEAC=1;MLEAF=0.500;MQ=40.86;MQ0=0;MQRankSum=0.319;QD=1.26;ReadPosRankSum=0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:88,13:101:99:155,0,2688 -chr1 41737 . G A 28.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.067;DP=98;Dels=0.00;FS=1.384;HaplotypeScore=41.8358;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=0;MQRankSum=-0.972;QD=0.29;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,9:98:57:57,0,2778 -chr1 41760 . C T 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=84;Dels=0.00;FS=4.638;HaplotypeScore=16.6682;MLEAC=1;MLEAF=0.500;MQ=38.94;MQ0=0;MQRankSum=2.250;QD=7.74;ReadPosRankSum=1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,26:84:99:678,0,1606 -chr1 41790 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.449;DP=72;Dels=0.00;FS=0.904;HaplotypeScore=22.5923;MLEAC=1;MLEAF=0.500;MQ=41.27;MQ0=0;MQRankSum=1.292;QD=12.39;ReadPosRankSum=1.235;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,34:72:99:920,0,1016 -chr1 41797 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=56;Dels=0.00;FS=17.110;HaplotypeScore=26.2547;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=0.349;QD=4.44;ReadPosRankSum=1.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:277,0,1304 -chr1 41816 . T C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.517;DP=70;Dels=0.00;FS=19.980;HaplotypeScore=12.2986;MLEAC=1;MLEAF=0.500;MQ=44.44;MQ0=0;MQRankSum=1.485;QD=5.95;ReadPosRankSum=0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:445,0,1433 -chr1 41832 . A G 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.295;DP=72;Dels=0.00;FS=47.755;HaplotypeScore=25.8822;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=-5.914;QD=4.62;ReadPosRankSum=0.334;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,25:72:99:361,0,1584 -chr1 41839 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.104;DP=75;Dels=0.00;FS=46.700;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=1;MQRankSum=-6.222;QD=5.20;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,27:75:99:418,0,1578 -chr1 41841 . A G 1684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=73;Dels=0.00;FS=17.617;HaplotypeScore=23.9247;MLEAC=1;MLEAF=0.500;MQ=46.38;MQ0=1;MQRankSum=3.993;QD=23.08;ReadPosRankSum=2.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,57:73:99:1713,0,219 -chr1 41855 . A G 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=75;Dels=0.00;FS=34.596;HaplotypeScore=5.5757;MLEAC=1;MLEAF=0.500;MQ=46.37;MQ0=4;MQRankSum=-4.879;QD=2.30;ReadPosRankSum=2.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,17:75:99:201,0,1834 -chr1 41867 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=76;Dels=0.00;FS=7.041;HaplotypeScore=8.7104;MLEAC=1;MLEAF=0.500;MQ=45.61;MQ0=4;MQRankSum=4.354;QD=8.84;ReadPosRankSum=-1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,24:76:99:700,0,1282 -chr1 41874 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=75;Dels=0.00;FS=14.535;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.20;MQ0=4;MQRankSum=-3.082;QD=0.37;ReadPosRankSum=2.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:66,9:75:56:56,0,1930 -chr1 41875 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.568;DP=73;Dels=0.00;FS=5.210;HaplotypeScore=9.9168;MLEAC=1;MLEAF=0.500;MQ=45.03;MQ0=4;MQRankSum=3.339;QD=10.49;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,25:73:99:794,0,1121 -chr1 41887 . T C 2160.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=18.1629;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=4;QD=30.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2189,175,0 -chr1 41891 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=76.6927;MLEAC=1;MLEAF=0.500;MQ=45.05;MQ0=4;MQRankSum=1.412;QD=10.65;ReadPosRankSum=0.443;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,24:69:99:763,0,786 -chr1 41899 . T A 1216.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=-2.812;DP=52;Dels=0.02;FS=6.283;HaplotypeScore=36.3869;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.157;QD=23.40;ReadPosRankSum=-0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,42:51:14:1245,14,0 -chr1 41900 . T C 1523.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.417;DP=52;Dels=0.00;FS=5.909;HaplotypeScore=45.3219;MLEAC=2;MLEAF=1.00;MQ=46.58;MQ0=4;MQRankSum=3.172;QD=29.30;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,43:52:29:1552,29,0 -chr1 41931 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=48.90;MQ0=3;MQRankSum=0.304;QD=11.97;ReadPosRankSum=1.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:806,0,1148 -chr1 41944 . C G 2024.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=51.55;MQ0=0;QD=32.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2053,156,0 -chr1 41946 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.696;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=51.55;MQ0=0;MQRankSum=-0.278;QD=14.11;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:776,0,935 -chr1 41952 . T C 1861.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.38;MQ0=0;QD=36.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1890,144,0 -chr1 41954 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.11;MQ0=0;MQRankSum=-0.942;QD=15.68;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:812,0,822 -chr1 41991 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=56;Dels=0.00;FS=7.656;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=1.035;QD=12.37;ReadPosRankSum=0.654;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:721,0,1091 -chr1 42007 . G A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.444;DP=51;Dels=0.00;FS=10.314;HaplotypeScore=2.4441;MLEAC=1;MLEAF=0.500;MQ=50.10;MQ0=0;MQRankSum=1.161;QD=13.51;ReadPosRankSum=-1.613;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:717,0,897 -chr1 42036 . A G 1816.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.7826;MLEAC=2;MLEAF=1.00;MQ=49.42;MQ0=1;QD=29.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1845,144,0 -chr1 42038 . G T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.265;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=5.5713;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=2.868;QD=10.28;ReadPosRankSum=0.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:532,0,906 -chr1 42046 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.504;DP=52;Dels=0.00;FS=2.418;HaplotypeScore=4.5717;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=1;MQRankSum=-3.243;QD=17.82;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:955,0,706 -chr1 42061 . C T 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.775;DP=49;Dels=0.00;FS=5.764;HaplotypeScore=4.9754;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=1;MQRankSum=3.673;QD=14.79;ReadPosRankSum=0.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:753,0,792 -chr1 42071 . C T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.982;DP=45;Dels=0.00;FS=4.388;HaplotypeScore=4.7774;MLEAC=1;MLEAF=0.500;MQ=49.26;MQ0=1;MQRankSum=-4.302;QD=15.22;ReadPosRankSum=-0.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:713,0,676 -chr1 42082 . T C 1927.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=49.55;MQ0=1;QD=25.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1956,150,0 -chr1 42083 . G T 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.128;DP=49;Dels=0.00;FS=4.144;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.42;MQ0=1;MQRankSum=-4.087;QD=13.97;ReadPosRankSum=1.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:713,0,858 -chr1 42106 . A G 1999.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.98;MQ0=2;QD=36.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2028,156,0 -chr1 42149 . T C 1779.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.012;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=10.4982;MLEAC=2;MLEAF=1.00;MQ=39.34;MQ0=6;MQRankSum=2.932;QD=26.56;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:9,58:67:99:1808,122,0 -chr1 42196 . C T 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=73;Dels=0.00;FS=15.517;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=35.03;MQ0=7;MQRankSum=3.313;QD=10.94;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,28:73:99:827,0,820 -chr1 42202 . T C 1564.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.114;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=23.7489;MLEAC=2;MLEAF=1.00;MQ=32.75;MQ0=6;MQRankSum=3.687;QD=24.84;ReadPosRankSum=-0.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:8,55:63:99:1593,107,0 -chr1 42204 . C T 644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.569;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=23.7489;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.649;QD=10.40;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:673,0,666 -chr1 42208 . C T 643.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=62;Dels=0.00;FS=14.833;HaplotypeScore=19.1747;MLEAC=1;MLEAF=0.500;MQ=32.93;MQ0=6;MQRankSum=3.599;QD=10.38;ReadPosRankSum=2.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,23:62:99:672,0,666 -chr1 42212 . T A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=60;Dels=0.00;FS=12.104;HaplotypeScore=19.4395;MLEAC=1;MLEAF=0.500;MQ=33.30;MQ0=6;MQRankSum=3.512;QD=10.15;ReadPosRankSum=2.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:637,0,656 -chr1 42218 . A G 1530.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.638;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.9344;MLEAC=2;MLEAF=1.00;MQ=32.94;MQ0=6;MQRankSum=-0.881;QD=24.30;ReadPosRankSum=-1.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,62:63:93:1559,93,0 -chr1 42221 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=65;Dels=0.00;FS=5.554;HaplotypeScore=8.9344;MLEAC=1;MLEAF=0.500;MQ=33.39;MQ0=6;MQRankSum=-1.189;QD=9.63;ReadPosRankSum=0.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,30:65:99:654,0,793 -chr1 42234 . A G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.221;DP=52;Dels=0.00;FS=7.954;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=36.56;MQ0=1;MQRankSum=-1.940;QD=11.46;ReadPosRankSum=0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:624,0,788 -chr1 42260 . T C 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.178;DP=42;Dels=0.00;FS=4.638;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=36.16;MQ0=0;MQRankSum=-1.412;QD=8.95;ReadPosRankSum=0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:404,0,716 -chr1 42263 . G A 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=37;Dels=0.00;FS=4.803;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=35.87;MQ0=0;MQRankSum=0.904;QD=14.56;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:567,0,421 -chr1 42280 . G A 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=36.50;MQ0=2;MQRankSum=0.805;QD=9.84;ReadPosRankSum=2.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:412,0,542 -chr1 42294 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.243;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=36.41;MQ0=2;MQRankSum=-0.883;QD=11.65;ReadPosRankSum=-0.558;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:436,0,494 -chr1 42305 . C T 1338.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.50;MQ0=2;QD=33.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1367,111,0 -chr1 42316 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=38.47;MQ0=2;MQRankSum=-1.556;QD=10.46;ReadPosRankSum=-0.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:457,0,721 -chr1 42344 . C T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.289;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7128;MLEAC=1;MLEAF=0.500;MQ=39.55;MQ0=2;MQRankSum=1.059;QD=16.22;ReadPosRankSum=1.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:823,0,592 -chr1 42360 . A G 1733.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.46;MQ0=1;QD=34.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1762,141,0 -chr1 42373 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.78;MQ0=0;MQRankSum=-1.866;QD=13.38;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:657,0,768 -chr1 42400 . A C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=4.7967;MLEAC=1;MLEAF=0.500;MQ=44.88;MQ0=0;MQRankSum=-2.723;QD=12.16;ReadPosRankSum=1.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:612,0,919 -chr1 42416 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.7990;MLEAC=1;MLEAF=0.500;MQ=44.11;MQ0=0;MQRankSum=2.735;QD=16.06;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:735,0,601 -chr1 42478 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.823;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.32;MQ0=1;MQRankSum=-2.431;QD=5.99;ReadPosRankSum=1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,10:21:99:154,0,359 -chr1 42479 . A G 606.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=1;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,22:22:54:635,54,0 -chr1 42486 . A G 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.373;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.44;MQ0=2;MQRankSum=-2.500;QD=6.25;ReadPosRankSum=0.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:172,0,350 -chr1 42503 . T A 579.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=2;QD=25.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:608,51,0 -chr1 42535 . G A 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.226;QD=12.17;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,18:33:99:430,0,463 -chr1 42539 . G A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.544;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4516;MLEAC=1;MLEAF=0.500;MQ=39.57;MQ0=2;MQRankSum=-1.381;QD=13.42;ReadPosRankSum=-0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,19:33:99:471,0,422 -chr1 42553 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=39.64;MQ0=2;MQRankSum=0.155;QD=15.72;ReadPosRankSum=-1.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:594,0,398 -chr1 42568 . A G 1099.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=40.82;MQ0=1;QD=33.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1128,87,0 -chr1 42617 . A T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=1;MQRankSum=0.049;QD=7.30;ReadPosRankSum=-1.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:240,0,633 -chr1 42618 . A G 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.87;MQ0=1;MQRankSum=-0.029;QD=7.03;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:211,0,532 -chr1 42641 . A G 782.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.44;MQ0=2;MQRankSum=1.595;QD=28.99;ReadPosRankSum=1.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,25:27:63:811,63,0 -chr1 42646 . G A 734.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.828;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.7330;MLEAC=2;MLEAF=1.00;MQ=36.88;MQ0=1;MQRankSum=1.306;QD=29.39;ReadPosRankSum=1.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:2,23:25:60:763,60,0 -chr1 42650 . A G 144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DP=22;Dels=0.00;FS=1.719;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=37.75;MQ0=1;MQRankSum=-2.354;QD=6.58;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,9:22:99:173,0,443 -chr1 42661 . T C 766.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.02;MQ0=1;QD=31.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,24:24:63:795,63,0 -chr1 42680 . G T 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.405;DP=23;Dels=0.00;FS=1.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.36;MQ0=1;MQRankSum=-0.922;QD=17.95;ReadPosRankSum=-0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:6,17:23:99:441,0,171 -chr1 42698 . A G 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.880;DP=34;Dels=0.00;FS=3.589;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=48.79;MQ0=1;MQRankSum=-0.707;QD=22.93;ReadPosRankSum=1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:9,25:34:99:808,0,202 -chr1 42700 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.444;DP=35;Dels=0.00;FS=3.712;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=1;MQRankSum=0.156;QD=5.31;ReadPosRankSum=-1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,9:35:99:214,0,848 -chr1 42716 . C A 1242.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=51.83;MQ0=0;QD=25.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1271,96,0 -chr1 42723 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.200;DP=39;Dels=0.00;FS=3.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=1.358;QD=5.20;ReadPosRankSum=-2.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:231,0,953 -chr1 42738 . G A 1423.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=54.09;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1452,108,0 -chr1 42747 . C T 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=-1.468;QD=21.23;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:835,0,401 -chr1 42749 . C T 342.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.407;DP=38;Dels=0.00;FS=1.475;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=55.27;MQ0=0;MQRankSum=2.557;QD=9.02;ReadPosRankSum=-1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:371,0,833 -chr1 42815 . T C 1223.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=1;QD=33.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,37:37:96:1252,96,0 -chr1 42840 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.801;DP=40;Dels=0.00;FS=1.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.73;MQ0=1;MQRankSum=0.745;QD=14.59;ReadPosRankSum=1.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:612,0,601 -chr1 42845 . A G 575.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=39;Dels=0.00;FS=1.210;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=0.482;QD=14.76;ReadPosRankSum=1.710;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:604,0,571 -chr1 42846 . G A 1308.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.65;MQ0=1;QD=33.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1337,102,0 -chr1 42848 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.965;DP=41;Dels=0.00;FS=1.189;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=1;MQRankSum=0.720;QD=14.29;ReadPosRankSum=1.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:614,0,573 -chr1 42865 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=50;Dels=0.00;FS=4.589;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.645;QD=6.80;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,14:50:99:368,0,1156 -chr1 42867 . G A 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=50;Dels=0.00;FS=2.949;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=1;MQRankSum=-0.500;QD=5.86;ReadPosRankSum=1.965;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,13:50:99:321,0,1202 -chr1 42868 . T C 1723.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1752,135,0 -chr1 42872 . C T 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=49;Dels=0.00;FS=2.969;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=1;MQRankSum=0.821;QD=23.85;ReadPosRankSum=-1.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:13,36:49:99:1197,0,340 -chr1 42885 . T C 1721.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.922;DP=50;Dels=0.00;FS=3.297;HaplotypeScore=2.9991;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=2;MQRankSum=-0.479;QD=34.44;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,48:50:99:1750,100,0 -chr1 42886 . C T 1072.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.810;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=2;MQRankSum=1.039;QD=21.46;ReadPosRankSum=1.761;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1101,0,484 -chr1 42890 . G T 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.510;DP=56;Dels=0.00;FS=1.156;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=2;MQRankSum=-0.672;QD=7.39;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,18:56:99:442,0,1293 -chr1 42926 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.287;DP=58;Dels=0.00;FS=7.798;HaplotypeScore=2.7439;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=-0.975;QD=20.50;ReadPosRankSum=0.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1217,0,729 -chr1 42931 . T C 2121.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7439;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=1;QD=32.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2150,163,0 -chr1 42980 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.991;QD=18.08;ReadPosRankSum=1.098;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:878,0,734 -chr1 43004 . A G 1350.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.45;MQ0=0;QD=34.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1379,105,0 -chr1 43009 . G A 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=0;MQRankSum=2.090;QD=14.47;ReadPosRankSum=0.512;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:578,0,652 -chr1 43016 . A G 1291.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.56;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1320,99,0 -chr1 43030 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=40;Dels=0.00;FS=1.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-2.465;QD=14.89;ReadPosRankSum=-0.325;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:624,0,708 -chr1 43039 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.020;DP=38;Dels=0.00;FS=2.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.44;MQ0=0;MQRankSum=-1.493;QD=12.99;ReadPosRankSum=0.606;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:522,0,755 -chr1 43040 . G A 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.177;DP=40;Dels=0.00;FS=4.756;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.41;MQ0=0;MQRankSum=-1.155;QD=13.87;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:583,0,758 -chr1 43050 . T C 1807.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.22;MQ0=0;QD=26.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1836,141,0 -chr1 43061 . T A 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.626;DP=49;Dels=0.00;FS=4.322;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=0;MQRankSum=1.606;QD=17.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:893,0,625 -chr1 43067 . C T 855.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=4.058;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-0.462;QD=16.78;ReadPosRankSum=2.101;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:884,0,760 -chr1 43068 . G T 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=2.286;QD=16.58;ReadPosRankSum=2.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:907,0,821 -chr1 43083 . G C 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.92;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,169,0 -chr1 43097 . T C 2191.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.07;MQ0=0;QD=28.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:57:99:2220,166,0 -chr1 43150 . T A 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.009;DP=54;Dels=0.00;FS=2.461;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.65;MQ0=0;MQRankSum=1.401;QD=18.50;ReadPosRankSum=-1.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1027,0,700 -chr1 43153 . G A 1106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.471;DP=58;Dels=0.00;FS=3.788;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=1.366;QD=19.08;ReadPosRankSum=-1.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1135,0,730 -chr1 43183 . T C 1947.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.34;MQ0=0;QD=33.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1976,147,0 -chr1 43187 . G A 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.656;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-0.333;QD=14.13;ReadPosRankSum=0.219;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:749,0,974 -chr1 43195 . A G 2077.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.472;DP=56;Dels=0.00;FS=5.362;HaplotypeScore=4.9656;MLEAC=2;MLEAF=1.00;MQ=50.45;MQ0=0;MQRankSum=0.283;QD=34.04;ReadPosRankSum=1.669;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,54:56:99:2106,123,0 -chr1 43197 . G A 1062.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=58;Dels=0.00;FS=1.101;HaplotypeScore=4.9656;MLEAC=1;MLEAF=0.500;MQ=50.81;MQ0=0;MQRankSum=0.868;QD=18.32;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1091,0,879 -chr1 43231 . C A 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.226;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=0;MQRankSum=-0.040;QD=12.06;ReadPosRankSum=0.473;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:36,22:58:99:728,0,1277 -chr1 43246 . T C 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=72;Dels=0.00;FS=7.335;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=53.67;MQ0=0;MQRankSum=-3.808;QD=0.61;ReadPosRankSum=-2.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,8:72:72:72,0,2204 -chr1 43265 . A T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.501;DP=75;Dels=0.00;FS=7.472;HaplotypeScore=3.7546;MLEAC=1;MLEAF=0.500;MQ=52.35;MQ0=0;MQRankSum=-3.233;QD=0.44;ReadPosRankSum=-2.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,7:75:61:61,0,2183 -chr1 43276 . G A 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.432;DP=69;Dels=0.00;FS=3.775;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-3.715;QD=1.13;ReadPosRankSum=1.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,9:69:99:106,0,2099 -chr1 43278 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.807;DP=70;Dels=0.00;FS=18.468;HaplotypeScore=9.7497;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=0;MQRankSum=-6.081;QD=5.05;ReadPosRankSum=2.009;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:52,18:70:99:382,0,1868 -chr1 43282 . A G 2155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.741;DP=72;Dels=0.00;FS=5.810;HaplotypeScore=18.7776;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=3.314;QD=29.94;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:10,62:72:99:2184,0,134 -chr1 43285 . G A 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.628;DP=73;Dels=0.00;FS=5.951;HaplotypeScore=50.5662;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-3.088;QD=1.42;ReadPosRankSum=2.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:132,0,2235 -chr1 43291 . C G 201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=74;Dels=0.00;FS=19.101;HaplotypeScore=33.7389;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-3.986;QD=2.73;ReadPosRankSum=0.439;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:230,0,2102 -chr1 43293 . A T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.021;DP=71;Dels=0.00;FS=10.885;HaplotypeScore=23.8257;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=1;MQRankSum=-3.987;QD=2.73;ReadPosRankSum=2.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:222,0,1937 -chr1 43298 . C T 2572.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=13.9125;MLEAC=2;MLEAF=1.00;MQ=49.91;MQ0=1;QD=27.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2601,199,0 -chr1 43315 . A C 2446.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=1;QD=24.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2475,196,0 -chr1 43326 . A T 2504.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=25.9658;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=1;QD=28.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2533,196,0 -chr1 43328 . C G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.840;DP=70;Dels=0.00;FS=18.175;HaplotypeScore=28.9637;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=1;MQRankSum=-1.433;QD=4.03;ReadPosRankSum=-2.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:54,16:70:99:310,0,1933 -chr1 43332 . G C 378.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.653;DP=68;Dels=0.00;FS=31.387;HaplotypeScore=27.9641;MLEAC=1;MLEAF=0.500;MQ=48.56;MQ0=2;MQRankSum=3.076;QD=5.57;ReadPosRankSum=0.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:407,0,1696 -chr1 43333 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.715;DP=63;Dels=0.00;FS=24.273;HaplotypeScore=25.9652;MLEAC=1;MLEAF=0.500;MQ=48.61;MQ0=2;MQRankSum=-3.220;QD=4.08;ReadPosRankSum=0.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:285,0,1646 -chr1 43371 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=73;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.66;MQ0=2;MQRankSum=2.809;QD=6.64;ReadPosRankSum=-0.324;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,18:73:99:513,0,1764 -chr1 43372 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=74;Dels=0.00;FS=22.148;HaplotypeScore=6.9922;MLEAC=1;MLEAF=0.500;MQ=51.31;MQ0=3;MQRankSum=2.584;QD=6.60;ReadPosRankSum=-0.403;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,18:74:99:517,0,1762 -chr1 43392 . C T 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.597;DP=82;Dels=0.00;FS=11.173;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=2;MQRankSum=3.354;QD=9.66;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,27:82:99:820,0,1545 -chr1 43419 . G A 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.314;DP=85;Dels=0.00;FS=4.704;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.922;QD=0.80;ReadPosRankSum=-1.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,15:85:96:96,0,2450 -chr1 43420 . T C 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=85;Dels=0.00;FS=8.730;HaplotypeScore=41.2098;MLEAC=1;MLEAF=0.500;MQ=52.49;MQ0=2;MQRankSum=-3.994;QD=1.48;ReadPosRankSum=-1.438;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,17:85:99:154,0,2361 -chr1 43424 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=86;Dels=0.00;FS=5.028;HaplotypeScore=83.0946;MLEAC=1;MLEAF=0.500;MQ=52.08;MQ0=2;MQRankSum=2.883;QD=9.25;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,27:86:99:824,0,1702 -chr1 43442 . C T 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=81;Dels=0.00;FS=4.587;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=51.64;MQ0=1;MQRankSum=-5.183;QD=2.57;ReadPosRankSum=1.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,18:81:99:236,0,2162 -chr1 43464 . T C 1004.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=83;Dels=0.00;FS=6.657;HaplotypeScore=7.8783;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-7.377;QD=12.11;ReadPosRankSum=-0.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,40:83:99:1033,0,1434 -chr1 43478 . C T 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=78;Dels=0.00;FS=2.728;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.85;MQ0=1;MQRankSum=-1.601;QD=4.14;ReadPosRankSum=-1.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,15:78:99:351,0,2012 -chr1 43479 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=78;Dels=0.00;FS=7.130;HaplotypeScore=27.3493;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-1.781;QD=0.23;ReadPosRankSum=0.470;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,8:78:46:46,0,2305 -chr1 43500 . C G 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=75;Dels=0.00;FS=9.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.12;MQ0=1;MQRankSum=3.454;QD=2.78;ReadPosRankSum=-0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,12:75:99:237,0,2108 -chr1 43510 . A G 135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=78;Dels=0.00;FS=13.593;HaplotypeScore=39.7676;MLEAC=1;MLEAF=0.500;MQ=48.31;MQ0=1;MQRankSum=3.326;QD=1.74;ReadPosRankSum=-1.053;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:78:99:164,0,2251 -chr1 43512 . T C 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=79;Dels=0.00;FS=5.766;HaplotypeScore=29.7717;MLEAC=1;MLEAF=0.500;MQ=48.16;MQ0=1;MQRankSum=-2.674;QD=5.09;ReadPosRankSum=-1.477;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:430,0,1984 -chr1 43517 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=74;Dels=0.00;FS=7.633;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=47.06;MQ0=1;MQRankSum=-2.543;QD=0.98;ReadPosRankSum=0.457;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:101,0,2153 -chr1 43520 . C A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=74;Dels=0.00;FS=3.451;HaplotypeScore=48.4896;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.123;QD=0.54;ReadPosRankSum=0.579;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,10:74:68:68,0,2205 -chr1 43523 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=77;Dels=0.00;FS=9.238;HaplotypeScore=43.3257;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=1;MQRankSum=2.335;QD=0.44;ReadPosRankSum=-0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,7:77:62:62,0,2240 -chr1 43525 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.632;DP=75;Dels=0.00;FS=2.429;HaplotypeScore=41.3363;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=1;MQRankSum=2.219;QD=4.41;ReadPosRankSum=0.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,15:75:99:359,0,1931 -chr1 43532 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=73;Dels=0.00;FS=11.099;HaplotypeScore=23.1272;MLEAC=1;MLEAF=0.500;MQ=45.27;MQ0=2;MQRankSum=1.051;QD=8.75;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:667,0,1489 -chr1 43535 . C G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=71;Dels=0.00;FS=13.340;HaplotypeScore=30.0213;MLEAC=1;MLEAF=0.500;MQ=44.73;MQ0=2;MQRankSum=1.228;QD=8.70;ReadPosRankSum=-0.541;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,24:71:99:646,0,1479 -chr1 43544 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=67;Dels=0.00;FS=8.590;HaplotypeScore=21.3628;MLEAC=1;MLEAF=0.500;MQ=43.73;MQ0=2;MQRankSum=-0.099;QD=12.70;ReadPosRankSum=1.165;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,30:67:99:879,0,1032 -chr1 43548 . T C 2142.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=18.0294;MLEAC=2;MLEAF=1.00;MQ=43.48;MQ0=1;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2171,171,0 -chr1 43554 . A G 1643.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=19.3162;MLEAC=2;MLEAF=1.00;MQ=40.15;MQ0=1;QD=32.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1672,135,0 -chr1 43556 . A T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=50;Dels=0.00;FS=20.048;HaplotypeScore=10.4239;MLEAC=1;MLEAF=0.500;MQ=40.15;MQ0=1;MQRankSum=1.405;QD=6.36;ReadPosRankSum=-0.232;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,981 -chr1 43562 . A C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.681;DP=50;Dels=0.00;FS=14.927;HaplotypeScore=31.3082;MLEAC=1;MLEAF=0.500;MQ=40.43;MQ0=1;MQRankSum=1.421;QD=7.74;ReadPosRankSum=-0.683;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:415,0,1027 -chr1 43569 . T C 1156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.578;DP=43;Dels=0.00;FS=13.268;HaplotypeScore=30.7711;MLEAC=1;MLEAF=0.500;MQ=39.33;MQ0=1;MQRankSum=-1.864;QD=26.90;ReadPosRankSum=1.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:4,39:43:35:1185,0,35 -chr1 43571 . A G 1091.86 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=1;QD=25.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:43:99:1234,99,0 -chr1 43572 . A G 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=45;Dels=0.00;FS=3.225;HaplotypeScore=32.6687;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=2;MQRankSum=-0.039;QD=6.37;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:315,0,750 -chr1 43594 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.410;DP=44;Dels=0.00;FS=5.674;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.55;MQ0=2;MQRankSum=0.307;QD=3.77;ReadPosRankSum=0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:34,10:44:99:194,0,793 -chr1 43610 . C T 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=33;Dels=0.00;FS=6.419;HaplotypeScore=4.5214;MLEAC=1;MLEAF=0.500;MQ=33.96;MQ0=2;MQRankSum=-0.609;QD=3.30;ReadPosRankSum=-0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:137,0,510 -chr1 43619 . T C 412.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=5.3349;MLEAC=2;MLEAF=1.00;MQ=30.87;MQ0=2;QD=17.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,23:23:36:441,36,0 -chr1 43627 . T G 140.9 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.23;MQ0=1;QD=9.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,15:15:15:169,15,0 -chr1 43635 . C T 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.559;DP=28;Dels=0.00;FS=10.098;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-0.717;QD=0.64;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,4:28:46:46,0,498 -chr1 43639 . C T 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=28;Dels=0.00;FS=3.565;HaplotypeScore=6.9461;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=1;MQRankSum=-1.029;QD=4.46;ReadPosRankSum=0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:153,0,405 -chr1 43643 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=13.8923;MLEAC=1;MLEAF=0.500;MQ=36.79;MQ0=1;MQRankSum=0.952;QD=1.16;ReadPosRankSum=-1.543;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,5:29:62:62,0,530 -chr1 43651 . G A 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=33;Dels=0.00;FS=1.393;HaplotypeScore=3.9569;MLEAC=1;MLEAF=0.500;MQ=39.46;MQ0=1;MQRankSum=1.499;QD=7.78;ReadPosRankSum=1.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:285,0,426 -chr1 43662 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.298;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=0;MQRankSum=0.474;QD=3.35;ReadPosRankSum=-0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,6:37:99:152,0,768 -chr1 43664 . A G 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=36;Dels=0.00;FS=5.877;HaplotypeScore=6.2383;MLEAC=1;MLEAF=0.500;MQ=45.71;MQ0=0;MQRankSum=-2.505;QD=4.72;ReadPosRankSum=-0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:24,11:36:99:198,0,750 -chr1 43668 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=39;Dels=0.00;FS=8.049;HaplotypeScore=10.2065;MLEAC=1;MLEAF=0.500;MQ=45.43;MQ0=0;MQRankSum=-2.825;QD=7.71;ReadPosRankSum=-0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:329,0,752 -chr1 43678 . T A 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=52;Dels=0.00;FS=11.972;HaplotypeScore=19.6024;MLEAC=1;MLEAF=0.500;MQ=44.28;MQ0=0;MQRankSum=-1.814;QD=3.86;ReadPosRankSum=1.661;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,12:52:99:229,0,1169 -chr1 43686 . T C 1665.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=13.0300;MLEAC=2;MLEAF=1.00;MQ=44.10;MQ0=0;QD=29.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:1694,138,0 -chr1 43688 . C T 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=30.3912;MLEAC=1;MLEAF=0.500;MQ=43.92;MQ0=0;MQRankSum=4.253;QD=8.54;ReadPosRankSum=1.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,17:55:99:498,0,1002 -chr1 43698 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;DP=67;Dels=0.00;FS=8.840;HaplotypeScore=47.7369;MLEAC=1;MLEAF=0.500;MQ=45.08;MQ0=0;MQRankSum=-4.239;QD=8.07;ReadPosRankSum=-0.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,26:67:99:569,0,1255 -chr1 43705 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=69;Dels=0.00;FS=3.045;HaplotypeScore=32.6622;MLEAC=1;MLEAF=0.500;MQ=45.16;MQ0=0;MQRankSum=-0.571;QD=2.33;ReadPosRankSum=0.145;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,10:69:99:189,0,1720 -chr1 43713 . A C 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.553;DP=77;Dels=0.00;FS=11.201;HaplotypeScore=42.6440;MLEAC=1;MLEAF=0.500;MQ=45.67;MQ0=0;MQRankSum=-5.163;QD=8.23;ReadPosRankSum=0.667;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,32:77:99:662,0,1440 -chr1 43719 . A T 122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=81;Dels=0.00;FS=4.781;HaplotypeScore=21.7031;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=-0.691;QD=1.52;ReadPosRankSum=-0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:70,10:81:99:151,0,2102 -chr1 43742 . A T 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.288;DP=82;Dels=0.00;FS=35.671;HaplotypeScore=38.7529;MLEAC=1;MLEAF=0.500;MQ=46.28;MQ0=0;MQRankSum=1.619;QD=4.07;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:67,15:82:99:362,0,1988 -chr1 43754 . G A 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.834;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.306;QD=4.89;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:424,0,1874 -chr1 43755 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.388;DP=81;Dels=0.00;FS=11.585;HaplotypeScore=3.8103;MLEAC=1;MLEAF=0.500;MQ=45.89;MQ0=0;MQRankSum=-4.189;QD=4.47;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:59,22:81:99:390,0,1864 -chr1 43771 . C T 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=17.4268;MLEAC=1;MLEAF=0.500;MQ=48.68;MQ0=0;MQRankSum=-0.578;QD=0.63;ReadPosRankSum=-0.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:75,9:84:81:81,0,2479 -chr1 43781 . A C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=89;Dels=0.00;FS=0.000;HaplotypeScore=27.2915;MLEAC=1;MLEAF=0.500;MQ=50.47;MQ0=0;MQRankSum=-1.448;QD=1.76;ReadPosRankSum=-0.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:89:99:185,0,2613 -chr1 43786 . G A 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=84;Dels=0.00;FS=1.288;HaplotypeScore=17.3780;MLEAC=1;MLEAF=0.500;MQ=51.33;MQ0=0;MQRankSum=-1.617;QD=1.74;ReadPosRankSum=-0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:174,0,2552 -chr1 43806 . T C 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=35.5387;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-6.251;QD=15.98;ReadPosRankSum=0.139;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,41:82:99:1339,0,1390 -chr1 43810 . C T 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.203;DP=79;Dels=0.00;FS=10.312;HaplotypeScore=35.5390;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=0;MQRankSum=-2.175;QD=1.48;ReadPosRankSum=1.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:68,10:79:99:145,0,2427 -chr1 43816 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.428;DP=76;Dels=0.00;FS=1.622;HaplotypeScore=86.3319;MLEAC=1;MLEAF=0.500;MQ=52.70;MQ0=0;MQRankSum=-2.822;QD=2.44;ReadPosRankSum=1.394;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:55,11:76:99:214,0,1931 -chr1 43818 . A G 2850.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=49.3811;MLEAC=2;MLEAF=1.00;MQ=52.68;MQ0=0;QD=33.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,74:75:99:2879,223,0 -chr1 43821 . G A 375.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.751;DP=80;Dels=0.00;FS=3.003;HaplotypeScore=41.4503;MLEAC=1;MLEAF=0.500;MQ=52.13;MQ0=2;MQRankSum=-3.694;QD=4.70;ReadPosRankSum=0.476;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,16:80:99:404,0,2083 -chr1 43823 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=47.4468;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=3.459;QD=8.60;ReadPosRankSum=0.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,24:81:99:725,0,1844 -chr1 43834 . A C 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.959;DP=87;Dels=0.00;FS=5.047;HaplotypeScore=27.3319;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=2;MQRankSum=-6.863;QD=11.49;ReadPosRankSum=1.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:47,40:87:99:1028,0,1538 -chr1 43840 . C T 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.139;DP=85;Dels=0.00;FS=1.532;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=2;MQRankSum=-0.945;QD=1.09;ReadPosRankSum=-1.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:74,11:85:99:121,0,2480 -chr1 43841 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=88;Dels=0.00;FS=8.668;HaplotypeScore=28.5959;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=2;MQRankSum=-6.447;QD=6.87;ReadPosRankSum=1.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:633,0,2003 -chr1 43851 . A G 3242.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=1.7273;MLEAC=2;MLEAF=1.00;MQ=50.57;MQ0=3;QD=29.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3271,253,0 -chr1 43863 . A G 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.312;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.86;MQ0=3;MQRankSum=-4.540;QD=0.20;ReadPosRankSum=0.738;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:83,14:97:48:48,0,2773 -chr1 43864 . G A 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.505;DP=94;Dels=0.00;FS=1.845;HaplotypeScore=54.7219;MLEAC=1;MLEAF=0.500;MQ=49.56;MQ0=3;MQRankSum=3.253;QD=11.17;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,34:94:99:1078,0,1669 -chr1 43866 . G C 1601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.813;DP=89;Dels=0.00;FS=2.991;HaplotypeScore=55.7192;MLEAC=1;MLEAF=0.500;MQ=48.76;MQ0=3;MQRankSum=6.796;QD=18.00;ReadPosRankSum=1.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,49:89:99:1630,0,963 -chr1 43877 . T G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.373;DP=82;Dels=0.00;FS=4.511;HaplotypeScore=22.6567;MLEAC=1;MLEAF=0.500;MQ=48.08;MQ0=3;MQRankSum=-6.816;QD=8.86;ReadPosRankSum=-0.734;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,34:82:99:755,0,1613 -chr1 43880 . G A 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=81;Dels=0.00;FS=3.784;HaplotypeScore=34.1328;MLEAC=1;MLEAF=0.500;MQ=47.59;MQ0=3;MQRankSum=4.821;QD=5.75;ReadPosRankSum=0.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,19:81:99:494,0,1845 -chr1 43886 . A G 2779.77 . AC=2;AF=1.00;AN=2;DP=83;Dels=0.00;FS=0.000;HaplotypeScore=36.7766;MLEAC=2;MLEAF=1.00;MQ=47.06;MQ0=3;QD=33.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,83:83:99:2808,223,0 -chr1 43895 . A G 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.900;DP=84;Dels=0.00;FS=3.557;HaplotypeScore=5.7833;MLEAC=1;MLEAF=0.500;MQ=47.29;MQ0=3;MQRankSum=3.874;QD=6.95;ReadPosRankSum=-0.792;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,22:84:99:612,0,1874 -chr1 43919 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.966;DP=90;Dels=0.00;FS=10.596;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=48.00;MQ0=3;MQRankSum=-3.047;QD=1.38;ReadPosRankSum=2.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:77,12:90:99:152,0,2472 -chr1 43921 . C T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.683;DP=89;Dels=0.00;FS=11.456;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=3;MQRankSum=-0.291;QD=12.58;ReadPosRankSum=1.796;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,38:89:99:1148,0,1412 -chr1 43929 . G C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.254;DP=96;Dels=0.00;FS=0.861;HaplotypeScore=31.8093;MLEAC=1;MLEAF=0.500;MQ=47.78;MQ0=4;MQRankSum=4.123;QD=8.49;ReadPosRankSum=0.847;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,31:96:99:843,0,1928 -chr1 43954 . G A 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=98;Dels=0.00;FS=3.403;HaplotypeScore=31.4020;MLEAC=1;MLEAF=0.500;MQ=48.81;MQ0=3;MQRankSum=-1.940;QD=5.12;ReadPosRankSum=-1.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:530,0,2436 -chr1 43958 . T C 1162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.883;DP=98;Dels=0.00;FS=0.772;HaplotypeScore=41.3969;MLEAC=1;MLEAF=0.500;MQ=49.49;MQ0=3;MQRankSum=-3.408;QD=11.86;ReadPosRankSum=0.154;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,42:98:99:1191,0,1753 -chr1 43959 . T C 3463.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=41.4115;MLEAC=2;MLEAF=1.00;MQ=49.49;MQ0=3;QD=29.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,98:98:99:3492,268,0 -chr1 43966 . G T 228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.214;DP=107;Dels=0.00;FS=4.094;HaplotypeScore=60.8308;MLEAC=1;MLEAF=0.500;MQ=49.53;MQ0=3;MQRankSum=-0.729;QD=2.14;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:93,14:107:99:257,0,2992 -chr1 43969 . G A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.432;DP=107;Dels=0.00;FS=1.978;HaplotypeScore=35.1970;MLEAC=1;MLEAF=0.500;MQ=49.50;MQ0=3;MQRankSum=-2.173;QD=5.55;ReadPosRankSum=-0.469;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:80,27:107:99:622,0,2650 -chr1 43976 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.740;DP=112;Dels=0.00;FS=3.944;HaplotypeScore=55.4395;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=4;MQRankSum=-1.018;QD=2.50;ReadPosRankSum=-0.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,15:112:99:308,0,3072 -chr1 43984 . G A 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=118;Dels=0.00;FS=2.892;HaplotypeScore=75.9412;MLEAC=1;MLEAF=0.500;MQ=50.30;MQ0=4;MQRankSum=0.547;QD=6.90;ReadPosRankSum=-0.638;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:89,29:118:99:842,0,2830 -chr1 43988 . A C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=116;Dels=0.00;FS=5.433;HaplotypeScore=43.4214;MLEAC=1;MLEAF=0.500;MQ=50.72;MQ0=4;MQRankSum=4.795;QD=7.25;ReadPosRankSum=-1.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:81,34:116:99:869,0,2451 -chr1 44002 . A G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=116;Dels=0.00;FS=0.958;HaplotypeScore=39.4904;MLEAC=1;MLEAF=0.500;MQ=51.56;MQ0=3;MQRankSum=-2.313;QD=3.79;ReadPosRankSum=1.726;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:96,20:116:99:468,0,2935 -chr1 44007 . T A 1436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.367;DP=111;Dels=0.00;FS=6.411;HaplotypeScore=43.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=3;MQRankSum=-6.177;QD=12.94;ReadPosRankSum=0.970;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,51:111:99:1465,0,1937 -chr1 44026 . T C 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.135;DP=110;Dels=0.00;FS=0.000;HaplotypeScore=6.8459;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=1;MQRankSum=-3.383;QD=0.29;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:98,12:110:60:60,0,3255 -chr1 44060 . T C 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=84;Dels=0.00;FS=2.470;HaplotypeScore=22.4896;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=4.395;QD=5.53;ReadPosRankSum=0.493;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:64,20:84:99:493,0,2021 -chr1 44069 . C A 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.048;DP=73;Dels=0.00;FS=3.136;HaplotypeScore=49.4176;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-5.204;QD=3.39;ReadPosRankSum=-0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,13:73:99:276,0,1726 -chr1 44072 . T A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=71;Dels=0.00;FS=1.293;HaplotypeScore=23.4451;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=1;MQRankSum=-3.737;QD=3.56;ReadPosRankSum=-1.197;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,14:71:99:281,0,1830 -chr1 44082 . C T 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=69;Dels=0.00;FS=10.437;HaplotypeScore=20.4044;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.783;QD=3.49;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,13:69:99:269,0,1813 -chr1 44096 . C T 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=19.4892;MLEAC=1;MLEAF=0.500;MQ=51.69;MQ0=0;MQRankSum=4.352;QD=10.13;ReadPosRankSum=1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,20:60:99:636,0,1132 -chr1 44099 . T G 1703.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=15.7767;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1732,132,0 -chr1 44100 . A T 1683.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=13.9885;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1712,129,0 -chr1 44102 . A C 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.658;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.00;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:122,0,1452 -chr1 44103 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=47;Dels=0.00;FS=10.637;HaplotypeScore=20.9826;MLEAC=1;MLEAF=0.500;MQ=55.51;MQ0=0;MQRankSum=-3.780;QD=2.14;ReadPosRankSum=1.539;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:40,7:47:99:129,0,1433 -chr1 44111 . T A 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=55;Dels=0.00;FS=2.927;HaplotypeScore=2.1550;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.824;QD=3.38;ReadPosRankSum=-0.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,13:55:99:214,0,1474 -chr1 44117 . C T 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.191;DP=61;Dels=0.00;FS=5.158;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-3.964;QD=2.88;ReadPosRankSum=0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,12:61:99:204,0,1632 -chr1 44120 . C T 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=63;Dels=0.00;FS=5.124;HaplotypeScore=10.4916;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-4.000;QD=2.69;ReadPosRankSum=1.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:51,12:63:99:198,0,1749 -chr1 44126 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.677;DP=63;Dels=0.00;FS=8.122;HaplotypeScore=17.4822;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=-4.789;QD=6.36;ReadPosRankSum=-1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,21:63:99:429,0,1420 -chr1 44133 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=64;Dels=0.00;FS=3.868;HaplotypeScore=13.3538;MLEAC=1;MLEAF=0.500;MQ=51.28;MQ0=0;MQRankSum=-2.947;QD=0.39;ReadPosRankSum=-2.323;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,7:64:53:53,0,1875 -chr1 44145 . T A 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.048;DP=72;Dels=0.00;FS=14.645;HaplotypeScore=3.9967;MLEAC=1;MLEAF=0.500;MQ=50.27;MQ0=0;MQRankSum=-4.480;QD=6.77;ReadPosRankSum=2.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:516,0,1706 -chr1 44157 . T C 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.780;DP=70;Dels=0.00;FS=5.275;HaplotypeScore=5.7502;MLEAC=1;MLEAF=0.500;MQ=49.89;MQ0=0;MQRankSum=-1.502;QD=1.11;ReadPosRankSum=2.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:60,10:70:99:106,0,2013 -chr1 44177 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.835;DP=73;Dels=0.00;FS=7.693;HaplotypeScore=14.5600;MLEAC=1;MLEAF=0.500;MQ=49.07;MQ0=0;MQRankSum=0.080;QD=7.48;ReadPosRankSum=0.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,20:73:99:574,0,1711 -chr1 44183 . T C 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=73;Dels=0.00;FS=3.202;HaplotypeScore=50.8308;MLEAC=1;MLEAF=0.500;MQ=49.60;MQ0=0;MQRankSum=-1.131;QD=1.08;ReadPosRankSum=-0.425;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:63,10:73:99:107,0,2164 -chr1 44188 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=74;Dels=0.00;FS=14.435;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=48.97;MQ0=0;MQRankSum=-4.140;QD=6.90;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,24:74:99:539,0,1696 -chr1 44191 . C G 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=78;Dels=0.00;FS=1.989;HaplotypeScore=30.4305;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=0;MQRankSum=3.081;QD=11.29;ReadPosRankSum=1.210;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,29:78:99:909,0,1490 -chr1 44202 . T C 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=70;Dels=0.00;FS=18.949;HaplotypeScore=45.1512;MLEAC=1;MLEAF=0.500;MQ=50.32;MQ0=0;MQRankSum=-3.780;QD=4.45;ReadPosRankSum=-1.041;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:53,17:70:99:340,0,1880 -chr1 44205 . T G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.786;DP=71;Dels=0.00;FS=2.009;HaplotypeScore=52.8564;MLEAC=1;MLEAF=0.500;MQ=50.01;MQ0=0;MQRankSum=2.066;QD=13.29;ReadPosRankSum=0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,30:71:99:972,0,1251 -chr1 44214 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=65;Dels=0.00;FS=6.471;HaplotypeScore=49.1081;MLEAC=1;MLEAF=0.500;MQ=49.76;MQ0=0;MQRankSum=-3.604;QD=0.55;ReadPosRankSum=-0.170;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,8:65:64:64,0,1916 -chr1 44224 . C T 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=65;Dels=0.00;FS=11.066;HaplotypeScore=41.7947;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=0;MQRankSum=3.011;QD=10.97;ReadPosRankSum=-1.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:741,0,1311 -chr1 44226 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.161;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=0.468;QD=10.58;ReadPosRankSum=1.342;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:663,0,1231 -chr1 44227 . T C 1771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=60;Dels=0.00;FS=3.739;HaplotypeScore=35.0888;MLEAC=1;MLEAF=0.500;MQ=48.89;MQ0=0;MQRankSum=3.270;QD=29.53;ReadPosRankSum=-1.934;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:7,52:60:43:1800,0,43 -chr1 44239 . C T 1746.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1775,138,0 -chr1 44240 . C T 507.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=2.627;HaplotypeScore=23.3747;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=2.800;QD=10.58;ReadPosRankSum=1.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:536,0,932 -chr1 44241 . T C 1696.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=23.3747;MLEAC=2;MLEAF=1.00;MQ=50.05;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1725,135,0 -chr1 44248 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.520;DP=48;Dels=0.00;FS=9.054;HaplotypeScore=23.3746;MLEAC=1;MLEAF=0.500;MQ=50.11;MQ0=0;MQRankSum=-4.405;QD=3.08;ReadPosRankSum=2.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,10:48:99:176,0,1356 -chr1 44249 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.419;DP=49;Dels=0.00;FS=8.239;HaplotypeScore=24.3740;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=0;MQRankSum=-4.565;QD=3.65;ReadPosRankSum=1.809;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:207,0,1354 -chr1 44258 . T A 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.562;DP=54;Dels=0.00;FS=4.366;HaplotypeScore=24.1638;MLEAC=1;MLEAF=0.500;MQ=48.73;MQ0=0;MQRankSum=4.329;QD=10.64;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:603,0,1025 -chr1 44278 . A G 1907.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=6.7023;MLEAC=2;MLEAF=1.00;MQ=46.93;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:1936,153,0 -chr1 44282 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=57;Dels=0.00;FS=1.055;HaplotypeScore=8.1141;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=0;MQRankSum=4.194;QD=11.70;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:33,24:57:99:695,0,881 -chr1 44295 . A T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.344;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=9.3874;MLEAC=1;MLEAF=0.500;MQ=43.43;MQ0=2;MQRankSum=-2.337;QD=0.18;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:56,7:63:39:39,0,1747 -chr1 44304 . T C 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.495;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=23.9832;MLEAC=1;MLEAF=0.500;MQ=43.23;MQ0=2;MQRankSum=4.033;QD=11.74;ReadPosRankSum=0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,25:62:99:756,0,963 -chr1 44307 . C G 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.815;DP=60;Dels=0.00;FS=6.252;HaplotypeScore=26.1832;MLEAC=1;MLEAF=0.500;MQ=43.38;MQ0=2;MQRankSum=-0.025;QD=7.33;ReadPosRankSum=-1.252;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:468,0,1201 -chr1 44311 . A G 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.265;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=30.9134;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=2;MQRankSum=-2.338;QD=10.90;ReadPosRankSum=-0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:31,29:60:99:682,0,949 -chr1 44317 . T A 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.835;DP=59;Dels=0.00;FS=4.227;HaplotypeScore=16.7737;MLEAC=1;MLEAF=0.500;MQ=42.80;MQ0=2;MQRankSum=0.606;QD=6.47;ReadPosRankSum=-2.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,17:59:99:410,0,1154 -chr1 44335 . T A 1721.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=18.1882;MLEAC=2;MLEAF=1.00;MQ=40.95;MQ0=2;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:1750,144,0 -chr1 44342 . C G 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=61;Dels=0.00;FS=4.324;HaplotypeScore=34.0871;MLEAC=1;MLEAF=0.500;MQ=42.11;MQ0=2;MQRankSum=-1.601;QD=6.18;ReadPosRankSum=0.691;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:39,16:61:99:405,0,1260 -chr1 44367 . C T 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=9.9194;MLEAC=1;MLEAF=0.500;MQ=42.27;MQ0=2;MQRankSum=2.251;QD=15.05;ReadPosRankSum=0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:886,0,731 -chr1 44402 . T C 1512.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=45.06;MQ0=0;QD=27.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1541,117,0 -chr1 44414 . C T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.135;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=14.3006;MLEAC=1;MLEAF=0.500;MQ=44.91;MQ0=0;MQRankSum=0.590;QD=12.70;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:714,0,919 -chr1 44417 . C T 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.333;DP=59;Dels=0.00;FS=7.276;HaplotypeScore=15.3006;MLEAC=1;MLEAF=0.500;MQ=45.19;MQ0=0;MQRankSum=-3.435;QD=2.13;ReadPosRankSum=-2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:154,0,1624 -chr1 44447 . T C 76.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.447;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.70;MQ0=0;MQRankSum=-0.207;QD=1.35;ReadPosRankSum=-0.960;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,7:57:99:105,0,1613 -chr1 44452 . G A 116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.071;DP=58;Dels=0.00;FS=3.537;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=44.96;MQ0=0;MQRankSum=-0.530;QD=2.01;ReadPosRankSum=-0.755;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:50,8:58:99:145,0,1592 -chr1 44473 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=69;Dels=0.00;FS=9.852;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=44.99;MQ0=0;MQRankSum=-4.187;QD=0.71;ReadPosRankSum=0.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:57,12:69:77:77,0,2026 -chr1 44477 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.028;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=0;MQRankSum=-0.984;QD=1.30;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:118,0,1985 -chr1 44478 . G C 84.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.175;DP=70;Dels=0.00;FS=1.536;HaplotypeScore=9.6363;MLEAC=1;MLEAF=0.500;MQ=45.34;MQ0=0;MQRankSum=-0.858;QD=1.21;ReadPosRankSum=2.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:62,8:70:99:113,0,2020 -chr1 44484 . A G 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.103;DP=69;Dels=0.00;FS=1.548;HaplotypeScore=36.7273;MLEAC=1;MLEAF=0.500;MQ=45.51;MQ0=0;MQRankSum=-1.246;QD=1.13;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:61,8:69:99:106,0,1981 -chr1 44498 . A C 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=59;Dels=0.03;FS=1.285;HaplotypeScore=66.6807;MLEAC=1;MLEAF=0.500;MQ=46.25;MQ0=0;MQRankSum=1.067;QD=5.03;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,12:57:99:325,0,1534 -chr1 44501 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.558;DP=54;Dels=0.00;FS=2.868;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.82;MQ0=0;MQRankSum=0.142;QD=6.25;ReadPosRankSum=-0.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:41,13:54:99:366,0,1280 -chr1 44503 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=55;Dels=0.00;FS=2.476;HaplotypeScore=45.5620;MLEAC=1;MLEAF=0.500;MQ=45.92;MQ0=0;MQRankSum=-0.130;QD=18.18;ReadPosRankSum=1.776;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1028,0,672 -chr1 44505 . T C 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.716;DP=56;Dels=0.00;FS=1.565;HaplotypeScore=46.3941;MLEAC=1;MLEAF=0.500;MQ=46.01;MQ0=0;MQRankSum=-0.697;QD=1.69;ReadPosRankSum=-0.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:56:99:123,0,1510 -chr1 44517 . G A 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=8.8138;MLEAC=1;MLEAF=0.500;MQ=44.77;MQ0=0;MQRankSum=-3.350;QD=2.42;ReadPosRankSum=2.577;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,11:54:99:159,0,1479 -chr1 44560 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.286;DP=43;Dels=0.00;FS=9.300;HaplotypeScore=4.7566;MLEAC=1;MLEAF=0.500;MQ=41.88;MQ0=0;MQRankSum=0.807;QD=9.95;ReadPosRankSum=-0.012;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:456,0,729 -chr1 44572 . C A 1243.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.646;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=41.69;MQ0=0;MQRankSum=0.866;QD=31.09;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:1,39:40:99:1272,105,0 -chr1 44587 . T C 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.665;DP=38;Dels=0.00;FS=13.265;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=40.46;MQ0=0;MQRankSum=-1.286;QD=9.10;ReadPosRankSum=-0.547;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:374,0,691 -chr1 44614 . C G 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.420;DP=43;Dels=0.00;FS=1.868;HaplotypeScore=14.4733;MLEAC=1;MLEAF=0.500;MQ=42.93;MQ0=0;MQRankSum=0.020;QD=1.11;ReadPosRankSum=0.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,6:43:76:76,0,1119 -chr1 44624 . G A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.102;DP=51;Dels=0.00;FS=12.856;HaplotypeScore=21.4215;MLEAC=1;MLEAF=0.500;MQ=42.84;MQ0=0;MQRankSum=-2.880;QD=0.20;ReadPosRankSum=1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,6:51:38:38,0,1509 -chr1 44632 . A T 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=54;Dels=0.00;FS=2.363;HaplotypeScore=21.5373;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=1.153;QD=12.81;ReadPosRankSum=-0.378;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:720,0,934 -chr1 44637 . C T 77.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=22.5160;MLEAC=1;MLEAF=0.500;MQ=42.79;MQ0=0;MQRankSum=-0.673;QD=1.44;ReadPosRankSum=0.812;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,9:54:99:106,0,1529 -chr1 44642 . C T 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.777;DP=52;Dels=0.00;FS=20.166;HaplotypeScore=24.5152;MLEAC=1;MLEAF=0.500;MQ=43.10;MQ0=0;MQRankSum=-3.351;QD=0.36;ReadPosRankSum=-0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:45,7:52:47:47,0,1525 -chr1 44646 . C T 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=50;Dels=0.00;FS=21.581;HaplotypeScore=15.6098;MLEAC=1;MLEAF=0.500;MQ=43.77;MQ0=0;MQRankSum=-3.383;QD=0.52;ReadPosRankSum=-0.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:43,7:50:54:54,0,1474 -chr1 44657 . C T 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=58;Dels=0.00;FS=2.599;HaplotypeScore=22.8584;MLEAC=1;MLEAF=0.500;MQ=44.43;MQ0=0;MQRankSum=2.619;QD=7.03;ReadPosRankSum=0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:42,15:58:99:436,0,1315 -chr1 44662 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=55;Dels=0.00;FS=16.338;HaplotypeScore=20.8592;MLEAC=1;MLEAF=0.500;MQ=44.81;MQ0=0;MQRankSum=-3.253;QD=0.34;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:49,6:55:47:47,0,1653 -chr1 44666 . T C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=4.523;HaplotypeScore=18.8632;MLEAC=1;MLEAF=0.500;MQ=45.50;MQ0=0;MQRankSum=-3.198;QD=5.00;ReadPosRankSum=0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:37,14:51:99:283,0,1321 -chr1 44682 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=48;Dels=0.00;FS=1.217;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=44.53;MQ0=0;MQRankSum=-2.438;QD=21.25;ReadPosRankSum=-0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:14,34:48:99:1048,0,416 -chr1 44699 . G A 1395.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=43.18;MQ0=0;QD=33.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1424,117,0 -chr1 44721 . A T 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.754;DP=38;Dels=0.00;FS=2.913;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.46;MQ0=0;MQRankSum=1.227;QD=11.65;ReadPosRankSum=1.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:471,0,475 -chr1 44722 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=40;Dels=0.00;FS=1.222;HaplotypeScore=8.5355;MLEAC=1;MLEAF=0.500;MQ=38.48;MQ0=0;MQRankSum=0.137;QD=8.77;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:379,0,602 -chr1 44747 . A G 853.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.64;MQ0=2;QD=23.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,36:36:75:882,75,0 -chr1 44750 . T C 772.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.71;MQ0=2;QD=22.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,35:35:69:801,69,0 -chr1 44764 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.890;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.22;MQ0=2;MQRankSum=-0.925;QD=0.33;ReadPosRankSum=0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 0/1:35,7:42:42:42,0,799 -chr1 44766 . G A 933.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.92;MQ0=2;QD=23.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00040|mRNA||GSCOCT00012436001|) GT:AD:DP:GQ:PL 1/1:0,40:40:81:962,81,0 -chr1 44844 . C T 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.998;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=13.6215;MLEAC=1;MLEAF=0.500;MQ=39.32;MQ0=0;MQRankSum=0.233;QD=13.06;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,25:50:99:681,0,649 -chr1 44846 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=13.5548;MLEAC=2;MLEAF=1.00;MQ=40.00;MQ0=0;QD=32.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1552,123,0 -chr1 44848 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=50;Dels=0.00;FS=1.565;HaplotypeScore=12.7662;MLEAC=1;MLEAF=0.500;MQ=40.79;MQ0=0;MQRankSum=-2.924;QD=0.54;ReadPosRankSum=1.522;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,8:50:55:55,0,1346 -chr1 44875 . C T 224.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.116;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=6.7552;MLEAC=1;MLEAF=0.500;MQ=43.15;MQ0=0;MQRankSum=-1.397;QD=3.57;ReadPosRankSum=-1.910;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,14:63:99:253,0,1577 -chr1 44905 . C G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.316;DP=72;Dels=0.00;FS=2.379;HaplotypeScore=14.6636;MLEAC=1;MLEAF=0.500;MQ=43.09;MQ0=1;MQRankSum=0.928;QD=8.39;ReadPosRankSum=-1.284;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:49,23:72:99:632,0,1456 -chr1 44912 . A G 1743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.677;DP=68;Dels=0.00;FS=1.336;HaplotypeScore=30.8580;MLEAC=1;MLEAF=0.500;MQ=43.96;MQ0=2;MQRankSum=-0.403;QD=25.64;ReadPosRankSum=-1.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,53:68:99:1772,0,267 -chr1 44920 . T C 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.714;DP=73;Dels=0.00;FS=7.931;HaplotypeScore=5.9984;MLEAC=1;MLEAF=0.500;MQ=42.33;MQ0=4;MQRankSum=-0.128;QD=5.48;ReadPosRankSum=1.793;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,21:73:99:428,0,1524 -chr1 44950 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=38.40;MQ0=5;MQRankSum=0.127;QD=7.52;ReadPosRankSum=1.502;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,23:72:99:570,0,1227 -chr1 44968 . A G 1512.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=4.8653;MLEAC=2;MLEAF=1.00;MQ=35.93;MQ0=5;QD=25.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,60:60:99:1541,132,0 -chr1 44980 . T G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=53;Dels=0.00;FS=1.794;HaplotypeScore=4.8653;MLEAC=1;MLEAF=0.500;MQ=32.25;MQ0=6;MQRankSum=0.207;QD=17.41;ReadPosRankSum=-1.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,47:53:53:951,0,53 -chr1 44999 . A G 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=6;MQRankSum=-2.111;QD=4.22;ReadPosRankSum=-0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:231,0,671 -chr1 45005 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.014;DP=44;Dels=0.00;FS=5.608;HaplotypeScore=21.5580;MLEAC=1;MLEAF=0.500;MQ=30.42;MQ0=4;MQRankSum=1.637;QD=10.11;ReadPosRankSum=1.096;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:473,0,341 -chr1 45011 . A G 805.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.6852;MLEAC=2;MLEAF=1.00;MQ=30.05;MQ0=2;QD=21.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:38:78:834,78,0 -chr1 45027 . C T 849.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.9559;MLEAC=2;MLEAF=1.00;MQ=31.41;MQ0=4;QD=20.23;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:78:878,78,0 -chr1 45055 . C T 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.634;DP=71;Dels=0.00;FS=12.767;HaplotypeScore=11.6629;MLEAC=1;MLEAF=0.500;MQ=43.94;MQ0=9;MQRankSum=-0.438;QD=0.94;ReadPosRankSum=-0.182;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:53,15:71:95:95,0,1604 -chr1 45090 . C T 1075.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.677;DP=87;Dels=0.00;FS=4.246;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.72;MQ0=1;MQRankSum=3.081;QD=12.37;ReadPosRankSum=-0.758;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,34:87:99:1104,0,1445 -chr1 45092 . C T 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=86;Dels=0.00;FS=18.933;HaplotypeScore=45.0201;MLEAC=1;MLEAF=0.500;MQ=49.98;MQ0=1;MQRankSum=-0.050;QD=0.57;ReadPosRankSum=-0.221;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:77,9:86:77:77,0,2524 -chr1 45093 . A C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.723;DP=84;Dels=0.04;FS=4.282;HaplotypeScore=44.0211;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=1;MQRankSum=-2.754;QD=0.47;ReadPosRankSum=0.306;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,16:81:68:68,0,2273 -chr1 45100 . A T 1063.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=91;Dels=0.00;FS=1.785;HaplotypeScore=46.2820;MLEAC=1;MLEAF=0.500;MQ=50.63;MQ0=1;MQRankSum=0.114;QD=11.69;ReadPosRankSum=1.119;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,34:91:99:1092,0,1575 -chr1 45104 . C T 1245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.511;DP=93;Dels=0.00;FS=5.290;HaplotypeScore=20.4240;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=1;MQRankSum=1.122;QD=13.40;ReadPosRankSum=-0.845;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,38:93:99:1274,0,1627 -chr1 45135 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.219;DP=93;Dels=0.00;FS=0.788;HaplotypeScore=3.1233;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=0.496;QD=15.87;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,46:93:99:1504,0,1552 -chr1 45155 . C T 3133.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.690;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=145.5703;MLEAC=2;MLEAF=1.00;MQ=50.31;MQ0=0;MQRankSum=1.436;QD=30.69;ReadPosRankSum=-0.338;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,81:82:99:3162,241,0 -chr1 45200 . A T 2113.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=1;QD=32.38;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2142,169,0 -chr1 45254 . G A 2049.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=47.40;MQ0=0;QD=29.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2078,156,0 -chr1 45271 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.331;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=0.761;QD=14.36;ReadPosRankSum=-0.072;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,26:58:99:861,0,1025 -chr1 45272 . C A 2207.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=3.1435;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=33.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2236,169,0 -chr1 45286 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7329;MLEAC=1;MLEAF=0.500;MQ=49.43;MQ0=0;MQRankSum=0.497;QD=16.06;ReadPosRankSum=0.752;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,31:64:99:1056,0,1087 -chr1 45290 . T A 1146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.598;DP=65;Dels=0.00;FS=2.073;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=49.75;MQ0=0;MQRankSum=-0.151;QD=17.64;ReadPosRankSum=0.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1175,0,1019 -chr1 45343 . T A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.611;DP=74;Dels=0.00;FS=3.119;HaplotypeScore=3.9919;MLEAC=1;MLEAF=0.500;MQ=51.54;MQ0=0;MQRankSum=1.189;QD=16.85;ReadPosRankSum=0.605;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,37:74:99:1275,0,1131 -chr1 45344 . G A 2859.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=2.9920;MLEAC=2;MLEAF=1.00;MQ=51.54;MQ0=0;QD=33.68;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2888,220,0 -chr1 45355 . T C 2778.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.98;MQ0=0;QD=24.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2807,211,0 -chr1 45366 . A C 2847.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.43;MQ0=0;QD=31.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2876,220,0 -chr1 45377 . C T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=72;Dels=0.00;FS=27.679;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.59;MQ0=0;MQRankSum=-2.895;QD=0.71;ReadPosRankSum=-1.328;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,9:72:79:79,0,2293 -chr1 45382 . A G 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.364;DP=74;Dels=0.00;FS=24.375;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.91;MQ0=0;MQRankSum=-3.126;QD=0.20;ReadPosRankSum=0.050;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,9:74:43:43,0,2344 -chr1 45385 . T A 2874.77 . AC=2;AF=1.00;AN=2;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=27.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:75:99:2903,220,0 -chr1 45401 . T G 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=75;Dels=0.00;FS=42.438;HaplotypeScore=1.8656;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-2.624;QD=2.74;ReadPosRankSum=2.484;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,13:75:99:234,0,2260 -chr1 45425 . T C 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=62;Dels=0.00;FS=32.888;HaplotypeScore=11.8192;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.715;QD=3.33;ReadPosRankSum=2.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,12:62:99:235,0,1811 -chr1 45428 . C A 2117.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=21.6418;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;QD=27.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2146,163,0 -chr1 45430 . C A 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.713;DP=50;Dels=0.00;FS=4.121;HaplotypeScore=21.6418;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=0.980;QD=12.74;ReadPosRankSum=0.446;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,20:50:99:665,0,987 -chr1 45435 . T C 1851.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=30.4494;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=26.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1880,141,0 -chr1 45436 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.196;DP=48;Dels=0.00;FS=17.629;HaplotypeScore=19.6275;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-3.668;QD=3.45;ReadPosRankSum=0.470;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:38,10:48:99:194,0,1412 -chr1 45442 . G A 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.766;DP=53;Dels=0.00;FS=20.851;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-3.761;QD=3.49;ReadPosRankSum=-0.055;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,11:53:99:213,0,1458 -chr1 45445 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=54;Dels=0.00;FS=3.890;HaplotypeScore=20.6274;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=0.857;QD=15.44;ReadPosRankSum=-0.441;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,26:54:99:862,0,877 -chr1 45455 . C T 1668.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=21.9167;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.46;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1697,132,0 -chr1 45456 . A G 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.281;DP=47;Dels=0.00;FS=15.317;HaplotypeScore=22.9164;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=0;MQRankSum=-2.324;QD=20.91;ReadPosRankSum=-1.560;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,31:47:99:1011,0,399 -chr1 45458 . C A 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.943;DP=49;Dels=0.00;FS=1.157;HaplotypeScore=24.9247;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=0.389;QD=9.83;ReadPosRankSum=0.305;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,17:49:99:510,0,1061 -chr1 45460 . C T 101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.945;DP=51;Dels=0.00;FS=20.268;HaplotypeScore=33.8333;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-2.966;QD=2.00;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,8:51:99:130,0,1482 -chr1 45468 . T C 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.974;DP=54;Dels=0.00;FS=11.572;HaplotypeScore=42.6787;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=3.688;QD=9.07;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:37,17:54:99:518,0,1120 -chr1 45469 . C G 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=54;Dels=0.00;FS=25.872;HaplotypeScore=26.8594;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-2.910;QD=1.38;ReadPosRankSum=-0.791;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,8:54:99:103,0,1615 -chr1 45473 . G A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.252;DP=57;Dels=0.00;FS=27.090;HaplotypeScore=18.7370;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=0;MQRankSum=-3.140;QD=1.47;ReadPosRankSum=-0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,9:57:99:112,0,1689 -chr1 45486 . T G 42.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=59;Dels=0.00;FS=26.386;HaplotypeScore=19.2723;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.044;QD=0.72;ReadPosRankSum=-0.122;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:51,8:59:71:71,0,1772 -chr1 45491 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.621;DP=56;Dels=0.00;FS=11.681;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=2.678;QD=7.98;ReadPosRankSum=-0.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:39,16:56:99:475,0,1141 -chr1 45492 . A C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=56;Dels=0.00;FS=36.390;HaplotypeScore=17.2627;MLEAC=1;MLEAF=0.500;MQ=51.49;MQ0=0;MQRankSum=-3.873;QD=1.34;ReadPosRankSum=-0.513;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,10:56:99:103,0,1545 -chr1 45515 . A C 249.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=55;Dels=0.00;FS=18.588;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.91;MQ0=0;MQRankSum=1.483;QD=4.54;ReadPosRankSum=1.105;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,11:55:99:278,0,1358 -chr1 45516 . T C 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=55;Dels=0.00;FS=32.991;HaplotypeScore=36.5629;MLEAC=1;MLEAF=0.500;MQ=47.72;MQ0=0;MQRankSum=-5.064;QD=1.89;ReadPosRankSum=0.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,12:55:99:132,0,1550 -chr1 45518 . C T 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.102;DP=57;Dels=0.00;FS=26.291;HaplotypeScore=37.5622;MLEAC=1;MLEAF=0.500;MQ=47.75;MQ0=0;MQRankSum=-5.240;QD=2.29;ReadPosRankSum=-0.162;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,13:57:99:159,0,1581 -chr1 45530 . G A 1057.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=61;Dels=0.00;FS=1.071;HaplotypeScore=2.8319;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=4.182;QD=17.34;ReadPosRankSum=-0.133;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,32:61:99:1086,0,615 -chr1 45538 . T C 2219.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.8319;MLEAC=2;MLEAF=1.00;MQ=45.96;MQ0=1;QD=33.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2248,175,0 -chr1 45549 . G A 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.457;DP=67;Dels=0.00;FS=21.346;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=45.62;MQ0=1;MQRankSum=1.140;QD=2.58;ReadPosRankSum=0.504;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:58,9:67:99:201,0,1627 -chr1 45550 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.636;DP=67;Dels=0.00;FS=0.940;HaplotypeScore=8.9982;MLEAC=1;MLEAF=0.500;MQ=46.27;MQ0=1;MQRankSum=-4.933;QD=9.31;ReadPosRankSum=0.982;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,33:67:99:652,0,1160 -chr1 45576 . A T 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=86;Dels=0.00;FS=0.996;HaplotypeScore=31.9081;MLEAC=1;MLEAF=0.500;MQ=44.67;MQ0=1;MQRankSum=-3.062;QD=5.30;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,26:86:99:484,0,1787 -chr1 45578 . A G 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.189;DP=84;Dels=0.00;FS=6.011;HaplotypeScore=57.3640;MLEAC=1;MLEAF=0.500;MQ=44.80;MQ0=1;MQRankSum=-6.448;QD=10.99;ReadPosRankSum=-1.326;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,44:84:99:951,0,1314 -chr1 45586 . T C 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.575;DP=80;Dels=0.00;FS=1.341;HaplotypeScore=88.2105;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.105;QD=0.92;ReadPosRankSum=-0.165;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:102,0,2084 -chr1 45587 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=80;Dels=0.00;FS=1.232;HaplotypeScore=75.5755;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-4.092;QD=1.20;ReadPosRankSum=-0.086;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,14:80:99:124,0,2088 -chr1 45588 . A G 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=81;Dels=0.00;FS=1.248;HaplotypeScore=76.3642;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=1;MQRankSum=-4.082;QD=1.15;ReadPosRankSum=0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:67,14:81:99:121,0,2109 -chr1 45600 . G A 1328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=109;Dels=0.00;FS=1.699;HaplotypeScore=36.6790;MLEAC=1;MLEAF=0.500;MQ=42.25;MQ0=2;MQRankSum=-6.013;QD=12.19;ReadPosRankSum=0.815;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:46,63:109:99:1357,0,1334 -chr1 45609 . A C 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=114;Dels=0.00;FS=0.838;HaplotypeScore=28.9230;MLEAC=1;MLEAF=0.500;MQ=42.08;MQ0=2;MQRankSum=-1.161;QD=6.55;ReadPosRankSum=1.490;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,34:114:99:775,0,2078 -chr1 45619 . C T 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=119;Dels=0.00;FS=2.580;HaplotypeScore=3.6750;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=2;MQRankSum=-0.216;QD=7.02;ReadPosRankSum=1.214;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:83,36:119:99:864,0,1946 -chr1 45632 . G T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=119;Dels=0.00;FS=0.893;HaplotypeScore=6.6304;MLEAC=1;MLEAF=0.500;MQ=40.17;MQ0=2;MQRankSum=-5.708;QD=2.94;ReadPosRankSum=1.745;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,37:119:99:378,0,2346 -chr1 45659 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.317;DP=120;Dels=0.00;FS=0.000;HaplotypeScore=71.6402;MLEAC=1;MLEAF=0.500;MQ=41.20;MQ0=3;MQRankSum=-6.632;QD=3.24;ReadPosRankSum=0.893;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,39:120:99:417,0,2397 -chr1 45660 . A G 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.966;DP=117;Dels=0.00;FS=2.575;HaplotypeScore=63.3294;MLEAC=1;MLEAF=0.500;MQ=41.50;MQ0=3;MQRankSum=-1.543;QD=0.31;ReadPosRankSum=1.048;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:117:64:64,0,2593 -chr1 45663 . C T 27.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.724;DP=116;Dels=0.00;FS=2.578;HaplotypeScore=119.3449;MLEAC=1;MLEAF=0.500;MQ=41.26;MQ0=3;MQRankSum=-1.489;QD=0.24;ReadPosRankSum=1.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,14:116:56:56,0,2716 -chr1 45672 . T G 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.828;DP=105;Dels=0.00;FS=0.751;HaplotypeScore=110.4878;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=2;MQRankSum=-5.196;QD=8.45;ReadPosRankSum=0.761;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,45:105:99:915,0,1759 -chr1 45673 . G A 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.793;DP=105;Dels=0.00;FS=0.897;HaplotypeScore=111.2217;MLEAC=1;MLEAF=0.500;MQ=43.63;MQ0=2;MQRankSum=-5.747;QD=1.35;ReadPosRankSum=1.937;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,24:105:99:170,0,2516 -chr1 45679 . C T 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.082;DP=116;Dels=0.00;FS=2.067;HaplotypeScore=85.5662;MLEAC=1;MLEAF=0.500;MQ=43.87;MQ0=2;MQRankSum=-0.621;QD=3.21;ReadPosRankSum=-0.794;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,23:116:99:401,0,2219 -chr1 45694 . A G 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=125;Dels=0.00;FS=4.243;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.00;MQ0=2;MQRankSum=-5.132;QD=1.74;ReadPosRankSum=-0.229;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,25:125:99:246,0,3244 -chr1 45707 . T C 2311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=121;Dels=0.00;FS=6.874;HaplotypeScore=39.0259;MLEAC=1;MLEAF=0.500;MQ=45.33;MQ0=2;MQRankSum=-7.286;QD=19.11;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,87:121:99:2340,0,940 -chr1 45717 . G A 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.975;DP=109;Dels=0.00;FS=1.591;HaplotypeScore=73.3895;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=2;MQRankSum=-1.982;QD=6.89;ReadPosRankSum=2.664;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:65,43:109:99:779,0,1809 -chr1 45724 . C G 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=100;Dels=0.00;FS=0.957;HaplotypeScore=83.7585;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=2;MQRankSum=-1.008;QD=5.78;ReadPosRankSum=1.509;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,25:100:99:606,0,1819 -chr1 45725 . C T 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.812;DP=98;Dels=0.00;FS=0.966;HaplotypeScore=96.3231;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=5.039;QD=4.35;ReadPosRankSum=-2.841;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,19:98:99:455,0,2414 -chr1 45727 . A G 3406.77 . AC=2;AF=1.00;AN=2;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=131.4140;MLEAC=2;MLEAF=1.00;MQ=46.96;MQ0=2;QD=34.41;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,99:99:99:3435,274,0 -chr1 45728 . T C 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.069;DP=100;Dels=0.00;FS=12.270;HaplotypeScore=130.4542;MLEAC=1;MLEAF=0.500;MQ=46.88;MQ0=2;MQRankSum=-0.733;QD=1.80;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,13:100:99:208,0,2628 -chr1 45729 . A G 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.199;DP=98;Dels=0.00;FS=7.239;HaplotypeScore=143.0188;MLEAC=1;MLEAF=0.500;MQ=47.26;MQ0=2;MQRankSum=-2.286;QD=9.53;ReadPosRankSum=1.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,35:98:99:962,0,1812 -chr1 45733 . C T 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.767;DP=103;Dels=0.00;FS=11.158;HaplotypeScore=175.1243;MLEAC=1;MLEAF=0.500;MQ=45.48;MQ0=2;MQRankSum=-0.096;QD=2.07;ReadPosRankSum=2.500;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:90,13:103:99:241,0,2768 -chr1 45744 . A T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=97;Dels=0.00;FS=3.403;HaplotypeScore=141.3914;MLEAC=1;MLEAF=0.500;MQ=43.52;MQ0=6;MQRankSum=-2.164;QD=0.15;ReadPosRankSum=0.983;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,11:97:43:43,0,2548 -chr1 45746 . C G 1081.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.871;DP=98;Dels=0.00;FS=5.658;HaplotypeScore=144.7874;MLEAC=1;MLEAF=0.500;MQ=43.28;MQ0=6;MQRankSum=-2.422;QD=11.04;ReadPosRankSum=-1.217;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:57,41:98:99:1110,0,1505 -chr1 45749 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.332;DP=105;Dels=0.00;FS=20.438;HaplotypeScore=99.1311;MLEAC=1;MLEAF=0.500;MQ=42.61;MQ0=6;MQRankSum=-1.228;QD=0.58;ReadPosRankSum=1.410;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:93,12:105:89:89,0,2686 -chr1 45752 . C A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.973;DP=107;Dels=0.00;FS=0.000;HaplotypeScore=60.4379;MLEAC=1;MLEAF=0.500;MQ=42.32;MQ0=7;MQRankSum=3.784;QD=2.22;ReadPosRankSum=3.512;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:91,16:107:99:266,0,2493 -chr1 45756 . T C 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.279;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=54.1966;MLEAC=1;MLEAF=0.500;MQ=41.83;MQ0=7;MQRankSum=3.711;QD=3.90;ReadPosRankSum=2.139;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:86,19:105:99:438,0,2316 -chr1 45774 . G A 2856.77 . AC=2;AF=1.00;AN=2;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=1.8661;MLEAC=2;MLEAF=1.00;MQ=40.57;MQ0=8;QD=29.15;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,98:98:99:2885,247,0 -chr1 45792 . A T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=73;Dels=0.00;FS=9.059;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.74;MQ0=7;MQRankSum=-2.340;QD=8.15;ReadPosRankSum=-0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,26:73:99:623,0,946 -chr1 45793 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=74;Dels=0.00;FS=6.479;HaplotypeScore=58.8320;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=-1.025;QD=10.97;ReadPosRankSum=-1.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:42,32:74:99:840,0,770 -chr1 45796 . T A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=73;Dels=0.03;FS=11.097;HaplotypeScore=57.0004;MLEAC=1;MLEAF=0.500;MQ=32.88;MQ0=7;MQRankSum=-0.761;QD=2.38;ReadPosRankSum=3.011;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:55,16:71:99:202,0,1418 -chr1 45803 . C T 2095.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=66.1329;MLEAC=2;MLEAF=1.00;MQ=33.59;MQ0=6;QD=27.58;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,76:76:99:2124,183,0 -chr1 45826 . A T 1113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=78;Dels=0.01;FS=3.363;HaplotypeScore=5.1586;MLEAC=1;MLEAF=0.500;MQ=36.05;MQ0=3;MQRankSum=-3.121;QD=14.28;ReadPosRankSum=2.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,46:77:99:1142,0,798 -chr1 45844 . T A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.235;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=38.54;MQ0=3;MQRankSum=-3.089;QD=4.97;ReadPosRankSum=0.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,25:96:99:505,0,2123 -chr1 45863 . A T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.601;DP=97;Dels=0.00;FS=0.931;HaplotypeScore=2.8214;MLEAC=1;MLEAF=0.500;MQ=39.70;MQ0=1;MQRankSum=3.322;QD=5.27;ReadPosRankSum=-0.737;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,22:97:99:539,0,2180 -chr1 45895 . C T 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.467;DP=86;Dels=0.00;FS=3.221;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=40.11;MQ0=2;MQRankSum=2.945;QD=7.57;ReadPosRankSum=1.653;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:61,25:86:99:679,0,1779 -chr1 45899 . T G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=84;Dels=0.00;FS=5.870;HaplotypeScore=19.6124;MLEAC=1;MLEAF=0.500;MQ=39.85;MQ0=3;MQRankSum=-2.045;QD=4.13;ReadPosRankSum=-0.184;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,20:84:99:375,0,1957 -chr1 45911 . C T 1407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=77;Dels=0.00;FS=0.933;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.22;MQ0=3;MQRankSum=-3.291;QD=18.28;ReadPosRankSum=1.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,51:77:99:1436,0,660 -chr1 45928 . G A 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.364;DP=63;Dels=0.00;FS=1.202;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-2.063;QD=3.84;ReadPosRankSum=-0.054;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,13:63:99:270,0,1333 -chr1 45929 . C G 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.620;DP=63;Dels=0.00;FS=1.173;HaplotypeScore=13.5950;MLEAC=1;MLEAF=0.500;MQ=38.77;MQ0=3;MQRankSum=-1.844;QD=3.39;ReadPosRankSum=0.603;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:48,15:63:99:242,0,1410 -chr1 45934 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=10.8117;MLEAC=1;MLEAF=0.500;MQ=38.27;MQ0=3;MQRankSum=-1.596;QD=3.36;ReadPosRankSum=0.489;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,14:55:99:213,0,1231 -chr1 45957 . T C 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=26;Dels=0.00;FS=2.754;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=3;MQRankSum=-0.385;QD=3.11;ReadPosRankSum=0.385;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,7:26:99:109,0,455 -chr1 45965 . T C 275.78 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.61;MQ0=2;QD=19.70;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,14:14:27:304,27,0 -chr1 45991 . T C 138.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.85;MQ0=1;QD=19.84;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:15:167,15,0 -chr1 46015 . T A 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.89;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:83:83,0,581 -chr1 46016 . G T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=29;Dels=0.00;FS=2.093;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.27;MQ0=6;MQRankSum=-1.304;QD=1.96;ReadPosRankSum=0.559;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,5:29:85:85,0,588 -chr1 46017 . A G 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=30.40;MQ0=7;MQRankSum=-1.457;QD=0.72;ReadPosRankSum=1.386;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,4:33:52:52,0,712 -chr1 46033 . A C 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.857;DP=62;Dels=0.00;FS=17.444;HaplotypeScore=12.6635;MLEAC=1;MLEAF=0.500;MQ=30.48;MQ0=9;MQRankSum=0.683;QD=2.08;ReadPosRankSum=0.683;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,8:62:99:157,0,1251 -chr1 46036 . C T 1669.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=12.6635;MLEAC=2;MLEAF=1.00;MQ=29.79;MQ0=10;QD=25.69;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,65:65:99:1698,141,0 -chr1 46051 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.580;DP=90;Dels=0.00;FS=6.369;HaplotypeScore=23.7978;MLEAC=1;MLEAF=0.500;MQ=30.89;MQ0=10;MQRankSum=-1.053;QD=5.56;ReadPosRankSum=1.556;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:64,26:90:99:529,0,1416 -chr1 46062 . T A 1644.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.702;DP=97;Dels=0.00;FS=0.875;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.34;MQ0=10;MQRankSum=2.289;QD=16.96;ReadPosRankSum=2.106;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,62:97:99:1673,0,454 -chr1 46064 . T C 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.201;DP=99;Dels=0.00;FS=7.151;HaplotypeScore=24.1654;MLEAC=1;MLEAF=0.500;MQ=31.03;MQ0=10;MQRankSum=-1.046;QD=0.26;ReadPosRankSum=-0.955;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:54:54,0,2051 -chr1 46073 . A T 1710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=18.4418;MLEAC=1;MLEAF=0.500;MQ=30.65;MQ0=10;MQRankSum=3.059;QD=15.41;ReadPosRankSum=3.428;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,64:111:99:1739,0,618 -chr1 46082 . C T 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=119;Dels=0.00;FS=2.762;HaplotypeScore=10.8856;MLEAC=1;MLEAF=0.500;MQ=30.51;MQ0=11;MQRankSum=-0.591;QD=0.29;ReadPosRankSum=1.598;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:105,14:119:63:63,0,2389 -chr1 46123 . T A 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=118;Dels=0.00;FS=2.620;HaplotypeScore=14.0204;MLEAC=1;MLEAF=0.500;MQ=29.74;MQ0=16;MQRankSum=0.492;QD=1.49;ReadPosRankSum=-1.118;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:204,0,2132 -chr1 46130 . G C 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.815;DP=113;Dels=0.00;FS=0.000;HaplotypeScore=12.9254;MLEAC=1;MLEAF=0.500;MQ=28.94;MQ0=18;MQRankSum=2.438;QD=9.95;ReadPosRankSum=0.465;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:59,54:113:99:1153,0,946 -chr1 46134 . A C 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=28.45;MQ0=19;MQRankSum=3.071;QD=10.54;ReadPosRankSum=0.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,52:106:99:1146,0,745 -chr1 46151 . A C 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.894;DP=96;Dels=0.00;FS=0.000;HaplotypeScore=29.0289;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=23;MQRankSum=2.003;QD=2.89;ReadPosRankSum=2.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,22:96:99:306,0,1339 -chr1 46158 . G C 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.411;DP=96;Dels=0.00;FS=1.341;HaplotypeScore=39.0149;MLEAC=1;MLEAF=0.500;MQ=26.29;MQ0=24;MQRankSum=1.288;QD=2.65;ReadPosRankSum=2.514;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,22:96:99:283,0,1187 -chr1 46169 . C A 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=33.7549;MLEAC=1;MLEAF=0.500;MQ=29.68;MQ0=25;MQRankSum=0.853;QD=1.55;ReadPosRankSum=-0.449;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,14:105:99:191,0,1752 -chr1 46178 . A G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=106;Dels=0.00;FS=0.000;HaplotypeScore=40.5352;MLEAC=1;MLEAF=0.500;MQ=29.80;MQ0=26;MQRankSum=1.065;QD=5.13;ReadPosRankSum=-0.715;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:72,32:106:99:572,0,1382 -chr1 46199 . T G 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.172;DP=90;Dels=0.00;FS=0.000;HaplotypeScore=146.8097;MLEAC=1;MLEAF=0.500;MQ=35.49;MQ0=8;MQRankSum=0.538;QD=3.53;ReadPosRankSum=-0.275;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,17:90:99:346,0,1892 -chr1 46203 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.356;DP=95;Dels=0.00;FS=4.713;HaplotypeScore=115.8313;MLEAC=1;MLEAF=0.500;MQ=36.73;MQ0=7;MQRankSum=2.951;QD=8.13;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:63,30:95:99:801,0,1544 -chr1 46204 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=99;Dels=0.00;FS=1.263;HaplotypeScore=104.3565;MLEAC=1;MLEAF=0.500;MQ=36.99;MQ0=7;MQRankSum=-3.158;QD=1.27;ReadPosRankSum=2.038;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,14:99:99:154,0,2379 -chr1 46209 . G C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.064;DP=105;Dels=0.00;FS=2.148;HaplotypeScore=73.4158;MLEAC=1;MLEAF=0.500;MQ=37.74;MQ0=6;MQRankSum=-0.435;QD=4.08;ReadPosRankSum=1.073;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,22:105:99:457,0,2172 -chr1 46217 . A T 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.595;DP=107;Dels=0.00;FS=7.349;HaplotypeScore=36.8004;MLEAC=1;MLEAF=0.500;MQ=38.39;MQ0=6;MQRankSum=2.982;QD=7.89;ReadPosRankSum=-0.040;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,33:107:99:872,0,1991 -chr1 46223 . A T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.004;DP=110;Dels=0.00;FS=16.066;HaplotypeScore=84.6532;MLEAC=1;MLEAF=0.500;MQ=39.41;MQ0=4;MQRankSum=3.566;QD=7.08;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:80,30:110:99:807,0,2258 -chr1 46259 . A C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.583;DP=125;Dels=0.00;FS=8.544;HaplotypeScore=18.7174;MLEAC=1;MLEAF=0.500;MQ=39.29;MQ0=5;MQRankSum=-2.002;QD=5.90;ReadPosRankSum=0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:68,35:125:99:766,0,2032 -chr1 46279 . G T 1314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.148;DP=126;Dels=0.00;FS=16.583;HaplotypeScore=16.7188;MLEAC=1;MLEAF=0.500;MQ=36.95;MQ0=11;MQRankSum=-2.173;QD=10.43;ReadPosRankSum=1.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:62,64:126:99:1343,0,1687 -chr1 46288 . A T 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=25.9225;MLEAC=1;MLEAF=0.500;MQ=35.56;MQ0=13;MQRankSum=-0.037;QD=2.17;ReadPosRankSum=0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:103,21:124:99:297,0,2552 -chr1 46293 . T A 3320.77 . AC=2;AF=1.00;AN=2;DP=124;Dels=0.00;FS=0.000;HaplotypeScore=27.7337;MLEAC=2;MLEAF=1.00;MQ=34.88;MQ0=13;QD=26.78;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,124:124:99:3349,268,0 -chr1 46297 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=123;Dels=0.00;FS=1.177;HaplotypeScore=28.4676;MLEAC=1;MLEAF=0.500;MQ=34.77;MQ0=13;MQRankSum=-1.404;QD=1.19;ReadPosRankSum=0.112;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,15:123:99:174,0,2572 -chr1 46303 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=113;Dels=0.00;FS=5.395;HaplotypeScore=31.8222;MLEAC=1;MLEAF=0.500;MQ=33.25;MQ0=13;MQRankSum=-0.279;QD=4.00;ReadPosRankSum=0.573;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:82,31:113:99:480,0,1952 -chr1 46311 . T C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=106;Dels=0.00;FS=4.629;HaplotypeScore=71.9889;MLEAC=1;MLEAF=0.500;MQ=31.67;MQ0=13;MQRankSum=-1.015;QD=2.43;ReadPosRankSum=1.472;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,25:106:99:286,0,1902 -chr1 46313 . T A 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=108;Dels=0.00;FS=12.679;HaplotypeScore=73.9836;MLEAC=1;MLEAF=0.500;MQ=31.59;MQ0=13;MQRankSum=-1.299;QD=2.52;ReadPosRankSum=0.178;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:85,23:108:99:300,0,1934 -chr1 46345 . G T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.751;DP=118;Dels=0.00;FS=1.369;HaplotypeScore=15.7222;MLEAC=1;MLEAF=0.500;MQ=30.78;MQ0=12;MQRankSum=0.291;QD=2.25;ReadPosRankSum=1.341;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:95,23:118:99:294,0,1983 -chr1 46349 . A G 370.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.226;DP=129;Dels=0.00;FS=0.000;HaplotypeScore=20.2580;MLEAC=1;MLEAF=0.500;MQ=32.38;MQ0=11;MQRankSum=4.078;QD=2.87;ReadPosRankSum=-1.669;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:107,22:129:99:399,0,2225 -chr1 46360 . A G 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.738;DP=121;Dels=0.00;FS=0.000;HaplotypeScore=144.3890;MLEAC=1;MLEAF=0.500;MQ=34.17;MQ0=10;MQRankSum=-0.032;QD=2.73;ReadPosRankSum=0.335;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:96,25:121:99:359,0,2284 -chr1 46365 . G T 168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.855;DP=118;Dels=0.00;FS=0.000;HaplotypeScore=86.2004;MLEAC=1;MLEAF=0.500;MQ=34.29;MQ0=10;MQRankSum=-0.261;QD=1.43;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:99,19:118:99:197,0,2403 -chr1 46370 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.186;DP=121;Dels=0.00;FS=0.988;HaplotypeScore=85.2005;MLEAC=1;MLEAF=0.500;MQ=35.94;MQ0=9;MQRankSum=3.941;QD=2.91;ReadPosRankSum=0.376;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:100,21:121:99:380,0,2395 -chr1 46385 . A T 1987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=132;Dels=0.00;FS=0.000;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=41.86;MQ0=1;MQRankSum=-4.706;QD=15.06;ReadPosRankSum=0.577;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:54,78:132:99:2016,0,1639 -chr1 46409 . G A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.697;DP=147;Dels=0.00;FS=5.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.328;QD=4.48;ReadPosRankSum=2.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:119,28:147:99:687,0,3761 -chr1 46413 . G A 5462.77 . AC=2;AF=1.00;AN=2;DP=150;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=45.19;MQ0=1;QD=31.52;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,150:150:99:5491,421,0 -chr1 46441 . G A 5317.77 . AC=2;AF=1.00;AN=2;DP=134;Dels=0.00;FS=0.000;HaplotypeScore=24.9609;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=1;QD=30.22;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,134:134:99:5346,400,0 -chr1 46442 . A T 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=132;Dels=0.00;FS=6.626;HaplotypeScore=24.9609;MLEAC=1;MLEAF=0.500;MQ=46.74;MQ0=1;MQRankSum=0.945;QD=6.40;ReadPosRankSum=2.434;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,31:132:99:873,0,3591 -chr1 46448 . T C 526.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.670;DP=120;Dels=0.00;FS=1.884;HaplotypeScore=45.9537;MLEAC=1;MLEAF=0.500;MQ=46.81;MQ0=1;MQRankSum=-1.356;QD=4.39;ReadPosRankSum=0.293;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,23:120:99:555,0,3478 -chr1 46453 . T A 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=109;Dels=0.00;FS=3.408;HaplotypeScore=1.9892;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=1;MQRankSum=-1.198;QD=4.26;ReadPosRankSum=1.024;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:89,20:109:99:493,0,3241 -chr1 46466 . T A 1384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.022;DP=98;Dels=0.00;FS=1.650;HaplotypeScore=38.9441;MLEAC=1;MLEAF=0.500;MQ=46.96;MQ0=1;MQRankSum=0.510;QD=14.13;ReadPosRankSum=0.930;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:52,46:98:99:1413,0,1799 -chr1 46486 . T A 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=62;Dels=0.00;FS=0.975;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=43.40;MQ0=1;MQRankSum=-0.195;QD=14.11;ReadPosRankSum=-0.137;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,29:62:99:903,0,1128 -chr1 46489 . A G 2225.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=42.98;MQ0=1;QD=30.18;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2254,175,0 -chr1 46505 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=39.03;MQ0=0;MQRankSum=1.388;QD=8.99;ReadPosRankSum=-1.130;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,8:24:99:244,0,502 -chr1 46511 . G C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=13;Dels=0.00;FS=2.920;HaplotypeScore=1.9890;MLEAC=1;MLEAF=0.500;MQ=36.55;MQ0=0;MQRankSum=0.592;QD=4.06;ReadPosRankSum=-1.099;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,3:13:81:81,0,328 -chr1 46521 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=33.95;MQ0=0;MQRankSum=-0.198;QD=2.13;ReadPosRankSum=0.198;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:5,2:7:43:43,0,159 -chr1 46524 . A C 63.23 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=2.9781;MLEAC=1;MLEAF=0.500;MQ=32.80;MQ0=0;QD=12.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:5:9:107,9,0 -chr1 46567 . T C 942.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.84;MQ0=0;QD=28.57;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:81:971,81,0 -chr1 46579 . T C 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.651;DP=54;Dels=0.00;FS=2.600;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=40.98;MQ0=0;MQRankSum=-0.248;QD=8.00;ReadPosRankSum=-0.266;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,18:54:99:460,0,1017 -chr1 46608 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=97;Dels=0.00;FS=7.798;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=45.77;MQ0=1;MQRankSum=0.169;QD=6.28;ReadPosRankSum=0.458;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,27:97:99:637,0,2291 -chr1 46649 . C G 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.383;DP=128;Dels=0.00;FS=5.797;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=50.51;MQ0=1;MQRankSum=0.828;QD=4.14;ReadPosRankSum=-0.170;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:102,26:128:99:558,0,3425 -chr1 46661 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=123;Dels=0.00;FS=0.000;HaplotypeScore=1.8874;MLEAC=1;MLEAF=0.500;MQ=52.82;MQ0=1;MQRankSum=-1.890;QD=4.49;ReadPosRankSum=-0.533;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:98,25:123:99:580,0,3412 -chr1 46669 . T C 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=111;Dels=0.00;FS=0.000;HaplotypeScore=71.8527;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=2;MQRankSum=-1.040;QD=2.79;ReadPosRankSum=0.046;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:94,17:111:99:338,0,3242 -chr1 46672 . T C 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.735;DP=101;Dels=0.00;FS=1.153;HaplotypeScore=51.8777;MLEAC=1;MLEAF=0.500;MQ=55.02;MQ0=2;MQRankSum=0.285;QD=2.14;ReadPosRankSum=1.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,13:101:99:244,0,3052 -chr1 46675 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;DP=100;Dels=0.00;FS=0.000;HaplotypeScore=49.8785;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=2;MQRankSum=0.732;QD=1.80;ReadPosRankSum=2.032;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:88,12:100:99:208,0,3050 -chr1 46676 . T C 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=65.8754;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=2;MQRankSum=0.553;QD=1.87;ReadPosRankSum=1.978;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:87,12:99:99:213,0,3001 -chr1 46677 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=103;Dels=0.00;FS=3.208;HaplotypeScore=64.9814;MLEAC=1;MLEAF=0.500;MQ=54.76;MQ0=2;MQRankSum=-2.102;QD=4.91;ReadPosRankSum=0.977;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:79,24:103:99:534,0,2803 -chr1 46680 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=105;Dels=0.00;FS=3.142;HaplotypeScore=55.7727;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=2;MQRankSum=-1.393;QD=4.65;ReadPosRankSum=1.009;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,23:105:99:516,0,2857 -chr1 46706 . T A 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.654;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=2.7898;MLEAC=1;MLEAF=0.500;MQ=51.38;MQ0=2;MQRankSum=0.757;QD=2.05;ReadPosRankSum=-0.339;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,17:91:99:215,0,2448 -chr1 46718 . A C 1001.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.273;DP=81;Dels=0.00;FS=1.893;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.582;QD=12.37;ReadPosRankSum=1.963;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,34:81:99:1030,0,1456 -chr1 46719 . A C 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=14.9370;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=2;MQRankSum=0.250;QD=3.16;ReadPosRankSum=-0.404;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:66,15:81:99:284,0,2191 -chr1 46726 . T C 2626.77 . AC=2;AF=1.00;AN=2;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=11.9384;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=2;QD=34.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,75:76:99:2655,202,0 -chr1 46731 . T C 2453.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=48.88;MQ0=2;QD=34.08;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2482,193,0 -chr1 46759 . C A 1490.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=9.8664;MLEAC=2;MLEAF=1.00;MQ=36.57;MQ0=2;QD=28.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1519,129,0 -chr1 46779 . T A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=47;Dels=0.00;FS=2.615;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.41;MQ0=8;MQRankSum=-1.409;QD=0.34;ReadPosRankSum=-0.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,14:47:44:44,0,779 -chr1 46829 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.094;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=28.31;MQ0=9;MQRankSum=-1.417;QD=3.18;ReadPosRankSum=-0.019;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:165,0,685 -chr1 46863 . T A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6918;MLEAC=1;MLEAF=0.500;MQ=34.16;MQ0=4;MQRankSum=1.021;QD=3.19;ReadPosRankSum=-0.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,10:31:99:127,0,637 -chr1 46875 . C T 193.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=0.391;QD=7.75;ReadPosRankSum=0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:222,0,386 -chr1 46877 . A G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.036;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.74;MQ0=4;MQRankSum=-0.391;QD=7.71;ReadPosRankSum=0.675;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,9:25:99:221,0,382 -chr1 46911 . T C 225.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.295;QD=11.88;ReadPosRankSum=1.120;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,13:19:99:254,0,170 -chr1 46912 . T C 139.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=-0.059;QD=7.36;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:168,0,256 -chr1 46921 . A T 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=31.99;MQ0=4;MQRankSum=1.120;QD=6.94;ReadPosRankSum=-1.237;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,6:19:99:160,0,232 -chr1 46929 . T C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=2.9987;MLEAC=1;MLEAF=0.500;MQ=30.25;MQ0=4;MQRankSum=1.826;QD=1.36;ReadPosRankSum=-1.396;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,2:16:50:50,0,263 -chr1 46930 . T C 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.382;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=0.382;QD=2.05;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,3:15:59:59,0,224 -chr1 46932 . T G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.597;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=29.49;MQ0=4;MQRankSum=-0.278;QD=10.05;ReadPosRankSum=0.597;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,11:15:99:179,0,100 -chr1 47124 . A G 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.189;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=2.616;QD=3.49;ReadPosRankSum=-0.713;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,5:30:99:133,0,417 -chr1 47130 . C A 109.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.139;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=6.6461;MLEAC=1;MLEAF=0.500;MQ=28.99;MQ0=5;MQRankSum=-0.972;QD=3.54;ReadPosRankSum=-0.417;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,8:31:99:138,0,432 -chr1 47133 . A T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.968;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=15.5825;MLEAC=1;MLEAF=0.500;MQ=29.36;MQ0=5;MQRankSum=2.905;QD=5.37;ReadPosRankSum=-1.743;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,7:32:99:200,0,418 -chr1 47143 . G A 25.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.890;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.6961;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.890;QD=0.78;ReadPosRankSum=1.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,3:33:54:54,0,575 -chr1 47144 . A G 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.060;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.9886;MLEAC=1;MLEAF=0.500;MQ=29.14;MQ0=5;MQRankSum=1.440;QD=17.39;ReadPosRankSum=-0.420;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,26:33:45:602,0,45 -chr1 47176 . T C 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.415;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.24;MQ0=6;MQRankSum=-3.114;QD=8.56;ReadPosRankSum=-0.467;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,20:32:99:302,0,299 -chr1 47177 . G A 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=14.0311;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=6;MQRankSum=0.027;QD=6.93;ReadPosRankSum=0.356;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,11:31:99:243,0,342 -chr1 47200 . T C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=28.35;MQ0=1;MQRankSum=0.312;QD=7.13;ReadPosRankSum=1.954;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:7,7:14:99:128,0,187 -chr1 47230 . T A 178.8 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=19.08;MQ0=3;QD=9.93;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:21:207,21,0 -chr1 47234 . T C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.58;MQ0=3;MQRankSum=-1.721;QD=2.61;ReadPosRankSum=1.721;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,13:21:83:83,0,132 -chr1 47250 . G A 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.640;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=5.7510;MLEAC=1;MLEAF=0.500;MQ=21.76;MQ0=5;MQRankSum=-1.456;QD=2.27;ReadPosRankSum=0.646;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:44,22:66:99:178,0,749 -chr1 47261 . A G 1410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=105;Dels=0.00;FS=0.000;HaplotypeScore=6.7299;MLEAC=1;MLEAF=0.500;MQ=24.69;MQ0=5;MQRankSum=-5.094;QD=13.44;ReadPosRankSum=1.015;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,92:105:99:1439,0,288 -chr1 47285 . A T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.781;DP=169;Dels=0.00;FS=25.466;HaplotypeScore=47.9098;MLEAC=1;MLEAF=0.500;MQ=25.11;MQ0=7;MQRankSum=-4.336;QD=4.42;ReadPosRankSum=3.540;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:101,68:169:99:776,0,2136 -chr1 47298 . G A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=190;Dels=0.00;FS=15.234;HaplotypeScore=62.4649;MLEAC=1;MLEAF=0.500;MQ=25.20;MQ0=9;MQRankSum=0.954;QD=0.07;ReadPosRankSum=-0.318;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:171,18:190:41:41,0,3305 -chr1 47310 . A T 485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.824;DP=205;Dels=0.00;FS=0.000;HaplotypeScore=49.7328;MLEAC=1;MLEAF=0.500;MQ=25.09;MQ0=7;MQRankSum=4.634;QD=2.37;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:176,29:205:99:514,0,2996 -chr1 47323 . G A 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.212;DP=211;Dels=0.00;FS=17.070;HaplotypeScore=51.7365;MLEAC=1;MLEAF=0.500;MQ=25.41;MQ0=8;MQRankSum=-0.372;QD=4.96;ReadPosRankSum=0.233;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:139,72:211:99:1074,0,2488 -chr1 47338 . C T 938.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.180;DP=186;Dels=0.02;FS=12.473;HaplotypeScore=79.8806;MLEAC=1;MLEAF=0.500;MQ=25.59;MQ0=8;MQRankSum=-2.645;QD=5.05;ReadPosRankSum=-1.238;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:110,73:183:99:967,0,2144 -chr1 47343 . A C 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.678;DP=175;Dels=0.00;FS=24.414;HaplotypeScore=63.4079;MLEAC=1;MLEAF=0.500;MQ=25.75;MQ0=8;MQRankSum=-4.741;QD=1.42;ReadPosRankSum=-2.918;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:123,52:175:99:276,0,2689 -chr1 47371 . T C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.308;DP=89;Dels=0.00;FS=1.351;HaplotypeScore=13.6568;MLEAC=1;MLEAF=0.500;MQ=24.59;MQ0=7;MQRankSum=-0.275;QD=11.91;ReadPosRankSum=-0.593;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,70:89:99:1088,0,261 -chr1 47393 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.335;DP=52;Dels=0.00;FS=11.083;HaplotypeScore=2.6277;MLEAC=1;MLEAF=0.500;MQ=22.57;MQ0=6;MQRankSum=-1.494;QD=0.31;ReadPosRankSum=1.210;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:41,11:52:44:44,0,511 -chr1 47428 . T C 338.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.940;DP=69;Dels=0.00;FS=2.933;HaplotypeScore=8.8333;MLEAC=1;MLEAF=0.500;MQ=23.55;MQ0=5;MQRankSum=3.350;QD=4.91;ReadPosRankSum=0.000;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:47,22:69:99:367,0,707 -chr1 47434 . T C 785.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.090;DP=72;Dels=0.00;FS=5.763;HaplotypeScore=21.1457;MLEAC=1;MLEAF=0.500;MQ=23.17;MQ0=5;MQRankSum=-4.249;QD=10.91;ReadPosRankSum=1.041;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:15,57:72:99:814,0,307 -chr1 47443 . G A 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=18.3434;MLEAC=1;MLEAF=0.500;MQ=20.97;MQ0=15;MQRankSum=-0.420;QD=0.53;ReadPosRankSum=1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:81,18:99:81:81,0,1206 -chr1 47486 . T C 1453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.037;DP=155;Dels=0.00;FS=0.000;HaplotypeScore=12.8061;MLEAC=1;MLEAF=0.500;MQ=22.09;MQ0=28;MQRankSum=-5.676;QD=9.38;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:36,119:155:99:1482,0,780 -chr1 47491 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.483;DP=156;Dels=0.00;FS=0.000;HaplotypeScore=17.2378;MLEAC=1;MLEAF=0.500;MQ=22.27;MQ0=26;MQRankSum=5.308;QD=3.06;ReadPosRankSum=-1.409;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:133,23:156:99:506,0,1813 -chr1 47535 . C T 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=93;Dels=0.02;FS=0.000;HaplotypeScore=38.1338;MLEAC=1;MLEAF=0.500;MQ=21.13;MQ0=22;MQRankSum=2.066;QD=3.23;ReadPosRankSum=1.772;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:73,16:91:99:329,0,900 -chr1 47567 . G A 567.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.580;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=4.7649;MLEAC=2;MLEAF=1.00;MQ=23.23;MQ0=4;MQRankSum=0.223;QD=17.74;ReadPosRankSum=-1.561;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:6,26:32:31:596,31,0 -chr1 47584 . T C 27.75 LowQual AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.33;MQ0=4;QD=4.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,2:6:6:55,6,0 -chr1 47788 . G A 57.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.406;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.71;MQ0=14;MQRankSum=1.537;QD=2.86;ReadPosRankSum=0.406;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:17,3:20:9:85,9,0 -chr1 47807 . T C 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=14.86;MQ0=12;MQRankSum=-1.709;QD=0.70;ReadPosRankSum=-2.534;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,18:27:47:47,0,128 -chr1 47841 . C A 85.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=1;MLEAF=0.500;MQ=15.69;MQ0=10;MQRankSum=0.024;QD=2.26;ReadPosRankSum=0.315;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:38:99:114,0,159 -chr1 47868 . A G 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=14.6837;MLEAC=1;MLEAF=0.500;MQ=16.29;MQ0=5;MQRankSum=0.408;QD=1.05;ReadPosRankSum=0.168;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,10:33:63:63,0,165 -chr1 47905 . T C 76.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.123;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=14.10;MQ0=0;MQRankSum=-0.919;QD=4.47;ReadPosRankSum=1.531;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,16:17:12:104,12,0 -chr1 47908 . G C 76.03 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.35;MQ0=0;QD=5.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,15:15:12:104,12,0 -chr1 48010 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.319;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.5644;MLEAC=1;MLEAF=0.500;MQ=17.06;MQ0=4;MQRankSum=1.490;QD=1.24;ReadPosRankSum=1.149;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,5:32:68:68,0,115 -chr1 48044 . T C 74.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.952;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=15.75;MQ0=6;MQRankSum=0.905;QD=2.20;ReadPosRankSum=1.323;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,12:34:99:103,0,101 -chr1 48062 . T C 149.84 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.286;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=16.25;MQ0=3;MQRankSum=1.884;QD=5.99;ReadPosRankSum=0.171;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:4,21:25:18:178,18,0 -chr1 48067 . T C 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.033;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=16.25;MQ0=3;MQRankSum=-0.560;QD=0.99;ReadPosRankSum=-0.033;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,11:25:53:53,0,86 -chr1 48077 . G A 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.200;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=11.66;MQ0=2;MQRankSum=0.000;QD=0.65;ReadPosRankSum=1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,5:16:15:38,0,15 -chr1 48103 . C T 10.33 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.365;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=13.51;MQ0=0;MQRankSum=0.000;QD=1.03;ReadPosRankSum=1.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,4:10:15:38,0,15 -chr1 69651 . C A 54.28 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.77;MQ0=1;QD=6.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:9:82,9,0 -chr1 69661 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0 -chr1 69674 . T C 54.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=13.92;MQ0=2;QD=6.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,9:9:9:82,9,0 -chr1 69693 . C G 54.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.747;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.15;MQ0=2;MQRankSum=0.747;QD=5.43;ReadPosRankSum=0.747;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,9:10:9:82,9,0 -chr1 69699 . C T 41.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.03;MQ0=2;MQRankSum=-0.762;QD=3.81;ReadPosRankSum=1.666;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,9:11:15:70,0,15 -chr1 69764 . A G 449.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.331;DP=37;Dels=0.00;FS=9.031;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=23.29;MQ0=17;MQRankSum=2.126;QD=12.15;ReadPosRankSum=0.047;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:7:477,0,7 -chr1 69840 . G A 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.6917;MLEAC=1;MLEAF=0.500;MQ=29.33;MQ0=7;MQRankSum=-2.507;QD=16.16;ReadPosRankSum=0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,31:36:55:610,0,55 -chr1 69869 . T C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.277;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.44;MQ0=9;MQRankSum=-2.380;QD=0.76;ReadPosRankSum=1.273;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,11:46:63:63,0,767 -chr1 69912 . A G 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.049;DP=89;Dels=0.00;FS=2.410;HaplotypeScore=43.2151;MLEAC=1;MLEAF=0.500;MQ=28.97;MQ0=20;MQRankSum=-2.202;QD=0.85;ReadPosRankSum=-1.327;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:71,18:89:99:104,0,1176 -chr1 69914 . T A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=89;Dels=0.00;FS=2.466;HaplotypeScore=31.1187;MLEAC=1;MLEAF=0.500;MQ=28.72;MQ0=20;MQRankSum=-2.123;QD=0.55;ReadPosRankSum=-0.877;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,15:89:77:77,0,1075 -chr1 69917 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.757;DP=93;Dels=0.00;FS=4.107;HaplotypeScore=21.6983;MLEAC=1;MLEAF=0.500;MQ=28.07;MQ0=21;MQRankSum=6.024;QD=8.30;ReadPosRankSum=3.447;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:60,33:93:99:800,0,323 -chr1 69936 . T C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.032;DP=99;Dels=0.00;FS=7.704;HaplotypeScore=13.1641;MLEAC=1;MLEAF=0.500;MQ=29.72;MQ0=22;MQRankSum=-2.828;QD=0.58;ReadPosRankSum=-0.226;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,24:99:86:86,0,1391 -chr1 69952 . G A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=98;Dels=0.00;FS=10.410;HaplotypeScore=7.2476;MLEAC=1;MLEAF=0.500;MQ=31.15;MQ0=22;MQRankSum=-3.094;QD=1.13;ReadPosRankSum=1.550;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:74,23:98:99:139,0,1447 -chr1 70044 . T C 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.831;DP=64;Dels=0.00;FS=17.302;HaplotypeScore=1.4972;MLEAC=1;MLEAF=0.500;MQ=39.43;MQ0=5;MQRankSum=-6.056;QD=6.00;ReadPosRankSum=-3.773;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:35,29:64:99:412,0,1246 -chr1 70061 . A T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=133;Dels=0.00;FS=7.265;HaplotypeScore=20.7708;MLEAC=1;MLEAF=0.500;MQ=36.02;MQ0=7;MQRankSum=-0.379;QD=2.95;ReadPosRankSum=-1.067;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:108,25:133:99:420,0,2776 -chr1 70083 . T A 2582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=229;Dels=0.00;FS=16.594;HaplotypeScore=75.2516;MLEAC=1;MLEAF=0.500;MQ=35.83;MQ0=10;MQRankSum=-6.665;QD=11.28;ReadPosRankSum=-0.109;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:50,97:229:99:2611,0,1502 -chr1 70125 . G T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=250;Dels=0.00;FS=22.446;HaplotypeScore=27.9709;MLEAC=1;MLEAF=0.500;MQ=34.24;MQ0=12;MQRankSum=6.009;QD=2.97;ReadPosRankSum=-1.398;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:216,34:250:99:771,0,5278 -chr1 70150 . A T 2213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=239;Dels=0.00;FS=21.127;HaplotypeScore=368.1172;MLEAC=1;MLEAF=0.500;MQ=33.77;MQ0=11;MQRankSum=1.765;QD=9.26;ReadPosRankSum=0.325;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:156,83:239:99:2242,0,3406 -chr1 70216 . A C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=108;Dels=0.00;FS=9.502;HaplotypeScore=1.7297;MLEAC=1;MLEAF=0.500;MQ=29.27;MQ0=14;MQRankSum=-0.174;QD=5.67;ReadPosRankSum=-0.831;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:70,38:108:99:641,0,1179 -chr1 70250 . G A 1741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.529;DP=135;Dels=0.00;FS=13.533;HaplotypeScore=55.9122;MLEAC=1;MLEAF=0.500;MQ=30.56;MQ0=13;MQRankSum=-4.770;QD=12.90;ReadPosRankSum=-1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,110:135:99:1770,0,694 -chr1 70260 . T A 1494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=159;Dels=0.00;FS=11.693;HaplotypeScore=60.0297;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=12;MQRankSum=3.229;QD=9.40;ReadPosRankSum=-1.725;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:97,62:159:99:1523,0,1679 -chr1 70302 . G C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.849;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=38.7004;MLEAC=1;MLEAF=0.500;MQ=30.81;MQ0=27;MQRankSum=2.779;QD=0.09;ReadPosRankSum=-0.062;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:234,14:250:51:51,0,4942 -chr1 70324 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.298;DP=250;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=36;MQRankSum=-1.206;QD=1.62;ReadPosRankSum=-0.310;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:212,38:250:99:433,0,4781 -chr1 70330 . T C 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.778;DP=247;Dels=0.00;FS=0.000;HaplotypeScore=72.4821;MLEAC=1;MLEAF=0.500;MQ=29.87;MQ0=39;MQRankSum=4.681;QD=4.35;ReadPosRankSum=0.440;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:201,45:247:99:1102,0,3835 -chr1 70352 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.133;DP=231;Dels=0.00;FS=0.000;HaplotypeScore=38.6164;MLEAC=1;MLEAF=0.500;MQ=29.11;MQ0=43;MQRankSum=-0.256;QD=4.09;ReadPosRankSum=1.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:164,67:231:99:973,0,3380 -chr1 70354 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=228;Dels=0.00;FS=0.000;HaplotypeScore=36.7869;MLEAC=1;MLEAF=0.500;MQ=28.93;MQ0=43;MQRankSum=0.019;QD=2.38;ReadPosRankSum=1.450;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:181,47:228:99:571,0,3676 -chr1 70360 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.327;DP=214;Dels=0.00;FS=0.000;HaplotypeScore=31.5616;MLEAC=1;MLEAF=0.500;MQ=28.34;MQ0=42;MQRankSum=0.615;QD=3.26;ReadPosRankSum=0.618;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:163,51:214:99:725,0,3164 -chr1 70400 . A G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.039;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.22;MQ0=0;MQRankSum=-1.795;QD=15.51;ReadPosRankSum=0.535;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,14:23:99:385,0,241 -chr1 70409 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.14;MQ0=0;MQRankSum=-2.381;QD=13.95;ReadPosRankSum=0.958;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,14:25:99:377,0,326 -chr1 70454 . T A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=38;Dels=0.00;FS=4.521;HaplotypeScore=2.5142;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=-4.169;QD=10.55;ReadPosRankSum=0.264;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,17:38:99:429,0,678 -chr1 70455 . G C 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=46.06;MQ0=0;MQRankSum=4.198;QD=16.99;ReadPosRankSum=-0.382;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,21:38:99:674,0,427 -chr1 70467 . G A 1182.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.7803;MLEAC=2;MLEAF=1.00;MQ=47.26;MQ0=0;QD=33.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1211,99,0 -chr1 70476 . C T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=28;Dels=0.00;FS=1.583;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.00;MQ0=0;MQRankSum=-4.339;QD=6.71;ReadPosRankSum=-2.613;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,10:28:99:216,0,597 -chr1 70481 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.212;DP=29;Dels=0.00;FS=3.696;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.39;MQ0=0;MQRankSum=-4.266;QD=5.23;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:180,0,720 -chr1 70487 . G A 100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=31;Dels=0.00;FS=7.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=0;MQRankSum=-3.992;QD=3.25;ReadPosRankSum=-0.685;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,7:31:99:129,0,866 -chr1 70488 . G C 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.493;DP=30;Dels=0.00;FS=12.454;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.88;MQ0=0;MQRankSum=-3.759;QD=3.33;ReadPosRankSum=-0.026;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,6:30:99:128,0,824 -chr1 70508 . A G 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=31;Dels=0.00;FS=8.915;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.10;MQ0=0;MQRankSum=3.902;QD=21.83;ReadPosRankSum=2.250;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,20:31:99:705,0,304 -chr1 70513 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.673;DP=29;Dels=0.00;FS=6.306;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=0;MQRankSum=-3.512;QD=7.10;ReadPosRankSum=-0.966;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,9:29:99:234,0,716 -chr1 70534 . A T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.500;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.15;MQ0=0;MQRankSum=4.082;QD=15.43;ReadPosRankSum=1.082;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:661,0,570 -chr1 70544 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.245;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.74;MQ0=0;MQRankSum=-3.969;QD=13.14;ReadPosRankSum=0.202;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,24:47:99:646,0,706 -chr1 70546 . C G 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.85;MQ0=0;MQRankSum=-3.859;QD=14.29;ReadPosRankSum=0.413;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,25:48:99:714,0,704 -chr1 70565 . A G 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.227;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.21;MQ0=0;MQRankSum=-2.949;QD=14.94;ReadPosRankSum=2.436;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:805,0,789 -chr1 70576 . T C 838.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.260;DP=58;Dels=0.00;FS=5.843;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.49;MQ0=0;MQRankSum=-3.297;QD=14.46;ReadPosRankSum=2.442;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,29:58:99:867,0,930 -chr1 70628 . T G 997.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.810;DP=62;Dels=0.00;FS=3.540;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=52.03;MQ0=0;MQRankSum=-0.331;QD=16.09;ReadPosRankSum=0.416;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,32:62:99:1026,0,961 -chr1 70637 . G A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=57;Dels=0.00;FS=1.010;HaplotypeScore=4.7315;MLEAC=1;MLEAF=0.500;MQ=53.93;MQ0=0;MQRankSum=0.813;QD=17.19;ReadPosRankSum=-0.748;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,30:57:99:1008,0,828 -chr1 70655 . A G 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=53;Dels=0.00;FS=1.090;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-0.769;QD=16.79;ReadPosRankSum=-2.051;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:53:99:918,0,834 -chr1 70662 . T G 2101.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=56.72;MQ0=0;QD=34.63;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2130,160,0 -chr1 70684 . C T 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=57;Dels=0.00;FS=3.772;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=1;MQRankSum=1.273;QD=17.59;ReadPosRankSum=-0.173;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1031,0,872 -chr1 70716 . A G 976.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.361;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=1;MQRankSum=-0.680;QD=16.01;ReadPosRankSum=-0.621;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1005,0,945 -chr1 70722 . G A 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.241;DP=64;Dels=0.00;FS=0.968;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=1;MQRankSum=-0.310;QD=14.48;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,30:64:99:955,0,1044 -chr1 70732 . T G 1039.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=0.419;QD=16.25;ReadPosRankSum=0.186;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1068,0,1033 -chr1 70757 . A G 1003.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=57;Dels=0.00;FS=2.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=2;MQRankSum=0.704;QD=17.61;ReadPosRankSum=-0.908;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1032,0,802 -chr1 70801 . T C 1321.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.33;MQ0=1;QD=31.86;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1350,102,0 -chr1 70805 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.701;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=-0.638;QD=11.39;ReadPosRankSum=3.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:427,0,704 -chr1 70806 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=1;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=3.192;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,14:36:99:431,0,755 -chr1 70808 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=1;MQRankSum=-0.461;QD=11.99;ReadPosRankSum=2.671;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,14:34:99:436,0,682 -chr1 70814 . A T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=1;MQRankSum=-0.281;QD=14.22;ReadPosRankSum=1.333;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,779 -chr1 70860 . G C 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.732;QD=15.72;ReadPosRankSum=-0.025;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,28:55:99:893,0,931 -chr1 70872 . A T 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.806;QD=14.49;ReadPosRankSum=-0.247;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,28:57:99:854,0,1019 -chr1 70927 . T A 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.885;QD=15.03;ReadPosRankSum=0.833;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:840,0,984 -chr1 70928 . C T 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.069;DP=54;Dels=0.00;FS=2.239;HaplotypeScore=28.8784;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.173;QD=14.92;ReadPosRankSum=0.642;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,25:54:99:834,0,975 -chr1 70958 . G A 884.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.312;DP=57;Dels=0.00;FS=1.019;HaplotypeScore=3.9961;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.008;QD=15.52;ReadPosRankSum=-0.855;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:30,27:57:99:913,0,1033 -chr1 70978 . A C 1879.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.75;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1908,144,0 -chr1 71024 . T A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.209;QD=10.97;ReadPosRankSum=0.418;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,15:38:99:445,0,742 -chr1 71043 . A G 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=38;Dels=0.00;FS=1.271;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.530;QD=10.86;ReadPosRankSum=-0.257;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,14:38:99:441,0,841 -chr1 71062 . G A 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.996;DP=39;Dels=0.00;FS=9.774;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.61;MQ0=0;MQRankSum=-1.775;QD=10.92;ReadPosRankSum=-1.342;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,15:39:99:454,0,819 -chr1 71078 . A G 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.024;DP=46;Dels=0.00;FS=9.879;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-2.684;QD=7.15;ReadPosRankSum=1.952;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,13:46:99:357,0,1152 -chr1 71081 . T G 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=45;Dels=0.00;FS=9.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-2.992;QD=7.59;ReadPosRankSum=1.991;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,13:45:99:370,0,1120 -chr1 71151 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=48;Dels=0.00;FS=6.211;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.755;QD=14.79;ReadPosRankSum=0.962;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,22:48:99:738,0,906 -chr1 71164 . T G 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=52;Dels=0.00;FS=5.816;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.829;QD=13.75;ReadPosRankSum=2.635;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,23:52:99:743,0,987 -chr1 71175 . C T 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.190;DP=49;Dels=0.00;FS=8.135;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.410;QD=15.79;ReadPosRankSum=2.570;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,24:49:99:802,0,806 -chr1 71183 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=50;Dels=0.00;FS=5.868;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=-0.740;QD=13.42;ReadPosRankSum=3.290;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:699,0,927 -chr1 71188 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=50;Dels=0.00;FS=4.061;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=-1.246;QD=13.50;ReadPosRankSum=2.647;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,23:50:99:703,0,954 -chr1 71222 . A C 1672.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.6203;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1701,129,0 -chr1 71229 . C T 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.588;QD=9.33;ReadPosRankSum=-2.495;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,14:42:99:420,0,1008 -chr1 71244 . A T 184.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.527;QD=4.99;ReadPosRankSum=-1.716;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,8:37:99:213,0,1037 -chr1 71245 . C T 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.080;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-3.757;QD=4.10;ReadPosRankSum=-1.239;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:29,7:36:99:176,0,1059 -chr1 71254 . G T 68.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-3.568;QD=1.91;ReadPosRankSum=-0.412;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,5:36:97:97,0,1070 -chr1 71258 . C T 1176.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=34.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1205,99,0 -chr1 71280 . T C 924.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:75:953,75,0 -chr1 71284 . T C 956.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:985,78,0 -chr1 71319 . G A 770.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:799,63,0 -chr1 71344 . G C 750.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:779,60,0 -chr1 71359 . G T 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.564;DP=32;Dels=0.00;FS=18.730;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=8.59;ReadPosRankSum=-1.888;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:303,0,699 -chr1 71365 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=15.204;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.18;MQ0=0;MQRankSum=-4.593;QD=9.83;ReadPosRankSum=-1.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:323,0,626 -chr1 71371 . C T 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=34;Dels=0.00;FS=14.526;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.775;QD=8.11;ReadPosRankSum=0.414;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:304,0,729 -chr1 71381 . C T 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=32;Dels=0.00;FS=11.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.56;MQ0=0;MQRankSum=-4.690;QD=9.18;ReadPosRankSum=2.316;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:322,0,668 -chr1 71388 . T C 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=35;Dels=0.00;FS=18.303;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.04;MQ0=0;MQRankSum=-4.813;QD=8.08;ReadPosRankSum=3.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:311,0,784 -chr1 71570 . G A 897.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.40;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:926,69,0 -chr1 71608 . A G 632.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.26;MQ0=0;QD=28.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:661,51,0 -chr1 71631 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.385;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.055;QD=11.37;ReadPosRankSum=-2.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:301,0,519 -chr1 71646 . A G 281.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=21;Dels=0.00;FS=9.840;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-3.873;QD=13.42;ReadPosRankSum=-0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:310,0,392 -chr1 71649 . C T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=20;Dels=0.00;FS=10.263;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.18;MQ0=0;MQRankSum=-3.799;QD=14.19;ReadPosRankSum=-0.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,9:20:99:312,0,385 -chr1 71668 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.732;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.94;ReadPosRankSum=2.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:181,0,541 -chr1 71670 . C T 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.518;DP=21;Dels=0.00;FS=12.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.16;MQ0=0;MQRankSum=-3.542;QD=7.42;ReadPosRankSum=2.997;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,6:21:99:184,0,526 -chr1 71673 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.72;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:176,0,563 -chr1 71675 . T C 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.848;DP=22;Dels=0.00;FS=9.185;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=-3.575;QD=6.63;ReadPosRankSum=3.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,6:22:99:174,0,568 -chr1 71676 . A G 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.455;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-3.606;QD=5.99;ReadPosRankSum=3.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:166,0,592 -chr1 71693 . T G 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.595;DP=27;Dels=0.00;FS=8.671;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-3.703;QD=4.03;ReadPosRankSum=1.895;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:137,0,745 -chr1 71715 . A T 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=27.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0 -chr1 71716 . A T 611.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=32.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:640,48,0 -chr1 71717 . A T 625.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=35.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:654,48,0 -chr1 71718 . A T 704.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.94;MQ0=0;QD=28.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:733,54,0 -chr1 71734 . G A 950.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.031;DP=49;Dels=0.00;FS=6.300;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=2.206;QD=19.40;ReadPosRankSum=2.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:979,0,585 -chr1 71751 . T C 1954.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.88;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1983,147,0 -chr1 71752 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.360;DP=52;Dels=0.00;FS=8.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=1;MQRankSum=-0.751;QD=11.90;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:647,0,1034 -chr1 71768 . T G 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.210;DP=50;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=0.630;QD=13.48;ReadPosRankSum=1.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:702,0,834 -chr1 71769 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=6.329;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-0.010;QD=13.47;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,24:48:99:675,0,839 -chr1 71772 . C T 1772.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9984;MLEAC=2;MLEAF=1.00;MQ=58.12;MQ0=0;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1801,135,0 -chr1 71809 . A C 2024.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=57.48;MQ0=1;QD=30.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2053,153,0 -chr1 71829 . C A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=56;Dels=0.00;FS=2.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=1;MQRankSum=0.563;QD=19.05;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1095,0,684 -chr1 71834 . T C 1044.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=51;Dels=0.00;FS=2.568;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.86;MQ0=1;MQRankSum=0.212;QD=20.49;ReadPosRankSum=-0.758;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,33:51:99:1073,0,570 -chr1 71853 . T C 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.834;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=55.00;MQ0=1;MQRankSum=-0.422;QD=19.24;ReadPosRankSum=0.084;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:971,0,612 -chr1 71859 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=49;Dels=0.00;FS=1.079;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=1;MQRankSum=-1.148;QD=16.89;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:856,0,696 -chr1 71860 . A T 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.606;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=1;MQRankSum=-0.374;QD=17.77;ReadPosRankSum=1.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:881,0,668 -chr1 71878 . T C 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.614;DP=44;Dels=0.00;FS=2.696;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=1;MQRankSum=-1.741;QD=16.99;ReadPosRankSum=1.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:776,0,611 -chr1 71879 . G T 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.817;DP=45;Dels=0.00;FS=2.750;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=52.60;MQ0=1;MQRankSum=-1.880;QD=16.79;ReadPosRankSum=1.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,24:45:99:784,0,584 -chr1 71900 . G A 544.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=26.2859;MLEAC=1;MLEAF=0.500;MQ=50.73;MQ0=0;MQRankSum=0.829;QD=13.97;ReadPosRankSum=-0.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:573,0,657 -chr1 71921 . G C 513.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.24;MQ0=0;QD=27.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:542,42,0 -chr1 71950 . T A 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.058;DP=28;Dels=0.00;FS=21.924;HaplotypeScore=4.3987;MLEAC=1;MLEAF=0.500;MQ=32.58;MQ0=2;MQRankSum=-0.462;QD=3.24;ReadPosRankSum=-1.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:119,0,331 -chr1 71973 . C A 115.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.018;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=5.0534;MLEAC=1;MLEAF=0.500;MQ=13.29;MQ0=15;MQRankSum=2.752;QD=1.90;ReadPosRankSum=3.058;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:54,7:61:75:144,0,75 -chr1 71995 . C T 106.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.495;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=22.9908;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=18;MQRankSum=2.453;QD=1.44;ReadPosRankSum=3.369;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:66,8:74:99:135,0,173 -chr1 72037 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.481;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=8.0800;MLEAC=1;MLEAF=0.500;MQ=11.16;MQ0=17;MQRankSum=2.289;QD=0.63;ReadPosRankSum=2.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:61,2:63:68:68,0,74 -chr1 72059 . T C 106.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.241;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.7351;MLEAC=2;MLEAF=1.00;MQ=11.90;MQ0=9;MQRankSum=1.061;QD=2.65;ReadPosRankSum=-2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:9,31:40:12:134,12,0 -chr1 72137 . C T 135.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.983;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=6;MQRankSum=3.138;QD=5.63;ReadPosRankSum=0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:16,7:24:12:163,12,0 -chr1 72198 . A G 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.408;DP=34;Dels=0.03;FS=0.000;HaplotypeScore=32.2822;MLEAC=1;MLEAF=0.500;MQ=18.40;MQ0=8;MQRankSum=0.642;QD=0.79;ReadPosRankSum=-0.803;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,3:33:55:55,0,194 -chr1 72220 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=8.1644;MLEAC=1;MLEAF=0.500;MQ=16.77;MQ0=8;MQRankSum=2.009;QD=1.02;ReadPosRankSum=2.679;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,3:33:62:62,0,141 -chr1 72245 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=1.052;QD=0.99;ReadPosRankSum=-1.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,3:30:58:58,0,156 -chr1 72246 . G T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.144;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=3.7817;MLEAC=1;MLEAF=0.500;MQ=17.26;MQ0=4;MQRankSum=2.261;QD=0.99;ReadPosRankSum=-0.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,2:30:58:58,0,154 -chr1 72269 . T C 18.83 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.122;DP=23;Dels=0.00;FS=4.771;HaplotypeScore=5.5051;MLEAC=1;MLEAF=0.500;MQ=11.28;MQ0=6;MQRankSum=-0.537;QD=0.82;ReadPosRankSum=2.293;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,7:23:39:47,0,39 -chr1 72271 . T C 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=22;Dels=0.00;FS=4.771;HaplotypeScore=4.7711;MLEAC=1;MLEAF=0.500;MQ=11.53;MQ0=6;MQRankSum=1.799;QD=0.51;ReadPosRankSum=-1.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,10:22:39:39,0,47 -chr1 72309 . T G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.537;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=9.6153;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=2.041;QD=2.45;ReadPosRankSum=-0.107;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:65:65,0,114 -chr1 72313 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.788;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=12.8714;MLEAC=1;MLEAF=0.500;MQ=23.14;MQ0=3;MQRankSum=-1.000;QD=4.38;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:6,9:15:86:94,0,86 -chr1 72362 . A G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=21.15;MQ0=4;MQRankSum=0.000;QD=3.98;ReadPosRankSum=0.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,6:14:61:84,0,61 -chr1 72457 . T G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.362;DP=19;Dels=0.00;FS=3.979;HaplotypeScore=10.4309;MLEAC=1;MLEAF=0.500;MQ=16.41;MQ0=1;MQRankSum=-0.453;QD=0.68;ReadPosRankSum=2.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,8:19:41:41,0,92 -chr1 72490 . A G 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=17.81;MQ0=2;MQRankSum=2.538;QD=5.57;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,11:24:54:162,0,54 -chr1 72511 . C T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.336;DP=23;Dels=0.00;FS=3.424;HaplotypeScore=8.8927;MLEAC=1;MLEAF=0.500;MQ=21.05;MQ0=2;MQRankSum=2.216;QD=0.61;ReadPosRankSum=-2.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,2:23:42:42,0,231 -chr1 72546 . G A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.714;DP=18;Dels=0.00;FS=3.010;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=22.48;MQ0=2;MQRankSum=2.143;QD=0.77;ReadPosRankSum=0.873;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:18:42:42,0,183 -chr1 72554 . C T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=24.02;MQ0=2;MQRankSum=2.073;QD=1.59;ReadPosRankSum=1.678;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:13,2:15:52:52,0,163 -chr1 72558 . C T 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4964;MLEAC=1;MLEAF=0.500;MQ=22.45;MQ0=2;MQRankSum=0.289;QD=1.91;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,4:14:55:55,0,130 -chr1 72562 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=12;Dels=0.00;FS=8.751;HaplotypeScore=4.2846;MLEAC=1;MLEAF=0.500;MQ=22.65;MQ0=2;MQRankSum=1.271;QD=2.23;ReadPosRankSum=1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:10,2:12:55:55,0,77 -chr1 72602 . G A 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.822;DP=19;Dels=0.00;FS=10.000;HaplotypeScore=6.4109;MLEAC=1;MLEAF=0.500;MQ=20.13;MQ0=4;MQRankSum=1.734;QD=1.88;ReadPosRankSum=-0.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,2:19:64:64,0,89 -chr1 72626 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.482;DP=23;Dels=0.00;FS=3.332;HaplotypeScore=8.3126;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=5;MQRankSum=0.796;QD=2.34;ReadPosRankSum=0.515;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,6:23:82:82,0,124 -chr1 72630 . G A 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=5;MQRankSum=0.787;QD=1.32;ReadPosRankSum=-1.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,9:24:60:60,0,147 -chr1 72631 . T C 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.646;DP=25;Dels=0.00;FS=2.680;HaplotypeScore=11.7259;MLEAC=1;MLEAF=0.500;MQ=18.06;MQ0=5;MQRankSum=1.905;QD=2.15;ReadPosRankSum=0.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,3:25:82:82,0,124 -chr1 72638 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=22.7383;MLEAC=1;MLEAF=0.500;MQ=17.66;MQ0=5;MQRankSum=-0.417;QD=3.96;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,17:29:95:143,0,95 -chr1 72646 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=2.219;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=1.020;QD=0.60;ReadPosRankSum=1.080;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,9:33:48:48,0,249 -chr1 72647 . A T 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.883;DP=33;Dels=0.00;FS=2.141;HaplotypeScore=9.5448;MLEAC=1;MLEAF=0.500;MQ=18.45;MQ0=5;MQRankSum=-1.102;QD=2.24;ReadPosRankSum=-1.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,12:33:99:102,0,158 -chr1 72688 . A C 22.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.304;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.2417;MLEAC=1;MLEAF=0.500;MQ=17.84;MQ0=5;MQRankSum=0.604;QD=0.76;ReadPosRankSum=-0.986;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,9:30:51:51,0,209 -chr1 72693 . A G,T 93.3 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.315;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=3.4300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=17.69;MQ0=3;MQRankSum=0.315;QD=4.06;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:3,13,7:23:82:195,82,86,97,0,107 -chr1 72717 . T C 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.369;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=16.28;MQ0=1;MQRankSum=0.555;QD=3.41;ReadPosRankSum=-0.660;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:7,7:14:32:76,0,32 -chr1 72825 . G C 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.350;QD=1.40;ReadPosRankSum=1.050;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,4:39:83:83,0,118 -chr1 72829 . C T 54.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.750;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=6.6451;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=20;MQRankSum=1.050;QD=1.40;ReadPosRankSum=1.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:35,4:39:83:83,0,121 -chr1 72855 . A G 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.464;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=16.6819;MLEAC=1;MLEAF=0.500;MQ=16.39;MQ0=10;MQRankSum=-0.705;QD=0.45;ReadPosRankSum=-1.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:12,14:27:40:40,0,130 -chr1 72858 . G A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.321;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=11.8688;MLEAC=1;MLEAF=0.500;MQ=16.70;MQ0=9;MQRankSum=1.415;QD=2.30;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,4:26:82:88,0,82 -chr1 72865 . G A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.456;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=9.3724;MLEAC=1;MLEAF=0.500;MQ=17.99;MQ0=8;MQRankSum=1.004;QD=0.55;ReadPosRankSum=0.091;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,3:22:40:40,0,130 -chr1 72880 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.386;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=20.39;MQ0=5;MQRankSum=-0.546;QD=0.99;ReadPosRankSum=-1.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:8,7:15:43:43,0,103 -chr1 72889 . T A 11.83 LowQual AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=21.37;MQ0=0;QD=2.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:3:38,3,0 -chr1 73036 . T A 208.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.62;MQ0=0;QD=34.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:237,18,0 -chr1 73048 . A G 266.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=33.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:295,24,0 -chr1 73057 . T C 276.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.49;MQ0=0;QD=34.60;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:305,24,0 -chr1 73065 . G A 343.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.86;MQ0=0;QD=34.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:372,30,0 -chr1 73081 . G A 317.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.59;MQ0=1;QD=28.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:346,27,0 -chr1 73149 . G C 249.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.69;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:278,21,0 -chr1 73163 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=26.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 73175 . G C 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.65;MQ0=0;QD=27.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 73190 . T C 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.190;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-0.021;QD=8.71;ReadPosRankSum=4.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:307,0,753 -chr1 73232 . T G 932.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.025;QD=21.20;ReadPosRankSum=1.585;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:961,0,450 -chr1 73255 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.483;DP=47;Dels=0.00;FS=6.570;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=-2.077;QD=9.48;ReadPosRankSum=-0.977;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,16:47:99:474,0,1089 -chr1 73261 . C A 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.379;DP=44;Dels=0.00;FS=4.722;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.183;QD=21.88;ReadPosRankSum=1.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:991,0,472 -chr1 73263 . C G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=44;Dels=0.00;FS=2.932;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.964;QD=21.31;ReadPosRankSum=1.671;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:966,0,458 -chr1 73275 . C T 999.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.486;DP=44;Dels=0.00;FS=1.263;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.535;QD=22.72;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,29:44:99:1028,0,450 -chr1 73316 . C T 2034.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2063,157,0 -chr1 73353 . T C 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.342;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.881;QD=11.40;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:587,0,1121 -chr1 73399 . A G 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.278;DP=55;Dels=0.00;FS=1.104;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.735;QD=9.60;ReadPosRankSum=2.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,18:55:99:556,0,1319 -chr1 73405 . A T 1043.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.503;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.482;QD=21.30;ReadPosRankSum=-0.975;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1072,0,626 -chr1 73409 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=50;Dels=0.00;FS=1.111;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-1.396;QD=19.28;ReadPosRankSum=-0.295;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:992,0,686 -chr1 73415 . A C 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.654;DP=46;Dels=0.00;FS=2.689;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-0.221;QD=17.91;ReadPosRankSum=0.198;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,629 -chr1 73486 . T A 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.8288;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.472;QD=15.77;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:864,0,913 -chr1 73498 . T G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=60;Dels=0.00;FS=7.060;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.598;QD=16.43;ReadPosRankSum=-1.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1014,0,976 -chr1 73526 . G C 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.141;DP=55;Dels=0.00;FS=5.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.947;QD=18.87;ReadPosRankSum=-1.408;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1066,0,776 -chr1 73533 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.024;DP=53;Dels=0.00;FS=1.107;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.014;QD=17.51;ReadPosRankSum=0.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:956,0,715 -chr1 73553 . C T 2145.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=31.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2174,160,0 -chr1 73559 . G C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.866;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.050;QD=12.94;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:33,23:56:99:753,0,1151 -chr1 73601 . T C 1170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.426;DP=64;Dels=0.00;FS=0.969;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.995;QD=18.29;ReadPosRankSum=-0.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1199,0,892 -chr1 73621 . C T 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.511;DP=67;Dels=0.00;FS=0.922;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.292;QD=18.98;ReadPosRankSum=-0.019;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,37:67:99:1300,0,965 -chr1 73648 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.955;DP=69;Dels=0.00;FS=2.001;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=-0.776;QD=13.56;ReadPosRankSum=0.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:37,32:69:99:964,0,1308 -chr1 73726 . T A 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.877;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.512;QD=18.38;ReadPosRankSum=1.487;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:800,0,577 -chr1 73823 . G C 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.311;QD=16.01;ReadPosRankSum=1.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:877,0,914 -chr1 73849 . G A 1301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.816;DP=62;Dels=0.00;FS=1.017;HaplotypeScore=3.9989;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.015;QD=21.00;ReadPosRankSum=-0.146;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,39:62:99:1330,0,730 -chr1 73870 . G A 1246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=62;Dels=0.00;FS=3.539;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.230;QD=20.11;ReadPosRankSum=0.861;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1275,0,847 -chr1 73877 . A G 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.674;DP=64;Dels=0.00;FS=3.431;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=-0.836;QD=17.84;ReadPosRankSum=1.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1170,0,987 -chr1 73917 . A G 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.277;DP=66;Dels=0.00;FS=2.047;HaplotypeScore=1.9912;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.905;QD=16.80;ReadPosRankSum=-0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1137,0,1083 -chr1 73927 . T C 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.691;DP=59;Dels=0.00;FS=3.614;HaplotypeScore=2.6984;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.812;QD=17.32;ReadPosRankSum=-1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:1050,0,941 -chr1 73941 . C G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.144;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6987;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=0.313;QD=14.74;ReadPosRankSum=0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:839,0,1011 -chr1 73956 . A C 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-0.468;QD=13.53;ReadPosRankSum=0.514;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:637,0,849 -chr1 74024 . G C 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.254;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=3;MQRankSum=-2.569;QD=14.19;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:681,0,673 -chr1 74047 . G A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=52;Dels=0.00;FS=6.153;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.43;MQ0=4;MQRankSum=-3.097;QD=12.90;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,28:52:99:699,0,647 -chr1 74080 . G A 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=58;Dels=0.00;FS=2.389;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=48.01;MQ0=4;MQRankSum=-5.098;QD=10.86;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:658,0,902 -chr1 74086 . A T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.43;MQ0=1;MQRankSum=-6.245;QD=9.29;ReadPosRankSum=1.114;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:530,0,995 -chr1 74089 . T G 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=1;MQRankSum=-6.297;QD=9.30;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:540,0,1006 -chr1 74105 . G A 433.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=50.74;MQ0=1;MQRankSum=-6.154;QD=8.18;ReadPosRankSum=-0.700;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:462,0,1044 -chr1 74115 . A G 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=50.24;MQ0=1;MQRankSum=-5.772;QD=6.19;ReadPosRankSum=-0.920;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:319,0,952 -chr1 74119 . A G 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.277;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=50.57;MQ0=1;MQRankSum=-5.551;QD=7.02;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:337,0,895 -chr1 74274 . A T 879.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.47;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:908,69,0 -chr1 74343 . C T 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.338;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.918;QD=17.18;ReadPosRankSum=3.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:973,0,882 -chr1 74475 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.652;DP=61;Dels=0.00;FS=12.530;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.79;MQ0=0;MQRankSum=-6.052;QD=16.83;ReadPosRankSum=2.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1055,0,1074 -chr1 74477 . T C 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.511;DP=59;Dels=0.00;FS=10.241;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-5.936;QD=17.84;ReadPosRankSum=2.070;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1081,0,1017 -chr1 74481 . G A 1104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.304;DP=60;Dels=0.00;FS=7.540;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-5.682;QD=18.41;ReadPosRankSum=1.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,32:60:99:1133,0,933 -chr1 74490 . A G 836.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.635;DP=62;Dels=0.00;FS=5.488;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=5.728;QD=13.50;ReadPosRankSum=1.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:36,26:62:99:865,0,1275 -chr1 74532 . C T 1134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.207;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=0;MQRankSum=-1.874;QD=18.60;ReadPosRankSum=-1.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1163,0,974 -chr1 74539 . T A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.904;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-2.447;QD=15.63;ReadPosRankSum=0.686;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:935,0,1102 -chr1 74540 . A T 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.639;QD=15.55;ReadPosRankSum=0.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:930,0,1112 -chr1 74544 . T C 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=1.937;QD=16.08;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,30:63:99:1041,0,1120 -chr1 74554 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=62;Dels=0.00;FS=0.939;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.760;QD=15.63;ReadPosRankSum=1.056;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:997,0,1066 -chr1 74559 . A G 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.648;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.806;QD=16.03;ReadPosRankSum=1.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,30:60:99:990,0,1042 -chr1 74590 . G A 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=0.903;QD=14.71;ReadPosRankSum=2.690;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:808,0,980 -chr1 74638 . C T 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.820;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.49;MQ0=0;MQRankSum=1.355;QD=14.74;ReadPosRankSum=-1.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:839,0,868 -chr1 74648 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=53;Dels=0.00;FS=3.775;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=1.331;QD=14.88;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:817,0,917 -chr1 74652 . T C 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.459;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=1.026;QD=14.20;ReadPosRankSum=-1.085;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:738,0,887 -chr1 74691 . C T 1222.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1251,96,0 -chr1 74732 . C A 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.435;DP=42;Dels=0.00;FS=18.002;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.102;QD=12.26;ReadPosRankSum=-0.615;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:543,0,832 -chr1 74805 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=32;Dels=0.00;FS=11.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.183;QD=8.59;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:303,0,769 -chr1 74809 . A G 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.788;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.297;QD=7.10;ReadPosRankSum=0.432;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:227,0,624 -chr1 74810 . C T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.348;DP=28;Dels=0.00;FS=11.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-0.687;QD=7.67;ReadPosRankSum=0.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:243,0,706 -chr1 74816 . A T 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.472;DP=30;Dels=0.00;FS=8.475;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=2.064;QD=5.89;ReadPosRankSum=-0.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,7:30:99:205,0,702 -chr1 74826 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9448;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.122;QD=28.38;ReadPosRankSum=2.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:4,19:23:88:681,0,88 -chr1 74830 . A T 738.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.315;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=17.9789;MLEAC=2;MLEAF=1.00;MQ=59.00;MQ0=0;MQRankSum=1.419;QD=33.58;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,21:22:25:767,25,0 -chr1 74836 . A T 949.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=18.7128;MLEAC=2;MLEAF=1.00;MQ=59.12;MQ0=0;QD=28.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:978,75,0 -chr1 74877 . C T 1344.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.09;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1373,105,0 -chr1 74921 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.720;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-0.573;QD=6.31;ReadPosRankSum=1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:249,0,790 -chr1 75391 . G T 704.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.040;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=3.7544;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-0.901;QD=28.19;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:25:733,25,0 -chr1 75393 . T C 692.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.069;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=2.9658;MLEAC=2;MLEAF=1.00;MQ=48.50;MQ0=0;MQRankSum=-1.040;QD=27.71;ReadPosRankSum=1.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:1,24:25:24:721,24,0 -chr1 75399 . C A 731.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.96;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,24:24:60:760,60,0 -chr1 75407 . G A 466.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:495,39,0 -chr1 75408 . T C 474.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=0;QD=27.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,17:17:39:503,39,0 -chr1 75441 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0 -chr1 75443 . A G 77.28 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.70;MQ0=0;QD=19.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,4:4:9:105,9,0 -chr1 75447 . C T 75.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:103,9,0 -chr1 75675 . G T 46.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:74,6,0 -chr1 75678 . G T 88.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:116,9,0 -chr1 75695 . T C 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=34;Dels=0.00;FS=1.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.62;MQ0=1;MQRankSum=-0.738;QD=15.23;ReadPosRankSum=0.018;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:546,0,545 -chr1 75719 . C T 1840.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=1;QD=26.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1869,138,0 -chr1 75727 . A G 2171.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.64;MQ0=0;QD=34.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2200,163,0 -chr1 75762 . C T 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=56;Dels=0.00;FS=11.912;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.737;QD=13.66;ReadPosRankSum=-0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:793,0,1062 -chr1 75763 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.486;QD=13.21;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:755,0,1074 -chr1 75764 . A G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.339;DP=55;Dels=0.00;FS=9.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=0.930;QD=13.14;ReadPosRankSum=-0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:751,0,1072 -chr1 75807 . A C 597.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.697;DP=47;Dels=0.00;FS=1.116;HaplotypeScore=3.2018;MLEAC=1;MLEAF=0.500;MQ=55.41;MQ0=0;MQRankSum=-0.075;QD=12.72;ReadPosRankSum=-0.181;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:626,0,814 -chr1 75832 . A G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.198;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=13.9498;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-3.243;QD=6.99;ReadPosRankSum=3.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,7:22:99:182,0,490 -chr1 75838 . A C,T 525.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=11.9502;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.83;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:0,7,12:19:99:664,409,388,255,0,222 -chr1 75850 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.400;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-1.228;QD=19.73;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:9,14:23:99:482,0,253 -chr1 75905 . T G 911.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.627;DP=45;Dels=0.00;FS=4.849;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=1;MQRankSum=-0.699;QD=20.26;ReadPosRankSum=-0.337;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:940,0,570 -chr1 75930 . T C 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=54;Dels=0.00;FS=8.156;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=1;MQRankSum=-2.270;QD=12.68;ReadPosRankSum=-0.996;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:713,0,1060 -chr1 75970 . C G 1604.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.17;MQ0=1;QD=31.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1633,120,0 -chr1 76013 . T G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.758;DP=38;Dels=0.00;FS=1.402;HaplotypeScore=1.9956;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=1;MQRankSum=0.479;QD=12.73;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,658 -chr1 76032 . A T 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.051;DP=43;Dels=0.00;FS=5.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.57;MQ0=1;MQRankSum=1.973;QD=12.72;ReadPosRankSum=-0.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:575,0,722 -chr1 76087 . C A 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=51;Dels=0.00;FS=11.471;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=1.732;QD=14.84;ReadPosRankSum=0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:785,0,818 -chr1 76168 . T C 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=43;Dels=0.00;FS=2.727;HaplotypeScore=5.8324;MLEAC=1;MLEAF=0.500;MQ=56.98;MQ0=1;MQRankSum=-0.743;QD=19.58;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,26:43:99:870,0,570 -chr1 76236 . C A 728.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=13.5311;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:757,57,0 -chr1 76283 . C A 1892.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.84;MQ0=0;QD=28.55;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1921,147,0 -chr1 76328 . C T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.666;DP=51;Dels=0.00;FS=4.307;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.62;MQ0=0;MQRankSum=-0.205;QD=10.86;ReadPosRankSum=-2.893;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:582,0,977 -chr1 76334 . A G 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.425;DP=45;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=2.653;QD=12.17;ReadPosRankSum=-1.587;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:576,0,815 -chr1 76427 . A C 759.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.347;DP=54;Dels=0.00;FS=12.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=-0.169;QD=14.07;ReadPosRankSum=0.508;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:788,0,919 -chr1 76443 . T C 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.715;DP=59;Dels=0.00;FS=11.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=1;MQRankSum=0.451;QD=14.91;ReadPosRankSum=-0.513;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:908,0,963 -chr1 76465 . C T 822.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.671;DP=50;Dels=0.00;FS=19.919;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=1;MQRankSum=-1.733;QD=16.46;ReadPosRankSum=-0.711;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:851,0,769 -chr1 76478 . G T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.821;DP=48;Dels=0.00;FS=13.782;HaplotypeScore=145.9761;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=-2.207;QD=15.77;ReadPosRankSum=0.565;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:785,0,657 -chr1 76500 . G T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.996;DP=35;Dels=0.00;FS=1.972;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=0.959;QD=0.57;ReadPosRankSum=-3.137;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,4:35:48:48,0,1103 -chr1 76506 . T G 1303.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.25;MQ0=0;QD=30.53;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1332,99,0 -chr1 76543 . A C,T 956.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.625;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=9.9300;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.99;MQ0=0;MQRankSum=0.542;QD=29.88;ReadPosRankSum=0.650;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/2:1,12,19:32:99:1134,701,665,433,0,376 -chr1 76552 . C A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.464;DP=33;Dels=0.00;FS=1.376;HaplotypeScore=16.6986;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-3.019;QD=17.72;ReadPosRankSum=0.524;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:613,0,416 -chr1 76554 . A T 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=14.9106;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.480;QD=15.93;ReadPosRankSum=0.827;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:570,0,574 -chr1 76667 . C A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=50;Dels=0.00;FS=2.539;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=-0.616;QD=22.38;ReadPosRankSum=2.961;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1147,0,573 -chr1 76736 . T C 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.2657;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.771;QD=21.09;ReadPosRankSum=-0.603;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:956,0,527 -chr1 76758 . A G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.695;DP=38;Dels=0.00;FS=1.289;HaplotypeScore=16.4637;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.370;QD=19.39;ReadPosRankSum=0.103;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:765,0,537 -chr1 76765 . A T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=38;Dels=0.00;FS=1.281;HaplotypeScore=62.8561;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=0.219;QD=17.55;ReadPosRankSum=1.535;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:695,0,601 -chr1 76784 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.258;QD=14.59;ReadPosRankSum=-1.433;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:670,0,738 -chr1 76813 . G T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.627;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.777;QD=19.61;ReadPosRankSum=-1.476;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,32:52:99:1048,0,649 -chr1 76827 . C T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.020;DP=50;Dels=0.00;FS=1.117;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-1.020;QD=19.94;ReadPosRankSum=-1.218;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1025,0,663 -chr1 76831 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=-0.124;QD=19.94;ReadPosRankSum=-1.136;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1105,0,628 -chr1 76885 . G C 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.785;DP=51;Dels=0.00;FS=8.452;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.280;QD=21.15;ReadPosRankSum=0.878;EFF=UTR_3_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1107,0,632 -chr1 76963 . A G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.690;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.421;QD=19.62;ReadPosRankSum=0.589;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V46A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:715,0,396 -chr1 76964 . C A 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.051;DP=35;Dels=0.00;FS=1.313;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.364;QD=19.68;ReadPosRankSum=0.791;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V46L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:14,21:35:99:717,0,439 -chr1 76995 . T C 912.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=34.12;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A35|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,24:24:72:941,72,0 -chr1 77019 . T G 807.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=28.76;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggA/ggC|G27|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,22:22:66:836,66,0 -chr1 77028 . G T 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.026;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.083;QD=11.11;ReadPosRankSum=-0.305;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S24R|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:15,10:25:99:306,0,525 -chr1 77030 . T C 1001.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=33.45;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S24G|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1030,78,0 -chr1 77036 . C G 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=2.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.482;QD=9.75;ReadPosRankSum=1.399;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Ctc|V22L|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,10:29:99:311,0,667 -chr1 77040 . A C 1106.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atT/atG|I20M|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,31:31:87:1135,87,0 -chr1 77066 . C T 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.686;QD=15.94;ReadPosRankSum=2.051;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcc/Acc|A12T|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:18,19:38:99:634,0,588 -chr1 77068 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.949;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-2.131;QD=16.28;ReadPosRankSum=2.336;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V11A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:647,0,593 -chr1 77072 . G C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.606;DP=38;Dels=0.00;FS=5.701;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.518;QD=15.65;ReadPosRankSum=2.628;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L10V|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,19:38:99:623,0,636 -chr1 77092 . C G 1448.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.9948;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.69;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gCg|G3A|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 1/1:0,42:43:99:1477,111,0 -chr1 77096 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=45;Dels=0.00;FS=6.823;HaplotypeScore=2.9948;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.215;QD=17.06;ReadPosRankSum=0.534;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E2K|Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:22,23:45:99:796,0,679 -chr1 77106 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.785;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.12;MQ0=0;MQRankSum=-1.035;QD=17.26;ReadPosRankSum=-1.240;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,24:45:99:805,0,662 -chr1 77122 . A G 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.595;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-1.700;QD=14.32;ReadPosRankSum=-0.728;EFF=START_GAINED(LOW||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:19,15:34:99:515,0,632 -chr1 77126 . A T 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.204;DP=37;Dels=0.00;FS=7.143;HaplotypeScore=3.7335;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-1.844;QD=14.97;ReadPosRankSum=-0.808;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:20,17:37:99:582,0,647 -chr1 77144 . A C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.300;DP=41;Dels=0.00;FS=4.506;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-1.265;QD=15.85;ReadPosRankSum=0.170;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:21,20:41:99:678,0,682 -chr1 77180 . C A 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.879;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=4.1179;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.179;QD=17.54;ReadPosRankSum=-0.594;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|Exon_chr1_76277_77218) GT:AD:DP:GQ:PL 0/1:16,24:40:99:730,0,535 -chr1 77221 . C G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=43;Dels=0.00;FS=14.813;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.319;QD=20.88;ReadPosRankSum=-0.163;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:16,27:43:99:926,0,502 -chr1 77244 . G C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=39;Dels=0.00;FS=5.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.512;QD=21.81;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:14,25:39:99:879,0,425 -chr1 77298 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.048;DP=35;Dels=0.00;FS=5.506;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-1.901;QD=23.14;ReadPosRankSum=1.190;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:838,0,318 -chr1 77325 . T A 1222.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=55.78;MQ0=0;QD=37.76;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1251,96,0 -chr1 77332 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=32;Dels=0.00;FS=3.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-0.516;QD=22.34;ReadPosRankSum=0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:11,21:32:99:743,0,352 -chr1 77376 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.170;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=83.6545;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.434;QD=15.40;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:783,0,747 -chr1 77378 . A C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=124.2479;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=-2.053;QD=15.32;ReadPosRankSum=0.431;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:779,0,892 -chr1 77438 . C T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.363;DP=53;Dels=0.00;FS=15.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.633;QD=16.94;ReadPosRankSum=-2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:926,0,869 -chr1 77442 . T G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=51;Dels=0.00;FS=15.703;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.218;QD=15.02;ReadPosRankSum=3.474;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,934 -chr1 77449 . T C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=48;Dels=0.00;FS=11.196;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.972;QD=13.39;ReadPosRankSum=2.206;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:671,0,945 -chr1 77450 . A G 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.917;DP=46;Dels=0.00;FS=11.459;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.853;QD=14.34;ReadPosRankSum=1.673;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:688,0,862 -chr1 77458 . A T 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.272;DP=51;Dels=0.00;FS=16.807;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=1;MQRankSum=2.301;QD=15.23;ReadPosRankSum=0.146;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:805,0,791 -chr1 77464 . G A 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=49;Dels=0.00;FS=17.115;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=-0.908;QD=16.95;ReadPosRankSum=-1.610;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:859,0,697 -chr1 77489 . G A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.648;DP=46;Dels=0.00;FS=12.506;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.16;MQ0=2;MQRankSum=-0.625;QD=14.45;ReadPosRankSum=2.345;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:693,0,690 -chr1 77491 . A G 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=45;Dels=0.00;FS=15.152;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.71;MQ0=2;MQRankSum=2.203;QD=12.71;ReadPosRankSum=-1.489;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:600,0,730 -chr1 77495 . A G 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.505;DP=41;Dels=0.00;FS=16.483;HaplotypeScore=1.9545;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=2;MQRankSum=2.237;QD=11.36;ReadPosRankSum=-0.476;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:494,0,766 -chr1 77531 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=49;Dels=0.00;FS=11.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=3;MQRankSum=4.899;QD=15.53;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:789,0,677 -chr1 77535 . C T 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=49;Dels=0.00;FS=13.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=3;MQRankSum=-5.229;QD=14.63;ReadPosRankSum=-2.065;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:745,0,801 -chr1 77544 . C T 633.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.557;DP=48;Dels=0.00;FS=11.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.09;MQ0=3;MQRankSum=-5.517;QD=13.20;ReadPosRankSum=-0.330;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:662,0,770 -chr1 77549 . C G 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.738;DP=50;Dels=0.00;FS=10.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=3;MQRankSum=-5.596;QD=12.14;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:635,0,869 -chr1 77557 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.869;DP=45;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=3;MQRankSum=-5.553;QD=14.15;ReadPosRankSum=0.416;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:665,0,732 -chr1 77577 . T G 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=3;MQRankSum=-3.998;QD=6.89;ReadPosRankSum=2.292;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:290,0,880 -chr1 77581 . T G 1321.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.74;MQ0=2;QD=31.22;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1350,99,0 -chr1 77582 . A G 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=55.61;MQ0=2;QD=29.89;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,99,0 -chr1 77589 . C T 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=42;Dels=0.00;FS=4.743;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=2;MQRankSum=-2.271;QD=11.95;ReadPosRankSum=-0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:530,0,807 -chr1 77592 . G A 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=2.439;QD=16.46;ReadPosRankSum=0.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:736,0,657 -chr1 77593 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=43;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-1.969;QD=15.04;ReadPosRankSum=-0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:675,0,722 -chr1 77615 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.765;DP=43;Dels=0.00;FS=2.820;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=2;MQRankSum=-0.327;QD=16.53;ReadPosRankSum=-0.327;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:739,0,655 -chr1 77617 . C T 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.975;DP=42;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.58;MQ0=2;MQRankSum=0.488;QD=16.40;ReadPosRankSum=0.027;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:20,22:42:99:717,0,653 -chr1 77620 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.342;DP=43;Dels=0.00;FS=2.687;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=2;MQRankSum=0.013;QD=12.79;ReadPosRankSum=0.781;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,17:43:99:578,0,822 -chr1 77633 . G A 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.964;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=1;MQRankSum=1.015;QD=11.33;ReadPosRankSum=-0.555;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:504,0,850 -chr1 77648 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.970;DP=44;Dels=0.00;FS=1.269;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=1;MQRankSum=0.304;QD=8.81;ReadPosRankSum=-0.569;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:416,0,909 -chr1 77650 . T C 1540.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=1;QD=31.92;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1569,120,0 -chr1 77695 . A G 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.171;DP=48;Dels=0.00;FS=11.450;HaplotypeScore=1.9984;MLEAC=1;MLEAF=0.500;MQ=56.59;MQ0=1;MQRankSum=-1.215;QD=11.39;ReadPosRankSum=-2.156;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:575,0,980 -chr1 77770 . C T 2115.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=2;QD=26.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2144,163,0 -chr1 77798 . A G 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.110;DP=51;Dels=0.00;FS=4.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-0.292;QD=13.56;ReadPosRankSum=-0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:720,0,928 -chr1 77814 . G T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.710;DP=51;Dels=0.00;FS=4.322;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=54.03;MQ0=1;MQRankSum=-1.124;QD=18.72;ReadPosRankSum=0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:983,0,686 -chr1 77873 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=1.065;QD=20.19;ReadPosRankSum=-2.142;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:937,0,508 -chr1 77951 . C A 2019.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.7336;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2048,159,0 -chr1 77986 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=56;Dels=0.00;FS=5.494;HaplotypeScore=1.9774;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-1.712;QD=14.80;ReadPosRankSum=0.778;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,28:56:99:857,0,933 -chr1 78007 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.299;DP=43;Dels=0.00;FS=1.315;HaplotypeScore=19.9836;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.842;QD=11.18;ReadPosRankSum=0.565;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:509,0,882 -chr1 78009 . C T 864.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.704;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-1.014;QD=19.65;ReadPosRankSum=-0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:893,0,579 -chr1 78012 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.563;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.037;QD=18.65;ReadPosRankSum=-0.185;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:830,0,589 -chr1 78019 . T C 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.817;DP=44;Dels=0.00;FS=3.112;HaplotypeScore=24.9845;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-0.446;QD=10.13;ReadPosRankSum=2.105;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:29,15:44:99:474,0,1015 -chr1 78027 . T C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.359;DP=44;Dels=0.00;FS=12.758;HaplotypeScore=6.9973;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.701;QD=1.72;ReadPosRankSum=-1.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:38,6:44:99:104,0,1372 -chr1 78118 . T A 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.504;DP=54;Dels=0.00;FS=1.040;HaplotypeScore=35.7719;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.892;QD=19.46;ReadPosRankSum=1.994;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1079,0,770 -chr1 78134 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.779;DP=54;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=0.099;QD=11.72;ReadPosRankSum=-0.958;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:34,20:54:99:661,0,1176 -chr1 78240 . T C 1102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=57;Dels=0.00;FS=3.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.234;QD=19.35;ReadPosRankSum=0.444;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1131,0,782 -chr1 78243 . T A 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=58;Dels=0.00;FS=5.380;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=0.361;QD=19.34;ReadPosRankSum=0.848;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1150,0,823 -chr1 78259 . A G 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.319;DP=58;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=1.330;QD=17.05;ReadPosRankSum=0.319;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1017,0,977 -chr1 78296 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=35;Dels=0.00;FS=5.073;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.286;QD=20.34;ReadPosRankSum=1.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:740,0,458 -chr1 78417 . A G 2257.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=1;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2286,172,0 -chr1 78420 . T C 2412.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=1;QD=32.78;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2441,184,0 -chr1 78459 . A G 1049.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=56;Dels=0.00;FS=1.071;HaplotypeScore=2.7605;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=4;MQRankSum=1.156;QD=18.75;ReadPosRankSum=1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,33:56:99:1078,0,681 -chr1 78480 . G T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=4;MQRankSum=-1.866;QD=7.95;ReadPosRankSum=-1.529;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:418,0,1082 -chr1 78503 . A C 1406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.844;DP=60;Dels=0.00;FS=2.699;HaplotypeScore=42.4334;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=3;MQRankSum=1.437;QD=23.45;ReadPosRankSum=2.809;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,45:60:99:1435,0,403 -chr1 78548 . T A 2170.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=24.73;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2199,166,0 -chr1 78601 . G A 1151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.289;DP=48;Dels=0.00;FS=5.335;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=0;MQRankSum=-0.133;QD=24.00;ReadPosRankSum=-0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,33:48:99:1180,0,463 -chr1 78639 . C A 1912.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1941,147,0 -chr1 78753 . G T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.473;DP=65;Dels=0.00;FS=0.960;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.007;QD=12.77;ReadPosRankSum=-0.353;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:38,27:65:99:858,0,1336 -chr1 78787 . G A 1365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.554;DP=61;Dels=0.00;FS=1.030;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.660;QD=22.39;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,40:61:99:1394,0,614 -chr1 78815 . A G 1168.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.008;DP=57;Dels=0.00;FS=3.773;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.336;QD=20.50;ReadPosRankSum=1.320;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,35:57:99:1197,0,695 -chr1 78892 . C T 925.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.979;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.584;QD=15.69;ReadPosRankSum=0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:954,0,1057 -chr1 78931 . G A 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.869;DP=63;Dels=0.00;FS=11.290;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.796;QD=16.93;ReadPosRankSum=-1.025;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1095,0,1023 -chr1 78981 . T C 131.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.954;DP=27;Dels=0.00;FS=12.207;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.904;QD=4.88;ReadPosRankSum=2.537;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:160,0,693 -chr1 78994 . T A 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.138;DP=38;Dels=0.00;FS=22.047;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=2.492;QD=20.10;ReadPosRankSum=-0.738;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,25:38:99:792,0,376 -chr1 79011 . A T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.991;DP=42;Dels=0.00;FS=18.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.654;QD=7.21;ReadPosRankSum=1.573;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:331,0,1024 -chr1 79031 . C A 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=45;Dels=0.00;FS=23.835;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=2.704;QD=20.24;ReadPosRankSum=0.386;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,28:45:99:939,0,503 -chr1 79032 . T C 1667.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.02;FS=0.000;HaplotypeScore=16.9978;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=32.21;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1696,126,0 -chr1 79035 . C G 1664.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.115;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;MQRankSum=1.578;QD=32.37;ReadPosRankSum=0.654;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,44:45:92:1693,92,0 -chr1 79092 . A C 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.296;DP=56;Dels=0.00;FS=20.015;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-1.258;QD=7.25;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:41,15:56:99:434,0,1487 -chr1 79155 . A G 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.851;DP=43;Dels=0.00;FS=24.229;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.433;QD=4.20;ReadPosRankSum=1.776;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,9:43:99:209,0,1210 -chr1 79179 . A G 1612.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.02;MQ0=0;QD=29.41;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1641,126,0 -chr1 79211 . G A 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=44;Dels=0.00;FS=24.701;HaplotypeScore=3.9990;MLEAC=1;MLEAF=0.500;MQ=55.60;MQ0=0;MQRankSum=-4.230;QD=6.36;ReadPosRankSum=2.095;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,12:44:99:308,0,1153 -chr1 79215 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.314;DP=46;Dels=0.00;FS=28.108;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.80;MQ0=0;MQRankSum=-3.940;QD=5.84;ReadPosRankSum=2.539;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,12:46:99:297,0,1207 -chr1 79219 . C T 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=48;Dels=0.00;FS=32.959;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.417;QD=5.62;ReadPosRankSum=2.464;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:298,0,1293 -chr1 79223 . A C 1751.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=2;MLEAF=1.00;MQ=55.80;MQ0=0;QD=31.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1780,135,0 -chr1 79242 . C T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.484;DP=54;Dels=0.00;FS=36.287;HaplotypeScore=13.9681;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-5.699;QD=8.00;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:460,0,1314 -chr1 79253 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.069;DP=49;Dels=0.00;FS=18.054;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.73;MQ0=0;MQRankSum=5.556;QD=23.30;ReadPosRankSum=2.594;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,32:49:99:1170,0,488 -chr1 79258 . C T 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=50;Dels=0.00;FS=15.207;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.996;QD=7.74;ReadPosRankSum=-1.397;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:415,0,1279 -chr1 79284 . A T 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.956;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-4.938;QD=8.83;ReadPosRankSum=1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:452,0,1222 -chr1 79288 . G C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=48;Dels=0.00;FS=2.747;HaplotypeScore=25.1292;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-5.205;QD=8.68;ReadPosRankSum=1.690;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:445,0,1219 -chr1 79300 . T A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-4.876;QD=8.74;ReadPosRankSum=1.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,14:44:99:413,0,1090 -chr1 79321 . G C 581.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.836;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.16;MQ0=0;MQRankSum=-4.816;QD=15.72;ReadPosRankSum=-0.137;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:610,0,654 -chr1 79322 . C A 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.35;MQ0=0;QD=35.79;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0 -chr1 79337 . G A 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.043;DP=33;Dels=0.00;FS=3.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-4.610;QD=14.14;ReadPosRankSum=1.392;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:495,0,617 -chr1 79397 . C A 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.587;DP=32;Dels=0.00;FS=32.017;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-4.602;QD=9.12;ReadPosRankSum=-2.420;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,11:32:99:320,0,754 -chr1 79404 . T A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.453;DP=40;Dels=0.00;FS=20.081;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.252;QD=10.74;ReadPosRankSum=-1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:458,0,853 -chr1 79408 . T A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.460;DP=42;Dels=0.00;FS=18.695;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.17;MQ0=0;MQRankSum=-4.894;QD=11.90;ReadPosRankSum=-1.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:528,0,853 -chr1 79425 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.446;DP=44;Dels=0.00;FS=12.871;HaplotypeScore=3.5215;MLEAC=1;MLEAF=0.500;MQ=56.34;MQ0=0;MQRankSum=-3.990;QD=9.90;ReadPosRankSum=1.522;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,15:44:99:464,0,918 -chr1 79451 . G A 406.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.625;DP=45;Dels=0.00;FS=2.772;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.017;QD=9.04;ReadPosRankSum=1.361;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:435,0,1059 -chr1 79452 . A T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.469;DP=46;Dels=0.00;FS=2.785;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=-1.218;QD=9.36;ReadPosRankSum=1.148;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:459,0,1031 -chr1 79468 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-0.623;QD=14.00;ReadPosRankSum=-0.748;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:700,0,913 -chr1 79478 . G C 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=1.6648;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.471;QD=16.94;ReadPosRankSum=-1.753;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:926,0,881 -chr1 79598 . C T 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.841;DP=38;Dels=0.00;FS=9.653;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=0;MQRankSum=-3.061;QD=4.23;ReadPosRankSum=-0.877;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,8:38:99:189,0,1018 -chr1 79615 . T C 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=23.6444;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.17;ReadPosRankSum=0.428;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:475,0,803 -chr1 79617 . T A 190.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=40;Dels=0.00;FS=9.975;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-4.200;QD=4.77;ReadPosRankSum=0.762;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,8:40:99:219,0,844 -chr1 79618 . G A 138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.167;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-3.364;QD=3.47;ReadPosRankSum=0.254;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,8:40:99:167,0,1124 -chr1 79619 . C T 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.201;DP=40;Dels=0.00;FS=4.786;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-5.315;QD=11.09;ReadPosRankSum=1.256;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:472,0,808 -chr1 79624 . C T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=37;Dels=0.00;FS=12.746;HaplotypeScore=31.2856;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.605;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,974 -chr1 79626 . G A 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.125;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.83;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:207,0,1010 -chr1 79627 . A G 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.531;DP=37;Dels=0.00;FS=13.178;HaplotypeScore=23.5003;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=0;MQRankSum=-3.007;QD=4.86;ReadPosRankSum=1.900;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:208,0,1015 -chr1 79640 . C T 478.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.230;DP=51;Dels=0.00;FS=14.590;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-1.369;QD=9.39;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,17:51:99:507,0,1160 -chr1 79641 . G A 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=51;Dels=0.00;FS=3.858;HaplotypeScore=7.9961;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-3.463;QD=1.92;ReadPosRankSum=3.189;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:44,7:51:99:126,0,1543 -chr1 79670 . A G 688.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.536;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=-3.131;QD=14.97;ReadPosRankSum=1.235;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:717,0,801 -chr1 79675 . C T 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=2.704;HaplotypeScore=18.9737;MLEAC=1;MLEAF=0.500;MQ=55.22;MQ0=0;MQRankSum=-2.223;QD=15.51;ReadPosRankSum=0.765;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:695,0,699 -chr1 79697 . C A 978.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=24.70;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1007,78,0 -chr1 79745 . C G 1250.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=25.03;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1279,93,0 -chr1 79753 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.941;DP=37;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=0.411;QD=13.21;ReadPosRankSum=0.290;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:517,0,675 -chr1 79807 . C T 1019.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=7.7317;MLEAC=2;MLEAF=1.00;MQ=56.83;MQ0=0;QD=31.02;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1048,81,0 -chr1 79827 . C T 1289.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.78;MQ0=0;QD=35.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1318,99,0 -chr1 79840 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.767;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.127;QD=12.11;ReadPosRankSum=0.055;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:428,0,660 -chr1 79842 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.603;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=1.492;QD=20.75;ReadPosRankSum=-0.608;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:713,0,391 -chr1 79860 . G A 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.431;DP=38;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.839;QD=14.44;ReadPosRankSum=0.000;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:577,0,643 -chr1 80003 . A T 1616.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=28.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1645,123,0 -chr1 80017 . T A 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.877;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=0.458;QD=12.63;ReadPosRankSum=0.340;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:508,0,721 -chr1 80041 . T C 415.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.861;DP=37;Dels=0.00;FS=2.846;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.611;QD=11.24;ReadPosRankSum=-1.174;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:444,0,776 -chr1 80045 . G C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.955;DP=36;Dels=0.00;FS=1.366;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.811;QD=21.47;ReadPosRankSum=1.548;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,23:36:99:801,0,403 -chr1 80079 . G C 459.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.802;DP=36;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.481;QD=12.77;ReadPosRankSum=-2.952;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:488,0,737 -chr1 80117 . C T 1871.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1900,141,0 -chr1 80171 . A G 1589.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=19.9948;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=31.59;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1618,120,0 -chr1 80184 . G A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.229;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.084;QD=20.44;ReadPosRankSum=-1.173;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:846,0,495 -chr1 80244 . T C 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.038;DP=32;Dels=0.00;FS=7.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.62;MQ0=0;MQRankSum=-3.927;QD=16.96;ReadPosRankSum=1.888;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,17:32:99:571,0,493 -chr1 80416 . C A 796.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.16;MQ0=0;QD=33.46;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:825,63,0 -chr1 80710 . A G 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.494;DP=36;Dels=0.00;FS=5.334;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-1.350;QD=10.69;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:413,0,777 -chr1 80861 . C T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=39;Dels=0.00;FS=2.826;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.328;QD=19.05;ReadPosRankSum=1.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:771,0,477 -chr1 80867 . T C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.071;DP=39;Dels=0.00;FS=2.869;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.827;QD=16.40;ReadPosRankSum=1.374;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,22:39:99:668,0,541 -chr1 80925 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.311;DP=44;Dels=0.00;FS=22.159;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=0.041;QD=7.20;ReadPosRankSum=0.203;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:345,0,1053 -chr1 80926 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.372;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-0.744;QD=6.37;ReadPosRankSum=0.200;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:302,0,1088 -chr1 80927 . G A 269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=43;Dels=0.00;FS=19.771;HaplotypeScore=1.3670;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=0.057;QD=6.27;ReadPosRankSum=0.372;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,12:43:99:298,0,1101 -chr1 80933 . T G 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=45;Dels=0.00;FS=23.434;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-1.225;QD=7.17;ReadPosRankSum=0.856;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,13:45:99:351,0,1105 -chr1 80959 . T A 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.398;DP=45;Dels=0.00;FS=5.002;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=1;MQRankSum=0.940;QD=10.44;ReadPosRankSum=-0.121;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:498,0,944 -chr1 80967 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=44;Dels=0.00;FS=5.002;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=1;MQRankSum=0.490;QD=11.29;ReadPosRankSum=0.666;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,17:44:99:525,0,924 -chr1 81012 . C G 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=40;Dels=0.00;FS=4.442;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.019;QD=17.52;ReadPosRankSum=1.672;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:729,0,588 -chr1 81069 . C A 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.275;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.919;QD=12.97;ReadPosRankSum=0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:599,0,905 -chr1 81071 . T C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=44;Dels=0.00;FS=23.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.373;QD=12.54;ReadPosRankSum=0.060;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:580,0,911 -chr1 81072 . C G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.097;DP=45;Dels=0.00;FS=20.102;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.286;QD=12.66;ReadPosRankSum=-0.081;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,18:45:99:598,0,942 -chr1 81095 . C G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.970;DP=57;Dels=0.00;FS=23.054;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.781;QD=8.77;ReadPosRankSum=-1.073;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:39,18:57:99:528,0,1396 -chr1 81130 . T G 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.726;QD=8.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:440,0,1117 -chr1 81131 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-1.523;QD=8.78;ReadPosRankSum=0.422;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:432,0,1127 -chr1 81133 . T C 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.253;DP=45;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=-0.951;QD=9.33;ReadPosRankSum=0.349;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,15:45:99:448,0,1081 -chr1 81169 . A G 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.374;DP=49;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.172;QD=13.10;ReadPosRankSum=2.091;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:670,0,987 -chr1 81178 . C A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.881;DP=50;Dels=0.00;FS=8.297;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.71;MQ0=0;MQRankSum=-3.555;QD=11.28;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:592,0,991 -chr1 81185 . G A 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.606;DP=41;Dels=0.00;FS=12.377;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.19;MQ0=0;MQRankSum=-3.568;QD=11.26;ReadPosRankSum=1.403;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:490,0,818 -chr1 81268 . T C 1503.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1532,114,0 -chr1 81303 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.18;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1707,126,0 -chr1 81317 . C T 1738.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=59.35;MQ0=0;QD=33.51;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1767,132,0 -chr1 81331 . A C 1662.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=2.3989;MLEAC=2;MLEAF=1.00;MQ=59.33;MQ0=0;QD=37.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1691,129,0 -chr1 81371 . G A 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.908;DP=48;Dels=0.00;FS=4.645;HaplotypeScore=1.9957;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.473;QD=6.60;ReadPosRankSum=-2.001;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,16:48:99:345,0,1127 -chr1 81408 . A G 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=53;Dels=0.00;FS=20.792;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.12;MQ0=0;MQRankSum=-4.943;QD=8.94;ReadPosRankSum=2.754;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:502,0,1182 -chr1 81418 . C T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.718;DP=50;Dels=0.00;FS=21.604;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=0;MQRankSum=-4.962;QD=9.28;ReadPosRankSum=2.375;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:492,0,1136 -chr1 81422 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.035;DP=48;Dels=0.00;FS=21.618;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=0;MQRankSum=5.281;QD=21.62;ReadPosRankSum=-2.242;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1066,0,457 -chr1 81453 . C A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-4.476;QD=8.15;ReadPosRankSum=0.442;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:403,0,1150 -chr1 81455 . G A 369.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.036;DP=46;Dels=0.00;FS=16.375;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.808;QD=8.04;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:398,0,1139 -chr1 81456 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.245;DP=47;Dels=0.00;FS=15.915;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-4.013;QD=8.02;ReadPosRankSum=0.384;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,14:47:99:405,0,1154 -chr1 81457 . G A 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.062;DP=46;Dels=0.00;FS=15.915;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=-3.617;QD=8.36;ReadPosRankSum=0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:413,0,1151 -chr1 81482 . G T 1236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.464;DP=50;Dels=0.00;FS=4.620;HaplotypeScore=1.7206;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=2.035;QD=24.74;ReadPosRankSum=0.265;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1265,0,325 -chr1 81533 . A G 1828.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.609;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;MQRankSum=2.352;QD=28.88;ReadPosRankSum=-0.619;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:2,48:50:99:1857,123,0 -chr1 81544 . A G 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.466;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8400;MLEAC=1;MLEAF=0.500;MQ=56.30;MQ0=0;MQRankSum=2.542;QD=8.41;ReadPosRankSum=-0.370;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:32,14:46:99:415,0,1040 -chr1 81580 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=43;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=1.644;QD=14.60;ReadPosRankSum=-2.471;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:656,0,776 -chr1 81581 . G A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=4.524;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=0.767;QD=15.18;ReadPosRankSum=-2.496;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:681,0,762 -chr1 81594 . G A 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.680;DP=41;Dels=0.00;FS=1.230;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-0.251;QD=19.53;ReadPosRankSum=1.919;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:829,0,565 -chr1 81600 . T G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.9968;MLEAC=1;MLEAF=0.500;MQ=56.66;MQ0=0;MQRankSum=-2.660;QD=16.65;ReadPosRankSum=2.588;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:744,0,706 -chr1 81603 . C G,T 1331.29 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=1.491;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.66;MQ0=0;MQRankSum=-0.443;QD=30.96;ReadPosRankSum=1.249;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/2:1,19,23:43:99:1506,809,783,668,0,633 -chr1 81634 . A G 2035.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.31;MQ0=0;QD=30.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2064,154,0 -chr1 81638 . C T 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.96;MQ0=0;MQRankSum=-2.108;QD=15.37;ReadPosRankSum=-1.219;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:843,0,879 -chr1 81650 . C T 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.645;DP=59;Dels=0.00;FS=0.989;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=1.677;QD=16.42;ReadPosRankSum=0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,31:59:99:997,0,893 -chr1 81655 . A T 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=50.82;MQ0=1;MQRankSum=-1.189;QD=14.60;ReadPosRankSum=-0.497;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:846,0,959 -chr1 81660 . C G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.26;MQ0=1;MQRankSum=-1.272;QD=14.65;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:834,0,917 -chr1 81676 . T A 1209.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.535;DP=37;Dels=0.03;FS=3.136;HaplotypeScore=2.9325;MLEAC=2;MLEAF=1.00;MQ=45.14;MQ0=1;MQRankSum=-1.733;QD=32.70;ReadPosRankSum=1.634;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:65:1238,65,0 -chr1 81684 . T C 421.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.407;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.850;QD=11.40;ReadPosRankSum=1.572;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:450,0,653 -chr1 81688 . G A 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=37;Dels=0.00;FS=3.014;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.14;MQ0=1;MQRankSum=-3.947;QD=10.94;ReadPosRankSum=2.054;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:433,0,686 -chr1 81689 . T C 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=36;Dels=0.00;FS=2.958;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=1;MQRankSum=-3.750;QD=10.77;ReadPosRankSum=1.950;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:416,0,612 -chr1 81693 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.747;DP=38;Dels=0.00;FS=4.815;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.42;MQ0=1;MQRankSum=-3.581;QD=12.68;ReadPosRankSum=1.143;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:510,0,642 -chr1 81698 . T C 1307.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.87;MQ0=1;QD=30.86;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1336,105,0 -chr1 81707 . T C 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=47;Dels=0.00;FS=1.176;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.19;MQ0=1;MQRankSum=3.636;QD=11.87;ReadPosRankSum=-0.268;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:586,0,810 -chr1 81724 . T C 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.003;DP=44;Dels=0.00;FS=1.986;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.23;MQ0=1;MQRankSum=-0.378;QD=1.27;ReadPosRankSum=0.609;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:36,8:44:84:84,0,1258 -chr1 81739 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.481;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.48;MQ0=1;MQRankSum=-2.983;QD=19.66;ReadPosRankSum=0.454;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,28:42:99:854,0,419 -chr1 81751 . G A 1532.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.00;MQ0=0;QD=26.66;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1561,114,0 -chr1 81778 . A G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.868;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.08;MQ0=3;MQRankSum=0.964;QD=8.94;ReadPosRankSum=2.043;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:493,0,1122 -chr1 81794 . A C 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.402;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.07;MQ0=3;MQRankSum=0.029;QD=18.77;ReadPosRankSum=-0.488;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,30:54:99:1042,0,496 -chr1 81819 . A G 1360.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=45.13;MQ0=3;QD=31.65;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1389,105,0 -chr1 81854 . T C 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.60;MQ0=0;QD=30.67;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0 -chr1 81866 . G C 932.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.99;MQ0=0;QD=30.61;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:961,72,0 -chr1 81879 . A G 1084.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=46.18;MQ0=0;QD=34.99;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,30:31:84:1113,84,0 -chr1 81881 . G A 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=46.68;MQ0=0;MQRankSum=-0.097;QD=21.21;ReadPosRankSum=2.511;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:12,20:32:99:707,0,302 -chr1 81889 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.311;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=49.01;MQ0=0;MQRankSum=-0.851;QD=9.17;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:340,0,730 -chr1 81914 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.672;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.95;MQ0=0;MQRankSum=0.503;QD=17.79;ReadPosRankSum=-3.004;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,22:40:99:740,0,520 -chr1 81927 . C T 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.72;MQ0=0;QD=28.57;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,123,0 -chr1 81935 . A T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.440;DP=43;Dels=0.00;FS=1.237;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.74;MQ0=0;MQRankSum=-0.335;QD=12.44;ReadPosRankSum=1.279;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,17:43:99:563,0,831 -chr1 81947 . T A 1397.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.54;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1426,108,0 -chr1 81948 . G C 1380.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=31.38;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1409,105,0 -chr1 81951 . T C 1385.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.24;MQ0=0;QD=25.32;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,37:38:99:1414,105,0 -chr1 81995 . G A 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.114;QD=12.73;ReadPosRankSum=0.458;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:512,0,740 -chr1 82003 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.877;QD=9.37;ReadPosRankSum=3.261;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:375,0,858 -chr1 82004 . A G 351.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.910;QD=9.51;ReadPosRankSum=3.326;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:380,0,857 -chr1 82005 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.190;DP=37;Dels=0.00;FS=1.392;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-3.358;QD=9.53;ReadPosRankSum=3.293;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,12:37:99:381,0,863 -chr1 82009 . T C 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.836;DP=36;Dels=0.00;FS=3.018;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-3.574;QD=10.05;ReadPosRankSum=2.970;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:390,0,731 -chr1 82011 . G C 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.763;DP=35;Dels=0.00;FS=1.421;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.35;MQ0=0;MQRankSum=-3.736;QD=10.42;ReadPosRankSum=2.763;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:393,0,756 -chr1 82025 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.275;DP=40;Dels=0.00;FS=4.364;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.59;MQ0=0;MQRankSum=-4.604;QD=16.92;ReadPosRankSum=0.244;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:705,0,617 -chr1 82036 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.824;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.13;MQ0=0;MQRankSum=-4.538;QD=19.31;ReadPosRankSum=-0.103;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:762,0,463 -chr1 82050 . C T 743.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.144;DP=35;Dels=0.00;FS=10.665;HaplotypeScore=49.2919;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-4.080;QD=21.25;ReadPosRankSum=-1.280;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,22:35:99:772,0,401 -chr1 82064 . T C 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.141;DP=31;Dels=0.00;FS=8.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-4.343;QD=19.41;ReadPosRankSum=1.501;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,18:31:99:630,0,427 -chr1 82080 . C T 1151.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1180,87,0 -chr1 82081 . C T 1143.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1172,87,0 -chr1 82082 . A G 1146.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=28.52;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1175,87,0 -chr1 82096 . T A 1128.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.09;MQ0=0;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1157,93,0 -chr1 82126 . G A 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.199;DP=37;Dels=0.00;FS=3.009;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-1.977;QD=16.02;ReadPosRankSum=-0.169;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:621,0,501 -chr1 82156 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.862;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-0.011;QD=14.34;ReadPosRankSum=0.990;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:702,0,724 -chr1 82158 . T A 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=0.352;QD=13.81;ReadPosRankSum=1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:705,0,824 -chr1 82161 . C G 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.131;QD=16.63;ReadPosRankSum=-1.578;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:843,0,731 -chr1 82181 . T C 1791.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.84;MQ0=0;QD=33.17;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:51:99:1820,138,0 -chr1 82212 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.113;DP=55;Dels=0.00;FS=1.075;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.113;QD=17.12;ReadPosRankSum=0.788;EFF=UPSTREAM(MODIFIER||||Cc01g00050|mRNA||GSCOCT00012435001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:970,0,654 -chr1 82270 . A C 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=48;Dels=0.00;FS=7.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=-0.969;QD=11.54;ReadPosRankSum=0.224;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,18:48:99:582,0,945 -chr1 82315 . C T 1935.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.36;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1964,150,0 -chr1 82352 . G C 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.780;QD=14.59;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:787,0,872 -chr1 82367 . G A 907.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.433;DP=60;Dels=0.00;FS=0.988;HaplotypeScore=2.7001;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.509;QD=15.13;ReadPosRankSum=-0.630;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,28:60:99:936,0,959 -chr1 82385 . G T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.579;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=81.3181;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.230;QD=0.21;ReadPosRankSum=-3.378;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:55,6:62:41:41,0,1896 -chr1 82434 . T C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.253;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.61;MQ0=0;MQRankSum=-1.087;QD=14.15;ReadPosRankSum=1.842;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:52:99:764,0,957 -chr1 82440 . G C 859.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=49;Dels=0.00;FS=1.092;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=0.955;QD=17.55;ReadPosRankSum=-1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:888,0,719 -chr1 82482 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=1.064;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=-1.757;QD=14.52;ReadPosRankSum=-1.194;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,24:51:99:769,0,899 -chr1 82487 . T A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=50;Dels=0.00;FS=1.101;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=1;MQRankSum=-0.850;QD=15.32;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:794,0,848 -chr1 82613 . T C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-1.183;QD=12.44;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,964 -chr1 82614 . A G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=1;MQRankSum=-0.539;QD=12.44;ReadPosRankSum=0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:675,0,934 -chr1 82616 . G C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=1;MQRankSum=-2.266;QD=11.86;ReadPosRankSum=0.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,23:53:99:657,0,973 -chr1 82648 . A G 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.315;DP=45;Dels=0.00;FS=5.254;HaplotypeScore=6.9393;MLEAC=1;MLEAF=0.500;MQ=52.78;MQ0=3;MQRankSum=-4.177;QD=3.93;ReadPosRankSum=-0.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,12:45:99:205,0,1095 -chr1 82650 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.065;DP=43;Dels=0.00;FS=5.772;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=3;MQRankSum=-4.146;QD=2.51;ReadPosRankSum=0.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:33,10:43:99:136,0,1090 -chr1 82656 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=3;MQRankSum=4.699;QD=22.29;ReadPosRankSum=0.901;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,27:41:99:942,0,189 -chr1 82658 . T G 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.383;DP=42;Dels=0.00;FS=3.333;HaplotypeScore=4.9694;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=3;MQRankSum=-4.050;QD=2.66;ReadPosRankSum=-1.617;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:140,0,1017 -chr1 82668 . A C 1112.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.88;MQ0=3;QD=30.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,36:36:90:1141,90,0 -chr1 82690 . G T 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=40;Dels=0.00;FS=5.301;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=1;MQRankSum=-2.041;QD=8.64;ReadPosRankSum=-2.488;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:374,0,898 -chr1 82792 . T A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.636;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=0.289;QD=19.32;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:743,0,494 -chr1 82795 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.114;QD=11.86;ReadPosRankSum=1.314;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:467,0,769 -chr1 82814 . G A 330.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.079;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.958;QD=8.48;ReadPosRankSum=0.707;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:359,0,871 -chr1 82877 . T C 1238.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.481;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.5775;MLEAC=2;MLEAF=1.00;MQ=59.05;MQ0=0;MQRankSum=0.385;QD=34.41;ReadPosRankSum=1.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,35:36:67:1267,67,0 -chr1 82878 . C T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=36;Dels=0.00;FS=2.928;HaplotypeScore=2.5775;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.111;QD=15.72;ReadPosRankSum=-2.244;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:594,0,499 -chr1 82887 . T C 410.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.631;DP=36;Dels=0.00;FS=1.344;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.257;QD=11.41;ReadPosRankSum=2.246;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:439,0,686 -chr1 82936 . A T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.839;DP=28;Dels=0.00;FS=10.544;HaplotypeScore=8.7318;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.839;QD=7.03;ReadPosRankSum=1.551;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:20,8:28:99:225,0,697 -chr1 82937 . G A 1059.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=7.7653;MLEAC=2;MLEAF=1.00;MQ=58.58;MQ0=0;QD=29.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1088,84,0 -chr1 82946 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.977;DP=34;Dels=0.00;FS=20.808;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.942;QD=14.52;ReadPosRankSum=1.353;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:522,0,487 -chr1 82981 . A C 1508.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=33.7746;MLEAC=2;MLEAF=1.00;MQ=57.89;MQ0=0;QD=32.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1537,117,0 -chr1 83013 . A T 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=48;Dels=0.00;FS=46.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.792;QD=11.70;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:590,0,915 -chr1 83024 . A G 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=42.658;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.86;MQ0=1;MQRankSum=-2.045;QD=10.57;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:472,0,804 -chr1 83033 . A G 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.157;DP=39;Dels=0.00;FS=31.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.45;MQ0=1;MQRankSum=-3.862;QD=6.79;ReadPosRankSum=2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,12:39:99:293,0,843 -chr1 83044 . C T 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.349;DP=37;Dels=0.00;FS=27.416;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=1;MQRankSum=-4.362;QD=6.40;ReadPosRankSum=2.278;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,11:37:99:265,0,839 -chr1 83083 . T C 872.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=27.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,23:23:66:901,66,0 -chr1 83091 . A G 855.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=28.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:884,66,0 -chr1 83162 . C T 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9867;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UPSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:682,51,0 -chr1 83337 . A C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.588;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.48;MQ0=1;MQRankSum=-2.646;QD=10.34;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:9,8:17:99:204,0,330 -chr1 83398 . G T 94.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.192;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=47.10;MQ0=1;MQRankSum=0.778;QD=6.32;ReadPosRankSum=2.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83279_83401) GT:AD:DP:GQ:PL 0/1:11,4:15:99:123,0,311 -chr1 83404 . G A 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9845;MLEAC=1;MLEAF=0.500;MQ=45.65;MQ0=1;MQRankSum=-1.157;QD=4.34;ReadPosRankSum=-1.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:9,5:14:89:89,0,317 -chr1 83532 . G T 196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.264;DP=30;Dels=0.00;FS=5.946;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.56;MQ0=2;MQRankSum=-3.188;QD=6.56;ReadPosRankSum=1.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_5_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83509_83569) GT:AD:DP:GQ:PL 0/1:18,12:30:99:225,0,597 -chr1 83605 . A G 62.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=24;Dels=0.00;FS=7.799;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.85;MQ0=0;MQRankSum=-2.167;QD=2.62;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:18,6:24:91:91,0,606 -chr1 83629 . T G 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;DP=19;Dels=0.00;FS=4.713;HaplotypeScore=1.7880;MLEAC=1;MLEAF=0.500;MQ=41.28;MQ0=0;MQRankSum=-2.268;QD=2.04;ReadPosRankSum=-1.991;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:14,5:19:67:67,0,465 -chr1 83691 . T G 192.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=35;Dels=0.00;FS=8.175;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=42.05;MQ0=0;MQRankSum=-0.020;QD=5.51;ReadPosRankSum=-1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,8:35:99:221,0,947 -chr1 83704 . C T 1319.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.35;MQ0=1;QD=32.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1348,102,0 -chr1 83837 . G A 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.636;DP=30;Dels=0.00;FS=14.239;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.28;MQ0=2;MQRankSum=-3.738;QD=5.23;ReadPosRankSum=-0.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_83730_84064) GT:AD:DP:GQ:PL 0/1:20,10:30:99:185,0,667 -chr1 84090 . G T 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.235;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.8663;MLEAC=1;MLEAF=0.500;MQ=55.21;MQ0=0;MQRankSum=0.440;QD=13.44;ReadPosRankSum=-0.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:539,0,732 -chr1 84156 . C T 1240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.552;DP=56;Dels=0.00;FS=6.157;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-1.818;QD=22.16;ReadPosRankSum=0.463;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:17,39:56:99:1269,0,542 -chr1 84243 . G A 1544.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1573,120,0 -chr1 84266 . A C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.232;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.392;QD=11.12;ReadPosRankSum=-0.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:484,0,881 -chr1 84467 . C A 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.341;DP=48;Dels=0.00;FS=5.874;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.321;QD=14.87;ReadPosRankSum=1.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,877 -chr1 84548 . G T 1008.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=61;Dels=0.00;FS=3.670;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=2.402;QD=16.54;ReadPosRankSum=1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:1037,0,988 -chr1 84596 . C T 2308.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.50;MQ0=0;QD=26.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2337,178,0 -chr1 84601 . C T 1275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.270;DP=65;Dels=0.00;FS=2.135;HaplotypeScore=1.9664;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.172;QD=19.63;ReadPosRankSum=-0.797;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:26,39:65:99:1304,0,773 -chr1 84805 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.168;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.505;QD=19.46;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S113|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,30:50:99:1001,0,641 -chr1 84858 . A C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.541;DP=42;Dels=0.00;FS=8.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.322;QD=16.95;ReadPosRankSum=1.876;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aCa|K131T|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:20,22:42:99:740,0,673 -chr1 84868 . C T 1590.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=28.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V134|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1619,123,0 -chr1 84880 . G A 1477.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L138|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1506,114,0 -chr1 84886 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.437;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.521;QD=14.58;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V140|Cc01g00060|mRNA||GSCOCT00012434001|Exon_chr1_84706_84991) GT:AD:DP:GQ:PL 0/1:21,18:39:99:597,0,712 -chr1 85016 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.347;QD=17.45;ReadPosRankSum=-0.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:988,0,847 -chr1 85055 . A G 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.265;DP=59;Dels=0.00;FS=7.450;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.599;QD=16.34;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:992,0,999 -chr1 85064 . T C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=54;Dels=0.00;FS=3.998;HaplotypeScore=2.4875;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.488;QD=14.61;ReadPosRankSum=0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:817,0,887 -chr1 85114 . A G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.117;DP=47;Dels=0.00;FS=2.488;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=-1.011;QD=16.40;ReadPosRankSum=-0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:799,0,742 -chr1 85206 . A G 805.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=-0.412;QD=14.65;ReadPosRankSum=-1.338;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:834,0,932 -chr1 85257 . C T 2136.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=60.19;MQ0=0;QD=25.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,55:56:99:2165,163,0 -chr1 85259 . T C 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.311;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=26.7919;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.070;QD=17.50;ReadPosRankSum=0.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,924 -chr1 85307 . G T 2188.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=23.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),INTRON(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2217,166,0 -chr1 85388 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=56;Dels=0.00;FS=2.338;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.972;QD=17.91;ReadPosRankSum=2.060;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1031,0,826 -chr1 85403 . A G 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.803;DP=53;Dels=0.00;FS=3.822;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.045;QD=20.00;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1088,0,713 -chr1 85446 . T G 2073.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2102,157,0 -chr1 85454 . C A 1996.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2025,150,0 -chr1 85460 . A C 857.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.217;DP=48;Dels=0.00;FS=4.180;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=17.87;ReadPosRankSum=-2.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:886,0,741 -chr1 85552 . A C 1841.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.742;QD=31.35;ReadPosRankSum=-0.035;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 1/1:1,48:49:99:1870,141,0 -chr1 85658 . T A 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.903;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.2566;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.933;QD=12.97;ReadPosRankSum=2.850;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:560,0,680 -chr1 85709 . T A 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=30;Dels=0.00;FS=3.431;HaplotypeScore=15.9845;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-0.209;QD=17.76;ReadPosRankSum=1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:561,0,349 -chr1 85779 . A G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.928;DP=32;Dels=0.00;FS=10.207;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.042;QD=6.27;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,9:32:99:229,0,795 -chr1 85837 . A T 1322.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1351,102,0 -chr1 85866 . G A 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.539;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=15.4975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.788;QD=15.93;ReadPosRankSum=-1.286;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:506,0,472 -chr1 85928 . G A 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.190;DP=31;Dels=0.00;FS=1.566;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.021;QD=22.54;ReadPosRankSum=1.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,21:31:99:727,0,300 -chr1 85964 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=32;Dels=0.00;FS=3.848;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.936;QD=26.59;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,24:32:99:879,0,222 -chr1 85983 . T C 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.457;QD=24.67;ReadPosRankSum=-0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:793,0,280 -chr1 85984 . A T 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.413;QD=24.19;ReadPosRankSum=-0.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:778,0,283 -chr1 86057 . T A 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.117;QD=16.34;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:796,0,802 -chr1 86096 . T C 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.383;DP=47;Dels=0.00;FS=6.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQ0=0;MQRankSum=1.171;QD=18.42;ReadPosRankSum=0.952;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:894,0,583 -chr1 86197 . A G 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.957;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.775;QD=15.83;ReadPosRankSum=1.413;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:614,0,592 -chr1 86283 . T G 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.233;DP=81;Dels=0.00;FS=11.183;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.22;MQ0=1;MQRankSum=-1.581;QD=7.98;ReadPosRankSum=-5.926;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:45,36:81:99:675,0,1045 -chr1 86295 . G A 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=1;MQRankSum=-0.694;QD=2.69;ReadPosRankSum=-1.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,17:79:99:241,0,1690 -chr1 86334 . C T 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=-1.600;QD=18.65;ReadPosRankSum=0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:942,0,629 -chr1 86368 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.611;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.010;QD=17.87;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:904,0,769 -chr1 86487 . C T 1135.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.006;DP=60;Dels=0.00;FS=3.617;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-2.588;QD=18.93;ReadPosRankSum=1.410;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1164,0,811 -chr1 86494 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.597;DP=62;Dels=0.00;FS=1.012;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.077;QD=11.83;ReadPosRankSum=-0.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:762,0,1311 -chr1 86710 . C T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.161;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;QD=15.58;ReadPosRankSum=-1.135;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:667,0,725 -chr1 86780 . T C 1962.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1991,150,0 -chr1 86783 . T C 814.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.254;DP=51;Dels=0.00;FS=1.083;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.98;ReadPosRankSum=0.141;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:843,0,891 -chr1 86812 . C G 2201.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=28.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2230,172,0 -chr1 86874 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.055;DP=46;Dels=0.00;FS=2.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.587;QD=18.63;ReadPosRankSum=0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,26:46:99:885,0,605 -chr1 86928 . A T 1814.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=28.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1843,138,0 -chr1 86945 . C T 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.551;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.651;QD=15.59;ReadPosRankSum=-1.292;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:792,0,917 -chr1 87016 . C T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.274;DP=53;Dels=0.00;FS=2.380;HaplotypeScore=46.7458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.134;QD=15.01;ReadPosRankSum=0.597;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:824,0,910 -chr1 87161 . A G 1557.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=15.2776;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1586,117,0 -chr1 87182 . A G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.190;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=65.7226;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.562;QD=16.77;ReadPosRankSum=-1.948;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:716,0,647 -chr1 87257 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.809;DP=42;Dels=0.00;FS=2.756;HaplotypeScore=3.9986;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.202;QD=14.71;ReadPosRankSum=-0.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:646,0,809 -chr1 87282 . C T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=11.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.581;QD=17.97;ReadPosRankSum=-0.708;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:783,0,641 -chr1 87399 . T A 662.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.840;DP=43;Dels=0.00;FS=4.388;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.426;QD=15.41;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),DOWNSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:691,0,818 -chr1 87964 . T C 1652.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=31.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R2079|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_87910_88146) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1681,126,0 -chr1 88214 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.856;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4710;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=1.316;QD=17.04;ReadPosRankSum=2.984;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,23:45:99:795,0,623 -chr1 88242 . A C 1458.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9734;MLEAC=2;MLEAF=1.00;MQ=59.07;MQ0=0;QD=31.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1487,111,0 -chr1 88243 . G A 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.274;DP=40;Dels=0.00;FS=2.817;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=0.465;QD=19.67;ReadPosRankSum=-2.818;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:815,0,487 -chr1 88460 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.222;DP=41;Dels=0.00;FS=4.561;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.874;QD=15.80;ReadPosRankSum=-0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:676,0,700 -chr1 88534 . T C 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.499;DP=50;Dels=0.00;FS=13.391;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=0.545;QD=14.54;ReadPosRankSum=-1.363;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1964|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_88510_88890) GT:AD:DP:GQ:PL 0/1:27,23:50:99:755,0,913 -chr1 88912 . A C 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.131;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-1.268;QD=13.31;ReadPosRankSum=-0.971;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:627,0,862 -chr1 88959 . C T 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.476;DP=56;Dels=0.00;FS=9.559;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=-0.590;QD=15.78;ReadPosRankSum=0.574;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:912,0,1002 -chr1 88961 . C G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=58;Dels=0.00;FS=11.723;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=0.661;QD=17.50;ReadPosRankSum=-0.521;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1043,0,950 -chr1 88987 . A G 2405.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=30.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2434,184,0 -chr1 89344 . G C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.526;DP=61;Dels=0.00;FS=5.322;HaplotypeScore=2.9937;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=1;MQRankSum=-0.052;QD=16.77;ReadPosRankSum=-0.304;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1051,0,895 -chr1 89418 . A T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.659;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=0.521;QD=18.45;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1793|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89391_89495) GT:AD:DP:GQ:PL 0/1:19,25:44:99:840,0,514 -chr1 89522 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.620;DP=45;Dels=0.00;FS=11.478;HaplotypeScore=103.5819;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.517;QD=13.15;ReadPosRankSum=-1.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:620,0,881 -chr1 89531 . A G 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=114.0798;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=1;MQRankSum=-0.041;QD=1.14;ReadPosRankSum=-1.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,9:50:85:85,0,1381 -chr1 89635 . T G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.207;DP=56;Dels=0.00;FS=7.797;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.737;QD=18.12;ReadPosRankSum=0.339;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Cat|N1762H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1043,0,749 -chr1 89720 . T C 1891.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.88;MQ0=0;QD=30.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q1733|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1920,144,0 -chr1 89745 . A G 1759.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M1725T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1788,135,0 -chr1 89792 . G A 2016.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V1709|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_89618_89905) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2045,159,0 -chr1 89954 . T C 1227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.449;DP=64;Dels=0.00;FS=2.069;HaplotypeScore=2.6551;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.884;QD=19.18;ReadPosRankSum=1.359;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,37:64:99:1256,0,894 -chr1 90005 . A G 1150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=58;Dels=0.00;FS=3.623;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.523;QD=19.84;ReadPosRankSum=0.502;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1179,0,842 -chr1 90289 . C T 1801.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A1597T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1830,141,0 -chr1 90303 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.343;DP=46;Dels=0.00;FS=5.030;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.388;QD=13.49;ReadPosRankSum=0.720;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I1592T|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_90065_90416) GT:AD:DP:GQ:PL 0/1:26,20:46:99:649,0,883 -chr1 90520 . C T 496.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=7.375;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-0.693;QD=23.66;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:18:525,0,18 -chr1 90521 . C T 488.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.441;DP=21;Dels=0.00;FS=8.316;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=56.05;MQ0=1;MQRankSum=-1.197;QD=23.24;ReadPosRankSum=2.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:3,18:21:12:516,0,12 -chr1 90525 . C T 577.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=43.4929;MLEAC=2;MLEAF=1.00;MQ=55.62;MQ0=1;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,18:19:51:606,51,0 -chr1 90567 . G A 583.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=15.0334;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=34.34;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:612,48,0 -chr1 90588 . A G 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.589;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=1.768;QD=8.06;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:262,0,686 -chr1 90590 . T C 1086.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=3.1875;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1115,84,0 -chr1 90591 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.430;DP=30;Dels=0.00;FS=1.987;HaplotypeScore=3.1875;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=0.387;QD=21.59;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00060|mRNA||GSCOCT00012434001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,19:30:99:676,0,304 -chr1 90977 . G T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.999;DP=45;Dels=0.00;FS=4.453;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=-0.857;QD=13.48;ReadPosRankSum=-1.633;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:635,0,845 -chr1 90985 . T C 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=47;Dels=0.00;FS=4.385;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=1.160;QD=12.29;ReadPosRankSum=0.228;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:606,0,909 -chr1 91106 . T C 1596.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.51;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1625,120,0 -chr1 91526 . G C 509.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=2.865;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.065;QD=12.14;ReadPosRankSum=-0.842;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:538,0,882 -chr1 91614 . A C 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.445;QD=17.90;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:1013,0,821 -chr1 91617 . T A 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.797;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.288;QD=18.19;ReadPosRankSum=1.043;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1047,0,834 -chr1 91650 . C A 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.554;DP=42;Dels=0.00;FS=1.831;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.893;QD=0.88;ReadPosRankSum=-2.796;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caG/caT|Q1346H|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:37,5:42:65:65,0,1325 -chr1 91722 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.741;DP=50;Dels=0.00;FS=4.367;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.000;QD=10.08;ReadPosRankSum=0.676;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggA|G1322|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91645_91760) GT:AD:DP:GQ:PL 0/1:33,17:50:99:532,0,996 -chr1 91774 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.165;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.765;QD=13.25;ReadPosRankSum=-1.230;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:823,0,1195 -chr1 91973 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.239;QD=15.71;ReadPosRankSum=-1.901;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A1269|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:20,22:42:99:688,0,658 -chr1 91976 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.609;DP=46;Dels=0.00;FS=6.133;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.277;QD=12.97;ReadPosRankSum=2.338;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C1268|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:26,20:46:99:625,0,846 -chr1 92011 . A C 1093.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=56;Dels=0.00;FS=7.262;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.813;QD=19.53;ReadPosRankSum=1.995;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S1257A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1122,0,788 -chr1 92186 . G A 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.573;DP=35;Dels=0.00;FS=5.368;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.083;QD=16.51;ReadPosRankSum=-0.083;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S1198|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_91853_92230) GT:AD:DP:GQ:PL 0/1:16,19:35:99:606,0,541 -chr1 92279 . A G 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=41;Dels=0.00;FS=6.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.090;QD=18.92;ReadPosRankSum=0.775;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:804,0,592 -chr1 92300 . C G 1407.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.55;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1436,108,0 -chr1 92325 . T C 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.810;DP=44;Dels=0.00;FS=6.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.692;QD=16.40;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:750,0,740 -chr1 92362 . A G 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.701;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.214;QD=14.48;ReadPosRankSum=0.097;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:752,0,920 -chr1 92420 . A C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=46;Dels=0.00;FS=6.635;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.404;QD=10.39;ReadPosRankSum=0.519;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,16:46:99:506,0,1054 -chr1 92426 . C T 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=42;Dels=0.00;FS=9.664;HaplotypeScore=12.9977;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.680;QD=9.99;ReadPosRankSum=0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:448,0,1021 -chr1 92459 . G A 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=41;Dels=0.00;FS=2.858;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.521;QD=11.87;ReadPosRankSum=-0.174;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:515,0,892 -chr1 92463 . G A 558.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=43;Dels=0.00;FS=2.743;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.406;QD=12.99;ReadPosRankSum=-0.529;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:587,0,880 -chr1 92529 . T A 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=1.253;QD=16.77;ReadPosRankSum=0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:984,0,918 -chr1 92647 . A G 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.840;QD=9.40;ReadPosRankSum=0.680;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:423,0,976 -chr1 92758 . T A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.338;DP=53;Dels=0.00;FS=3.955;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.930;QD=10.18;ReadPosRankSum=1.380;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:568,0,1136 -chr1 92787 . A G 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=68;Dels=0.00;FS=3.335;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=0;MQRankSum=0.142;QD=13.50;ReadPosRankSum=0.377;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,30:68:99:946,0,1223 -chr1 92856 . G C 2242.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.58;MQ0=1;QD=29.11;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2271,172,0 -chr1 92881 . G T 1034.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.472;DP=57;Dels=0.00;FS=9.783;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=1;MQRankSum=1.051;QD=18.15;ReadPosRankSum=-0.803;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1063,0,740 -chr1 92887 . A G 874.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.408;DP=56;Dels=0.00;FS=2.506;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=1;MQRankSum=0.126;QD=15.62;ReadPosRankSum=0.008;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:903,0,715 -chr1 92906 . T C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.983;DP=64;Dels=0.00;FS=2.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=2;MQRankSum=1.450;QD=13.48;ReadPosRankSum=0.728;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,30:64:99:891,0,1127 -chr1 93051 . G C 1300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=67;Dels=0.00;FS=0.945;HaplotypeScore=2.9966;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.436;QD=19.41;ReadPosRankSum=-0.576;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,38:67:99:1329,0,959 -chr1 93126 . T G 1178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.349;QD=21.83;ReadPosRankSum=-0.099;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1207,0,605 -chr1 93129 . C T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.066;DP=54;Dels=0.00;FS=5.804;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=0.905;QD=22.01;ReadPosRankSum=0.242;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1217,0,604 -chr1 93143 . G C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.109;DP=51;Dels=0.00;FS=2.448;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.287;QD=11.86;ReadPosRankSum=-1.357;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:51:99:633,0,1071 -chr1 93221 . G C 960.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=59;Dels=0.00;FS=0.998;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.371;QD=16.28;ReadPosRankSum=0.387;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:989,0,965 -chr1 93235 . G A 1138.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=63;Dels=0.00;FS=2.089;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=1.110;QD=18.08;ReadPosRankSum=-0.779;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,34:63:99:1167,0,900 -chr1 93270 . T C 2111.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.10;MQ0=0;QD=30.32;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2140,160,0 -chr1 93280 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.487;DP=52;Dels=0.00;FS=4.010;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.194;QD=13.11;ReadPosRankSum=3.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:710,0,1066 -chr1 93282 . G C 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.616;DP=49;Dels=0.00;FS=4.055;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.636;QD=14.02;ReadPosRankSum=3.222;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:715,0,961 -chr1 93283 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.394;DP=50;Dels=0.00;FS=2.447;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.10;MQ0=0;MQRankSum=-1.065;QD=14.36;ReadPosRankSum=2.746;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:746,0,976 -chr1 93306 . A T 2098.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.20;MQ0=0;QD=32.01;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2127,160,0 -chr1 93333 . C T 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.258;DP=53;Dels=0.00;FS=5.940;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=0.454;QD=15.32;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:840,0,924 -chr1 93352 . T C 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=57;Dels=0.00;FS=11.817;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.745;QD=15.03;ReadPosRankSum=1.402;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:885,0,1090 -chr1 93358 . A C 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.132;DP=56;Dels=0.00;FS=12.410;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.19;MQ0=0;MQRankSum=-0.231;QD=14.50;ReadPosRankSum=1.615;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,1093 -chr1 93504 . G A 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.233;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.560;QD=16.00;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,29:59:99:972,0,962 -chr1 93508 . G C 2130.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=2.9988;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.10;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2159,163,0 -chr1 93567 . A G 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=59;Dels=0.00;FS=2.347;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.177;QD=9.56;ReadPosRankSum=0.344;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,20:59:99:592,0,1326 -chr1 93595 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=4.620;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.830;QD=7.95;ReadPosRankSum=-0.586;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,14:49:99:418,0,1282 -chr1 93676 . A G 942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.019;QD=17.14;ReadPosRankSum=1.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F1167|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93628_93699) GT:AD:DP:GQ:PL 0/1:27,28:55:99:971,0,908 -chr1 93754 . T A 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.413;DP=58;Dels=0.00;FS=5.597;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=11.58;ReadPosRankSum=-0.111;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,23:58:99:700,0,1216 -chr1 93879 . T C 1833.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.96;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1137|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1862,141,0 -chr1 93903 . G T 747.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.782;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.011;QD=16.62;ReadPosRankSum=-0.261;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I1129|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:22,23:45:99:776,0,668 -chr1 93906 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.482;DP=47;Dels=0.00;FS=6.054;HaplotypeScore=1.9830;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.098;QD=14.46;ReadPosRankSum=0.309;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K1128|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_93813_93975) GT:AD:DP:GQ:PL 0/1:25,22:47:99:708,0,860 -chr1 93998 . A G 2112.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=2.5774;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.68;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2141,163,0 -chr1 94001 . A G 893.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=53;Dels=0.00;FS=2.323;HaplotypeScore=1.5782;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.240;QD=16.86;ReadPosRankSum=0.827;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,27:53:99:922,0,890 -chr1 94020 . G C 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.912;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.331;QD=15.44;ReadPosRankSum=1.733;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:785,0,888 -chr1 94164 . A G 839.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.633;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.879;QD=15.00;ReadPosRankSum=-0.501;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y1084|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94102_94193) GT:AD:DP:GQ:PL 0/1:30,26:56:99:868,0,1033 -chr1 94307 . G A 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.017;DP=48;Dels=0.00;FS=1.133;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.403;QD=17.66;ReadPosRankSum=-0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:876,0,754 -chr1 94331 . G T 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.887;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.692;QD=15.95;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:714,0,748 -chr1 94476 . G T 1018.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.404;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=1;MQRankSum=0.350;QD=18.87;ReadPosRankSum=-1.498;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1047,0,739 -chr1 94499 . C T 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.740;DP=55;Dels=0.00;FS=1.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.531;QD=13.83;ReadPosRankSum=0.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:789,0,1061 -chr1 94679 . A G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.046;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.612;QD=15.70;ReadPosRankSum=-0.198;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1005|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94543_94708) GT:AD:DP:GQ:PL 0/1:26,25:51:99:829,0,859 -chr1 94743 . G A 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.225;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-1.258;QD=9.38;ReadPosRankSum=3.272;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:366,0,807 -chr1 94753 . A C 357.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.995;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.8896;MLEAC=1;MLEAF=0.500;MQ=61.17;MQ0=0;MQRankSum=-0.225;QD=9.94;ReadPosRankSum=0.898;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:386,0,718 -chr1 94840 . A C 753.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.135;DP=58;Dels=0.00;FS=0.999;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.272;QD=13.00;ReadPosRankSum=-0.455;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S985A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:33,25:58:99:782,0,1167 -chr1 94856 . C T 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.040;QD=18.01;ReadPosRankSum=0.523;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L979|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1055,0,767 -chr1 94898 . G A 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.088;DP=57;Dels=0.00;FS=2.219;HaplotypeScore=1.6649;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.679;QD=16.35;ReadPosRankSum=-2.038;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L965|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_94808_94919) GT:AD:DP:GQ:PL 0/1:27,30:57:99:960,0,917 -chr1 94963 . C A 867.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.638;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.668;QD=16.69;ReadPosRankSum=-0.503;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:896,0,874 -chr1 94973 . A T 2138.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2167,163,0 -chr1 95134 . T C 2154.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T933A|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95058_95208) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2183,169,0 -chr1 95594 . A G 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.180;DP=53;Dels=0.00;FS=5.738;HaplotypeScore=2.6552;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=0.085;QD=17.22;ReadPosRankSum=0.349;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G817|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_95323_95596) GT:AD:DP:GQ:PL 0/1:24,28:53:99:941,0,742 -chr1 95809 . G A 1511.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.57;MQ0=0;QD=34.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1540,114,0 -chr1 96016 . C T 1313.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.43;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1342,99,0 -chr1 96111 . A C 1249.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.76;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1278,96,0 -chr1 96124 . A G 1357.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.72;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1386,105,0 -chr1 96214 . A T 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.364;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.622;QD=15.04;ReadPosRankSum=0.321;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1036,0,1067 -chr1 96224 . G A 924.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.656;QD=15.16;ReadPosRankSum=-2.171;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,30:61:99:953,0,1050 -chr1 96308 . T C 2053.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.62;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2082,154,0 -chr1 96309 . A G 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.522;DP=54;Dels=0.00;FS=7.971;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.262;QD=13.66;ReadPosRankSum=-2.029;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:766,0,1037 -chr1 96335 . G T 1948.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;QD=30.44;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1977,147,0 -chr1 96360 . G A 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.447;DP=58;Dels=0.00;FS=3.832;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=1.081;QD=15.86;ReadPosRankSum=-0.864;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,883 -chr1 96399 . T G 905.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=51;Dels=0.00;FS=8.273;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=1.902;QD=17.76;ReadPosRankSum=1.618;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:934,0,788 -chr1 96448 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.536;DP=51;Dels=0.00;FS=4.093;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.121;QD=17.09;ReadPosRankSum=-1.479;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:900,0,792 -chr1 96485 . A T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.292;DP=44;Dels=0.00;FS=2.672;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=0.141;QD=15.77;ReadPosRankSum=0.987;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acA|T806|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:23,21:44:99:722,0,775 -chr1 96530 . G A 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.746;QD=18.04;ReadPosRankSum=0.526;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N791|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_96455_96617) GT:AD:DP:GQ:PL 0/1:19,24:43:99:804,0,602 -chr1 96637 . G A 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.628;QD=15.17;ReadPosRankSum=-1.798;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:741,0,788 -chr1 96789 . C T 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.380;DP=69;Dels=0.00;FS=0.918;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=1;MQRankSum=0.417;QD=15.65;ReadPosRankSum=1.436;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1108,0,1126 -chr1 96791 . T C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.571;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=1.110;QD=15.59;ReadPosRankSum=1.543;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:1057,0,1086 -chr1 96809 . C T 2747.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=1;QD=26.52;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2776,205,0 -chr1 96822 . T G 1272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=73;Dels=0.00;FS=1.969;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=1;MQRankSum=-0.475;QD=17.44;ReadPosRankSum=-0.328;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,40:73:99:1301,0,1128 -chr1 96868 . A T 1270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.180;DP=72;Dels=0.00;FS=7.826;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.65;MQ0=0;MQRankSum=0.620;QD=17.65;ReadPosRankSum=0.631;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1299,0,1177 -chr1 96880 . C T 1144.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.650;DP=65;Dels=0.00;FS=3.414;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.795;QD=17.61;ReadPosRankSum=-0.729;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1173,0,1062 -chr1 96881 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.233;DP=62;Dels=0.00;FS=4.010;HaplotypeScore=12.9967;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.752;QD=8.00;ReadPosRankSum=0.101;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,18:62:99:524,0,1555 -chr1 96885 . G T 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=2.212;HaplotypeScore=11.9973;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.053;QD=17.23;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1045,0,994 -chr1 97080 . A G 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.185;DP=53;Dels=0.00;FS=3.844;HaplotypeScore=4.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.312;QD=15.58;ReadPosRankSum=-1.630;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L759S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:28,25:53:99:854,0,987 -chr1 97141 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.017;DP=35;Dels=0.00;FS=7.260;HaplotypeScore=3.5776;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.183;QD=19.31;ReadPosRankSum=2.450;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Tcc|P739S|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:15,20:35:99:704,0,461 -chr1 97145 . G A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=37;Dels=0.00;FS=2.995;HaplotypeScore=5.4724;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.461;QD=20.48;ReadPosRankSum=1.021;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P737|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97071_97171) GT:AD:DP:GQ:PL 0/1:13,23:37:99:786,0,395 -chr1 97223 . A C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=2.9971;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=0.412;QD=14.31;ReadPosRankSum=0.443;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,28:58:99:858,0,1018 -chr1 97268 . G T 803.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.938;DP=63;Dels=0.00;FS=2.132;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.326;QD=12.76;ReadPosRankSum=-0.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:832,0,1288 -chr1 97299 . A G 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.601;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=1.648;QD=14.48;ReadPosRankSum=-0.290;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,28:62:99:926,0,1199 -chr1 97312 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.498;DP=67;Dels=0.00;FS=0.988;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=1.608;QD=13.74;ReadPosRankSum=1.761;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1344 -chr1 97491 . T G 2512.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=1.7219;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=30.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2541,193,0 -chr1 97631 . G C 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.243;DP=55;Dels=0.00;FS=2.478;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.377;QD=11.76;ReadPosRankSum=-0.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gGt|A723G|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_97615_97666) GT:AD:DP:GQ:PL 0/1:34,21:55:99:675,0,1153 -chr1 97696 . C T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.902;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.101;QD=12.26;ReadPosRankSum=1.362;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,18:46:99:592,0,888 -chr1 97749 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.914;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.748;QD=13.02;ReadPosRankSum=-0.831;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:653,0,801 -chr1 97919 . A T 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.901;DP=46;Dels=0.00;FS=4.288;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.066;QD=16.41;ReadPosRankSum=-0.945;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:783,0,771 -chr1 97946 . C G 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.771;DP=41;Dels=0.00;FS=2.814;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=0.879;QD=14.68;ReadPosRankSum=-1.799;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,20:41:99:630,0,670 -chr1 98038 . A G 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.277;DP=50;Dels=0.00;FS=1.115;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.019;QD=17.68;ReadPosRankSum=0.564;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:912,0,770 -chr1 98051 . A T 1890.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=31.05;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1919,144,0 -chr1 98140 . A G 1419.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=31.65;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1448,108,0 -chr1 98179 . G T 887.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.164;DP=54;Dels=0.00;FS=3.840;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.099;QD=16.44;ReadPosRankSum=1.013;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:916,0,864 -chr1 98231 . T A 2348.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.96;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2377,178,0 -chr1 98270 . A T 2354.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=28.54;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2383,178,0 -chr1 98294 . A G 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=52;Dels=0.00;FS=8.574;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-1.000;QD=15.21;ReadPosRankSum=0.707;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:819,0,922 -chr1 98466 . A G 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.245;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.607;QD=15.61;ReadPosRankSum=-2.224;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:762,0,808 -chr1 98495 . G A 994.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=51;Dels=0.00;FS=4.035;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=0.390;QD=19.51;ReadPosRankSum=-1.113;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:1023,0,696 -chr1 98562 . A C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=55;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.698;QD=12.67;ReadPosRankSum=-0.572;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,23:55:99:725,0,1123 -chr1 98613 . T C 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=41;Dels=0.00;FS=4.457;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.327;QD=14.31;ReadPosRankSum=1.011;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:615,0,801 -chr1 98666 . A T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.742;DP=47;Dels=0.00;FS=2.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=1.116;QD=18.97;ReadPosRankSum=-3.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:920,0,631 -chr1 98933 . A T 1037.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.557;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=1;MQRankSum=-0.034;QD=16.22;ReadPosRankSum=0.612;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1066,0,1072 -chr1 99114 . A T 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.229;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.092;QD=14.05;ReadPosRankSum=-1.037;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atA|I608|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:28,24:52:99:759,0,894 -chr1 99351 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=45;Dels=0.00;FS=2.527;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.683;QD=11.93;ReadPosRankSum=0.637;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctA|L529|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,18:45:99:565,0,935 -chr1 99567 . T G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=49;Dels=0.00;FS=12.036;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.79;MQ0=0;MQRankSum=0.412;QD=14.02;ReadPosRankSum=-0.533;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaC|E457D|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:27,22:49:99:715,0,877 -chr1 99633 . A G 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.770;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.9944;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=1.259;QD=13.09;ReadPosRankSum=-0.599;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S435|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,731 -chr1 99642 . C T 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.111;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-0.702;QD=11.25;ReadPosRankSum=-0.579;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V432|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:25,18:43:99:512,0,818 -chr1 99729 . G A 977.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.652;DP=53;Dels=0.00;FS=3.841;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.298;QD=18.45;ReadPosRankSum=-1.670;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G403|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:22,31:53:99:1006,0,723 -chr1 99861 . A G 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.654;DP=48;Dels=0.00;FS=2.555;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.822;QD=18.89;ReadPosRankSum=-1.581;EFF=SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S359|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_98997_99978) GT:AD:DP:GQ:PL 0/1:19,29:48:99:935,0,572 -chr1 100026 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.071;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=-0.156;QD=20.77;ReadPosRankSum=-0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:859,0,407 -chr1 100458 . A C 2457.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttT/ttG|F240L|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100334_100464) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2486,187,0 -chr1 100484 . A C 2630.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.86;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2659,199,0 -chr1 100660 . T C 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.498;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.981;QD=10.20;ReadPosRankSum=1.005;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:569,0,1225 -chr1 100710 . A C 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.633;DP=58;Dels=0.00;FS=1.023;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.213;QD=16.46;ReadPosRankSum=-1.944;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F235C|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,29:58:99:983,0,1001 -chr1 100778 . A T 1005.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.399;DP=60;Dels=0.00;FS=2.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.139;QD=16.76;ReadPosRankSum=0.888;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A212|Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_100701_100860) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1034,0,964 -chr1 100875 . C A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=46;Dels=0.00;FS=1.178;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.963;QD=14.84;ReadPosRankSum=-0.794;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:711,0,861 -chr1 100917 . T C 205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.969;DP=54;Dels=0.00;FS=3.266;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.189;QD=3.81;ReadPosRankSum=-3.129;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,10:54:99:234,0,1538 -chr1 101397 . A G 870.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=1;MQRankSum=0.492;QD=15.28;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:899,0,799 -chr1 101547 . A G 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=65;Dels=0.00;FS=10.521;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.833;QD=15.89;ReadPosRankSum=-0.151;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1061,0,1064 -chr1 101623 . T C 2368.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=24.90;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2397,181,0 -chr1 101683 . C T 508.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.992;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.040;QD=12.41;ReadPosRankSum=0.437;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:537,0,822 -chr1 101684 . A G 505.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.439;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.910;QD=13.31;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:534,0,741 -chr1 101745 . G A 861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.536;DP=56;Dels=0.00;FS=3.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.107;QD=15.39;ReadPosRankSum=0.715;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:890,0,1039 -chr1 101797 . C A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.276;DP=66;Dels=0.00;FS=0.940;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.032;QD=16.34;ReadPosRankSum=-0.494;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,32:66:99:1107,0,1179 -chr1 101798 . C T 1122.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=69;Dels=0.00;FS=1.986;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.198;QD=16.27;ReadPosRankSum=-0.582;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:69:99:1151,0,1212 -chr1 101823 . C T 2664.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.40;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2693,202,0 -chr1 101901 . C T 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.165;DP=38;Dels=0.00;FS=6.942;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.407;QD=20.49;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:807,0,440 -chr1 101928 . T A 1680.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=38.41;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1709,129,0 -chr1 101943 . G C 988.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.433;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.144;QD=21.97;ReadPosRankSum=-0.445;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,30:45:99:1017,0,464 -chr1 101964 . A T 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.379;QD=14.30;ReadPosRankSum=-0.037;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:643,0,818 -chr1 102084 . T C 1022.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.787;DP=61;Dels=0.00;FS=0.974;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.816;QD=16.77;ReadPosRankSum=0.440;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1051,0,930 -chr1 102113 . A C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=-1.220;QD=15.40;ReadPosRankSum=0.579;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:860,0,828 -chr1 102117 . C A 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=55;Dels=0.00;FS=2.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=1;MQRankSum=-1.307;QD=14.85;ReadPosRankSum=1.030;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:845,0,861 -chr1 102158 . T C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=54;Dels=0.00;FS=2.323;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=1;MQRankSum=1.951;QD=15.22;ReadPosRankSum=0.526;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:850,0,846 -chr1 102167 . G A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=57;Dels=0.00;FS=5.494;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=2;MQRankSum=0.806;QD=16.59;ReadPosRankSum=-2.418;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:974,0,828 -chr1 102180 . T A 2213.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=2;QD=25.80;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2242,166,0 -chr1 102205 . T C 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=59;Dels=0.00;FS=1.030;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-0.661;QD=15.50;ReadPosRankSum=0.770;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:943,0,978 -chr1 102214 . G C 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.23;MQ0=1;MQRankSum=-2.208;QD=15.30;ReadPosRankSum=-1.135;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,29:59:99:931,0,1005 -chr1 102348 . T G 800.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.766;DP=44;Dels=0.00;FS=11.766;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.295;QD=18.20;ReadPosRankSum=-0.554;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:829,0,650 -chr1 102411 . T A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.145;DP=43;Dels=0.00;FS=2.999;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.308;QD=18.02;ReadPosRankSum=-0.382;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:803,0,602 -chr1 102443 . C T 1665.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=69.5886;MLEAC=2;MLEAF=1.00;MQ=58.97;MQ0=0;QD=30.29;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1694,126,0 -chr1 102454 . T A 778.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.682;DP=46;Dels=0.00;FS=19.456;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=1.572;QD=16.93;ReadPosRankSum=-1.352;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:807,0,705 -chr1 102506 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.117;DP=36;Dels=0.00;FS=5.231;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=-1.950;QD=17.69;ReadPosRankSum=0.317;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:665,0,522 -chr1 102514 . T C 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.939;DP=39;Dels=0.00;FS=7.216;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=1;MQRankSum=0.617;QD=14.10;ReadPosRankSum=-0.264;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:578,0,741 -chr1 102576 . C G 1795.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.71;MQ0=2;QD=31.84;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1824,135,0 -chr1 102597 . T A 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.154;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=-0.495;QD=17.25;ReadPosRankSum=1.374;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:839,0,693 -chr1 102632 . G A 1747.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=1;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1776,135,0 -chr1 102685 . T C 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=48;Dels=0.00;FS=11.229;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-2.270;QD=15.41;ReadPosRankSum=-0.310;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:768,0,789 -chr1 102745 . G A 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=57;Dels=0.00;FS=1.037;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.626;QD=12.54;ReadPosRankSum=0.203;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:743,0,1192 -chr1 102828 . T A 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.030;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.556;QD=13.44;ReadPosRankSum=-1.748;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:687,0,969 -chr1 102840 . C T 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.773;DP=49;Dels=0.00;FS=2.600;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.317;QD=11.49;ReadPosRankSum=-0.425;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:591,0,1069 -chr1 102853 . A T 1069.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=51;Dels=0.00;FS=4.012;HaplotypeScore=1.9978;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.453;QD=20.98;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1098,0,644 -chr1 103138 . A T 1021.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.059;DP=57;Dels=0.00;FS=3.801;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.010;QD=17.93;ReadPosRankSum=-0.653;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1050,0,812 -chr1 103150 . T C 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=53;Dels=0.00;FS=2.466;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=2;MQRankSum=0.274;QD=14.58;ReadPosRankSum=-0.632;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:801,0,943 -chr1 103189 . A G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.202;DP=55;Dels=0.00;FS=4.291;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=1;MQRankSum=0.854;QD=12.70;ReadPosRankSum=1.329;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:727,0,1140 -chr1 103225 . G A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.322;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=1;MQRankSum=1.023;QD=15.72;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,26:54:99:877,0,949 -chr1 103405 . C T 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=57;Dels=0.00;FS=2.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.280;QD=17.24;ReadPosRankSum=1.223;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1011,0,920 -chr1 103515 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=2.536;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.222;QD=13.79;ReadPosRankSum=-0.778;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:704,0,944 -chr1 103542 . G C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.229;DP=44;Dels=0.00;FS=2.800;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.991;QD=19.31;ReadPosRankSum=-1.492;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:878,0,558 -chr1 103599 . C G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.7842;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.583;QD=15.71;ReadPosRankSum=0.473;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,22:46:99:751,0,773 -chr1 103609 . A C 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=48;Dels=0.00;FS=4.201;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.330;QD=16.89;ReadPosRankSum=-1.218;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:839,0,793 -chr1 103612 . C T 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.050;DP=49;Dels=0.00;FS=1.101;HaplotypeScore=3.7837;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.130;QD=17.30;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:876,0,826 -chr1 103621 . G T 902.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.198;QD=17.70;ReadPosRankSum=-1.915;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:931,0,802 -chr1 103691 . C A 1271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.171;DP=60;Dels=0.00;FS=2.252;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-0.061;QD=21.20;ReadPosRankSum=2.646;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,37:60:99:1300,0,754 -chr1 103828 . C G 947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.716;DP=55;Dels=0.00;FS=7.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=0.227;QD=17.23;ReadPosRankSum=-0.109;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:976,0,894 -chr1 103856 . C T 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=49;Dels=0.00;FS=16.948;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=60.22;MQ0=0;MQRankSum=-1.149;QD=12.02;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:617,0,1000 -chr1 103995 . G A 806.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.761;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.440;QD=12.81;ReadPosRankSum=-0.510;EFF=INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,26:63:99:835,0,1325 -chr1 104120 . C G 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.402;DP=54;Dels=0.00;FS=5.785;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.227;QD=12.09;ReadPosRankSum=-1.032;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:681,0,1040 -chr1 104149 . G A 983.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.565;DP=51;Dels=0.00;FS=2.555;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.048;QD=19.29;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1012,0,605 -chr1 104155 . A G 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.401;DP=49;Dels=0.00;FS=4.412;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.798;QD=10.73;ReadPosRankSum=2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,17:49:99:554,0,1041 -chr1 104159 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=51;Dels=0.00;FS=4.244;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.89;MQ0=0;MQRankSum=-1.120;QD=11.25;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:602,0,1079 -chr1 104167 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.897;DP=51;Dels=0.00;FS=2.473;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.109;QD=12.25;ReadPosRankSum=1.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,20:51:99:653,0,1056 -chr1 104213 . C T 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.709;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.104;QD=13.73;ReadPosRankSum=-1.481;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:756,0,1034 -chr1 104372 . G A 2025.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2054,156,0 -chr1 104376 . T C 968.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.581;DP=53;Dels=0.00;FS=10.088;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.367;QD=18.28;ReadPosRankSum=-1.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,29:53:99:997,0,714 -chr1 104545 . A C 1079.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.282;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.847;QD=17.70;ReadPosRankSum=-0.007;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,33:61:99:1108,0,937 -chr1 104549 . C A 2426.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2455,184,0 -chr1 104570 . G T 1119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.314;DP=66;Dels=0.00;FS=2.084;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.212;QD=16.97;ReadPosRankSum=0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1148,0,1049 -chr1 104631 . T A 1016.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.341;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=2.7461;MLEAC=1;MLEAF=0.500;MQ=60.16;MQ0=0;MQRankSum=-1.676;QD=15.18;ReadPosRankSum=-0.596;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:1045,0,1181 -chr1 104738 . A T 1287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.183;DP=70;Dels=0.00;FS=10.396;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.242;QD=18.40;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1316,0,1019 -chr1 104775 . C A 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=61;Dels=0.00;FS=2.287;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=1.380;QD=20.29;ReadPosRankSum=0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,37:61:99:1266,0,700 -chr1 104901 . T G 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.076;DP=55;Dels=0.00;FS=2.401;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.582;QD=18.03;ReadPosRankSum=0.464;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1020,0,851 -chr1 104914 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.187;QD=15.35;ReadPosRankSum=-0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,26:54:99:857,0,929 -chr1 105215 . A G 1426.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.23;MQ0=0;QD=27.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1455,111,0 -chr1 105276 . A G 1014.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=49;Dels=0.02;FS=1.174;HaplotypeScore=2.9659;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.120;QD=20.71;ReadPosRankSum=0.930;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,29:48:99:1043,0,542 -chr1 105289 . C A 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=0.027;QD=19.57;ReadPosRankSum=0.587;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,31:54:99:1085,0,685 -chr1 105333 . G A 2241.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=1;QD=30.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2270,169,0 -chr1 105363 . G A 2110.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=1;QD=30.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2139,160,0 -chr1 105391 . A G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=59;Dels=0.00;FS=7.470;HaplotypeScore=3.5213;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=12.00;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,23:59:99:736,0,1250 -chr1 105594 . A G 2739.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=3.2358;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2768,214,0 -chr1 105636 . C T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=70;Dels=0.00;FS=8.071;HaplotypeScore=4.6697;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.786;QD=15.83;ReadPosRankSum=0.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,34:70:99:1136,0,1128 -chr1 105656 . G A 984.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.247;DP=63;Dels=0.00;FS=6.709;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-1.218;QD=15.63;ReadPosRankSum=-0.697;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,33:63:99:1013,0,1033 -chr1 105661 . T A 1957.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=36.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1986,147,0 -chr1 105662 . T A 2023.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=25.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2052,153,0 -chr1 105733 . T G 2248.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.503;DP=62;Dels=0.00;FS=3.153;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;MQRankSum=0.335;QD=30.29;ReadPosRankSum=1.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,61:62:99:2277,135,0 -chr1 105750 . C T 2320.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=0;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2349,175,0 -chr1 105769 . C G 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=68;Dels=0.00;FS=3.397;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.071;QD=13.58;ReadPosRankSum=1.453;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,31:68:99:952,0,1291 -chr1 105775 . A G 1185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.270;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=2.634;QD=17.97;ReadPosRankSum=-0.899;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1214,0,951 -chr1 105776 . C T 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.385;DP=66;Dels=0.00;FS=3.451;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.105;QD=13.42;ReadPosRankSum=0.822;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,31:66:99:914,0,1186 -chr1 105815 . C A 1124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.954;DP=65;Dels=0.00;FS=2.177;HaplotypeScore=2.3346;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=0.388;QD=17.30;ReadPosRankSum=-1.112;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),INTRON(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1153,0,982 -chr1 105914 . A G 985.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.125;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.402;QD=19.33;ReadPosRankSum=1.939;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1014,0,607 -chr1 105940 . A G 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.169;DP=55;Dels=0.00;FS=1.036;HaplotypeScore=6.1984;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.580;QD=11.83;ReadPosRankSum=1.117;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,21:55:99:679,0,1160 -chr1 106000 . G A 723.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.619;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.475;QD=15.08;ReadPosRankSum=-0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,23:48:99:752,0,840 -chr1 106003 . C T 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.730;QD=15.87;ReadPosRankSum=-0.650;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:25,24:49:99:806,0,839 -chr1 106222 . A T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.445;DP=56;Dels=0.00;FS=3.858;HaplotypeScore=2.9889;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-0.294;QD=10.64;ReadPosRankSum=-1.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:34,22:56:99:624,0,1107 -chr1 106301 . G A 1226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=76;Dels=0.00;FS=3.172;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.057;QD=16.14;ReadPosRankSum=-0.161;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,38:76:99:1255,0,1277 -chr1 106304 . C T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.244;DP=75;Dels=0.00;FS=3.136;HaplotypeScore=1.6988;MLEAC=1;MLEAF=0.500;MQ=60.14;MQ0=0;MQRankSum=0.178;QD=14.90;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 0/1:38,36:75:99:1146,0,1287 -chr1 106352 . T A 2717.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.81;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UTR_5_PRIME(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|Exon_chr1_105901_106373) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2746,208,0 -chr1 106447 . C A 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.452;DP=58;Dels=0.00;FS=3.667;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=1.169;QD=15.17;ReadPosRankSum=-0.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:908,0,1064 -chr1 106476 . T G 1349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.697;DP=77;Dels=0.00;FS=16.431;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=1.137;QD=17.53;ReadPosRankSum=2.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,40:77:99:1378,0,1148 -chr1 106481 . T C 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=76;Dels=0.00;FS=14.274;HaplotypeScore=3.8312;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=0.091;QD=12.37;ReadPosRankSum=-0.562;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,32:76:99:968,0,1489 -chr1 106482 . G A 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.300;DP=76;Dels=0.00;FS=17.089;HaplotypeScore=2.8316;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.404;QD=12.63;ReadPosRankSum=0.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,32:76:99:988,0,1538 -chr1 106502 . C T 1216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=80;Dels=0.00;FS=9.385;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.833;QD=15.21;ReadPosRankSum=0.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,38:80:99:1245,0,1351 -chr1 106522 . G C 1262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.345;DP=73;Dels=0.00;FS=7.905;HaplotypeScore=3.1224;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.745;QD=17.30;ReadPosRankSum=0.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,37:73:99:1291,0,1178 -chr1 106546 . A T 1107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.761;DP=68;Dels=0.00;FS=21.595;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.577;QD=16.29;ReadPosRankSum=0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,35:68:99:1136,0,1064 -chr1 106547 . T A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.040;DP=65;Dels=0.00;FS=19.861;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.581;QD=13.38;ReadPosRankSum=0.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:33,32:65:99:898,0,1081 -chr1 106583 . A C 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=51;Dels=0.00;FS=1.066;HaplotypeScore=1.8313;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.161;QD=18.17;ReadPosRankSum=-1.259;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:955,0,750 -chr1 106636 . C G 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.551;DP=53;Dels=0.00;FS=4.175;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.208;QD=12.96;ReadPosRankSum=0.713;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:715,0,996 -chr1 106713 . G T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.015;DP=52;Dels=0.00;FS=10.628;HaplotypeScore=24.7277;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.007;QD=15.17;ReadPosRankSum=0.623;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:817,0,902 -chr1 106753 . T A 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-2.249;DP=40;Dels=0.00;FS=2.183;HaplotypeScore=19.7108;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=0.900;QD=0.26;ReadPosRankSum=-1.963;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,5:40:38:38,0,1284 -chr1 106797 . G A 1867.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1896,141,0 -chr1 106811 . G A,C 1402.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,27,16:43:99:1616,598,517,1018,0,970 -chr1 106817 . C T 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=40;Dels=0.00;FS=2.928;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.801;QD=23.29;ReadPosRankSum=0.241;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:14,26:40:99:960,0,454 -chr1 106840 . C T 1108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.900;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.801;QD=25.20;ReadPosRankSum=1.029;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,31:44:99:1137,0,394 -chr1 106843 . G C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.852;DP=44;Dels=0.00;FS=2.926;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.206;QD=8.09;ReadPosRankSum=-1.260;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,13:44:99:384,0,1140 -chr1 106856 . G A 1422.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1451,108,0 -chr1 106885 . A T 744.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.646;QD=22.57;ReadPosRankSum=0.921;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:10,23:33:99:773,0,304 -chr1 106934 . T A 450.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=34.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:479,36,0 -chr1 106992 . T C 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0 -chr1 106996 . C T 120.03 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=26.08;MQ0=3;QD=15.00;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:3,5:8:12:148,12,0 -chr1 107014 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,6:7:12:149,12,0 -chr1 107015 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:1,5:6:12:149,12,0 -chr1 107020 . C T 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:6:12:149,12,0 -chr1 107021 . T C 121.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.11;MQ0=1;QD=20.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:149,12,0 -chr1 107045 . G A 121.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.88;MQ0=2;QD=17.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:2,5:7:12:149,12,0 -chr1 107068 . G A 83.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.13;MQ0=1;QD=16.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:111,9,0 -chr1 107156 . A T 10.9 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.26;MQ0=3;MQRankSum=0.736;QD=1.82;ReadPosRankSum=-0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:4,2:6:3:37,3,0 -chr1 107197 . C T 120.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.887;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.4725;MLEAC=2;MLEAF=1.00;MQ=12.97;MQ0=14;MQRankSum=2.957;QD=3.75;ReadPosRankSum=1.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:12:148,12,0 -chr1 107202 . G A 116.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.449;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.5362;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=13;MQRankSum=2.654;QD=3.63;ReadPosRankSum=1.674;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,14:32:12:144,12,0 -chr1 107216 . G T 87.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.623;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.1146;MLEAC=2;MLEAF=1.00;MQ=12.19;MQ0=12;MQRankSum=1.535;QD=2.73;ReadPosRankSum=0.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,6:32:9:115,9,0 -chr1 107223 . G A 78.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.529;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=3.0304;MLEAC=2;MLEAF=1.00;MQ=12.37;MQ0=12;MQRankSum=2.646;QD=2.45;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:27,5:32:9:106,9,0 -chr1 107234 . T C 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.256;DP=34;Dels=0.00;FS=10.000;HaplotypeScore=3.3679;MLEAC=1;MLEAF=0.500;MQ=15.56;MQ0=13;MQRankSum=2.161;QD=1.99;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,4:34:58:96,0,58 -chr1 107332 . A G 264.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.49;MQ0=1;QD=24.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:293,24,0 -chr1 107410 . T G 122.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.550;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.88;MQ0=4;MQRankSum=1.754;QD=11.09;ReadPosRankSum=-1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:7,4:11:12:150,12,0 -chr1 107457 . G A 251.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.263;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9157;MLEAC=2;MLEAF=1.00;MQ=19.81;MQ0=12;MQRankSum=3.308;QD=8.99;ReadPosRankSum=0.368;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,8:28:21:280,21,0 -chr1 107475 . G T 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.088;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.53;MQ0=12;MQRankSum=3.532;QD=9.13;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:19,9:30:24:302,24,0 -chr1 107492 . A G 271.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.144;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.9159;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.416;QD=9.37;ReadPosRankSum=0.722;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:20,9:29:24:300,24,0 -chr1 107493 . A C 268.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.847;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8490;MLEAC=2;MLEAF=1.00;MQ=19.86;MQ0=12;MQRankSum=3.281;QD=9.27;ReadPosRankSum=0.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:18,9:29:24:297,24,0 -chr1 107755 . G A 128.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.00;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:156,12,0 -chr1 107795 . G T 489.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=1;QD=34.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:518,39,0 -chr1 107900 . T C 502.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=33.52;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:531,42,0 -chr1 107903 . A G 489.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.86;MQ0=0;QD=32.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:518,42,0 -chr1 108008 . A T 911.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.22;MQ0=0;QD=25.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:72:940,72,0 -chr1 108057 . A G 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=2.204;QD=13.15;ReadPosRankSum=3.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:620,0,784 -chr1 108058 . C T 789.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.271;DP=45;Dels=0.00;FS=1.167;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.59;MQ0=1;MQRankSum=-1.780;QD=17.55;ReadPosRankSum=-2.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:818,0,619 -chr1 108069 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.51;MQ0=1;QD=25.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:901,66,0 -chr1 108088 . C T 944.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=29.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:973,72,0 -chr1 108089 . A G 933.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.22;MQ0=1;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:962,72,0 -chr1 108104 . G A 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.287;DP=47;Dels=0.00;FS=1.121;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.48;MQ0=0;MQRankSum=-4.097;QD=14.00;ReadPosRankSum=-5.544;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:686,0,806 -chr1 108110 . C T 1376.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.31;MQ0=0;QD=34.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1405,114,0 -chr1 108111 . A G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.878;QD=9.97;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:427,0,745 -chr1 108112 . G A 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.496;DP=40;Dels=0.00;FS=1.279;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.31;MQ0=0;MQRankSum=2.793;QD=9.94;ReadPosRankSum=4.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,14:40:99:426,0,750 -chr1 108120 . A C 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=48;Dels=0.00;FS=2.509;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.28;MQ0=0;MQRankSum=-2.348;QD=14.56;ReadPosRankSum=0.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:727,0,612 -chr1 108125 . T C 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.178;DP=46;Dels=0.00;FS=2.597;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=33.80;MQ0=0;MQRankSum=1.807;QD=11.10;ReadPosRankSum=-1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:539,0,755 -chr1 108127 . C T 1486.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.04;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1515,126,0 -chr1 108128 . A G 1489.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9987;MLEAC=2;MLEAF=1.00;MQ=33.75;MQ0=0;QD=33.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1518,126,0 -chr1 108131 . C T 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.573;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.012;QD=13.32;ReadPosRankSum=2.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:721,0,597 -chr1 108137 . T A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=-1.072;QD=13.30;ReadPosRankSum=4.498;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:720,0,593 -chr1 108138 . G C 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.272;DP=52;Dels=0.00;FS=5.913;HaplotypeScore=1.9987;MLEAC=1;MLEAF=0.500;MQ=31.93;MQ0=3;MQRankSum=0.952;QD=10.88;ReadPosRankSum=-4.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:594,0,722 -chr1 108168 . G A 896.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.18;MQ0=3;QD=25.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,35:35:81:925,81,0 -chr1 108170 . A G 268.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.18;MQ0=3;MQRankSum=0.019;QD=7.68;ReadPosRankSum=2.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:297,0,467 -chr1 108172 . A T 271.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.052;DP=34;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=29.06;MQ0=3;MQRankSum=0.020;QD=7.99;ReadPosRankSum=2.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:300,0,431 -chr1 108179 . A T 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;DP=31;Dels=0.00;FS=1.744;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=27.94;MQ0=3;MQRankSum=-0.092;QD=7.67;ReadPosRankSum=3.271;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:266,0,355 -chr1 108237 . T C 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.136;DP=52;Dels=0.00;FS=1.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=1;MQRankSum=0.076;QD=2.84;ReadPosRankSum=-3.358;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:176,0,1420 -chr1 108244 . C T 165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.012;DP=52;Dels=0.00;FS=3.548;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.507;QD=3.19;ReadPosRankSum=-2.533;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:194,0,1435 -chr1 108245 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.803;DP=52;Dels=0.00;FS=3.605;HaplotypeScore=34.2618;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=1;MQRankSum=0.358;QD=3.17;ReadPosRankSum=-2.508;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,9:52:99:193,0,1432 -chr1 108320 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.061;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.89;MQ0=0;MQRankSum=-1.995;QD=13.85;ReadPosRankSum=-0.737;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:804,0,1051 -chr1 108356 . C A 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=72;Dels=0.00;FS=1.099;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=1.076;QD=7.89;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:596,0,1658 -chr1 108358 . G C 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.113;DP=72;Dels=0.00;FS=2.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=0.603;QD=8.11;ReadPosRankSum=-0.180;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:50,22:72:99:612,0,1682 -chr1 108381 . C G 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.195;DP=57;Dels=0.00;FS=2.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=1.583;QD=9.47;ReadPosRankSum=-0.279;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,19:57:99:568,0,1331 -chr1 108383 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.245;DP=59;Dels=0.00;FS=2.367;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=0.657;QD=10.86;ReadPosRankSum=-0.768;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:669,0,1309 -chr1 108421 . T C 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=54;Dels=0.00;FS=5.922;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.455;QD=12.48;ReadPosRankSum=-1.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:702,0,1090 -chr1 108425 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.158;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=10.9950;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.604;QD=12.76;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:666,0,1049 -chr1 108449 . A G 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.445;DP=52;Dels=0.00;FS=6.027;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=1.139;QD=12.59;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:683,0,1017 -chr1 108459 . T C 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=57;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=1;MQRankSum=-0.379;QD=17.36;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,31:57:99:1018,0,841 -chr1 108471 . G A 2484.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=1;QD=27.75;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2513,190,0 -chr1 108482 . T C 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.027;DP=70;Dels=0.00;FS=6.663;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=1;MQRankSum=-0.510;QD=11.90;ReadPosRankSum=-0.092;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,28:70:99:861,0,1470 -chr1 108528 . T A 1085.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.439;DP=90;Dels=0.00;FS=2.962;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=3;MQRankSum=-0.509;QD=12.06;ReadPosRankSum=-0.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,37:90:99:1114,0,1842 -chr1 108603 . T C 724.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.997;DP=72;Dels=0.00;FS=5.096;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-1.165;QD=10.07;ReadPosRankSum=0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:48,24:72:99:753,0,1647 -chr1 108612 . T C 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=75;Dels=0.00;FS=7.991;HaplotypeScore=66.7830;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.528;QD=11.52;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:46,29:75:99:892,0,1572 -chr1 108628 . A C 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.110;DP=62;Dels=0.00;FS=2.268;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-0.346;QD=10.00;ReadPosRankSum=1.802;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:648,0,1375 -chr1 108660 . G A 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=51;Dels=0.00;FS=1.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.575;QD=16.15;ReadPosRankSum=-1.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:852,0,837 -chr1 108664 . C T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.192;DP=49;Dels=0.00;FS=2.568;HaplotypeScore=1.7820;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.551;QD=15.63;ReadPosRankSum=-1.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:794,0,758 -chr1 108691 . A T 981.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1010,78,0 -chr1 108698 . C G 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.147;DP=38;Dels=0.00;FS=8.656;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.27;MQ0=0;MQRankSum=0.998;QD=13.70;ReadPosRankSum=-4.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:549,0,669 -chr1 108709 . A C 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.320;DP=37;Dels=0.00;FS=12.587;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=0.442;QD=13.97;ReadPosRankSum=-0.411;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:545,0,634 -chr1 108759 . T A 790.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.087;DP=55;Dels=0.00;FS=33.086;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.45;MQ0=0;MQRankSum=1.155;QD=14.38;ReadPosRankSum=0.868;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:819,0,968 -chr1 108772 . G A 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=54;Dels=0.00;FS=28.588;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=0;MQRankSum=-1.120;QD=13.33;ReadPosRankSum=-0.805;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:748,0,1076 -chr1 108785 . C G 1842.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=29.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1871,141,0 -chr1 108796 . C T 1158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.176;DP=42;Dels=0.00;FS=2.508;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.950;QD=27.59;ReadPosRankSum=-0.858;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,33:42:99:1187,0,248 -chr1 108799 . G A 1078.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.972;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.684;QD=26.97;ReadPosRankSum=-0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:9,31:40:99:1107,0,249 -chr1 108827 . C T 383.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.074;DP=32;Dels=0.00;FS=27.227;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-3.223;QD=11.99;ReadPosRankSum=-0.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:412,0,643 -chr1 108889 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.037;DP=18;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=-1.616;QD=26.71;ReadPosRankSum=-1.335;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,16:18:33:509,0,33 -chr1 108893 . A G 636.84 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.770;DP=22;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.400;QD=28.95;ReadPosRankSum=-1.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:2,20:22:18:665,0,18 -chr1 108940 . T G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=35;Dels=0.00;FS=14.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.160;QD=22.74;ReadPosRankSum=1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:824,0,345 -chr1 108944 . A G 1416.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1445,108,0 -chr1 108956 . G A 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.064;DP=38;Dels=0.00;FS=10.987;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.354;QD=23.86;ReadPosRankSum=-2.157;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,27:38:99:935,0,334 -chr1 108987 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=30;Dels=0.00;FS=5.654;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.022;QD=9.69;ReadPosRankSum=-0.374;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:319,0,707 -chr1 108988 . A G,T 817.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=31.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:981,597,567,383,0,335 -chr1 108990 . G A,T 801.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.21;MQ0=0;QD=30.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/2:0,10,16:26:99:964,583,553,382,0,333 -chr1 109006 . G A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.423;DP=30;Dels=0.00;FS=9.472;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.963;QD=18.89;ReadPosRankSum=2.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:595,0,411 -chr1 109022 . A G 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=22;Dels=0.00;FS=2.126;HaplotypeScore=3.9974;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.672;QD=19.94;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:8,14:22:99:467,0,255 -chr1 109058 . A C 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=6.641;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=0;MQRankSum=-4.308;QD=19.07;ReadPosRankSum=0.467;EFF=DOWNSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:524,0,360 -chr1 109062 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.218;DP=27;Dels=0.00;FS=9.864;HaplotypeScore=13.9930;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=0;MQRankSum=-4.440;QD=16.55;ReadPosRankSum=1.626;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:475,0,443 -chr1 109083 . T C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.570;DP=34;Dels=0.00;FS=14.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=-3.295;QD=14.64;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:526,0,626 -chr1 109085 . G A 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.173;DP=37;Dels=0.00;FS=16.965;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-3.692;QD=15.80;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:613,0,599 -chr1 109091 . G A 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.910;DP=42;Dels=0.00;FS=18.757;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-1.845;QD=17.92;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:781,0,633 -chr1 109097 . T A 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.958;DP=44;Dels=0.00;FS=18.557;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=-2.652;QD=15.47;ReadPosRankSum=-1.072;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:709,0,666 -chr1 109115 . C T 693.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=42;Dels=0.00;FS=9.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=-1.862;QD=16.52;ReadPosRankSum=-1.233;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:722,0,721 -chr1 109169 . G C 974.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=46;Dels=0.00;FS=1.139;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.191;QD=21.19;ReadPosRankSum=-0.979;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:1003,0,590 -chr1 109252 . C T 1130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.266;DP=54;Dels=0.00;FS=7.888;HaplotypeScore=2.6437;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.461;QD=20.94;ReadPosRankSum=-0.763;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,33:54:99:1159,0,672 -chr1 109254 . G A 2185.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.6648;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=32.54;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2214,166,0 -chr1 109269 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.574;DP=54;Dels=0.00;FS=15.735;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=-0.175;QD=11.68;ReadPosRankSum=0.455;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:659,0,1060 -chr1 109311 . T A 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.611;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.952;QD=14.86;ReadPosRankSum=-0.651;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,26:50:99:771,0,715 -chr1 109317 . T C 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=48;Dels=0.00;FS=1.079;HaplotypeScore=2.3119;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.702;QD=13.12;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:658,0,763 -chr1 109405 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.645;DP=42;Dels=0.00;FS=6.930;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=2;MQRankSum=-0.585;QD=15.68;ReadPosRankSum=-0.938;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:687,0,600 -chr1 109412 . C A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.217;DP=47;Dels=0.00;FS=6.249;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=2;MQRankSum=1.422;QD=16.31;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:795,0,679 -chr1 109420 . A T 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=50;Dels=0.00;FS=1.145;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=2;MQRankSum=1.148;QD=15.90;ReadPosRankSum=-0.010;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:823,0,754 -chr1 109464 . C T 986.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.050;DP=60;Dels=0.00;FS=7.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=3;MQRankSum=-1.214;QD=16.45;ReadPosRankSum=-0.217;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1015,0,831 -chr1 109479 . G A 923.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.708;DP=53;Dels=0.00;FS=8.418;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=3;MQRankSum=2.123;QD=17.43;ReadPosRankSum=-1.356;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:952,0,701 -chr1 109530 . G A 1926.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=1;QD=29.57;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:1955,147,0 -chr1 109539 . T C 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.577;DP=51;Dels=0.00;FS=2.465;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=1;MQRankSum=1.378;QD=17.49;ReadPosRankSum=-0.518;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,29:51:99:920,0,726 -chr1 109549 . C T 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.389;DP=60;Dels=0.00;FS=1.044;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=1;MQRankSum=-0.603;QD=13.80;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1084 -chr1 109620 . A T 2529.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.89;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2558,199,0 -chr1 109646 . G A 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.540;DP=57;Dels=0.00;FS=1.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=-0.471;QD=16.52;ReadPosRankSum=0.311;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:970,0,961 -chr1 109673 . A T 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.120;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.499;QD=14.44;ReadPosRankSum=1.382;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:909,0,993 -chr1 109689 . C T 2343.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=36.47;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2372,175,0 -chr1 109734 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.181;DP=56;Dels=0.00;FS=2.436;HaplotypeScore=1.7608;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=0.033;QD=14.01;ReadPosRankSum=0.115;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:813,0,1012 -chr1 109767 . C T 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.208;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.31;MQ0=0;MQRankSum=-0.035;QD=13.44;ReadPosRankSum=1.596;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,25:54:99:754,0,928 -chr1 109788 . T C 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-3.116;QD=5.73;ReadPosRankSum=2.141;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,10:42:99:269,0,1133 -chr1 109814 . C T 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.124;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.18;MQ0=0;MQRankSum=-4.437;QD=10.59;ReadPosRankSum=-1.494;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,18:47:99:526,0,933 -chr1 109855 . C G 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.579;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1986;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=-5.305;QD=11.95;ReadPosRankSum=1.686;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:542,0,816 -chr1 109898 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.567;DP=42;Dels=0.00;FS=4.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=-4.596;QD=14.49;ReadPosRankSum=-0.038;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:637,0,754 -chr1 109948 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.655;DP=45;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.56;MQ0=0;MQRankSum=-4.171;QD=13.66;ReadPosRankSum=-0.931;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,26:45:99:643,0,655 -chr1 109992 . C G 1090.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=20.2910;MLEAC=2;MLEAF=1.00;MQ=38.79;MQ0=0;QD=25.97;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:90:1119,90,0 -chr1 110000 . T C 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.991;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=3.3547;MLEAC=1;MLEAF=0.500;MQ=40.16;MQ0=0;MQRankSum=-3.699;QD=6.42;ReadPosRankSum=0.672;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:330,0,703 -chr1 110006 . A G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.955;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.5657;MLEAC=1;MLEAF=0.500;MQ=41.04;MQ0=0;MQRankSum=-3.990;QD=5.89;ReadPosRankSum=0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:317,0,813 -chr1 110065 . T G 10.2 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.35;ReadPosRankSum=-1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:38:38,0,838 -chr1 110066 . T G 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;DP=29;Dels=0.00;FS=5.711;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-2.399;QD=0.38;ReadPosRankSum=-1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|),UTR_3_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,3:29:39:39,0,891 -chr1 110176 . A G 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=39;Dels=0.00;FS=2.780;HaplotypeScore=3.5109;MLEAC=1;MLEAF=0.500;MQ=46.75;MQ0=0;MQRankSum=-0.407;QD=13.61;ReadPosRankSum=-0.014;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T411|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:559,0,657 -chr1 110245 . A G 456.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.065;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.81;MQ0=0;MQRankSum=-0.531;QD=10.88;ReadPosRankSum=-0.142;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y388|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:485,0,885 -chr1 110253 . A C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.134;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.29;MQ0=0;MQRankSum=-0.744;QD=10.27;ReadPosRankSum=0.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S386A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_109059_110454),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,16:44:99:480,0,992 -chr1 110499 . C A 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.668;DP=57;Dels=0.00;FS=7.487;HaplotypeScore=1.9858;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=0.040;QD=15.54;ReadPosRankSum=1.365;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:914,0,969 -chr1 110535 . G A 2517.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=0;QD=29.61;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2546,193,0 -chr1 110567 . C A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.335;DP=65;Dels=0.00;FS=12.462;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.072;QD=17.29;ReadPosRankSum=-0.965;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:31,34:65:99:1152,0,1057 -chr1 110655 . A G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=49;Dels=0.00;FS=10.545;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.344;QD=18.79;ReadPosRankSum=-0.414;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:21,28:49:99:949,0,664 -chr1 110660 . G C 1835.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.79;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1864,141,0 -chr1 110836 . G C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.562;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.256;QD=13.11;ReadPosRankSum=0.128;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:25,17:42:99:579,0,858 -chr1 110841 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.455;DP=42;Dels=0.00;FS=1.210;HaplotypeScore=18.3458;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.025;QD=14.76;ReadPosRankSum=-0.783;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,793 -chr1 110897 . G T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.379;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=-0.138;QD=16.14;ReadPosRankSum=-0.344;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:577,0,566 -chr1 110902 . G A 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=36;Dels=0.00;FS=1.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.792;QD=15.33;ReadPosRankSum=-0.032;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:580,0,630 -chr1 110931 . T A 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=46;Dels=0.00;FS=4.246;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.242;QD=17.30;ReadPosRankSum=-1.440;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:824,0,677 -chr1 110948 . T A 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=55;Dels=0.00;FS=1.028;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.81;MQ0=0;MQRankSum=0.416;QD=17.70;ReadPosRankSum=-0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|atA/atT|I314|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:1002,0,664 -chr1 110974 . T G 1390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=77;Dels=0.00;FS=4.904;HaplotypeScore=1.9464;MLEAC=1;MLEAF=0.500;MQ=54.88;MQ0=3;MQRankSum=-1.165;QD=18.06;ReadPosRankSum=-0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|Aga/Cga|R306|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:28,49:77:99:1419,0,866 -chr1 111002 . G A 3102.77 . AC=2;AF=1.00;AN=2;DP=92;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=2;MLEAF=1.00;MQ=52.54;MQ0=3;QD=33.73;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G296|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,92:92:99:3131,241,0 -chr1 111012 . A G 148.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.621;DP=99;Dels=0.00;FS=4.879;HaplotypeScore=1.9775;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=2;MQRankSum=-2.017;QD=1.50;ReadPosRankSum=1.985;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aCa|I293T|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:85,14:99:99:177,0,2833 -chr1 111037 . C T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.209;DP=91;Dels=0.00;FS=27.980;HaplotypeScore=5.8656;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=1;MQRankSum=-5.776;QD=7.67;ReadPosRankSum=1.097;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggg/Agg|G285R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:61,30:91:99:726,0,2033 -chr1 111047 . C T 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.018;DP=95;Dels=0.00;FS=36.143;HaplotypeScore=18.9090;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=2;MQRankSum=-6.952;QD=8.96;ReadPosRankSum=-0.167;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L281|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,39:95:99:879,0,1831 -chr1 111053 . G A 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.068;DP=94;Dels=0.00;FS=22.160;HaplotypeScore=52.4073;MLEAC=1;MLEAF=0.500;MQ=50.62;MQ0=2;MQRankSum=2.884;QD=5.07;ReadPosRankSum=-0.550;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y279|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:75,19:94:99:505,0,2239 -chr1 111063 . G A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.458;DP=88;Dels=0.00;FS=26.842;HaplotypeScore=20.7019;MLEAC=1;MLEAF=0.500;MQ=49.44;MQ0=2;MQRankSum=-5.090;QD=3.58;ReadPosRankSum=-0.104;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T276M|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_110936_111082),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,21:88:99:343,0,2305 -chr1 111093 . T G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.555;DP=72;Dels=0.00;FS=18.592;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.32;MQ0=2;MQRankSum=-5.719;QD=9.66;ReadPosRankSum=1.059;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:72:99:724,0,1232 -chr1 111097 . C T 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.318;DP=72;Dels=0.00;FS=35.215;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.27;MQ0=2;MQRankSum=-6.753;QD=9.77;ReadPosRankSum=1.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:37,35:72:99:732,0,1245 -chr1 111100 . A G 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.870;DP=71;Dels=0.00;FS=28.661;HaplotypeScore=4.3003;MLEAC=1;MLEAF=0.500;MQ=48.11;MQ0=2;MQRankSum=-5.937;QD=9.72;ReadPosRankSum=0.950;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:40,31:71:99:718,0,1230 -chr1 111136 . T C 1449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.884;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=59.2005;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=0;MQRankSum=-5.507;QD=20.14;ReadPosRankSum=1.606;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:23,49:72:99:1478,0,710 -chr1 111137 . T A 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.429;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=58.2007;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=5.353;QD=9.45;ReadPosRankSum=-1.274;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:49,22:71:99:699,0,1451 -chr1 111146 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.640;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=19.0679;MLEAC=1;MLEAF=0.500;MQ=51.24;MQ0=1;MQRankSum=-5.478;QD=4.65;ReadPosRankSum=0.664;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:53,21:74:99:372,0,1862 -chr1 111162 . G A 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.513;DP=77;Dels=0.00;FS=4.192;HaplotypeScore=2.5773;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=1;MQRankSum=-4.854;QD=3.78;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:57,20:77:99:319,0,1968 -chr1 111178 . A G 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.787;DP=88;Dels=0.00;FS=4.774;HaplotypeScore=23.6084;MLEAC=1;MLEAF=0.500;MQ=51.68;MQ0=1;MQRankSum=-2.409;QD=9.66;ReadPosRankSum=0.590;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:58,30:88:99:878,0,1739 -chr1 111187 . C T 395.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.713;DP=91;Dels=0.00;FS=21.798;HaplotypeScore=61.2603;MLEAC=1;MLEAF=0.500;MQ=52.52;MQ0=1;MQRankSum=-5.366;QD=4.35;ReadPosRankSum=-0.991;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),SPLICE_SITE_DONOR(HIGH||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:69,22:91:99:424,0,2409 -chr1 111193 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=1;MQRankSum=-4.830;QD=5.18;ReadPosRankSum=-0.680;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Agg|W268R|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:479,0,2299 -chr1 111194 . G A 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.569;DP=87;Dels=0.00;FS=25.534;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.42;MQ0=1;MQRankSum=-4.830;QD=5.11;ReadPosRankSum=-0.649;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y267|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:67,20:87:99:473,0,2303 -chr1 111218 . A G 1531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.345;DP=85;Dels=0.00;FS=28.288;HaplotypeScore=40.8045;MLEAC=1;MLEAF=0.500;MQ=53.15;MQ0=1;MQRankSum=-6.832;QD=18.02;ReadPosRankSum=0.372;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D259|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:35,50:85:99:1560,0,1149 -chr1 111221 . A G 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.974;DP=85;Dels=0.00;FS=2.368;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-0.591;QD=5.79;ReadPosRankSum=0.772;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggT/ggC|G258|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,21:85:99:520,0,2174 -chr1 111222 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.901;DP=85;Dels=0.00;FS=52.665;HaplotypeScore=41.6986;MLEAC=1;MLEAF=0.500;MQ=53.00;MQ0=1;MQRankSum=-6.297;QD=9.76;ReadPosRankSum=-0.509;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G258D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:55,30:85:99:858,0,1882 -chr1 111233 . C A 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.154;DP=83;Dels=0.00;FS=8.074;HaplotypeScore=21.7535;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=0.985;QD=6.33;ReadPosRankSum=-0.484;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P254|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:63,20:83:99:554,0,2166 -chr1 111239 . C T 1826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.821;DP=83;Dels=0.00;FS=18.536;HaplotypeScore=20.7540;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-5.866;QD=22.01;ReadPosRankSum=-0.753;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111188_111241),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:27,56:83:99:1855,0,817 -chr1 111265 . T C 944.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=74;Dels=0.00;FS=53.983;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.93;MQ0=0;MQRankSum=-6.988;QD=12.77;ReadPosRankSum=2.319;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,32:74:99:973,0,1429 -chr1 111274 . T C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.905;DP=65;Dels=0.00;FS=22.427;HaplotypeScore=13.9941;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=4.440;QD=9.60;ReadPosRankSum=-1.326;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:652,0,1525 -chr1 111296 . T A 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.855;DP=60;Dels=0.00;FS=47.063;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.47;MQ0=0;MQRankSum=-6.194;QD=11.68;ReadPosRankSum=-0.038;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:729,0,1223 -chr1 111307 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.080;DP=61;Dels=0.00;FS=45.484;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.52;MQ0=0;MQRankSum=-6.030;QD=8.75;ReadPosRankSum=-0.269;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:41,20:61:99:562,0,1377 -chr1 111315 . A T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.943;DP=53;Dels=0.00;FS=25.441;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-4.672;QD=4.07;ReadPosRankSum=-2.694;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:244,0,1509 -chr1 111318 . C T 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=50;Dels=0.00;FS=22.968;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-4.247;QD=3.04;ReadPosRankSum=-2.686;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 0/1:42,8:50:99:180,0,1475 -chr1 111328 . C T 2042.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.58;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|),UPSTREAM(MODIFIER||||Cc01g00070|mRNA||GSCOCT00012432001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2071,162,0 -chr1 111397 . G A 2124.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.93;MQ0=1;QD=28.28;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2153,166,0 -chr1 111485 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.983;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=-1.024;QD=15.81;ReadPosRankSum=1.190;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q223|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111401_111565) GT:AD:DP:GQ:PL 0/1:23,26:49:99:803,0,742 -chr1 111592 . T A 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=60;Dels=0.00;FS=3.582;HaplotypeScore=1.6006;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.112;QD=13.36;ReadPosRankSum=-0.246;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:830,0,1146 -chr1 111732 . A G 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.751;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=-1.026;QD=14.15;ReadPosRankSum=1.868;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:764,0,902 -chr1 111733 . G A 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.217;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=2.274;QD=17.17;ReadPosRankSum=-2.142;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:904,0,661 -chr1 111744 . G A 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.681;DP=48;Dels=0.00;FS=2.691;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=0.557;QD=16.14;ReadPosRankSum=-0.227;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:803,0,707 -chr1 111927 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.084;DP=61;Dels=0.00;FS=8.983;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.791;QD=18.34;ReadPosRankSum=0.399;EFF=SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q139|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1147,0,896 -chr1 111933 . G A 1065.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=59;Dels=0.00;FS=11.534;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.586;QD=18.06;ReadPosRankSum=0.936;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I137|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 0/1:27,32:59:99:1094,0,890 -chr1 112070 . T C 1601.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.25;MQ0=0;QD=27.83;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I92V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_111756_112103) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1630,123,0 -chr1 112145 . T C 969.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.317;DP=47;Dels=0.00;FS=8.803;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=0;MQRankSum=-2.922;QD=20.63;ReadPosRankSum=0.908;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,29:47:99:998,0,587 -chr1 112157 . A T 1725.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=24.4498;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1754,129,0 -chr1 112214 . G A 579.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.778;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.89;MQ0=2;MQRankSum=0.106;QD=14.87;ReadPosRankSum=-2.021;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:608,0,645 -chr1 112312 . C G 1042.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=44;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-0.391;QD=23.70;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,30:44:99:1071,0,416 -chr1 112332 . G A 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.487;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=1.8666;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.961;QD=7.80;ReadPosRankSum=-0.320;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,12:42:99:356,0,1063 -chr1 112390 . A T 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.639;DP=47;Dels=0.00;FS=2.499;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.835;QD=11.10;ReadPosRankSum=-0.271;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:550,0,929 -chr1 112486 . A C 689.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.749;DP=57;Dels=0.00;FS=12.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=0.008;QD=12.10;ReadPosRankSum=-1.976;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,23:57:99:718,0,1139 -chr1 112608 . A G 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=62;Dels=0.00;FS=0.979;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.596;QD=13.66;ReadPosRankSum=-0.185;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,27:62:99:875,0,1208 -chr1 112714 . A C 1539.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.662;DP=44;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;MQRankSum=-0.873;QD=34.99;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,42:44:59:1568,59,0 -chr1 112726 . A G 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=45;Dels=0.00;FS=1.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.059;QD=10.97;ReadPosRankSum=-0.925;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:522,0,972 -chr1 112738 . A G 1769.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.86;EFF=INTRON(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1798,138,0 -chr1 112792 . A G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=41;Dels=0.00;FS=7.053;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.535;QD=16.53;ReadPosRankSum=0.561;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L68|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:20,21:41:99:706,0,681 -chr1 112909 . A C 1038.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=31.52;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttg/Gtg|L29V|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1067,81,0 -chr1 112926 . A T 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.603;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=24.1961;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-0.021;QD=14.43;ReadPosRankSum=-3.139;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gAt|V23D|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,16:30:99:461,0,376 -chr1 112983 . A G 1239.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.7883;MLEAC=2;MLEAF=1.00;MQ=57.43;MQ0=0;QD=33.51;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V4A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1268,99,0 -chr1 112990 . T C 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.117;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=3.3109;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=0.352;QD=7.05;ReadPosRankSum=-0.185;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Acg/Gcg|T2A|Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:24,12:36:99:282,0,828 -chr1 112999 . T C 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.4558;MLEAC=1;MLEAF=0.500;MQ=57.95;MQ0=0;MQRankSum=1.333;QD=22.16;ReadPosRankSum=-0.622;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:11,24:35:99:804,0,241 -chr1 113028 . T C 261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.3184;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=-1.835;QD=9.35;ReadPosRankSum=0.000;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:17,11:28:99:290,0,593 -chr1 113037 . G T 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.102;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=20.2844;MLEAC=1;MLEAF=0.500;MQ=56.42;MQ0=0;MQRankSum=-2.110;QD=8.84;ReadPosRankSum=-0.220;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:14,9:25:99:258,0,479 -chr1 113038 . A T 187.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.888;DP=25;Dels=0.04;FS=0.000;HaplotypeScore=19.2851;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-0.827;QD=7.51;ReadPosRankSum=0.582;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:16,8:24:99:216,0,560 -chr1 113090 . A C 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.412;DP=41;Dels=0.00;FS=2.417;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=55.93;MQ0=2;MQRankSum=0.949;QD=0.51;ReadPosRankSum=-0.532;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:37,4:41:49:49,0,1144 -chr1 113092 . C T 1222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.600;DP=42;Dels=0.00;FS=2.442;HaplotypeScore=13.9009;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=2;MQRankSum=-1.195;QD=29.11;ReadPosRankSum=0.789;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:4,38:42:40:1251,0,40 -chr1 113105 . T A 1562.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.66;MQ0=2;QD=30.97;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1591,117,0 -chr1 113115 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.012;DP=45;Dels=0.00;FS=1.232;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=2;MQRankSum=1.145;QD=17.44;ReadPosRankSum=-0.628;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,27:45:99:813,0,572 -chr1 113119 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.534;DP=45;Dels=0.00;FS=2.776;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=2;MQRankSum=0.335;QD=11.11;ReadPosRankSum=0.907;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:28,17:45:99:528,0,850 -chr1 113161 . C T 1227.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=2.5015;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=29.79;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1256,96,0 -chr1 113173 . T C 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.461;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=1.037;QD=10.59;ReadPosRankSum=0.148;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:18,12:30:99:346,0,540 -chr1 113177 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=25.30;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1027,78,0 -chr1 113178 . G A 1046.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.92;MQ0=0;QD=29.64;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,28:28:81:1075,81,0 -chr1 113190 . C G 241.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.023;DP=29;Dels=0.00;FS=1.585;HaplotypeScore=1.7883;MLEAC=1;MLEAF=0.500;MQ=58.58;MQ0=0;MQRankSum=-0.665;QD=8.34;ReadPosRankSum=-1.996;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:19,10:29:99:270,0,614 -chr1 113238 . G A 92.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.041;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=20.8374;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=0;MQRankSum=-0.586;QD=3.57;ReadPosRankSum=2.277;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,5:26:99:121,0,747 -chr1 113268 . T G 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.540;DP=36;Dels=0.00;FS=5.290;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.353;QD=10.83;ReadPosRankSum=-0.257;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:21,15:36:99:418,0,717 -chr1 113287 . A C 1111.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.97;MQ0=0;QD=29.47;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1140,90,0 -chr1 113306 . A C 1268.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=31.06;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1297,99,0 -chr1 113324 . C A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=34;Dels=0.00;FS=1.524;HaplotypeScore=1.9977;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-0.248;QD=20.79;ReadPosRankSum=0.071;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:13,21:34:99:735,0,408 -chr1 113358 . G A 385.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.203;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.134;QD=29.68;ReadPosRankSum=1.470;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 0/1:1,12:13:2:412,0,2 -chr1 113386 . A G 130.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.51;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,4:4:12:158,12,0 -chr1 113396 . T C 43.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=21.87;EFF=UTR_5_PRIME(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 -chr1 113410 . A T 156.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.38;EFF=START_GAINED(LOW||||Cc01g00080|mRNA||GSCOCT00012431001|Exon_chr1_112754_113429) GT:AD:DP:GQ:PL 1/1:0,5:5:15:185,15,0 -chr1 113431 . A G 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.03;MQ0=0;MQRankSum=1.920;QD=18.85;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,5:8:82:179,0,82 -chr1 113440 . T A 180.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=26.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:209,15,0 -chr1 113444 . T A 178.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=31.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:207,15,0 -chr1 113446 . A C 181.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.82;MQ0=0;QD=27.48;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:210,15,0 -chr1 113450 . A T 214.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.19;MQ0=0;QD=31.14;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:243,18,0 -chr1 113468 . G C 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.78;MQ0=0;MQRankSum=-2.670;QD=1.59;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,3:15:52:52,0,418 -chr1 113483 . T C 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.061;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.57;MQ0=0;MQRankSum=-0.354;QD=1.10;ReadPosRankSum=-2.239;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,2:11:40:40,0,313 -chr1 113488 . T C 240.8 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=30.10;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:21:269,21,0 -chr1 113492 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.39;MQ0=0;QD=33.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:298,24,0 -chr1 113500 . T C 242.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=34.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:271,21,0 -chr1 113503 . T C 254.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=27.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:283,21,0 -chr1 113505 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.30;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:266,21,0 -chr1 113522 . T C 153.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.02;MQ0=0;QD=30.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:182,15,0 -chr1 114239 . A C 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.00;MQ0=0;QD=28.37;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr1 114264 . C G 551.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.91;MQ0=0;QD=32.00;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,15:15:42:580,42,0 -chr1 114287 . G A 771.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=28.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:800,63,0 -chr1 114304 . A G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.688;DP=21;Dels=0.00;FS=5.898;HaplotypeScore=11.6441;MLEAC=1;MLEAF=0.500;MQ=54.71;MQ0=0;MQRankSum=-2.064;QD=10.66;ReadPosRankSum=-1.195;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,8:21:99:252,0,383 -chr1 114311 . G A 481.18 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.217;DP=16;Dels=0.00;FS=7.270;HaplotypeScore=3.6636;MLEAC=2;MLEAF=1.00;MQ=53.36;MQ0=0;MQRankSum=-0.868;QD=30.07;ReadPosRankSum=1.302;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:1,15:16:10:509,10,0 -chr1 114312 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.329;DP=16;Dels=0.00;FS=6.726;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.36;MQ0=0;MQRankSum=-2.223;QD=11.05;ReadPosRankSum=-1.799;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:205,0,294 -chr1 114313 . G C 227.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.261;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=3.6636;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=0.722;QD=13.40;ReadPosRankSum=2.646;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,8:17:99:256,0,295 -chr1 114326 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.959;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=0.249;QD=12.27;ReadPosRankSum=0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,9:21:99:286,0,380 -chr1 114330 . T C 355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.239;DP=21;Dels=0.00;FS=4.010;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.20;MQ0=0;MQRankSum=-0.462;QD=16.94;ReadPosRankSum=-0.320;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,12:21:99:384,0,253 -chr1 114353 . C A 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.002;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=-1.591;QD=11.18;ReadPosRankSum=-0.648;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:196,0,307 -chr1 114354 . A T 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.237;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.945;QD=18.85;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:311,0,195 -chr1 114356 . G T 283.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.05;MQ0=0;MQRankSum=1.120;QD=18.92;ReadPosRankSum=0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,9:15:99:312,0,191 -chr1 114371 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.9971;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=-0.899;QD=13.75;ReadPosRankSum=0.417;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:427,0,524 -chr1 114439 . T C 631.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.119;DP=37;Dels=0.00;FS=3.179;HaplotypeScore=1.5781;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=0.445;QD=17.07;ReadPosRankSum=0.230;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,21:37:99:660,0,452 -chr1 114460 . C A 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.748;DP=36;Dels=0.00;FS=9.728;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-0.398;QD=13.74;ReadPosRankSum=-1.894;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:523,0,607 -chr1 114463 . T G 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.778;DP=35;Dels=0.00;FS=5.449;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-0.579;QD=14.34;ReadPosRankSum=2.434;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,19:35:99:530,0,535 -chr1 114470 . T G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.856;DP=26;Dels=0.00;FS=7.707;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=1.004;QD=4.38;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,6:26:99:142,0,623 -chr1 114472 . A C 864.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.84;MQ0=0;QD=34.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:893,69,0 -chr1 114475 . A G 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.177;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.350;QD=5.47;ReadPosRankSum=1.813;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:165,0,582 -chr1 114476 . G C 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.686;DP=25;Dels=0.00;FS=7.908;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-0.223;QD=5.75;ReadPosRankSum=2.004;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:172,0,560 -chr1 114480 . C A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.623;DP=25;Dels=0.00;FS=7.952;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.84;MQ0=0;MQRankSum=-1.304;QD=5.71;ReadPosRankSum=2.450;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,6:25:99:171,0,583 -chr1 114486 . T G 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.268;DP=31;Dels=0.00;FS=17.994;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.46;MQ0=0;MQRankSum=0.434;QD=8.86;ReadPosRankSum=0.681;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:303,0,607 -chr1 114494 . C G 1000.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=30.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1029,78,0 -chr1 114501 . G A 815.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.64;MQ0=0;QD=33.99;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:844,66,0 -chr1 114552 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.040;DP=25;Dels=0.00;FS=11.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=0.245;QD=17.19;ReadPosRankSum=1.006;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:458,0,356 -chr1 114576 . A T 643.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.58;MQ0=0;QD=37.73;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:672,51,0 -chr1 114578 . T C 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=4.533;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.41;MQ0=0;MQRankSum=0.381;QD=7.32;ReadPosRankSum=1.778;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:204,0,601 -chr1 114603 . A C 1082.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.79;MQ0=0;QD=29.78;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1111,84,0 -chr1 114617 . G A 1458.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=28.9952;MLEAC=2;MLEAF=1.00;MQ=46.56;MQ0=0;QD=27.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1487,114,0 -chr1 114621 . G A 1401.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.91;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1430,111,0 -chr1 114645 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.436;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=37.7265;MLEAC=1;MLEAF=0.500;MQ=45.53;MQ0=0;MQRankSum=-1.288;QD=20.49;ReadPosRankSum=1.767;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,23:34:99:725,0,274 -chr1 114719 . A G 12.77 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:39,3,0 -chr1 114726 . A G 10.9 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:37,3,0 -chr1 114739 . T C 14.68 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.89;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:41,3,0 -chr1 114740 . C T 11.83 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=3.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:38,3,0 -chr1 114744 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0 -chr1 114746 . A G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=5.22;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:42,3,0 -chr1 114752 . A G 13.72 LowQual AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.57;MQ0=0;QD=4.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:3:40,3,0 -chr1 114770 . G C 44.74 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.49;MQ0=0;QD=8.95;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:6:72,6,0 -chr1 114788 . T C 46.74 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.96;MQ0=0;QD=11.69;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:4:6:74,6,0 -chr1 114810 . T G 15.65 LowQual AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.41;MQ0=0;QD=7.83;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,2:2:3:42,3,0 -chr1 114906 . T G 147.9 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=21.13;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:15:176,15,0 -chr1 114967 . A T 395.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.734;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.69;MQ0=0;MQRankSum=2.100;QD=28.28;ReadPosRankSum=0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,12:14:15:424,15,0 -chr1 115005 . G A 307.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.086;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=29.1197;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=23.64;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:335,9,0 -chr1 115006 . C T 312.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.099;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=33.6508;MLEAC=2;MLEAF=1.00;MQ=34.93;MQ0=0;MQRankSum=1.678;QD=24.02;ReadPosRankSum=-1.086;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,11:13:9:340,9,0 -chr1 115080 . G A 659.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.90;MQ0=0;QD=24.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:688,51,0 -chr1 115081 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=17;Dels=0.00;FS=1.957;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=0.433;QD=16.63;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,275 -chr1 115090 . T C 776.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.86;MQ0=0;QD=33.63;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:805,60,0 -chr1 115098 . G T 841.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.28;MQ0=0;QD=32.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:870,66,0 -chr1 115143 . A G 816.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;QD=26.49;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:845,63,0 -chr1 115156 . A G 687.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.36;MQ0=0;QD=31.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:716,54,0 -chr1 115169 . T C 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=0;QD=28.56;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,21:21:60:808,60,0 -chr1 115181 . T G 1085.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.15;MQ0=0;QD=34.25;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1114,84,0 -chr1 115198 . A G 817.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.246;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;MQRankSum=-1.201;QD=34.05;ReadPosRankSum=2.246;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,22:24:11:845,11,0 -chr1 115206 . C T 1077.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1106,81,0 -chr1 115249 . G A 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.086;DP=53;Dels=0.00;FS=9.816;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.278;QD=13.15;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:725,0,1025 -chr1 115259 . A G 2107.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.59;MQ0=0;QD=29.15;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2136,166,0 -chr1 115271 . A G 935.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.303;DP=57;Dels=0.00;FS=11.864;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=1.031;QD=16.42;ReadPosRankSum=-3.364;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:964,0,858 -chr1 115276 . G T 881.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.719;DP=60;Dels=0.00;FS=6.930;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=0.956;QD=14.70;ReadPosRankSum=-2.838;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:910,0,1060 -chr1 115303 . C T 2271.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2300,172,0 -chr1 115305 . A G 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.643;DP=56;Dels=0.00;FS=5.501;HaplotypeScore=51.1251;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=3.741;QD=14.66;ReadPosRankSum=-0.379;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:849,0,1091 -chr1 115352 . T C 875.96 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.787;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.250;QD=32.44;ReadPosRankSum=2.268;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:5:903,5,0 -chr1 115355 . A G 885.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.694;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;MQRankSum=-1.157;QD=32.81;ReadPosRankSum=1.898;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,25:27:6:913,6,0 -chr1 115360 . T C 783.56 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.463;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=-1.129;QD=31.34;ReadPosRankSum=1.965;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,22:25:7:811,0,7 -chr1 115381 . A G 1182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.28;MQ0=1;MQRankSum=4.365;QD=21.12;ReadPosRankSum=5.503;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,35:56:99:1211,0,406 -chr1 115385 . C T 2076.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.28;MQ0=1;QD=35.26;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2105,160,0 -chr1 115399 . G T 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.993;DP=58;Dels=0.00;FS=5.640;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-3.684;QD=11.55;ReadPosRankSum=-2.448;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:698,0,1158 -chr1 115400 . C T 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.919;DP=58;Dels=0.00;FS=5.893;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=1;MQRankSum=-2.871;QD=11.38;ReadPosRankSum=-2.415;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:688,0,1133 -chr1 115414 . A G 1203.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=64;Dels=0.00;FS=3.517;HaplotypeScore=52.2248;MLEAC=1;MLEAF=0.500;MQ=55.46;MQ0=1;MQRankSum=2.511;QD=18.81;ReadPosRankSum=-0.519;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,35:64:99:1232,0,864 -chr1 115418 . T C 1129.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.624;DP=66;Dels=0.00;FS=0.952;HaplotypeScore=30.9607;MLEAC=1;MLEAF=0.500;MQ=55.61;MQ0=1;MQRankSum=3.185;QD=17.12;ReadPosRankSum=0.112;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,34:66:99:1158,0,983 -chr1 115440 . A C 941.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.049;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9932;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=0.387;QD=14.95;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:970,0,1095 -chr1 115476 . T C 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.547;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.880;QD=13.59;ReadPosRankSum=1.676;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,22:52:99:735,0,938 -chr1 115480 . C A 1943.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.95;MQ0=0;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1972,150,0 -chr1 115485 . T C 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=5.136;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.179;QD=16.48;ReadPosRankSum=0.288;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:984,0,900 -chr1 115540 . T C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.408;DP=54;Dels=0.00;FS=4.135;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=0;MQRankSum=-0.444;QD=11.44;ReadPosRankSum=-1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:646,0,1164 -chr1 115548 . T C 2024.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=26.84;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2053,157,0 -chr1 115568 . T A 987.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=26.97;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:1016,75,0 -chr1 115569 . G A 945.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=25.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:974,72,0 -chr1 115571 . T A 938.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.17;MQ0=0;QD=27.94;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:967,75,0 -chr1 115574 . C T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.756;DP=37;Dels=0.00;FS=4.170;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=0;MQRankSum=-1.454;QD=3.64;ReadPosRankSum=1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,7:37:99:163,0,1074 -chr1 115602 . G C 1954.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.30;MQ0=0;QD=29.47;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1983,147,0 -chr1 115617 . C T 2393.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=58.36;MQ0=0;QD=29.55;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2422,184,0 -chr1 115730 . A G 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.644;DP=35;Dels=0.00;FS=8.346;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.007;QD=16.96;ReadPosRankSum=-1.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:622,0,576 -chr1 115732 . G A 512.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.309;DP=34;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.103;QD=15.08;ReadPosRankSum=-1.033;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:541,0,583 -chr1 115738 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.838;DP=37;Dels=0.00;FS=5.540;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-0.229;QD=16.99;ReadPosRankSum=-2.088;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:657,0,575 -chr1 115746 . A C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=38;Dels=0.00;FS=7.279;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.905;QD=15.23;ReadPosRankSum=-1.401;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:607,0,655 -chr1 115752 . C A 1480.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=34.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1509,114,0 -chr1 115793 . G A 2310.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.47;MQ0=0;QD=27.91;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2339,175,0 -chr1 115811 . T G 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.352;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.283;QD=12.62;ReadPosRankSum=2.897;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:697,0,1114 -chr1 115814 . T G 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=53;Dels=0.00;FS=10.487;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-2.500;QD=12.67;ReadPosRankSum=2.987;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:700,0,1111 -chr1 115817 . A C 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.839;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.670;QD=12.35;ReadPosRankSum=3.005;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:683,0,1076 -chr1 115818 . G A 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.244;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.507;QD=12.73;ReadPosRankSum=2.771;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:703,0,1078 -chr1 115819 . T A 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.977;DP=53;Dels=0.00;FS=8.267;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-1.995;QD=12.52;ReadPosRankSum=2.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:692,0,1062 -chr1 115824 . T C 906.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=64;Dels=0.00;FS=0.970;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=3.857;QD=14.17;ReadPosRankSum=1.430;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:35,29:64:99:935,0,1177 -chr1 115872 . T C 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=37;Dels=0.00;FS=13.443;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=56.26;MQ0=0;MQRankSum=-0.564;QD=17.59;ReadPosRankSum=2.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:679,0,570 -chr1 115884 . G T 431.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=32;Dels=0.00;FS=10.606;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.397;QD=13.49;ReadPosRankSum=-2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:460,0,582 -chr1 115887 . A T 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.104;DP=30;Dels=0.00;FS=8.202;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=0;MQRankSum=0.395;QD=16.23;ReadPosRankSum=2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:515,0,435 -chr1 115890 . T C 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.658;DP=29;Dels=0.00;FS=5.988;HaplotypeScore=5.4965;MLEAC=1;MLEAF=0.500;MQ=56.14;MQ0=0;MQRankSum=-1.060;QD=15.58;ReadPosRankSum=2.211;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,15:29:99:480,0,414 -chr1 115900 . C A 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.934;DP=29;Dels=0.00;FS=2.129;HaplotypeScore=9.4946;MLEAC=1;MLEAF=0.500;MQ=56.43;MQ0=0;MQRankSum=0.375;QD=1.51;ReadPosRankSum=-2.050;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,5:29:72:72,0,793 -chr1 115966 . T A 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=49;Dels=0.00;FS=6.121;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=2;MQRankSum=0.798;QD=14.42;ReadPosRankSum=-0.543;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:735,0,712 -chr1 115983 . T C 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=55;Dels=0.00;FS=2.393;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=-0.139;QD=17.10;ReadPosRankSum=-0.278;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:969,0,769 -chr1 115998 . C G 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.525;DP=62;Dels=0.00;FS=5.215;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=0.776;QD=15.22;ReadPosRankSum=-0.747;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:31,31:62:99:972,0,1040 -chr1 116012 . A T 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.443;DP=65;Dels=0.00;FS=1.013;HaplotypeScore=4.5213;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=1;MQRankSum=0.189;QD=14.12;ReadPosRankSum=0.486;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:946,0,1099 -chr1 116022 . G C 2223.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=2.7333;MLEAC=2;MLEAF=1.00;MQ=57.61;MQ0=1;QD=34.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,62:64:99:2252,175,0 -chr1 116026 . T A 1054.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.724;DP=65;Dels=0.00;FS=2.157;HaplotypeScore=2.6644;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=1;MQRankSum=-0.182;QD=16.23;ReadPosRankSum=-0.155;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1083,0,932 -chr1 116035 . G T 2393.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=3.3036;MLEAC=2;MLEAF=1.00;MQ=57.52;MQ0=1;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2422,181,0 -chr1 116068 . A G 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.699;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-1.678;QD=17.75;ReadPosRankSum=-0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:898,0,730 -chr1 116073 . T C 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.379;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=57.91;MQ0=0;MQRankSum=-1.194;QD=15.54;ReadPosRankSum=0.884;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:805,0,790 -chr1 116082 . G A 1794.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=40.8500;MLEAC=2;MLEAF=1.00;MQ=57.87;MQ0=0;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1823,138,0 -chr1 116106 . C T 1595.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=57.28;MQ0=0;QD=30.04;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1624,120,0 -chr1 116191 . G A 419.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.858;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=3.7255;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=0.684;QD=10.49;ReadPosRankSum=-2.599;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,17:40:99:448,0,731 -chr1 116284 . G T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.326;DP=43;Dels=0.00;FS=1.216;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=50.07;MQ0=2;MQRankSum=-1.787;QD=15.72;ReadPosRankSum=-0.352;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,696 -chr1 116327 . C T 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.305;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=46.31;MQ0=1;MQRankSum=-3.916;QD=5.32;ReadPosRankSum=0.305;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:193,0,788 -chr1 116350 . T G 775.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.53;MQ0=0;QD=33.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:804,60,0 -chr1 116354 . A G 750.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.28;MQ0=0;QD=33.75;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:779,57,0 -chr1 116368 . G T 687.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=24;Dels=0.00;FS=2.291;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.36;MQ0=0;MQRankSum=2.706;QD=28.66;ReadPosRankSum=1.920;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:3,21:24:26:716,0,26 -chr1 116375 . G A 873.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.89;MQ0=0;QD=33.23;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:902,69,0 -chr1 116391 . T A 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.605;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-2.880;QD=4.61;ReadPosRankSum=-0.433;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:162,0,816 -chr1 116393 . A T 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.688;DP=29;Dels=0.00;FS=7.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.81;MQ0=0;MQRankSum=-3.134;QD=4.65;ReadPosRankSum=-0.127;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,7:29:99:163,0,804 -chr1 116410 . T C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.59;MQ0=0;QD=30.57;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0 -chr1 116422 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.301;DP=31;Dels=0.00;FS=12.035;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=51.97;MQ0=0;MQRankSum=-3.613;QD=9.83;ReadPosRankSum=1.590;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,11:31:99:333,0,662 -chr1 116436 . T G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.291;DP=37;Dels=0.00;FS=10.037;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.32;MQ0=0;MQRankSum=-1.109;QD=14.97;ReadPosRankSum=-0.957;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:582,0,665 -chr1 116453 . C T 1640.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.49;MQ0=0;QD=26.27;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1669,123,0 -chr1 116488 . G A 1609.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.82;MQ0=0;QD=32.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1638,123,0 -chr1 116492 . T C 1557.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=31.39;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:40:99:1586,117,0 -chr1 116493 . C T 555.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.591;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=0.670;QD=13.56;ReadPosRankSum=-2.010;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:584,0,810 -chr1 116506 . A G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=41;Dels=0.00;FS=2.694;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-2.600;QD=16.68;ReadPosRankSum=-2.058;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,21:41:99:712,0,659 -chr1 116529 . G A 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.134;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=-3.948;QD=16.90;ReadPosRankSum=2.053;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:755,0,724 -chr1 116532 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=43;Dels=0.00;FS=2.649;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=0;MQRankSum=3.827;QD=15.97;ReadPosRankSum=-2.199;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:715,0,752 -chr1 116537 . C T 1663.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.13;MQ0=0;QD=26.41;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1692,126,0 -chr1 116554 . A C 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.179;DP=42;Dels=0.00;FS=9.199;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.68;MQ0=0;MQRankSum=-3.792;QD=19.64;ReadPosRankSum=0.436;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:853,0,555 -chr1 116565 . C T 832.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=41;Dels=0.00;FS=6.909;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.92;MQ0=0;MQRankSum=-3.782;QD=20.31;ReadPosRankSum=-0.628;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:861,0,489 -chr1 116576 . G A 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=44;Dels=0.02;FS=4.546;HaplotypeScore=1.9662;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-3.188;QD=18.47;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,25:43:99:841,0,592 -chr1 116582 . A T 943.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=48;Dels=0.00;FS=2.552;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=0;MQRankSum=-2.973;QD=19.66;ReadPosRankSum=-0.611;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,29:48:99:972,0,614 -chr1 116595 . T G 1623.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=57.42;MQ0=0;QD=28.53;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1652,129,0 -chr1 116602 . A C 1697.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9914;MLEAC=2;MLEAF=1.00;MQ=57.59;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1726,138,0 -chr1 116621 . G A 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.163;DP=41;Dels=0.00;FS=2.820;HaplotypeScore=1.9914;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=1.938;QD=12.04;ReadPosRankSum=-1.029;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,16:41:99:522,0,880 -chr1 116650 . A G 1523.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.47;MQ0=1;QD=28.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1552,117,0 -chr1 116679 . C T 1348.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.24;MQ0=1;QD=35.33;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1377,105,0 -chr1 116681 . A G 1459.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.89;MQ0=1;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1488,114,0 -chr1 116708 . T C 152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.97;MQ0=0;MQRankSum=-0.735;QD=6.64;ReadPosRankSum=0.035;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:181,0,612 -chr1 116711 . T C 651.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=30.82;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:680,51,0 -chr1 116712 . G A 681.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=20.1188;MLEAC=2;MLEAF=1.00;MQ=53.31;MQ0=0;QD=29.36;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:710,54,0 -chr1 116724 . T A 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.705;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-0.054;QD=21.55;ReadPosRankSum=-2.007;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,10:16:99:373,0,200 -chr1 116728 . T A 622.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=28.11;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:651,48,0 -chr1 116732 . A G 647.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.89;MQ0=0;QD=27.29;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:676,51,0 -chr1 116749 . A T 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.320;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.87;MQ0=0;MQRankSum=-0.553;QD=15.18;ReadPosRankSum=0.456;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:787,0,824 -chr1 116757 . G A 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.651;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.743;QD=12.68;ReadPosRankSum=1.259;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:637,0,796 -chr1 116793 . G C 1565.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=26.79;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1594,120,0 -chr1 116804 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.442;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=0.704;QD=12.06;ReadPosRankSum=0.418;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:559,0,846 -chr1 116809 . G A 1767.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=35.74;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1796,138,0 -chr1 116816 . A T 1677.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.31;MQ0=0;QD=29.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1706,129,0 -chr1 116822 . T A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.282;DP=39;Dels=0.00;FS=1.310;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.493;QD=13.92;ReadPosRankSum=1.507;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:571,0,715 -chr1 116824 . T C 1298.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=28.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1327,99,0 -chr1 116906 . C A 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.149;QD=12.02;ReadPosRankSum=-2.562;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,19:45:99:569,0,916 -chr1 116917 . A G 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.610;DP=47;Dels=0.00;FS=1.154;HaplotypeScore=1.9931;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-0.501;QD=12.89;ReadPosRankSum=-2.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:634,0,880 -chr1 116943 . A G 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.102;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.695;QD=18.14;ReadPosRankSum=-2.536;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:881,0,663 -chr1 116949 . G A 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=0.854;QD=13.97;ReadPosRankSum=3.146;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:713,0,926 -chr1 116959 . G A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.008;DP=55;Dels=0.00;FS=1.029;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=1.355;QD=14.94;ReadPosRankSum=2.113;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:850,0,924 -chr1 116971 . G A 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.651;DP=50;Dels=0.00;FS=2.386;HaplotypeScore=3.2789;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-0.283;QD=17.90;ReadPosRankSum=0.870;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:22,28:50:99:923,0,717 -chr1 117007 . C T 1395.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.49;MQ0=0;QD=29.86;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1424,114,0 -chr1 117050 . G A 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.324;QD=6.57;ReadPosRankSum=-1.528;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:14,5:19:99:153,0,501 -chr1 117051 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.267;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.099;QD=7.10;ReadPosRankSum=-1.971;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:156,0,470 -chr1 117054 . T G 130.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.971;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.887;QD=7.26;ReadPosRankSum=-1.183;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:13,5:18:99:159,0,429 -chr1 117071 . G A 293.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.080;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.164;QD=9.79;ReadPosRankSum=0.783;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:322,0,621 -chr1 117077 . G C 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=33;Dels=0.00;FS=1.434;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=1.029;QD=10.75;ReadPosRankSum=1.740;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:383,0,738 -chr1 117104 . C T 671.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-2.211;QD=13.17;ReadPosRankSum=-0.335;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:700,0,1034 -chr1 117130 . C A 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.251;DP=72;Dels=0.00;FS=18.205;HaplotypeScore=5.9991;MLEAC=1;MLEAF=0.500;MQ=57.64;MQ0=4;MQRankSum=-4.097;QD=0.80;ReadPosRankSum=-0.505;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:61,11:72:86:86,0,2246 -chr1 117148 . G T 1083.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.492;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=1;MQRankSum=0.824;QD=14.65;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:39,35:74:99:1112,0,1310 -chr1 117150 . C T 1112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=75;Dels=0.00;FS=0.883;HaplotypeScore=8.7758;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.114;QD=14.84;ReadPosRankSum=1.763;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:40,35:75:99:1141,0,1350 -chr1 117157 . A G 1202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=75;Dels=0.00;FS=1.938;HaplotypeScore=5.7880;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=1;MQRankSum=0.827;QD=16.04;ReadPosRankSum=2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:38,37:75:99:1231,0,1283 -chr1 117161 . G A 1326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=76;Dels=0.00;FS=3.158;HaplotypeScore=3.9994;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.545;QD=17.46;ReadPosRankSum=0.900;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:36,40:76:99:1355,0,1228 -chr1 117175 . T G 248.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.270;DP=78;Dels=0.00;FS=22.021;HaplotypeScore=9.9969;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=0.164;QD=3.19;ReadPosRankSum=-2.376;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:58,12:78:99:277,0,2135 -chr1 117193 . G A 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=65;Dels=0.00;FS=7.705;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.404;QD=13.73;ReadPosRankSum=-0.470;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,28:65:99:921,0,1261 -chr1 117202 . G T 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=61;Dels=0.00;FS=10.025;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=1.292;QD=12.16;ReadPosRankSum=0.170;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:37,24:61:99:770,0,1299 -chr1 117240 . G A 248.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.71;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:277,21,0 -chr1 117248 . A G 170.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.18;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:199,15,0 -chr1 117260 . C G 86.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:114,9,0 -chr1 117286 . A G 714.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.70;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:743,57,0 -chr1 117350 . A T 879.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.016;DP=63;Dels=0.00;FS=4.058;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=52.64;MQ0=0;MQRankSum=-6.819;QD=13.96;ReadPosRankSum=-3.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,30:63:99:908,0,1176 -chr1 117353 . G A 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.169;DP=62;Dels=0.00;FS=6.115;HaplotypeScore=4.6334;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=6.744;QD=18.04;ReadPosRankSum=2.271;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:29,33:62:99:1147,0,898 -chr1 117361 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.041;DP=50;Dels=0.00;FS=2.729;HaplotypeScore=10.5317;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-5.755;QD=9.76;ReadPosRankSum=1.270;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:516,0,1175 -chr1 117411 . T C 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.758;DP=23;Dels=0.00;FS=39.846;HaplotypeScore=10.9973;MLEAC=1;MLEAF=0.500;MQ=46.04;MQ0=1;MQRankSum=-3.989;QD=6.82;ReadPosRankSum=-2.011;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,11:23:99:185,0,421 -chr1 117420 . A T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.462;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=-0.092;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,370 -chr1 117422 . G T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.523;DP=24;Dels=0.00;FS=41.720;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.07;MQ0=1;MQRankSum=-4.093;QD=9.03;ReadPosRankSum=0.215;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:245,0,369 -chr1 117438 . G C 551.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.413;DP=32;Dels=0.00;FS=52.903;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.12;MQ0=1;MQRankSum=-3.851;QD=17.24;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,23:32:99:580,0,237 -chr1 117455 . T A,G 486.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.25;MQ0=1;QD=24.31;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,9,11:20:99:628,311,284,317,0,287 -chr1 117461 . G C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.770;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.298;QD=9.92;ReadPosRankSum=1.591;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,309 -chr1 117462 . T C 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.123;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.887;QD=9.92;ReadPosRankSum=1.827;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117464 . C T 158.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.652;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.652;QD=9.92;ReadPosRankSum=1.709;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:187,0,285 -chr1 117465 . T A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.416;DP=16;Dels=0.00;FS=28.543;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=-2.062;QD=9.86;ReadPosRankSum=1.355;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,7:16:99:186,0,295 -chr1 117467 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.550;DP=18;Dels=0.00;FS=28.543;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=1;MQRankSum=-3.224;QD=12.82;ReadPosRankSum=0.241;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:9,9:18:99:259,0,257 -chr1 117527 . C A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.031;DP=38;Dels=0.00;FS=14.618;HaplotypeScore=0.9867;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=2;MQRankSum=-4.256;QD=7.26;ReadPosRankSum=2.631;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:27,11:38:99:304,0,852 -chr1 117551 . C G 73.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.950;DP=19;Dels=0.00;FS=5.815;HaplotypeScore=15.9941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.750;QD=3.88;ReadPosRankSum=-1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:15,4:19:99:102,0,544 -chr1 117615 . A C 375.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=23.38;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:404,30,0 -chr1 117624 . G A 445.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:474,36,0 -chr1 117647 . T G 493.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.12;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:39:522,39,0 -chr1 117656 . A G 537.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;QD=29.60;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:566,42,0 -chr1 117663 . A T 499.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:528,39,0 -chr1 117688 . T C 420.53 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;QD=32.35;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,12:13:36:488,36,0 -chr1 117772 . T G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117777 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117778 . A G 238.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.62;MQ0=2;QD=23.88;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:267,21,0 -chr1 117787 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.86;MQ0=2;QD=21.76;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,9:9:18:224,18,0 -chr1 117923 . C T 159.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.922;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.24;MQ0=3;MQRankSum=1.495;QD=15.99;ReadPosRankSum=-1.495;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:5,5:10:15:188,15,0 -chr1 117938 . T A 245.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=24.58;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:21:274,21,0 -chr1 117939 . T C 282.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=2;QD=28.28;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:2,8:10:24:311,24,0 -chr1 117954 . T G 632.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.29;MQ0=2;QD=33.30;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:661,51,0 -chr1 117967 . C T 371.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.351;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.465;QD=11.99;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:400,0,581 -chr1 117972 . C G 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.218;DP=31;Dels=0.00;FS=12.308;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.54;MQ0=2;MQRankSum=-0.686;QD=12.02;ReadPosRankSum=-4.539;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:401,0,578 -chr1 117996 . T C 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.341;DP=34;Dels=0.00;FS=8.609;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=2;MQRankSum=-1.468;QD=9.26;ReadPosRankSum=0.635;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:343,0,658 -chr1 118063 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.05;MQ0=0;MQRankSum=3.026;QD=21.04;ReadPosRankSum=3.377;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:6,13:19:36:428,0,36 -chr1 118067 . T A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.792;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.566;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:60:418,0,60 -chr1 118068 . G A 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.426;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=50.20;MQ0=0;MQRankSum=3.170;QD=19.49;ReadPosRankSum=3.487;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:7,13:20:69:418,0,69 -chr1 118069 . G A 26.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.483;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.31;MQ0=0;MQRankSum=-3.541;QD=1.07;ReadPosRankSum=-1.362;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:18,7:25:55:55,0,547 -chr1 118098 . G A 673.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=32;Dels=0.00;FS=5.979;HaplotypeScore=17.1556;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=3.923;QD=21.06;ReadPosRankSum=-0.468;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:10,22:32:99:702,0,186 -chr1 118118 . A G 810.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.220;DP=42;Dels=0.00;FS=2.745;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=2.888;QD=19.30;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:839,0,403 -chr1 118122 . C A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.130;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-1.111;QD=9.81;ReadPosRankSum=-0.447;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:411,0,831 -chr1 118131 . A G 556.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.931;DP=44;Dels=0.00;FS=2.548;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.24;MQ0=0;MQRankSum=-0.837;QD=12.65;ReadPosRankSum=-1.638;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:585,0,736 -chr1 118140 . T A 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-3.047;QD=12.91;ReadPosRankSum=-0.299;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:622,0,857 -chr1 118262 . C A 945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.769;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.037;QD=21.49;ReadPosRankSum=2.452;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:16,28:44:99:974,0,497 -chr1 118324 . A G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=0;MQRankSum=-1.355;QD=10.63;ReadPosRankSum=-2.135;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:528,0,851 -chr1 118347 . T A 946.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.543;DP=42;Dels=0.00;FS=5.576;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.125;QD=22.54;ReadPosRankSum=0.181;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:12,30:42:99:975,0,281 -chr1 118393 . C G 1571.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=4.1872;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1600,120,0 -chr1 118394 . C G 687.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.473;DP=43;Dels=0.00;FS=9.242;HaplotypeScore=4.1872;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=1.960;QD=15.99;ReadPosRankSum=0.524;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:716,0,621 -chr1 118403 . G A 1580.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=41.1140;MLEAC=2;MLEAF=1.00;MQ=57.24;MQ0=0;QD=27.67;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1609,123,0 -chr1 118423 . C A,T 1500.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.60;MQ0=0;QD=30.62;EFF=UPSTREAM(MODIFIER||||Cc01g00080|mRNA||GSCOCT00012431001|) GT:AD:DP:GQ:PL 1/2:0,26,23:49:99:1727,749,670,978,0,915 -chr1 118436 . T A 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.005;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=2.6648;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.756;QD=14.47;ReadPosRankSum=-1.770;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:27,26:53:99:795,0,854 -chr1 118461 . T C 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.460;DP=47;Dels=0.00;FS=1.192;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=3;MQRankSum=1.167;QD=15.68;ReadPosRankSum=-1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,27:47:99:765,0,667 -chr1 118483 . G C 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=44;Dels=0.00;FS=4.457;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=3;MQRankSum=-1.011;QD=12.18;ReadPosRankSum=0.197;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,21:44:99:564,0,783 -chr1 118552 . C T 844.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:66:873,66,0 -chr1 118569 . G A 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=29;Dels=0.00;FS=5.142;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.85;MQ0=0;MQRankSum=-3.742;QD=0.68;ReadPosRankSum=-3.419;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,6:29:48:48,0,779 -chr1 118577 . A G 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.12;MQ0=0;MQRankSum=-3.972;QD=1.53;ReadPosRankSum=-1.520;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,7:30:74:74,0,821 -chr1 118586 . T C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.704;DP=28;Dels=0.00;FS=1.906;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=-4.094;QD=3.21;ReadPosRankSum=-0.992;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,8:28:99:118,0,717 -chr1 118591 . C T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.306;DP=26;Dels=0.00;FS=4.471;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=3.972;QD=23.84;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:8,18:26:99:648,0,124 -chr1 118613 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.661;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.81;MQ0=0;MQRankSum=-3.748;QD=6.56;ReadPosRankSum=3.244;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:179,0,510 -chr1 118618 . T A 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=23;Dels=0.00;FS=4.419;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=51.52;MQ0=0;MQRankSum=-3.181;QD=6.60;ReadPosRankSum=3.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,9:23:99:180,0,492 -chr1 118625 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=18;Dels=0.00;FS=4.708;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-2.950;QD=6.32;ReadPosRankSum=2.763;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:12,6:18:99:142,0,434 -chr1 118632 . G T 625.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=2.6647;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=34.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:654,51,0 -chr1 118676 . G T 1157.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=30.42;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1186,90,0 -chr1 118776 . A G 1200.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=23.9732;MLEAC=2;MLEAF=1.00;MQ=59.04;MQ0=0;QD=33.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,35:36:99:1229,99,0 -chr1 118792 . T A 957.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=28.12;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:986,75,0 -chr1 118793 . T A 946.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.04;FS=0.000;HaplotypeScore=15.9088;MLEAC=2;MLEAF=1.00;MQ=56.73;MQ0=0;QD=32.62;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,25:25:75:975,75,0 -chr1 118806 . G A 1063.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.10;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1092,84,0 -chr1 118812 . G A 1035.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=24.64;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1064,84,0 -chr1 118868 . G A 529.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.576;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=0;MQRankSum=-4.743;QD=17.09;ReadPosRankSum=1.211;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,17:31:99:558,0,461 -chr1 118880 . C T 637.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=0;QD=33.88;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:666,51,0 -chr1 118885 . A G 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=1.7335;MLEAC=1;MLEAF=0.500;MQ=57.62;MQ0=0;MQRankSum=1.002;QD=15.42;ReadPosRankSum=-0.530;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:6,9:16:99:275,0,201 -chr1 118899 . A G 656.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.35;MQ0=0;QD=30.20;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,18:18:51:685,51,0 -chr1 118943 . A G 601.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.62;MQ0=6;QD=23.14;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,21:26:48:630,48,0 -chr1 118947 . T A 569.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.71;MQ0=6;QD=22.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:45:598,45,0 -chr1 118954 . C T 416.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.33;MQ0=6;QD=19.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,16:21:33:445,33,0 -chr1 118958 . C T 374.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.73;MQ0=6;QD=18.74;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,15:20:30:403,30,0 -chr1 118973 . C T 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.10;MQ0=1;MQRankSum=-0.456;QD=17.38;ReadPosRankSum=2.100;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:2,13:15:48:289,0,48 -chr1 118991 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.347;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.50;MQ0=1;MQRankSum=1.561;QD=10.94;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,20:21:33:258,33,0 -chr1 119018 . C T 229.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.520;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.12;MQ0=5;MQRankSum=1.561;QD=9.19;ReadPosRankSum=-1.734;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:5,20:25:33:258,33,0 -chr1 119028 . G A 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.598;DP=28;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.29;MQ0=5;MQRankSum=2.693;QD=1.21;ReadPosRankSum=-2.784;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,3:28:62:62,0,217 -chr1 119038 . C G 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.913;DP=27;Dels=0.00;FS=5.880;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.72;MQ0=5;MQRankSum=2.679;QD=2.07;ReadPosRankSum=-2.775;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,3:27:84:84,0,217 -chr1 119044 . T A 84.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=21.19;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:27:113,0,27 -chr1 119050 . A T 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.727;QD=20.94;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:28:112,0,28 -chr1 119051 . C G 125.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.26;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,4:4:12:153,12,0 -chr1 119228 . A C 261.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=30.03;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,7:7:21:290,21,0 -chr1 119229 . G A 301.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=33.85;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:330,24,0 -chr1 119234 . G A 305.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=26.59;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:334,24,0 -chr1 119294 . T A 812.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.23;MQ0=0;QD=26.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:841,63,0 -chr1 119318 . T C 804.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=19.9457;MLEAC=2;MLEAF=1.00;MQ=58.88;MQ0=0;QD=34.99;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,23:23:63:833,63,0 -chr1 119339 . A G 715.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=23.07;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:57:744,57,0 -chr1 119555 . C A 1140.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.628;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.523;QD=34.57;ReadPosRankSum=-1.628;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,32:33:96:1169,96,0 -chr1 119677 . C T 48.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.65;MQ0=0;MQRankSum=0.736;QD=16.25;ReadPosRankSum=-0.736;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:1,2:3:6:76,6,0 -chr1 119803 . C T 34.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=17.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:62,6,0 -chr1 119816 . G A 33.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:61,6,0 -chr1 119819 . C T 32.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=16.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:60,6,0 -chr1 119830 . A G 36.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.77;MQ0=0;QD=18.37;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,2:2:6:64,6,0 -chr1 119840 . C T 68.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=22.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:96,9,0 -chr1 119841 . T C 65.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=21.76;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:93,9,0 -chr1 119862 . G T 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr1 119869 . T C 73.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=0;QD=24.43;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,3:3:9:101,9,0 -chr1 119921 . A T 289.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=61.65;MQ0=0;QD=30.13;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,8:8:24:318,24,0 -chr1 119961 . G C 77.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=65.19;MQ0=0;MQRankSum=0.727;QD=19.44;ReadPosRankSum=0.727;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:1,3:4:26:106,0,26 -chr1 119977 . T G 253.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=13;Dels=0.00;FS=9.792;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.49;MQ0=0;MQRankSum=-1.466;QD=19.52;ReadPosRankSum=0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,9:13:99:282,0,121 -chr1 120103 . C G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;DP=41;Dels=0.00;FS=9.770;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.26;MQ0=0;MQRankSum=0.468;QD=3.29;ReadPosRankSum=1.299;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:34,7:41:99:163,0,1266 -chr1 120119 . G A 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.960;DP=37;Dels=0.00;FS=4.862;HaplotypeScore=2.9458;MLEAC=1;MLEAF=0.500;MQ=60.29;MQ0=0;MQRankSum=0.258;QD=14.67;ReadPosRankSum=-0.623;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,19:37:99:571,0,599 -chr1 120128 . T C 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.522;DP=34;Dels=0.00;FS=3.329;HaplotypeScore=1.9459;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=1;MQRankSum=1.099;QD=15.88;ReadPosRankSum=-0.594;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,18:34:99:568,0,540 -chr1 120143 . T C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282;DP=27;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=1;MQRankSum=1.487;QD=14.95;ReadPosRankSum=0.154;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:432,0,438 -chr1 120179 . C T 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=1;MQRankSum=-0.517;QD=13.45;ReadPosRankSum=0.680;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:378,0,440 -chr1 120186 . T C 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.610;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.83;MQ0=1;MQRankSum=-0.268;QD=12.74;ReadPosRankSum=0.903;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,12:28:99:385,0,463 -chr1 120227 . C T 580.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.140;DP=38;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=1;MQRankSum=1.322;QD=15.28;ReadPosRankSum=-1.565;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,18:38:99:609,0,620 -chr1 120238 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=41;Dels=0.00;FS=7.160;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.231;QD=16.41;ReadPosRankSum=0.177;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,23:41:99:701,0,597 -chr1 120278 . C A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=49;Dels=0.00;FS=4.269;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=1;MQRankSum=0.282;QD=18.55;ReadPosRankSum=-0.366;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,29:49:99:937,0,665 -chr1 120311 . T C 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.855;DP=42;Dels=0.00;FS=1.163;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.780;QD=16.54;ReadPosRankSum=0.101;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:723,0,713 -chr1 120315 . G A 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.790;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.036;QD=15.72;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:704,0,762 -chr1 120371 . T C 692.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=23.27;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,19:19:54:721,54,0 -chr1 120437 . C T 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.001;DP=32;Dels=0.00;FS=22.212;HaplotypeScore=1.9985;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=0;MQRankSum=-1.284;QD=14.02;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:477,0,541 -chr1 120508 . C T 1393.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.10;MQ0=0;QD=30.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1422,108,0 -chr1 120513 . C G 436.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=35;Dels=0.00;FS=5.287;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-1.317;QD=12.48;ReadPosRankSum=0.883;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,15:35:99:465,0,629 -chr1 120525 . G A 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.734;DP=32;Dels=0.00;FS=5.486;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=55.77;MQ0=1;MQRankSum=0.337;QD=12.46;ReadPosRankSum=0.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,15:32:99:427,0,557 -chr1 120532 . T A 382.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.856;DP=34;Dels=0.00;FS=7.806;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=55.37;MQ0=1;MQRankSum=-0.055;QD=11.26;ReadPosRankSum=0.856;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,15:34:99:411,0,622 -chr1 120546 . C A 1112.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.7256;MLEAC=2;MLEAF=1.00;MQ=55.59;MQ0=1;QD=34.77;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1141,90,0 -chr1 120550 . C G 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.115;DP=33;Dels=0.00;FS=3.269;HaplotypeScore=2.4595;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-0.422;QD=10.60;ReadPosRankSum=0.806;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:378,0,603 -chr1 120567 . A T 60.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=25;Dels=0.00;FS=2.671;HaplotypeScore=15.7066;MLEAC=1;MLEAF=0.500;MQ=53.60;MQ0=1;MQRankSum=-2.312;QD=2.43;ReadPosRankSum=1.987;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,5:25:89:89,0,628 -chr1 120592 . G C 609.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=1.9995;MLEAC=2;MLEAF=1.00;MQ=55.83;MQ0=0;QD=31.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,17:17:51:638,51,0 -chr1 120670 . A G 746.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.31;MQ0=0;QD=33.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:60:775,60,0 -chr1 120698 . C T 666.53 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.689;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=0;MQRankSum=2.693;QD=28.98;ReadPosRankSum=0.959;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:3,20:23:3:693,0,3 -chr1 120702 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=1.6006;MLEAC=2;MLEAF=1.00;MQ=50.14;MQ0=0;QD=34.35;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,22:22:63:784,63,0 -chr1 120717 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=1.7333;MLEAC=2;MLEAF=1.00;MQ=47.61;MQ0=0;QD=34.34;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,20:20:57:715,57,0 -chr1 120722 . T C 592.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=3.000;QD=28.23;ReadPosRankSum=-0.403;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:4,17:21:43:621,0,43 -chr1 120723 . G T 738.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=46.92;MQ0=0;QD=32.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,21:21:60:767,60,0 -chr1 120725 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.120;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=46.92;MQ0=0;MQRankSum=-3.090;QD=0.71;ReadPosRankSum=0.224;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,4:21:43:43,0,578 -chr1 120730 . T C 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.805;DP=23;Dels=0.00;FS=1.935;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.58;MQ0=0;MQRankSum=-2.065;QD=3.77;ReadPosRankSum=-0.805;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,6:23:99:115,0,600 -chr1 120744 . C A 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.752;DP=27;Dels=0.00;FS=1.574;HaplotypeScore=6.9985;MLEAC=1;MLEAF=0.500;MQ=46.78;MQ0=0;MQRankSum=1.604;QD=19.32;ReadPosRankSum=0.864;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,16:27:99:550,0,301 -chr1 120759 . T C 295.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.164;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.96;MQ0=0;MQRankSum=-0.367;QD=15.57;ReadPosRankSum=-1.347;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:324,0,285 -chr1 120764 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.936;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.60;MQ0=0;MQRankSum=-0.599;QD=13.70;ReadPosRankSum=0.951;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,10:21:99:316,0,375 -chr1 120777 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.459;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=1.257;QD=12.14;ReadPosRankSum=-0.018;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,14:33:99:429,0,613 -chr1 120780 . G A 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.623;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=46.32;MQ0=0;MQRankSum=0.960;QD=11.94;ReadPosRankSum=0.354;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,14:35:99:446,0,633 -chr1 120787 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.328;DP=39;Dels=0.00;FS=1.273;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.62;MQ0=0;MQRankSum=-1.898;QD=14.64;ReadPosRankSum=2.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,19:39:99:599,0,603 -chr1 120802 . T C 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=45;Dels=0.00;FS=2.555;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=50.94;MQ0=0;MQRankSum=-3.970;QD=16.39;ReadPosRankSum=1.331;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,24:45:99:766,0,656 -chr1 120813 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.02;MQ0=0;MQRankSum=4.507;QD=14.68;ReadPosRankSum=-0.102;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,22:45:99:689,0,762 -chr1 120816 . A G 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.013;DP=41;Dels=0.00;FS=2.837;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=51.82;MQ0=0;MQRankSum=-4.264;QD=15.31;ReadPosRankSum=0.639;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:656,0,729 -chr1 120820 . T C 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.817;DP=40;Dels=0.00;FS=2.785;HaplotypeScore=13.9933;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-4.361;QD=15.12;ReadPosRankSum=1.517;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,684 -chr1 120826 . A G 1504.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=13.9933;MLEAC=2;MLEAF=1.00;MQ=52.41;MQ0=0;QD=34.96;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1533,114,0 -chr1 120838 . A C 1759.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.71;MQ0=1;QD=34.54;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1788,135,0 -chr1 120862 . T C 1676.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.45;MQ0=1;QD=31.05;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1705,132,0 -chr1 120875 . C T 493.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.870;DP=43;Dels=0.00;FS=4.561;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=1;MQRankSum=-5.022;QD=11.48;ReadPosRankSum=2.076;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,18:43:99:522,0,781 -chr1 120891 . T C 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.826;DP=23;Dels=0.00;FS=9.132;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.13;MQ0=0;MQRankSum=-3.019;QD=3.16;ReadPosRankSum=1.155;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,5:23:99:101,0,602 -chr1 120906 . C A 986.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=18.7330;MLEAC=2;MLEAF=1.00;MQ=54.05;MQ0=1;QD=27.45;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1015,78,0 -chr1 120925 . T A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.177;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.81;MQ0=1;MQRankSum=-1.123;QD=12.24;ReadPosRankSum=0.578;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,16:37:99:481,0,688 -chr1 120936 . T A 1380.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.96;MQ0=1;QD=27.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1409,108,0 -chr1 120960 . G C 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.936;DP=43;Dels=0.00;FS=2.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=1;MQRankSum=-1.055;QD=18.34;ReadPosRankSum=-1.309;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:817,0,617 -chr1 120966 . T C 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.430;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=-1.213;QD=16.55;ReadPosRankSum=-0.480;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:740,0,631 -chr1 120969 . G A 650.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.851;DP=43;Dels=0.00;FS=1.149;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.63;MQ0=1;MQRankSum=1.322;QD=15.13;ReadPosRankSum=-0.340;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:22,21:43:99:679,0,731 -chr1 120992 . C T 1474.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=1;QD=25.94;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1503,111,0 -chr1 120994 . C G 1506.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;QD=33.17;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1535,114,0 -chr1 121003 . A G 1781.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=30.81;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1810,135,0 -chr1 121015 . T C 903.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.582;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=0.989;QD=17.38;ReadPosRankSum=0.659;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:25,27:52:99:932,0,820 -chr1 121034 . T C 831.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.450;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.94;MQ0=0;MQRankSum=-0.850;QD=16.97;ReadPosRankSum=0.370;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,25:49:99:860,0,817 -chr1 121052 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=46;Dels=0.00;FS=8.862;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.022;QD=16.80;ReadPosRankSum=0.681;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,23:46:99:801,0,734 -chr1 121087 . G T 336.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.047;DP=40;Dels=0.00;FS=5.155;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=0.924;QD=8.42;ReadPosRankSum=0.579;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,16:40:99:365,0,767 -chr1 121102 . G T 1242.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=33.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1271,99,0 -chr1 121118 . T A 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=7.025;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-0.692;QD=16.94;ReadPosRankSum=0.890;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:10,12:22:99:401,0,296 -chr1 121148 . G A 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=27;Dels=0.00;FS=9.204;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=57.69;MQ0=0;MQRankSum=-0.655;QD=15.92;ReadPosRankSum=-0.849;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,14:27:99:458,0,425 -chr1 121152 . T C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.256;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.923;QD=15.84;ReadPosRankSum=-0.821;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:440,0,417 -chr1 121153 . C T 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=6.455;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.10;MQ0=0;MQRankSum=-0.615;QD=15.76;ReadPosRankSum=-0.872;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:13,13:26:99:438,0,430 -chr1 121409 . T C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.00;MQ0=0;QD=11.83;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 -chr1 121415 . G A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.544;DP=32;Dels=0.00;FS=8.557;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-2.657;QD=11.24;ReadPosRankSum=-0.094;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:16,16:32:99:388,0,539 -chr1 121429 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=46.16;MQ0=0;QD=22.24;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1604,126,0 -chr1 121448 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.767;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=3.811;QD=14.79;ReadPosRankSum=0.158;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,20:43:99:664,0,751 -chr1 121451 . G A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.157;DP=43;Dels=0.00;FS=11.590;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.05;MQ0=0;MQRankSum=-3.859;QD=16.34;ReadPosRankSum=0.816;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,23:43:99:731,0,659 -chr1 121462 . T A 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.155;DP=40;Dels=0.00;FS=9.593;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.80;MQ0=0;MQRankSum=-4.391;QD=16.62;ReadPosRankSum=0.204;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:18,22:40:99:693,0,595 -chr1 121471 . G C 11.83 LowQual AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.49;MQ0=14;QD=0.79;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:14,1:15:3:38,3,0 -chr1 122095 . T C 15.65 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=15.65;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,1:1:3:42,3,0 -chr1 122148 . T G 1209.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9947;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=35.61;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1238,93,0 -chr1 122173 . G T 646.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.745;DP=41;Dels=0.00;FS=1.248;HaplotypeScore=3.6993;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=0.176;QD=15.77;ReadPosRankSum=0.311;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,20:41:99:675,0,610 -chr1 122179 . T C 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.298;DP=44;Dels=0.00;FS=2.744;HaplotypeScore=2.7126;MLEAC=1;MLEAF=0.500;MQ=57.20;MQ0=0;MQRankSum=-0.813;QD=14.45;ReadPosRankSum=1.190;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,20:44:99:664,0,726 -chr1 122203 . A C 703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.560;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.51;MQ0=0;MQRankSum=-2.415;QD=16.76;ReadPosRankSum=0.352;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,21:42:99:732,0,674 -chr1 122216 . C G 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.587;DP=41;Dels=0.00;FS=2.755;HaplotypeScore=32.8942;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-1.343;QD=15.60;ReadPosRankSum=-0.117;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:21,20:41:99:668,0,646 -chr1 122277 . T C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.946;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=8.4826;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=1.650;QD=9.49;ReadPosRankSum=2.750;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,10:30:99:313,0,658 -chr1 122295 . G A 1172.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.24;MQ0=0;QD=26.60;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1201,90,0 -chr1 122297 . G A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.136;DP=32;Dels=0.00;FS=3.151;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.564;QD=11.15;ReadPosRankSum=2.511;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:20,12:32:99:385,0,654 -chr1 122301 . C T 1251.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.50;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1280,93,0 -chr1 122383 . C T 1913.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9989;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=25.00;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1942,144,0 -chr1 122415 . G A 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=43;Dels=0.00;FS=2.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.30;MQ0=0;MQRankSum=-0.135;QD=13.41;ReadPosRankSum=-0.746;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:24,19:43:99:605,0,828 -chr1 122424 . G A 1618.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.58;MQ0=0;QD=29.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1647,129,0 -chr1 122430 . G A 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=43;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.37;MQ0=1;MQRankSum=0.216;QD=18.23;ReadPosRankSum=-0.928;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:19,24:43:99:812,0,558 -chr1 122455 . G A,T 921.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=45.04;MQ0=2;QD=24.90;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,20,17:37:99:1105,544,493,561,0,513 -chr1 122456 . G T 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.745;DP=37;Dels=0.00;FS=5.023;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.04;MQ0=2;MQRankSum=-0.480;QD=12.51;ReadPosRankSum=-0.712;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:17,20:37:99:491,0,496 -chr1 122464 . G A 961.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.23;MQ0=2;QD=30.06;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,32:32:84:990,84,0 -chr1 122469 . A G 726.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=37.29;MQ0=2;QD=27.95;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,26:26:66:755,66,0 -chr1 122471 . G A 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=26;Dels=0.00;FS=3.892;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=37.29;MQ0=2;MQRankSum=1.101;QD=11.64;ReadPosRankSum=-0.811;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,12:26:99:331,0,295 -chr1 122483 . G A 191.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.303;DP=23;Dels=0.00;FS=4.036;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=35.66;MQ0=2;MQRankSum=-2.429;QD=8.34;ReadPosRankSum=2.429;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:11,12:23:99:220,0,312 -chr1 122487 . T A 132.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.241;DP=20;Dels=0.05;FS=1.957;HaplotypeScore=10.7857;MLEAC=1;MLEAF=0.500;MQ=31.84;MQ0=2;MQRankSum=-2.454;QD=6.64;ReadPosRankSum=2.742;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:9,10:19:99:161,0,242 -chr1 122498 . T C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.141;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.9968;MLEAC=1;MLEAF=0.500;MQ=48.55;MQ0=1;MQRankSum=0.407;QD=14.02;ReadPosRankSum=-0.039;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:23,19:42:99:617,0,646 -chr1 122513 . T G 1544.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=1;QD=34.33;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1573,120,0 -chr1 122548 . C T 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.027;DP=35;Dels=0.00;FS=1.445;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.791;QD=19.42;ReadPosRankSum=2.576;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,21:35:99:708,0,420 -chr1 122565 . A T 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.454;DP=37;Dels=0.00;FS=7.957;HaplotypeScore=0.9933;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.391;QD=20.07;ReadPosRankSum=-0.673;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:14,23:37:99:771,0,457 -chr1 122594 . G T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.727;DP=54;Dels=0.00;FS=2.373;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.37;MQ0=0;MQRankSum=0.177;QD=12.25;ReadPosRankSum=2.129;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,21:54:99:690,0,1043 -chr1 122607 . G C 917.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=59;Dels=0.00;FS=3.662;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-0.387;QD=15.56;ReadPosRankSum=-0.751;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,28:59:99:946,0,1029 -chr1 122655 . T G 629.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=64;Dels=0.00;FS=1.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-0.915;QD=9.84;ReadPosRankSum=1.687;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,21:64:99:658,0,1417 -chr1 122658 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.967;DP=63;Dels=0.00;FS=2.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=0.303;QD=9.33;ReadPosRankSum=1.676;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:43,20:63:99:616,0,1391 -chr1 122661 . C T 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.722;DP=59;Dels=0.00;FS=3.946;HaplotypeScore=7.7321;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=0;MQRankSum=-0.511;QD=9.88;ReadPosRankSum=1.371;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:40,19:59:99:611,0,1272 -chr1 122745 . C A 1546.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=2;MLEAF=1.00;MQ=56.58;MQ0=0;QD=35.56;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1575,120,0 -chr1 122757 . A C,G 1142.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.27;MQ0=0;QD=30.87;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/2:0,15,22:37:99:1336,829,786,508,0,441 -chr1 122760 . T G 1421.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.36;MQ0=0;QD=30.21;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1450,108,0 -chr1 122767 . A C 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-5.113;QD=8.09;ReadPosRankSum=2.844;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:360,0,994 -chr1 122789 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-4.915;QD=8.73;ReadPosRankSum=1.209;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:26,12:38:99:360,0,925 -chr1 122826 . G A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.987;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.84;MQ0=0;MQRankSum=-3.853;QD=3.02;ReadPosRankSum=1.957;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,6:37:99:140,0,1158 -chr1 122828 . G A 176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.592;DP=40;Dels=0.00;FS=1.550;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.688;QD=4.42;ReadPosRankSum=0.423;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,8:40:99:205,0,1171 -chr1 122865 . C T 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.439;DP=49;Dels=0.00;FS=14.272;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=0.373;QD=9.81;ReadPosRankSum=0.501;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:33,16:49:99:509,0,1184 -chr1 122905 . C T 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.019;DP=42;Dels=0.00;FS=5.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.989;QD=6.14;ReadPosRankSum=0.901;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:32,10:42:99:286,0,1168 -chr1 122938 . C T 313.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.284;DP=41;Dels=0.00;FS=5.664;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=1;MQRankSum=-4.235;QD=7.65;ReadPosRankSum=-3.497;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:28,13:41:99:342,0,1011 -chr1 122969 . T C 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.007;DP=52;Dels=0.00;FS=11.610;HaplotypeScore=2.8266;MLEAC=1;MLEAF=0.500;MQ=58.04;MQ0=0;MQRankSum=-5.166;QD=13.00;ReadPosRankSum=1.641;EFF=INTERGENIC(MODIFIER||||||||) GT:AD:DP:GQ:PL 0/1:31,21:52:99:704,0,1092 -chr1 122976 . C T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=49;Dels=0.00;FS=12.245;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-3.283;QD=13.83;ReadPosRankSum=2.879;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,21:49:99:706,0,952 -chr1 122990 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.759;DP=52;Dels=0.00;FS=15.894;HaplotypeScore=2.9996;MLEAC=1;MLEAF=0.500;MQ=58.08;MQ0=0;MQRankSum=-4.241;QD=12.23;ReadPosRankSum=3.207;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:664,0,1073 -chr1 123012 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.417;DP=52;Dels=0.00;FS=6.555;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=0;MQRankSum=-3.786;QD=11.46;ReadPosRankSum=0.019;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,21:52:99:624,0,1045 -chr1 123034 . T C 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.523;DP=46;Dels=0.00;FS=4.428;HaplotypeScore=3.8314;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-1.707;QD=10.23;ReadPosRankSum=-1.707;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,17:46:99:499,0,1020 -chr1 123098 . A G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.078;DP=38;Dels=0.00;FS=7.718;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=1;MQRankSum=1.769;QD=9.86;ReadPosRankSum=-1.613;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:403,0,787 -chr1 123121 . C T 335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.802;DP=35;Dels=0.00;FS=3.247;HaplotypeScore=1.8273;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=1;MQRankSum=-1.207;QD=9.59;ReadPosRankSum=-1.907;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:364,0,645 -chr1 123176 . A T 1326.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.74;MQ0=0;QD=34.79;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1355,102,0 -chr1 123262 . G A 661.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=10.6984;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:690,51,0 -chr1 123294 . A G 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.444;DP=22;Dels=0.00;FS=6.897;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.901;QD=10.03;ReadPosRankSum=-0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:249,0,484 -chr1 123320 . T A 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.094;DP=23;Dels=0.00;FS=7.060;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.409;QD=11.56;ReadPosRankSum=2.425;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,9:23:99:294,0,487 -chr1 123328 . G C 229.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.557;DP=25;Dels=0.00;FS=6.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.878;QD=9.19;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:258,0,573 -chr1 123528 . G T 563.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.41;MQ0=3;QD=31.32;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,15:18:45:592,45,0 -chr1 123588 . T C 848.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.28;MQ0=3;QD=33.95;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,22:25:66:877,66,0 -chr1 123694 . A G 697.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.64;MQ0=0;QD=34.89;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:726,54,0 -chr1 123730 . T A 30.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=23;Dels=0.00;FS=5.969;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=55.45;MQ0=0;MQRankSum=-0.502;QD=1.34;ReadPosRankSum=-0.411;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,3:23:59:59,0,664 -chr1 123755 . C A 61.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=28;Dels=0.00;FS=5.305;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.20;MQ0=0;MQRankSum=0.624;QD=2.21;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,4:28:90:90,0,768 -chr1 123843 . T C 181.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=24;Dels=0.00;FS=16.510;HaplotypeScore=1.8663;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=0.889;QD=7.57;ReadPosRankSum=-0.191;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:210,0,577 -chr1 123903 . T A 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.580;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.500;QD=11.77;ReadPosRankSum=1.221;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:393,0,627 -chr1 123904 . G A 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.340;DP=31;Dels=0.00;FS=1.446;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.941;QD=11.67;ReadPosRankSum=1.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:390,0,619 -chr1 123916 . T G 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.496;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.276;QD=10.49;ReadPosRankSum=0.390;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:385,0,693 -chr1 123923 . C T 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.989;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=0.329;QD=9.32;ReadPosRankSum=-0.141;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:373,0,791 -chr1 123947 . C A 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=42;Dels=0.00;FS=1.259;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-1.321;QD=9.66;ReadPosRankSum=-0.867;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,14:42:99:434,0,970 -chr1 123966 . G A 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=11.9954;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-0.893;QD=8.91;ReadPosRankSum=-0.275;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:349,0,885 -chr1 123975 . T A 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=41;Dels=0.00;FS=1.345;HaplotypeScore=13.9928;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.124;QD=9.60;ReadPosRankSum=1.113;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:422,0,967 -chr1 124035 . T C 365.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.216;DP=34;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-0.378;QD=10.76;ReadPosRankSum=1.423;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,12:34:99:394,0,689 -chr1 124057 . G A 482.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.547;DP=38;Dels=0.00;FS=1.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.990;QD=12.70;ReadPosRankSum=0.754;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:511,0,655 -chr1 124075 . T G 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.223;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=-0.800;QD=11.92;ReadPosRankSum=1.082;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:362,0,542 -chr1 124090 . T C 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.741;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-3.362;QD=13.27;ReadPosRankSum=0.703;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:453,0,623 -chr1 124097 . G A 315.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.10;MQ0=0;MQRankSum=-3.549;QD=10.19;ReadPosRankSum=0.669;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,12:31:99:344,0,678 -chr1 124108 . A G 280.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=29;Dels=0.00;FS=3.834;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.38;MQ0=0;MQRankSum=-4.061;QD=9.68;ReadPosRankSum=1.124;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:309,0,669 -chr1 124113 . C A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.297;DP=32;Dels=0.00;FS=6.057;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.25;MQ0=0;MQRankSum=-3.923;QD=8.52;ReadPosRankSum=1.159;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:301,0,784 -chr1 124123 . A C 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.866;DP=31;Dels=0.00;FS=6.205;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-3.867;QD=8.61;ReadPosRankSum=-0.063;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:295,0,742 -chr1 124134 . C T 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=29;Dels=0.00;FS=10.056;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.44;MQ0=0;MQRankSum=3.001;QD=23.82;ReadPosRankSum=1.147;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:8,21:29:99:719,0,221 -chr1 124151 . C T 256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.49;MQ0=0;MQRankSum=1.104;QD=10.27;ReadPosRankSum=1.047;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:285,0,486 -chr1 124152 . A G 916.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.49;MQ0=0;QD=27.62;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:945,72,0 -chr1 124168 . C T 879.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.592;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=3.4667;MLEAC=2;MLEAF=1.00;MQ=42.46;MQ0=2;MQRankSum=2.281;QD=28.38;ReadPosRankSum=1.764;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:72:908,72,0 -chr1 124203 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.72;MQ0=2;QD=25.33;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:66:788,66,0 -chr1 124205 . A G 777.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.764;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.60;MQ0=2;MQRankSum=2.281;QD=25.09;ReadPosRankSum=-2.195;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:69:806,69,0 -chr1 124243 . G C 675.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.16;MQ0=2;QD=28.16;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:57:704,57,0 -chr1 124267 . G A 818.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.25;MQ0=0;QD=34.12;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:847,66,0 -chr1 124277 . A C 856.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.91;MQ0=0;QD=34.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:885,69,0 -chr1 124284 . C T 947.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.04;MQ0=0;QD=33.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:976,78,0 -chr1 124321 . C T 993.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.624;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.37;MQ0=0;MQRankSum=2.203;QD=33.13;ReadPosRankSum=1.788;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,28:30:78:1022,78,0 -chr1 124337 . C T 1115.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.315;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.29;MQ0=0;MQRankSum=2.239;QD=31.88;ReadPosRankSum=-0.107;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,33:35:90:1144,90,0 -chr1 124376 . A T 778.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.420;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.24;MQ0=2;MQRankSum=1.850;QD=25.12;ReadPosRankSum=-0.645;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,29:31:66:807,66,0 -chr1 124388 . C T 51.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.026;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.51;MQ0=0;MQRankSum=1.026;QD=12.94;ReadPosRankSum=-1.026;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:2,2:4:6:79,6,0 -chr1 124423 . T A 12.77 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.97;MQ0=9;QD=1.28;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:9,1:10:3:39,3,0 -chr1 124467 . G T 1086.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.37;MQ0=10;QD=27.17;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,33:40:84:1115,84,0 -chr1 124471 . G A 1113.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.55;MQ0=8;QD=29.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:7,31:38:87:1142,87,0 -chr1 124494 . G A 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.11;MQ0=0;MQRankSum=2.064;QD=19.94;ReadPosRankSum=4.069;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1025,0,663 -chr1 124512 . A C 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.300;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.557;QD=13.28;ReadPosRankSum=1.261;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:692,0,960 -chr1 124607 . T C 840.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.445;DP=50;Dels=0.00;FS=19.947;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.175;QD=16.82;ReadPosRankSum=1.106;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:869,0,855 -chr1 124731 . C A 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.538;DP=30;Dels=0.00;FS=18.572;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.727;QD=1.29;ReadPosRankSum=-2.688;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,4:30:67:67,0,818 -chr1 124820 . A T 638.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.078;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.600;QD=13.31;ReadPosRankSum=1.683;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,21:48:99:667,0,918 -chr1 124864 . T C 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.180;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.318;QD=14.06;ReadPosRankSum=-2.039;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:647,0,835 -chr1 124901 . T G 722.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.942;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.761;QD=16.06;ReadPosRankSum=0.874;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:751,0,736 -chr1 124917 . A T 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.090;DP=40;Dels=0.00;FS=2.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.79;MQ0=0;MQRankSum=0.251;QD=11.29;ReadPosRankSum=-1.145;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:480,0,891 -chr1 124920 . C T 376.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.922;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.054;QD=10.47;ReadPosRankSum=-1.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:405,0,807 -chr1 125002 . T C 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.594;DP=49;Dels=0.00;FS=1.202;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=2.069;QD=9.57;ReadPosRankSum=-1.460;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,17:49:99:497,0,1178 -chr1 125004 . A G 1137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.804;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=1.148;QD=23.22;ReadPosRankSum=1.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,32:49:99:1166,0,460 -chr1 125020 . A T 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.617;DP=46;Dels=0.00;FS=1.204;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-1.547;QD=9.95;ReadPosRankSum=0.375;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,15:46:99:486,0,1126 -chr1 125046 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.163;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.20;MQ0=0;MQRankSum=1.788;QD=12.74;ReadPosRankSum=0.293;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,19:47:99:627,0,985 -chr1 125096 . A G 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.345;HaplotypeScore=2.7212;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.887;QD=16.57;ReadPosRankSum=0.553;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:724,0,731 -chr1 125124 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.683;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=3.985;QD=26.36;ReadPosRankSum=0.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:7,26:33:99:898,0,147 -chr1 125126 . T C 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.859;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.029;QD=3.63;ReadPosRankSum=0.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:148,0,866 -chr1 125128 . G A 86.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.228;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=55.39;MQ0=0;MQRankSum=-4.011;QD=2.63;ReadPosRankSum=2.370;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,7:33:99:115,0,854 -chr1 125133 . C T 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.024;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-3.992;QD=3.99;ReadPosRankSum=2.622;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:152,0,843 -chr1 125134 . A G 1101.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=54.91;MQ0=0;QD=25.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1130,90,0 -chr1 125142 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=52.83;MQ0=0;MQRankSum=4.377;QD=22.16;ReadPosRankSum=-1.254;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,20:30:99:693,0,230 -chr1 125149 . G A 347.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=28;Dels=0.00;FS=1.690;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=50.58;MQ0=0;MQRankSum=-4.514;QD=12.42;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:376,0,460 -chr1 125166 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.120;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.66;MQ0=0;MQRankSum=-4.339;QD=9.10;ReadPosRankSum=0.264;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,10:28:99:283,0,577 -chr1 125168 . C T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.699;DP=30;Dels=0.00;FS=1.805;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.84;MQ0=0;MQRankSum=4.551;QD=18.83;ReadPosRankSum=0.826;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,18:30:99:593,0,339 -chr1 125175 . A G 1245.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=23.30;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1274,102,0 -chr1 125190 . C T 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=37;Dels=0.00;FS=4.233;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=52.15;MQ0=0;MQRankSum=-5.120;QD=10.53;ReadPosRankSum=0.820;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,15:37:99:418,0,736 -chr1 125195 . C T 1518.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.9963;MLEAC=2;MLEAF=1.00;MQ=51.70;MQ0=0;QD=25.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1547,123,0 -chr1 125207 . G A 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.326;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.99;ReadPosRankSum=2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:379,0,880 -chr1 125210 . C T 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.296;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.050;QD=8.89;ReadPosRankSum=2.309;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:375,0,828 -chr1 125216 . G C 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.307;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.26;MQ0=0;MQRankSum=-5.080;QD=8.81;ReadPosRankSum=1.918;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:372,0,862 -chr1 125248 . T C 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=49;Dels=0.00;FS=1.304;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=51.96;MQ0=1;MQRankSum=-3.990;QD=12.14;ReadPosRankSum=-0.686;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:623,0,932 -chr1 125250 . C T 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.022;DP=47;Dels=0.00;FS=2.895;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=52.33;MQ0=1;MQRankSum=4.261;QD=18.97;ReadPosRankSum=0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,27:47:99:920,0,541 -chr1 125267 . T C 1345.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.3302;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=32.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1374,111,0 -chr1 125269 . T C 1426.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=51.80;MQ0=1;QD=34.80;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1455,114,0 -chr1 125274 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=49.93;MQ0=1;MQRankSum=3.553;QD=15.80;ReadPosRankSum=0.624;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:755,0,576 -chr1 125306 . A T 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=36;Dels=0.00;FS=1.377;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=1;MQRankSum=-2.732;QD=11.44;ReadPosRankSum=1.772;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,17:36:99:440,0,654 -chr1 125310 . C T 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.769;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=9.9429;MLEAC=1;MLEAF=0.500;MQ=45.70;MQ0=1;MQRankSum=3.388;QD=16.64;ReadPosRankSum=-1.600;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:544,0,362 -chr1 125319 . C T 250.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.05;MQ0=1;MQRankSum=-3.282;QD=8.96;ReadPosRankSum=2.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:279,0,506 -chr1 125322 . T A 873.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.64;MQ0=1;QD=32.36;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:72:902,72,0 -chr1 125330 . T A 876.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.42;MQ0=1;QD=31.31;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,28:28:72:905,72,0 -chr1 125345 . C T 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.830;DP=23;Dels=0.00;FS=1.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.96;MQ0=0;MQRankSum=-3.132;QD=9.86;ReadPosRankSum=-0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:255,0,427 -chr1 125408 . C T 195.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:224,18,0 -chr1 125409 . C G 191.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=31.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:220,18,0 -chr1 125410 . C G 194.84 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.01;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,6:6:18:223,18,0 -chr1 125416 . G T 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=14;Dels=0.00;FS=2.963;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.55;MQ0=0;MQRankSum=1.734;QD=1.00;ReadPosRankSum=-0.822;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,2:14:42:42,0,418 -chr1 125441 . A G 103.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.742;DP=24;Dels=0.00;FS=1.760;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.26;MQ0=1;MQRankSum=-3.324;QD=4.32;ReadPosRankSum=-3.905;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:132,0,545 -chr1 125444 . C T 548.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.594;DP=26;Dels=0.00;FS=1.697;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.30;MQ0=1;MQRankSum=3.652;QD=21.11;ReadPosRankSum=2.746;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,16:26:99:577,0,160 -chr1 125447 . G A 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.535;DP=24;Dels=0.00;FS=1.744;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.32;MQ0=1;MQRankSum=-3.937;QD=6.12;ReadPosRankSum=-2.551;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:175,0,501 -chr1 125453 . G A 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.271;DP=24;Dels=0.00;FS=3.963;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.60;MQ0=1;MQRankSum=-4.062;QD=7.91;ReadPosRankSum=-2.946;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,11:24:99:218,0,462 -chr1 125481 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.995;DP=33;Dels=0.00;FS=3.256;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.76;MQ0=1;MQRankSum=-4.758;QD=8.93;ReadPosRankSum=2.724;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:323,0,666 -chr1 125491 . G C 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.934;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.31;ReadPosRankSum=1.104;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:286,0,566 -chr1 125495 . G A 260.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.953;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.43;ReadPosRankSum=1.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:289,0,560 -chr1 125497 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.689;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.55;ReadPosRankSum=1.274;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:292,0,557 -chr1 125498 . C T 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=25;Dels=0.00;FS=1.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=0;MQRankSum=-4.105;QD=10.19;ReadPosRankSum=1.387;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,9:25:99:283,0,571 -chr1 125503 . A G 263.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.671;DP=26;Dels=0.00;FS=1.657;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.08;MQ0=0;MQRankSum=-4.042;QD=10.14;ReadPosRankSum=1.294;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:292,0,609 -chr1 125509 . C T 1210.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=28.40;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1239,93,0 -chr1 125530 . T C 1192.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.61;MQ0=0;QD=25.52;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1221,93,0 -chr1 125548 . C A 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.637;DP=29;Dels=0.00;FS=9.640;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=2.073;QD=16.13;ReadPosRankSum=0.153;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,15:29:99:496,0,417 -chr1 125550 . G A 1067.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=57.16;MQ0=0;QD=31.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1096,87,0 -chr1 125582 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.929;DP=28;Dels=0.00;FS=3.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.88;MQ0=1;MQRankSum=0.386;QD=21.10;ReadPosRankSum=-0.849;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:10,18:28:99:619,0,268 -chr1 125589 . A T 672.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.41;MQ0=0;QD=28.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,18:18:51:701,51,0 -chr1 125622 . A C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.336;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=1;MQRankSum=-0.542;QD=19.26;ReadPosRankSum=-0.251;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:837,0,537 -chr1 125640 . G T 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.195;DP=41;Dels=0.00;FS=2.681;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-1.405;QD=14.29;ReadPosRankSum=3.533;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:614,0,776 -chr1 125691 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=44;Dels=0.00;FS=4.165;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-2.085;QD=13.79;ReadPosRankSum=-0.308;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,19:44:99:635,0,863 -chr1 125721 . T G 219.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.694;DP=36;Dels=0.00;FS=1.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-1.754;QD=6.10;ReadPosRankSum=0.913;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,9:36:99:248,0,910 -chr1 125736 . T C 235.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.326;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-1.023;QD=7.61;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:264,0,762 -chr1 125740 . A G 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-1.249;QD=8.20;ReadPosRankSum=-1.014;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,9:29:99:266,0,653 -chr1 125759 . T C 320.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.697;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=-3.079;QD=11.06;ReadPosRankSum=-0.652;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:349,0,542 -chr1 125772 . C G 360.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.466;DP=26;Dels=0.00;FS=8.852;HaplotypeScore=17.6766;MLEAC=1;MLEAF=0.500;MQ=55.71;MQ0=0;MQRankSum=-4.089;QD=13.88;ReadPosRankSum=-0.489;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:389,0,400 -chr1 125787 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=26;Dels=0.00;FS=12.825;HaplotypeScore=2.9982;MLEAC=1;MLEAF=0.500;MQ=55.75;MQ0=0;MQRankSum=1.463;QD=0.57;ReadPosRankSum=-2.801;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,3:26:43:43,0,723 -chr1 125794 . C T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.246;DP=25;Dels=0.00;FS=1.697;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-4.243;QD=12.43;ReadPosRankSum=1.670;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:339,0,466 -chr1 125810 . G T 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.54;MQ0=0;MQRankSum=-4.808;QD=9.17;ReadPosRankSum=1.750;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:331,0,680 -chr1 125834 . T G 1147.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.621;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7719;MLEAC=2;MLEAF=1.00;MQ=58.76;MQ0=0;MQRankSum=-0.503;QD=26.31;ReadPosRankSum=-1.286;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,30:31:70:1176,70,0 -chr1 126025 . G A 1160.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=54.1245;MLEAC=2;MLEAF=1.00;MQ=47.94;MQ0=0;QD=26.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1189,90,0 -chr1 126059 . T C 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.273;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.52;ReadPosRankSum=-2.721;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:590,0,540 -chr1 126061 . T A 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.514;DP=34;Dels=0.00;FS=7.712;HaplotypeScore=13.5642;MLEAC=1;MLEAF=0.500;MQ=46.49;MQ0=0;MQRankSum=4.960;QD=16.40;ReadPosRankSum=-3.341;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:586,0,522 -chr1 126072 . G A 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.927;DP=28;Dels=0.00;FS=6.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.25;MQ0=0;MQRankSum=-4.480;QD=11.53;ReadPosRankSum=1.648;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:351,0,542 -chr1 126082 . A T 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.310;DP=19;Dels=0.00;FS=7.701;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.40;MQ0=0;MQRankSum=-3.592;QD=9.46;ReadPosRankSum=1.479;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,7:19:99:208,0,430 -chr1 126524 . G A 622.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.99;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:651,51,0 -chr1 126529 . T A 646.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=27.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:675,51,0 -chr1 126531 . C T 649.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=30.09;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:678,51,0 -chr1 126536 . G A 653.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.36;MQ0=0;QD=25.84;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:682,51,0 -chr1 126547 . G A 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=25;Dels=0.00;FS=13.262;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.44;MQ0=0;MQRankSum=0.082;QD=16.95;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,13:25:99:452,0,359 -chr1 126551 . A G 380.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.496;DP=25;Dels=0.00;FS=13.829;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=48.34;MQ0=0;MQRankSum=0.027;QD=15.23;ReadPosRankSum=4.215;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,12:25:99:409,0,391 -chr1 126556 . T C 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.263;DP=24;Dels=0.00;FS=26.945;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.95;MQ0=0;MQRankSum=-0.381;QD=12.41;ReadPosRankSum=4.070;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:326,0,444 -chr1 126572 . G C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.553;DP=49;Dels=0.00;FS=4.366;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=0;MQRankSum=-3.829;QD=8.40;ReadPosRankSum=0.618;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,15:49:99:440,0,1091 -chr1 126583 . C T 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.466;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-1.853;QD=19.55;ReadPosRankSum=5.365;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:947,0,591 -chr1 126584 . G A 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.103;DP=47;Dels=0.00;FS=2.763;HaplotypeScore=12.9923;MLEAC=1;MLEAF=0.500;MQ=50.69;MQ0=0;MQRankSum=-4.028;QD=8.53;ReadPosRankSum=1.677;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,15:47:99:429,0,1116 -chr1 126595 . A T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.488;DP=52;Dels=0.00;FS=2.606;HaplotypeScore=22.9737;MLEAC=1;MLEAF=0.500;MQ=51.73;MQ0=0;MQRankSum=-4.709;QD=8.67;ReadPosRankSum=2.092;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:479,0,1271 -chr1 126599 . G T 1355.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.510;DP=50;Dels=0.00;FS=1.289;HaplotypeScore=32.9690;MLEAC=1;MLEAF=0.500;MQ=52.25;MQ0=0;MQRankSum=-2.510;QD=27.12;ReadPosRankSum=-1.715;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:12,38:50:99:1384,0,313 -chr1 126603 . A G 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.988;DP=50;Dels=0.00;FS=2.527;HaplotypeScore=32.7034;MLEAC=1;MLEAF=0.500;MQ=52.38;MQ0=0;MQRankSum=-4.690;QD=8.90;ReadPosRankSum=4.066;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:34,16:50:99:473,0,1206 -chr1 126605 . C T 779.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.369;HaplotypeScore=32.7046;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=3.501;QD=15.29;ReadPosRankSum=-4.331;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:808,0,893 -chr1 126609 . C T 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.515;DP=50;Dels=0.00;FS=2.429;HaplotypeScore=30.7052;MLEAC=1;MLEAF=0.500;MQ=52.80;MQ0=0;MQRankSum=-2.243;QD=17.32;ReadPosRankSum=3.641;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,26:50:99:894,0,800 -chr1 126615 . T A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.333;DP=53;Dels=0.00;FS=8.297;HaplotypeScore=11.7855;MLEAC=1;MLEAF=0.500;MQ=54.30;MQ0=0;MQRankSum=-5.840;QD=8.94;ReadPosRankSum=4.602;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:502,0,1303 -chr1 126645 . G A 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.957;DP=65;Dels=0.00;FS=13.603;HaplotypeScore=100.5169;MLEAC=1;MLEAF=0.500;MQ=55.52;MQ0=0;MQRankSum=-5.977;QD=5.77;ReadPosRankSum=-1.607;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,16:65:99:403,0,1747 -chr1 126670 . C T 634.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.047;DP=54;Dels=0.00;FS=1.105;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-1.100;QD=11.75;ReadPosRankSum=-0.710;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:33,21:54:99:663,0,1180 -chr1 126698 . T C 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.857;DP=55;Dels=0.00;FS=8.472;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.76;MQ0=0;MQRankSum=2.036;QD=22.43;ReadPosRankSum=2.161;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1262,0,539 -chr1 126702 . T C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.824;DP=58;Dels=0.00;FS=16.756;HaplotypeScore=5.9982;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.515;QD=9.98;ReadPosRankSum=-2.609;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:38,20:58:99:607,0,1364 -chr1 126709 . C T 292.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.843;DP=54;Dels=0.00;FS=4.827;HaplotypeScore=4.9981;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.447;QD=5.42;ReadPosRankSum=-0.697;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:42,12:54:99:321,0,1519 -chr1 126712 . A T 2169.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=9.9949;MLEAC=2;MLEAF=1.00;MQ=59.76;MQ0=0;QD=27.57;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2198,166,0 -chr1 126725 . G T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=57;Dels=0.00;FS=9.993;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=1.729;QD=12.00;ReadPosRankSum=-1.418;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:35,22:57:99:712,0,1228 -chr1 126730 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=53;Dels=0.00;FS=6.032;HaplotypeScore=9.9931;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.467;QD=9.18;ReadPosRankSum=-2.601;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:515,0,1208 -chr1 126761 . C A 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.830;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=2.9989;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=1.910;QD=16.77;ReadPosRankSum=-0.350;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:850,0,808 -chr1 126795 . T A 1211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=58;Dels=0.00;FS=1.054;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.462;QD=20.89;ReadPosRankSum=1.685;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,35:58:99:1240,0,735 -chr1 126808 . C T 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.677;DP=61;Dels=0.00;FS=3.491;HaplotypeScore=16.9835;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-3.792;QD=1.68;ReadPosRankSum=-0.502;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:53,8:61:99:131,0,1927 -chr1 126813 . C A 98.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=62;Dels=0.00;FS=3.493;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.433;QD=1.59;ReadPosRankSum=0.304;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,8:62:99:127,0,1961 -chr1 126818 . A T 1188.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.396;DP=60;Dels=0.00;FS=3.656;HaplotypeScore=46.9121;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=-1.381;QD=19.81;ReadPosRankSum=-0.083;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:24,36:60:99:1217,0,765 -chr1 126828 . G A 1176.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.847;DP=64;Dels=0.00;FS=3.468;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.035;QD=18.39;ReadPosRankSum=0.616;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,36:64:99:1205,0,913 -chr1 126853 . C T 183.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=65;Dels=0.00;FS=24.367;HaplotypeScore=18.9957;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-2.099;QD=2.83;ReadPosRankSum=-0.102;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:54,11:65:99:212,0,1982 -chr1 126860 . A C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.719;DP=68;Dels=0.00;FS=20.308;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=1;MQRankSum=-1.259;QD=2.08;ReadPosRankSum=0.450;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,10:68:99:170,0,2073 -chr1 126861 . T A 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.510;DP=69;Dels=0.00;FS=6.505;HaplotypeScore=26.9946;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=0.043;QD=15.01;ReadPosRankSum=1.333;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:36,33:69:99:1064,0,1239 -chr1 126865 . G C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.017;DP=69;Dels=0.00;FS=24.072;HaplotypeScore=18.9966;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-0.684;QD=2.62;ReadPosRankSum=0.043;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:58,11:69:99:209,0,2116 -chr1 126883 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.091;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=0.724;QD=7.50;ReadPosRankSum=0.943;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:50,19:69:99:546,0,1802 -chr1 126896 . G T 1175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.676;DP=66;Dels=0.00;FS=6.828;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=1;MQRankSum=0.099;QD=17.81;ReadPosRankSum=-1.057;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1204,0,1011 -chr1 126923 . A G 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=68;Dels=0.00;FS=11.174;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=1;MQRankSum=1.555;QD=9.54;ReadPosRankSum=-1.395;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:46,22:68:99:677,0,1574 -chr1 126945 . A T 301.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.121;DP=63;Dels=0.00;FS=9.115;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=1;MQRankSum=0.380;QD=4.79;ReadPosRankSum=0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,14:63:99:330,0,1740 -chr1 126957 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.697;DP=59;Dels=0.00;FS=5.370;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=1;MQRankSum=0.773;QD=2.47;ReadPosRankSum=1.289;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:49,10:59:99:174,0,1767 -chr1 126959 . A G 174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=55;Dels=0.00;FS=5.678;HaplotypeScore=18.9933;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-0.116;QD=3.18;ReadPosRankSum=0.812;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:45,10:55:99:203,0,1601 -chr1 126963 . C A 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=54;Dels=0.00;FS=19.876;HaplotypeScore=17.9934;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-0.135;QD=13.01;ReadPosRankSum=0.695;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:731,0,1059 -chr1 126974 . G A 1026.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.932;DP=53;Dels=0.00;FS=4.336;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=1;MQRankSum=-0.448;QD=19.37;ReadPosRankSum=-0.858;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:21,32:53:99:1055,0,636 -chr1 126988 . T C 66.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.09;MQ0=1;MQRankSum=-0.179;QD=1.42;ReadPosRankSum=-0.636;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:40,7:47:95:95,0,1426 -chr1 127068 . T C 919.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.25;MQ0=0;QD=27.97;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:948,72,0 -chr1 127210 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.118;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=1.8245;MLEAC=1;MLEAF=0.500;MQ=53.31;MQ0=0;MQRankSum=1.532;QD=1.71;ReadPosRankSum=-1.296;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,2:11:47:47,0,276 -chr1 127231 . C A 235.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.94;MQ0=0;QD=33.69;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:264,21,0 -chr1 127271 . G A 273.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.262;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.35;MQ0=0;MQRankSum=2.262;QD=24.89;ReadPosRankSum=0.566;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:3,8:11:24:302,24,0 -chr1 127280 . C T 285.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=38.63;MQ0=2;QD=23.82;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:314,24,0 -chr1 127338 . C T 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.92;MQ0=0;MQRankSum=0.731;QD=15.01;ReadPosRankSum=0.731;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:1,4:5:12:103,0,12 -chr1 127348 . G A 75.03 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.720;DP=6;Dels=0.00;FS=6.021;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.23;MQ0=0;MQRankSum=0.720;QD=12.51;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:2,4:6:12:103,0,12 -chr1 127382 . C T 90.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.568;DP=10;Dels=0.00;FS=11.181;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=35.14;MQ0=0;MQRankSum=2.383;QD=9.08;ReadPosRankSum=-0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:6,4:10:43:119,0,43 -chr1 127438 . G T 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=27;Dels=0.00;FS=15.441;HaplotypeScore=6.0290;MLEAC=1;MLEAF=0.500;MQ=25.45;MQ0=5;MQRankSum=2.404;QD=11.51;ReadPosRankSum=1.469;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:13,14:27:56:339,0,56 -chr1 127457 . C T 504.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=2.419;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.1428;MLEAC=2;MLEAF=1.00;MQ=26.11;MQ0=5;MQRankSum=0.959;QD=18.03;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:5,23:28:51:533,51,0 -chr1 127490 . G A 323.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.41;MQ0=1;MQRankSum=1.488;QD=21.58;ReadPosRankSum=1.240;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:1,14:15:36:352,36,0 -chr1 127515 . T C 221.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.49;MQ0=0;QD=24.64;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,9:9:24:250,24,0 -chr1 127567 . G A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=35;Dels=0.00;FS=6.623;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=43.19;MQ0=2;MQRankSum=-4.564;QD=1.99;ReadPosRankSum=-3.380;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:23,12:35:98:98,0,737 -chr1 127579 . G C 89.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=39;Dels=0.00;FS=3.519;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.40;MQ0=2;MQRankSum=-4.786;QD=2.30;ReadPosRankSum=-2.028;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:118,0,827 -chr1 127590 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=42;Dels=0.00;FS=4.107;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.59;MQ0=2;MQRankSum=-4.885;QD=1.95;ReadPosRankSum=1.048;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:29,13:42:99:110,0,969 -chr1 127595 . T G 1307.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.28;MQ0=2;QD=29.72;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1336,111,0 -chr1 127637 . A G 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.819;DP=40;Dels=0.00;FS=12.746;HaplotypeScore=2.4098;MLEAC=1;MLEAF=0.500;MQ=51.13;MQ0=0;MQRankSum=-4.973;QD=2.04;ReadPosRankSum=-1.284;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:110,0,984 -chr1 127648 . G A 908.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.114;DP=35;Dels=0.00;FS=12.225;HaplotypeScore=1.8110;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=4.397;QD=25.96;ReadPosRankSum=3.076;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:9,26:35:99:937,0,111 -chr1 127656 . T C 1057.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.13;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1086,81,0 -chr1 127661 . C T 1052.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.96;MQ0=0;QD=32.43;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1081,81,0 -chr1 127677 . T C 998.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.78;MQ0=0;QD=30.02;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,25:27:75:1027,75,0 -chr1 127909 . T A 404.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.68;MQ0=5;QD=19.27;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:42:433,42,0 -chr1 127922 . T C 479.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.69;MQ0=4;QD=22.85;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,21:21:45:508,45,0 -chr1 127948 . A G 614.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.18;MQ0=4;QD=26.73;EFF=UPSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,23:23:51:643,51,0 -chr1 128047 . A G 823.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.02;MQ0=1;QD=29.22;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q26|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,23:23:63:852,63,0 -chr1 128090 . A T 825.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.66;MQ0=1;QD=25.81;EFF=STOP_GAINED(HIGH|NONSENSE|Aga/Tga|R41*|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,32:32:69:854,69,0 -chr1 128144 . C T 1024.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.67;MQ0=0;QD=31.05;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L59|Cc01g00090|mRNA||GSCOCT00012429001|Exon_chr1_127970_128260) GT:AD:DP:GQ:PL 1/1:0,33:33:81:1053,81,0 -chr1 128315 . C T 802.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=29.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 1/1:0,22:22:63:831,63,0 -chr1 128373 . T A 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.675;DP=31;Dels=0.00;FS=10.328;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.35;MQ0=0;MQRankSum=-3.475;QD=1.64;ReadPosRankSum=-1.875;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|) GT:AD:DP:GQ:PL 0/1:25,6:31:79:79,0,886 -chr1 128434 . A G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.517;DP=34;Dels=0.00;FS=10.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=-4.271;QD=13.76;ReadPosRankSum=1.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:496,0,567 -chr1 128435 . C A 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.620;DP=34;Dels=0.00;FS=13.315;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.34;MQ0=0;MQRankSum=4.202;QD=15.61;ReadPosRankSum=-1.929;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:559,0,495 -chr1 128484 . G A 511.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.879;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-4.478;QD=17.06;ReadPosRankSum=0.460;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:540,0,432 -chr1 128493 . A G 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.428;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.90;MQ0=0;MQRankSum=-4.008;QD=15.96;ReadPosRankSum=0.507;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:13,15:28:99:475,0,439 -chr1 128534 . G T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.215;DP=28;Dels=0.00;FS=5.632;HaplotypeScore=18.3580;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=0;MQRankSum=0.821;QD=1.99;ReadPosRankSum=-2.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,4:28:84:84,0,841 -chr1 128588 . C T 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=37;Dels=0.00;FS=28.800;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.381;QD=17.89;ReadPosRankSum=1.356;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:690,0,561 -chr1 128665 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.03;FS=0.000;HaplotypeScore=3.2953;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1204,93,0 -chr1 128691 . G A 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.043;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=4;MQRankSum=-0.764;QD=6.66;ReadPosRankSum=-0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,11:39:99:288,0,846 -chr1 128700 . T C 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=5;MQRankSum=-1.458;QD=4.21;ReadPosRankSum=-0.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,8:37:99:184,0,862 -chr1 128703 . A G 146.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.686;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-0.441;QD=4.19;ReadPosRankSum=-0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:175,0,799 -chr1 128705 . C T 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.53;MQ0=5;MQRankSum=-0.969;QD=4.27;ReadPosRankSum=0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:182,0,890 -chr1 128706 . A G 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.275;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.40;MQ0=5;MQRankSum=-1.471;QD=4.59;ReadPosRankSum=0.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:189,0,851 -chr1 128741 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.822;DP=49;Dels=0.00;FS=18.338;HaplotypeScore=2.9979;MLEAC=1;MLEAF=0.500;MQ=54.84;MQ0=3;MQRankSum=-1.889;QD=10.67;ReadPosRankSum=2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:551,0,903 -chr1 128751 . A G 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.379;DP=53;Dels=0.00;FS=22.251;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=3;MQRankSum=-1.700;QD=9.75;ReadPosRankSum=3.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:545,0,1055 -chr1 128795 . G A 820.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.675;DP=55;Dels=0.00;FS=5.871;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-3.881;QD=14.92;ReadPosRankSum=-1.456;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:849,0,927 -chr1 128807 . T C 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.729;DP=57;Dels=0.00;FS=5.835;HaplotypeScore=10.9974;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.485;QD=12.96;ReadPosRankSum=3.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:767,0,1052 -chr1 128808 . C T 2130.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=11.9972;MLEAC=2;MLEAF=1.00;MQ=56.00;MQ0=0;QD=30.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2159,165,0 -chr1 128816 . A G 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=56;Dels=0.00;FS=11.033;HaplotypeScore=23.9742;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=0.409;QD=5.35;ReadPosRankSum=-2.905;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,12:56:99:328,0,1466 -chr1 128821 . G T 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=54;Dels=0.00;FS=1.128;HaplotypeScore=13.9934;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=0;MQRankSum=-1.961;QD=19.50;ReadPosRankSum=3.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,34:54:99:1081,0,641 -chr1 128823 . C T 952.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;DP=51;Dels=0.00;FS=1.146;HaplotypeScore=22.8239;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-0.718;QD=18.68;ReadPosRankSum=2.727;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:981,0,699 -chr1 128833 . C T 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.443;DP=53;Dels=0.00;FS=6.025;HaplotypeScore=10.8296;MLEAC=1;MLEAF=0.500;MQ=57.48;MQ0=0;MQRankSum=-0.580;QD=3.51;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,10:53:99:214,0,1479 -chr1 128853 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=49;Dels=0.00;FS=11.665;HaplotypeScore=1.6634;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.294;QD=3.67;ReadPosRankSum=1.902;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:39,9:49:99:208,0,1382 -chr1 128899 . G A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.178;DP=38;Dels=0.00;FS=4.943;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=0;MQRankSum=-3.084;QD=11.84;ReadPosRankSum=-1.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:478,0,618 -chr1 128911 . T C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.951;DP=51;Dels=0.00;FS=1.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-2.607;QD=3.39;ReadPosRankSum=-3.817;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:201,0,1364 -chr1 128916 . G A 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.605;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-1.816;QD=3.41;ReadPosRankSum=-2.706;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:42,9:51:99:202,0,1455 -chr1 128946 . A G 568.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=60;Dels=0.00;FS=2.267;HaplotypeScore=13.9962;MLEAC=1;MLEAF=0.500;MQ=56.81;MQ0=0;MQRankSum=-1.741;QD=9.48;ReadPosRankSum=1.787;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:38,22:60:99:597,0,1331 -chr1 128948 . A C 588.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.669;DP=62;Dels=0.00;FS=1.018;HaplotypeScore=31.9736;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-2.302;QD=9.50;ReadPosRankSum=1.640;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:40,22:62:99:617,0,1424 -chr1 128956 . C G 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=47.9525;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=0.097;QD=7.15;ReadPosRankSum=1.620;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:493,0,1642 -chr1 128957 . T G 1312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=33.9668;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.149;QD=20.84;ReadPosRankSum=1.949;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1341,0,755 -chr1 128961 . G A 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.635;DP=63;Dels=0.00;FS=2.198;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.06;MQ0=0;MQRankSum=-1.577;QD=19.96;ReadPosRankSum=1.877;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:23,40:63:99:1286,0,756 -chr1 128975 . G T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=33.8278;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-0.350;QD=10.39;ReadPosRankSum=-0.311;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,23:68:99:735,0,1596 -chr1 128988 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.066;DP=73;Dels=0.00;FS=12.861;HaplotypeScore=23.3284;MLEAC=1;MLEAF=0.500;MQ=59.60;MQ0=0;MQRankSum=-0.345;QD=5.52;ReadPosRankSum=1.976;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:55,17:73:99:431,0,2010 -chr1 129160 . A T 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.395;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=53.02;MQ0=0;MQRankSum=-5.688;QD=4.52;ReadPosRankSum=-1.880;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:48,15:63:99:313,0,1702 -chr1 129165 . G T 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.047;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-5.619;QD=4.83;ReadPosRankSum=-1.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,15:61:99:323,0,1605 -chr1 129168 . A G 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.381;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-5.671;QD=4.71;ReadPosRankSum=-0.542;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:47,15:62:99:320,0,1616 -chr1 129170 . G T 2364.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.46;MQ0=0;QD=33.61;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2393,187,0 -chr1 129174 . T A 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.686;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.87;MQ0=0;MQRankSum=-5.798;QD=4.36;ReadPosRankSum=1.384;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:50,16:66:99:316,0,1690 -chr1 129186 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.619;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.94;MQ0=1;MQRankSum=-6.469;QD=6.53;ReadPosRankSum=1.121;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:46,23:69:99:479,0,1553 -chr1 129201 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.234;DP=58;Dels=0.00;FS=2.756;HaplotypeScore=12.9038;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=1;MQRankSum=1.307;QD=5.62;ReadPosRankSum=1.103;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:44,14:58:99:354,0,1347 -chr1 129215 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.088;DP=44;Dels=0.00;FS=1.218;HaplotypeScore=9.9234;MLEAC=1;MLEAF=0.500;MQ=51.67;MQ0=1;MQRankSum=-4.732;QD=10.43;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:487,0,829 -chr1 129227 . T C 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=2.3660;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=1;MQRankSum=-4.330;QD=5.34;ReadPosRankSum=1.719;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:199,0,742 -chr1 129279 . T G 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.257;DP=43;Dels=0.00;FS=7.514;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=55.76;MQ0=2;MQRankSum=-0.257;QD=20.27;ReadPosRankSum=-4.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,28:43:99:900,0,484 -chr1 129287 . G A 991.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.143;DP=45;Dels=0.00;FS=10.631;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=55.96;MQ0=2;MQRankSum=-1.076;QD=22.04;ReadPosRankSum=-3.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:14,31:45:99:1020,0,440 -chr1 129320 . T A 1123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.339;DP=51;Dels=0.00;FS=20.436;HaplotypeScore=2.9997;MLEAC=1;MLEAF=0.500;MQ=57.21;MQ0=3;MQRankSum=0.864;QD=22.03;ReadPosRankSum=3.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1152,0,502 -chr1 129323 . A G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.889;DP=48;Dels=0.00;FS=17.838;HaplotypeScore=3.9996;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=3;MQRankSum=0.605;QD=21.10;ReadPosRankSum=3.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,31:48:99:1041,0,518 -chr1 129341 . C G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=57;Dels=0.00;FS=17.030;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=6;MQRankSum=-1.618;QD=3.28;ReadPosRankSum=-3.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:43,14:57:99:215,0,1547 -chr1 129364 . G A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.104;DP=53;Dels=0.00;FS=30.019;HaplotypeScore=14.7852;MLEAC=1;MLEAF=0.500;MQ=56.85;MQ0=5;MQRankSum=-1.619;QD=5.17;ReadPosRankSum=0.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:37,16:53:99:302,0,1331 -chr1 129366 . C T 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.951;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=12.7857;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=5;MQRankSum=2.207;QD=16.03;ReadPosRankSum=-0.714;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,729 -chr1 129393 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.105;DP=49;Dels=0.00;FS=6.439;HaplotypeScore=51.4904;MLEAC=1;MLEAF=0.500;MQ=57.40;MQ0=1;MQRankSum=-1.665;QD=10.87;ReadPosRankSum=1.560;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:29,20:49:99:561,0,1020 -chr1 129409 . C T 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.755;DP=52;Dels=0.00;FS=15.514;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=1;MQRankSum=-1.292;QD=7.01;ReadPosRankSum=2.326;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,16:52:99:393,0,1247 -chr1 129415 . T G 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.131;DP=49;Dels=0.00;FS=10.402;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.60;MQ0=1;MQRankSum=-1.083;QD=4.57;ReadPosRankSum=1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,13:49:99:252,0,1255 -chr1 129421 . A G 204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.641;DP=47;Dels=0.00;FS=10.402;HaplotypeScore=14.7307;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.163;QD=4.36;ReadPosRankSum=1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:36,11:47:99:233,0,1272 -chr1 129428 . T A 80.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;DP=47;Dels=0.00;FS=11.605;HaplotypeScore=14.5195;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=0.749;QD=1.72;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:109,0,1365 -chr1 129430 . T C 1335.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.868;DP=47;Dels=0.00;FS=14.700;HaplotypeScore=13.5208;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.941;QD=28.42;ReadPosRankSum=-1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,40:47:99:1364,0,151 -chr1 129470 . A G 891.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.482;DP=34;Dels=0.00;FS=6.431;HaplotypeScore=3.9295;MLEAC=1;MLEAF=0.500;MQ=56.67;MQ0=0;MQRankSum=3.106;QD=26.23;ReadPosRankSum=3.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,26:34:99:920,0,161 -chr1 129498 . G A 174.9 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.78;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,6:6:15:203,15,0 -chr1 129499 . G A 154.94 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=6;Dels=0.00;FS=4.771;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=0;MQRankSum=0.736;QD=25.82;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:1,5:6:14:183,0,14 -chr1 129592 . A G 656.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.867;DP=20;Dels=0.00;FS=9.777;HaplotypeScore=22.2964;MLEAC=2;MLEAF=1.00;MQ=53.98;MQ0=0;MQRankSum=-1.387;QD=32.85;ReadPosRankSum=-1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,19:20:15:685,15,0 -chr1 129600 . G A 343.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=2.9992;MLEAC=1;MLEAF=0.500;MQ=53.77;MQ0=0;MQRankSum=1.557;QD=13.22;ReadPosRankSum=-0.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:372,0,498 -chr1 129610 . G T 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.411;DP=28;Dels=0.00;FS=28.641;HaplotypeScore=3.7875;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=-2.006;QD=30.10;ReadPosRankSum=0.446;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:3,25:28:36:871,0,36 -chr1 129625 . G A 379.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.306;DP=29;Dels=0.00;FS=12.308;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=56.07;MQ0=0;MQRankSum=-3.476;QD=13.10;ReadPosRankSum=1.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,12:29:99:408,0,556 -chr1 129672 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=10;Dels=0.00;FS=11.761;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.898;QD=1.69;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,2:10:45:45,0,294 -chr1 129688 . T C 517.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.96;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:546,42,0 -chr1 129768 . T C 363.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.11;MQ0=0;QD=30.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:392,30,0 -chr1 129773 . T C 324.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.65;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:27:353,27,0 -chr1 129786 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129790 . T C 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129791 . T A 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129792 . C T 88.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.43;MQ0=0;QD=17.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:116,9,0 -chr1 129814 . A G 86.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.45;MQ0=0;QD=17.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:114,9,0 -chr1 129819 . A T 123.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:151,12,0 -chr1 129823 . T C 124.03 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.28;MQ0=1;QD=17.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:12:152,12,0 -chr1 129890 . C T 551.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.187;DP=39;Dels=0.00;FS=4.523;HaplotypeScore=2.9153;MLEAC=2;MLEAF=1.00;MQ=26.19;MQ0=13;MQRankSum=2.769;QD=14.15;ReadPosRankSum=-2.891;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:15,24:39:28:580,28,0 -chr1 129897 . C A 631.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.036;DP=42;Dels=0.00;FS=4.559;HaplotypeScore=4.7472;MLEAC=2;MLEAF=1.00;MQ=26.06;MQ0=14;MQRankSum=2.939;QD=15.04;ReadPosRankSum=-2.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:18,24:42:37:660,37,0 -chr1 129936 . C T 516.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.057;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=2;MLEAF=1.00;MQ=25.05;MQ0=5;MQRankSum=1.999;QD=19.14;ReadPosRankSum=1.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:6,21:27:48:545,48,0 -chr1 129979 . T C 255.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.81;MQ0=2;QD=21.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:27:284,27,0 -chr1 129983 . C T 208.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=18.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:237,24,0 -chr1 129984 . T C 217.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.67;MQ0=2;QD=19.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,9:11:24:246,24,0 -chr1 130090 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.290;QD=16.48;ReadPosRankSum=-1.448;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,11:12:21:226,21,0 -chr1 130092 . A G 197.8 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.752;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=4.6635;MLEAC=2;MLEAF=1.00;MQ=23.48;MQ0=0;MQRankSum=0.752;QD=16.48;ReadPosRankSum=-0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:21:226,21,0 -chr1 130105 . T G 496.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.063;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=1.6988;MLEAC=2;MLEAF=1.00;MQ=30.50;MQ0=1;MQRankSum=1.449;QD=23.66;ReadPosRankSum=-1.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:3,18:21:45:525,45,0 -chr1 130186 . G A 309.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:338,30,0 -chr1 130188 . G A 307.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.10;MQ0=2;QD=25.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:2,10:12:30:336,30,0 -chr1 130195 . G A 303.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:332,30,0 -chr1 130203 . T C 188.8 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.02;MQ0=0;QD=26.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,7:7:21:217,21,0 -chr1 130297 . C T 396.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:425,33,0 -chr1 130299 . C T 391.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.47;MQ0=0;QD=32.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:420,33,0 -chr1 130317 . G A 482.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=28.92;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:511,39,0 -chr1 130321 . G A 485.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:514,39,0 -chr1 130322 . G A 476.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=31.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:505,39,0 -chr1 130326 . A G 488.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.36;MQ0=0;QD=27.14;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:517,39,0 -chr1 130345 . T C 618.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.48;MQ0=0;QD=32.54;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:647,48,0 -chr1 130362 . C T 595.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.33;MQ0=0;QD=29.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:624,48,0 -chr1 130369 . A G 530.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.78;MQ0=0;QD=34.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:559,42,0 -chr1 130374 . T C 645.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.35;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:674,51,0 -chr1 130382 . T C 389.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.395;DP=19;Dels=0.00;FS=9.745;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.14;MQ0=0;MQRankSum=-1.395;QD=20.51;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:418,0,230 -chr1 130392 . G A 275.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=16;Dels=0.00;FS=10.532;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.73;MQ0=0;MQRankSum=-1.059;QD=17.24;ReadPosRankSum=1.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:304,0,242 -chr1 130395 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.107;DP=17;Dels=0.00;FS=10.843;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.81;MQ0=0;MQRankSum=-1.107;QD=16.63;ReadPosRankSum=1.395;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:8,9:17:99:311,0,277 -chr1 130406 . G A 733.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=0;QD=33.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:762,57,0 -chr1 130422 . G A 680.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=27.30;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:709,54,0 -chr1 130428 . C T 234.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=20;Dels=0.00;FS=13.778;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=55.68;MQ0=0;MQRankSum=0.501;QD=11.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:12,8:20:99:263,0,382 -chr1 130463 . T A 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.131;DP=33;Dels=0.00;FS=33.092;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=0;MQRankSum=1.767;QD=13.30;ReadPosRankSum=0.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:467,0,604 -chr1 130464 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.665;DP=34;Dels=0.00;FS=25.025;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.02;MQ0=0;MQRankSum=-1.006;QD=16.52;ReadPosRankSum=-0.104;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:590,0,499 -chr1 130471 . G T 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.398;DP=36;Dels=0.00;FS=24.517;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.430;QD=13.85;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:527,0,659 -chr1 130515 . C T 710.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.442;DP=43;Dels=0.00;FS=6.930;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.717;QD=16.53;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:739,0,723 -chr1 130542 . C T 93.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.025;DP=53;Dels=0.00;FS=1.790;HaplotypeScore=19.9950;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.161;QD=1.77;ReadPosRankSum=-3.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:45,8:53:99:122,0,1658 -chr1 130586 . C T 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.100;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=0.060;QD=18.68;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:962,0,598 -chr1 130630 . G A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=19.8889;MLEAC=1;MLEAF=0.500;MQ=58.60;MQ0=0;MQRankSum=0.154;QD=17.07;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:745,0,563 -chr1 130682 . A C 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.424;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=-0.407;QD=11.69;ReadPosRankSum=-0.199;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:34,21:55:99:671,0,1176 -chr1 130699 . G A 1434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.851;QD=23.14;ReadPosRankSum=-0.956;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:20,42:62:99:1463,0,623 -chr1 130768 . C T 1247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=53;Dels=0.00;FS=14.260;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.41;MQ0=0;MQRankSum=0.829;QD=23.54;ReadPosRankSum=-1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1276,0,522 -chr1 130839 . A G 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=2.873;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.222;QD=17.69;ReadPosRankSum=1.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:665,0,568 -chr1 130852 . C G 1575.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.648;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.127;QD=22.42;ReadPosRankSum=0.887;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|) GT:AD:DP:GQ:PL 1/1:1,40:41:99:1604,120,0 -chr1 130914 . A G 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.017;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.258;QD=22.52;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1109,0,452 -chr1 130927 . A C 1100.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.739;DP=48;Dels=0.00;FS=6.248;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.498;QD=22.93;ReadPosRankSum=2.329;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,32:48:99:1129,0,467 -chr1 130951 . A G 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.242;DP=43;Dels=0.00;FS=7.186;HaplotypeScore=26.1290;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=-1.231;QD=23.90;ReadPosRankSum=1.205;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:1056,0,426 -chr1 130966 . A T 1310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=53;Dels=0.00;FS=6.248;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.819;QD=24.73;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,38:53:99:1339,0,440 -chr1 130976 . G C 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.645;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-0.337;QD=9.57;ReadPosRankSum=1.048;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:526,0,1151 -chr1 130992 . C T 1237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.042;DP=57;Dels=0.00;FS=3.924;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.112;QD=21.72;ReadPosRankSum=-1.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,37:57:99:1266,0,611 -chr1 131017 . C G 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.370;DP=49;Dels=0.00;FS=19.446;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=0.850;QD=16.36;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:830,0,803 -chr1 131080 . T C 532.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=39;Dels=0.00;FS=1.261;HaplotypeScore=9.7317;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-0.662;QD=13.66;ReadPosRankSum=-0.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:561,0,711 -chr1 131092 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.419;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=2.039;QD=20.12;ReadPosRankSum=0.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,25:40:99:833,0,436 -chr1 131093 . A T 208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.421;DP=40;Dels=0.00;FS=5.618;HaplotypeScore=29.6879;MLEAC=1;MLEAF=0.500;MQ=54.75;MQ0=0;MQRankSum=-0.234;QD=5.22;ReadPosRankSum=1.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:237,0,1057 -chr1 131106 . A G 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.361;DP=32;Dels=0.00;FS=8.080;HaplotypeScore=2.9994;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-2.945;QD=13.59;ReadPosRankSum=-0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:463,0,546 -chr1 131121 . C T 540.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.467;DP=34;Dels=0.00;FS=5.188;HaplotypeScore=15.7761;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-3.640;QD=15.90;ReadPosRankSum=-2.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:569,0,510 -chr1 131126 . C A 1433.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=15.7761;MLEAC=2;MLEAF=1.00;MQ=53.11;MQ0=0;QD=32.95;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1462,111,0 -chr1 131132 . C A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.426;DP=44;Dels=0.00;FS=15.097;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.78;MQ0=0;MQRankSum=4.844;QD=17.24;ReadPosRankSum=-1.049;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:787,0,609 -chr1 131154 . A T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=44;Dels=0.00;FS=23.397;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.56;MQ0=0;MQRankSum=-4.184;QD=14.54;ReadPosRankSum=2.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:668,0,759 -chr1 131158 . C T 549.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.954;DP=41;Dels=0.00;FS=21.509;HaplotypeScore=4.4675;MLEAC=1;MLEAF=0.500;MQ=52.27;MQ0=0;MQRankSum=-3.830;QD=13.41;ReadPosRankSum=2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:578,0,692 -chr1 131163 . T C 1650.77 . AC=2;AF=1.00;AN=2;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=3.4677;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=32.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,45:45:99:1679,129,0 -chr1 131170 . T G 560.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.488;DP=49;Dels=0.00;FS=38.825;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=51.91;MQ0=0;MQRankSum=-3.211;QD=11.44;ReadPosRankSum=1.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:589,0,938 -chr1 131184 . G A 432.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.436;DP=49;Dels=0.00;FS=38.784;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.16;MQ0=2;MQRankSum=-3.020;QD=8.83;ReadPosRankSum=-0.595;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:461,0,1001 -chr1 131207 . G T 418.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.185;DP=42;Dels=0.00;FS=27.416;HaplotypeScore=4.4038;MLEAC=1;MLEAF=0.500;MQ=48.07;MQ0=2;MQRankSum=-3.576;QD=9.97;ReadPosRankSum=-4.554;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:447,0,821 -chr1 131225 . C G 247.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.578;DP=40;Dels=0.00;FS=16.577;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.44;MQ0=3;MQRankSum=-2.808;QD=6.19;ReadPosRankSum=-0.548;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:276,0,822 -chr1 131249 . C T 126.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.731;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.12;MQ0=0;MQRankSum=0.731;QD=25.21;ReadPosRankSum=-0.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:1,4:5:12:154,12,0 -chr1 131267 . T A 654.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.56;MQ0=1;QD=34.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,19:19:51:683,51,0 -chr1 131275 . T C 693.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.79;MQ0=1;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,20:20:54:722,54,0 -chr1 131301 . T C 198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.737;DP=31;Dels=0.00;FS=14.239;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=57.02;MQ0=3;MQRankSum=0.331;QD=6.41;ReadPosRankSum=-2.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,10:31:99:227,0,719 -chr1 131355 . A G 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.377;DP=32;Dels=0.00;FS=6.200;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=1;MQRankSum=0.099;QD=15.24;ReadPosRankSum=0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:516,0,481 -chr1 131363 . A C 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.895;DP=30;Dels=0.00;FS=4.091;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=1;MQRankSum=-1.768;QD=15.03;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:479,0,438 -chr1 131370 . T C 438.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.262;DP=35;Dels=0.00;FS=6.017;HaplotypeScore=8.8267;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=1;MQRankSum=2.012;QD=12.54;ReadPosRankSum=0.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:467,0,650 -chr1 131393 . T A 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.277;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-1.006;QD=16.68;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:612,0,506 -chr1 131394 . T G 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.035;DP=35;Dels=0.00;FS=2.127;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.16;MQ0=1;MQRankSum=-2.497;QD=16.71;ReadPosRankSum=0.520;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:613,0,502 -chr1 131430 . C G 1471.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.04;MQ0=1;QD=27.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1500,117,0 -chr1 131432 . G C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.327;DP=42;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=1;MQRankSum=-1.274;QD=17.66;ReadPosRankSum=1.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:18,24:42:99:770,0,563 -chr1 131475 . G T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.053;DP=48;Dels=0.00;FS=2.505;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.99;MQ0=1;MQRankSum=0.096;QD=15.00;ReadPosRankSum=0.947;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:748,0,812 -chr1 131486 . C G 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.407;DP=50;Dels=0.00;FS=2.434;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.59;MQ0=0;MQRankSum=0.601;QD=16.58;ReadPosRankSum=-1.203;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:857,0,830 -chr1 131560 . C T 2155.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=30.7936;MLEAC=2;MLEAF=1.00;MQ=54.35;MQ0=0;QD=30.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2184,169,0 -chr1 131561 . A G 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=33.7934;MLEAC=1;MLEAF=0.500;MQ=52.54;MQ0=0;MQRankSum=4.289;QD=12.63;ReadPosRankSum=2.427;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,25:63:99:824,0,1054 -chr1 131579 . T A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.134;DP=55;Dels=0.00;FS=1.050;HaplotypeScore=2.6642;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=3.452;QD=14.49;ReadPosRankSum=-1.717;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,25:55:99:825,0,902 -chr1 131583 . G A 2053.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.6642;MLEAC=2;MLEAF=1.00;MQ=51.43;MQ0=0;QD=27.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2082,162,0 -chr1 131601 . G A 779.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=26.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:808,63,0 -chr1 131602 . T C 819.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.21;MQ0=0;QD=28.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:848,63,0 -chr1 131633 . G T 907.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.40;MQ0=0;QD=28.45;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:936,69,0 -chr1 131703 . T C 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=1;QD=34.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:55:99:2139,160,0 -chr1 131720 . T C 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.158;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.715;QD=13.65;ReadPosRankSum=4.883;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:779,0,1056 -chr1 131746 . G A 1546.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.95;MQ0=2;QD=31.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,42:43:99:1575,120,0 -chr1 131760 . C T 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.593;DP=39;Dels=0.00;FS=7.125;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.06;MQ0=2;MQRankSum=1.717;QD=15.71;ReadPosRankSum=0.927;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:641,0,573 -chr1 131770 . G A,C 1088.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=50.27;MQ0=3;QD=28.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/2:2,18,18:38:99:1278,681,630,597,0,543 -chr1 131775 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.080;DP=35;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQ0=2;MQRankSum=-1.927;QD=13.85;ReadPosRankSum=-1.171;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:513,0,603 -chr1 131776 . G A 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.441;DP=33;Dels=0.00;FS=3.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.73;MQ0=2;MQRankSum=-2.203;QD=12.42;ReadPosRankSum=-0.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:438,0,599 -chr1 131796 . A G 361.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.532;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.71;MQ0=2;MQRankSum=-2.445;QD=10.05;ReadPosRankSum=0.780;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,14:36:99:390,0,704 -chr1 131801 . A G 678.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.91;MQ0=2;MQRankSum=2.114;QD=19.39;ReadPosRankSum=-1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:707,0,371 -chr1 131805 . G C 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.002;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=2.434;QD=19.64;ReadPosRankSum=-1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:39:99:794,0,392 -chr1 131806 . A G 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.239;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.83;MQ0=2;MQRankSum=-2.752;QD=9.10;ReadPosRankSum=1.129;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:383,0,799 -chr1 131818 . T C 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.568;DP=39;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.16;MQ0=2;MQRankSum=-2.677;QD=7.05;ReadPosRankSum=0.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:303,0,803 -chr1 131851 . A G 306.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=41;Dels=0.00;FS=5.599;HaplotypeScore=20.1968;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=1;MQRankSum=-3.302;QD=7.48;ReadPosRankSum=-1.506;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:41:99:335,0,851 -chr1 131940 . C T 523.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=33;Dels=0.00;FS=13.038;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.25;MQ0=1;MQRankSum=0.537;QD=15.87;ReadPosRankSum=-0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:552,0,366 -chr1 131946 . T G 257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.071;DP=33;Dels=0.00;FS=13.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.15;MQ0=1;MQRankSum=-0.754;QD=7.81;ReadPosRankSum=-0.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:286,0,622 -chr1 131950 . G A 220.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.061;DP=33;Dels=0.00;FS=9.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.67;MQ0=1;MQRankSum=-0.793;QD=6.69;ReadPosRankSum=-0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:249,0,652 -chr1 131964 . T C 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.757;DP=27;Dels=0.00;FS=4.809;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.64;MQ0=1;MQRankSum=-0.976;QD=1.70;ReadPosRankSum=-2.017;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,5:27:74:74,0,639 -chr1 131985 . A T 612.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.63;MQ0=1;QD=29.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:51:641,51,0 -chr1 132042 . C T 418.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.17;MQ0=4;QD=19.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,21:21:36:447,36,0 -chr1 132048 . T A 299.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.822;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.89;MQ0=4;MQRankSum=1.734;QD=16.65;ReadPosRankSum=1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:6,12:18:27:328,27,0 -chr1 132089 . A T 110.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.747;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.9529;MLEAC=2;MLEAF=1.00;MQ=18.63;MQ0=4;MQRankSum=0.747;QD=9.17;ReadPosRankSum=-0.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:138,12,0 -chr1 132209 . C T 107.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=34.81;MQ0=0;QD=26.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:135,12,0 -chr1 132286 . C T 954.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.87;MQ0=1;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:78:983,78,0 -chr1 132307 . T C 759.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.61;MQ0=0;QD=29.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,25:26:63:788,63,0 -chr1 132327 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.844;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.266;QD=7.82;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,314 -chr1 132328 . A T 140.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.755;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.532;QD=7.82;ReadPosRankSum=1.644;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:169,0,315 -chr1 132332 . A T 137.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.400;DP=18;Dels=0.00;FS=4.832;HaplotypeScore=1.9663;MLEAC=1;MLEAF=0.500;MQ=44.38;MQ0=0;MQRankSum=-2.355;QD=7.65;ReadPosRankSum=1.555;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:10,8:18:99:166,0,314 -chr1 132348 . G A 209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.371;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=46.07;MQ0=0;MQRankSum=1.431;QD=8.74;ReadPosRankSum=1.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:15,9:24:99:238,0,433 -chr1 132356 . A C 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.968;DP=24;Dels=0.00;FS=4.738;HaplotypeScore=14.3879;MLEAC=1;MLEAF=0.500;MQ=45.87;MQ0=0;MQRankSum=-2.087;QD=16.82;ReadPosRankSum=-0.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,15:24:99:432,0,228 -chr1 132369 . A T 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.273;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.53;MQ0=0;MQRankSum=-0.634;QD=1.95;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,5:23:73:73,0,558 -chr1 132372 . A T 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.52;ReadPosRankSum=2.068;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:40:40,0,597 -chr1 132376 . T A 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.014;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.51;MQ0=0;MQRankSum=-0.203;QD=0.56;ReadPosRankSum=1.419;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,4:23:41:41,0,600 -chr1 132383 . A C 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.49;MQ0=0;MQRankSum=-0.142;QD=0.75;ReadPosRankSum=-0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,4:20:43:43,0,566 -chr1 132405 . G A 755.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.18;MQ0=2;QD=32.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:60:784,60,0 -chr1 132443 . C T 984.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.73;MQ0=2;QD=29.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1013,78,0 -chr1 132456 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.241;DP=28;Dels=0.00;FS=1.941;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=50.78;MQ0=2;MQRankSum=0.212;QD=22.35;ReadPosRankSum=0.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:9,18:28:99:654,0,184 -chr1 132468 . C G 1263.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.51;MQ0=2;QD=32.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1292,99,0 -chr1 132478 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.382;DP=36;Dels=0.00;FS=3.155;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.69;MQ0=2;MQRankSum=0.673;QD=9.83;ReadPosRankSum=-0.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:382,0,743 -chr1 132621 . A G 898.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=1.9970;MLEAC=2;MLEAF=1.00;MQ=54.48;MQ0=0;MQRankSum=-0.800;QD=34.57;ReadPosRankSum=1.600;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,25:26:42:927,42,0 -chr1 132697 . G T 1425.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.63;MQ0=1;QD=28.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1454,108,0 -chr1 132730 . G C 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=40;Dels=0.00;FS=1.399;HaplotypeScore=2.7317;MLEAC=1;MLEAF=0.500;MQ=52.84;MQ0=1;MQRankSum=-4.323;QD=6.12;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,11:40:99:273,0,1019 -chr1 132737 . C T 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.263;DP=48;Dels=0.00;FS=1.273;HaplotypeScore=23.7282;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=2;MQRankSum=-4.842;QD=7.04;ReadPosRankSum=0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,14:48:99:366,0,1103 -chr1 132780 . A G 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.056;DP=55;Dels=0.00;FS=28.806;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.41;MQ0=1;MQRankSum=2.043;QD=6.52;ReadPosRankSum=-0.819;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:387,0,1434 -chr1 132838 . G A 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.471;DP=60;Dels=0.00;FS=19.671;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.32;MQ0=0;MQRankSum=-0.669;QD=14.03;ReadPosRankSum=1.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:870,0,1128 -chr1 132869 . G T 2120.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.59;MQ0=0;QD=30.38;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2149,166,0 -chr1 132921 . T C 1226.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=47.64;MQ0=0;QD=32.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1255,96,0 -chr1 132922 . T C 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.652;QD=17.87;ReadPosRankSum=1.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:600,0,462 -chr1 132923 . G T 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.083;DP=32;Dels=0.00;FS=15.134;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=47.64;MQ0=0;MQRankSum=-1.842;QD=17.65;ReadPosRankSum=1.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,18:32:99:593,0,451 -chr1 132956 . T C 1509.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=64.3730;MLEAC=2;MLEAF=1.00;MQ=53.28;MQ0=0;QD=28.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1538,117,0 -chr1 133042 . G A 1488.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.72;MQ0=0;QD=34.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1517,120,0 -chr1 133059 . C T 705.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.463;DP=46;Dels=0.00;FS=11.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=0;MQRankSum=-2.139;QD=15.34;ReadPosRankSum=-0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:734,0,651 -chr1 133068 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.081;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=48.47;MQ0=0;MQRankSum=-2.420;QD=14.97;ReadPosRankSum=-0.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:687,0,652 -chr1 133104 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.990;DP=47;Dels=0.00;FS=4.125;HaplotypeScore=2.9633;MLEAC=1;MLEAF=0.500;MQ=52.43;MQ0=0;MQRankSum=1.309;QD=14.85;ReadPosRankSum=-0.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:726,0,732 -chr1 133115 . C G 712.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.406;DP=46;Dels=0.00;FS=2.550;HaplotypeScore=2.9394;MLEAC=1;MLEAF=0.500;MQ=52.55;MQ0=0;MQRankSum=-1.164;QD=15.49;ReadPosRankSum=0.505;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:741,0,689 -chr1 133160 . A T 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=24.1627;MLEAC=1;MLEAF=0.500;MQ=51.45;MQ0=0;MQRankSum=2.042;QD=14.09;ReadPosRankSum=0.744;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:592,0,613 -chr1 133168 . T A 1301.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=72.4881;MLEAC=2;MLEAF=1.00;MQ=50.41;MQ0=0;QD=30.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00090|mRNA||GSCOCT00012429001|),UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1330,105,0 -chr1 133318 . T G 1696.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=56.63;MQ0=0;QD=27.68;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1725,132,0 -chr1 133344 . T C 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.470;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=0.230;QD=15.59;ReadPosRankSum=0.150;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:792,0,735 -chr1 133348 . G T 1903.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.70;MQ0=0;QD=33.82;EFF=UPSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1932,150,0 -chr1 133404 . G T 940.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.824;DP=49;Dels=0.00;FS=1.131;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=3.143;QD=19.20;ReadPosRankSum=0.559;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:20,29:49:99:969,0,589 -chr1 133419 . G C 1742.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.29;MQ0=0;QD=33.58;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1771,138,0 -chr1 133433 . G A 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=0;MQRankSum=-4.245;QD=8.51;ReadPosRankSum=0.593;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:27,12:39:99:360,0,943 -chr1 133435 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=26.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1302,102,0 -chr1 133436 . A T 1250.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.76;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1279,99,0 -chr1 133437 . G C 1319.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.45;MQ0=0;QD=27.96;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1348,102,0 -chr1 133448 . C A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.362;DP=47;Dels=0.00;FS=1.146;HaplotypeScore=1.5317;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-4.461;QD=10.08;ReadPosRankSum=-0.365;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,17:47:99:502,0,1052 -chr1 133453 . C T 520.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.012;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=16.0294;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=0;MQRankSum=-4.142;QD=10.85;ReadPosRankSum=-0.245;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,18:48:99:549,0,976 -chr1 133491 . T A,G 1599.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=57.45;MQ0=0;QD=30.76;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 1/2:0,20,32:52:99:1838,1129,1068,710,0,616 -chr1 133511 . T G 1608.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=57.68;MQ0=0;QD=27.83;EFF=START_GAINED(LOW||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1637,126,0 -chr1 133553 . A G 417.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.865;DP=46;Dels=0.00;FS=8.994;HaplotypeScore=2.6278;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-4.347;QD=9.08;ReadPosRankSum=0.657;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:30,16:46:99:446,0,1041 -chr1 133580 . G T 655.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=46;Dels=0.00;FS=8.283;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=0;MQRankSum=-5.226;QD=14.26;ReadPosRankSum=-1.808;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,21:46:99:684,0,798 -chr1 133584 . G A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.057;DP=45;Dels=0.00;FS=4.288;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-5.037;QD=13.24;ReadPosRankSum=-1.450;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:25,20:45:99:624,0,830 -chr1 133629 . G A 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.488;DP=53;Dels=0.00;FS=2.379;HaplotypeScore=3.9941;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.817;QD=14.45;ReadPosRankSum=0.793;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:28,25:53:99:794,0,922 -chr1 133703 . G A 403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.177;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=53.94;MQ0=0;MQRankSum=-5.657;QD=8.59;ReadPosRankSum=0.492;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:29,18:47:99:432,0,1026 -chr1 133708 . C T 327.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=11.4011;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-4.162;QD=6.83;ReadPosRankSum=-1.463;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:34,14:48:99:356,0,1139 -chr1 133768 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.666;DP=35;Dels=0.00;FS=3.120;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.03;MQ0=0;MQRankSum=-3.499;QD=9.74;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:22,13:35:99:369,0,766 -chr1 133772 . T A 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.647;DP=31;Dels=0.00;FS=1.503;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.798;QD=11.86;ReadPosRankSum=-0.258;EFF=UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UTR_5_PRIME(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269) GT:AD:DP:GQ:PL 0/1:17,14:31:99:396,0,591 -chr1 133877 . G C 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=64;Dels=0.00;FS=2.113;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.82;MQ0=0;MQRankSum=-3.336;QD=12.97;ReadPosRankSum=1.698;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtC|V19|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:858,0,1194 -chr1 133880 . T G 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=9.9811;MLEAC=1;MLEAF=0.500;MQ=48.53;MQ0=0;MQRankSum=-1.770;QD=2.61;ReadPosRankSum=2.191;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcG|S20|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,10:62:99:190,0,1843 -chr1 133924 . C T 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.234;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=14.4642;MLEAC=1;MLEAF=0.500;MQ=50.02;MQ0=1;MQRankSum=-2.145;QD=5.48;ReadPosRankSum=0.419;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P35L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,12:50:99:302,0,1267 -chr1 133955 . C G 156.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.925;DP=31;Dels=0.00;FS=1.768;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=49.62;MQ0=0;MQRankSum=-2.415;QD=5.06;ReadPosRankSum=-1.377;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaC/gaG|D45E|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,8:31:99:185,0,789 -chr1 133985 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.181;DP=21;Dels=0.00;FS=15.849;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.52;MQ0=1;MQRankSum=-2.976;QD=1.42;ReadPosRankSum=-2.032;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C55|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,5:21:58:58,0,571 -chr1 134007 . G T 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.146;DP=26;Dels=0.00;FS=3.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.17;MQ0=1;MQRankSum=-3.466;QD=6.64;ReadPosRankSum=-0.903;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Ttg|V63L|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:201,0,596 -chr1 134011 . C T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=30;Dels=0.00;FS=3.630;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.39;MQ0=1;MQRankSum=-3.372;QD=7.46;ReadPosRankSum=-0.619;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCc/gTc|A64V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:252,0,660 -chr1 134033 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.577;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=39.69;MQ0=2;MQRankSum=-1.710;QD=0.33;ReadPosRankSum=-2.732;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L71|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,6:39:41:41,0,1056 -chr1 134148 . C T 488.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.729;DP=60;Dels=0.00;FS=15.632;HaplotypeScore=2.9570;MLEAC=1;MLEAF=0.500;MQ=39.89;MQ0=8;MQRankSum=1.349;QD=8.15;ReadPosRankSum=0.912;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R110C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,19:60:99:517,0,973 -chr1 134280 . A C 982.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=91;Dels=0.00;FS=2.074;HaplotypeScore=10.4073;MLEAC=1;MLEAF=0.500;MQ=34.28;MQ0=7;MQRankSum=1.802;QD=10.80;ReadPosRankSum=-0.414;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K154Q|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,38:91:99:1011,0,1041 -chr1 134333 . T C 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.529;DP=65;Dels=0.00;FS=5.430;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.88;MQ0=7;MQRankSum=0.576;QD=10.38;ReadPosRankSum=0.734;EFF=SYNONYMOUS_CODING(LOW|SILENT|taT/taC|Y171|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:703,0,1008 -chr1 134354 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.370;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=35.63;MQ0=7;MQRankSum=0.036;QD=9.56;ReadPosRankSum=-0.060;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A178|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:516,0,788 -chr1 134514 . T C 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.334;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.7876;MLEAC=1;MLEAF=0.500;MQ=37.13;MQ0=3;MQRankSum=-2.851;QD=7.28;ReadPosRankSum=-0.527;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgc/Cgc|C232R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:392,0,878 -chr1 134570 . T C 854.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.545;DP=44;Dels=0.00;FS=1.192;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=42.49;MQ0=0;MQRankSum=3.436;QD=19.43;ReadPosRankSum=-1.090;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F250|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:883,0,419 -chr1 134580 . C T 1494.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.09;MQ0=0;QD=33.97;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P254S|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1523,117,0 -chr1 134603 . G T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.9762;MLEAC=1;MLEAF=0.500;MQ=42.98;MQ0=0;MQRankSum=-4.437;QD=12.42;ReadPosRankSum=-1.075;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acT|T261|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:612,0,769 -chr1 134696 . G A 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.174;DP=25;Dels=0.00;FS=7.471;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=32.51;MQ0=1;MQRankSum=1.217;QD=13.63;ReadPosRankSum=-3.187;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R292|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:11,14:25:99:369,0,240 -chr1 134729 . G T 259.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.888;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=3.8313;MLEAC=2;MLEAF=1.00;MQ=20.10;MQ0=6;MQRankSum=1.678;QD=13.67;ReadPosRankSum=1.283;EFF=SYNONYMOUS_CODING(LOW|SILENT|ggG/ggT|G303|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,17:19:30:288,30,0 -chr1 134730 . T G 147.89 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.715;DP=17;Dels=0.00;FS=9.031;HaplotypeScore=3.8313;MLEAC=1;MLEAF=0.500;MQ=18.34;MQ0=6;MQRankSum=0.715;QD=8.70;ReadPosRankSum=1.931;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttc/Gtc|F304V|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:3,14:17:2:174,0,2 -chr1 134755 . G C 619.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.70;MQ0=7;QD=20.66;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S312T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:54:648,54,0 -chr1 134780 . T C 422.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.579;DP=42;Dels=0.00;FS=7.420;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=32.71;MQ0=7;MQRankSum=0.050;QD=10.07;ReadPosRankSum=1.871;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C320|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,16:42:99:451,0,502 -chr1 134807 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.282;DP=53;Dels=0.00;FS=2.402;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=34.74;MQ0=5;MQRankSum=-1.432;QD=14.07;ReadPosRankSum=0.010;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I329|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:774,0,584 -chr1 134822 . T C 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.627;DP=52;Dels=0.00;FS=4.058;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=36.11;MQ0=1;MQRankSum=-2.231;QD=16.55;ReadPosRankSum=0.789;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I334|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,33:52:99:889,0,575 -chr1 134927 . G C 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=5.3557;MLEAC=1;MLEAF=0.500;MQ=26.60;MQ0=9;MQRankSum=1.588;QD=7.44;ReadPosRankSum=-0.677;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E369D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,19:52:99:415,0,456 -chr1 135009 . A G 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.634;DP=56;Dels=0.00;FS=9.949;HaplotypeScore=1.8154;MLEAC=1;MLEAF=0.500;MQ=45.81;MQ0=1;MQRankSum=-2.335;QD=0.23;ReadPosRankSum=-2.281;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T397A|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,6:56:41:41,0,1637 -chr1 135029 . G C 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=68;Dels=0.00;FS=9.976;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.96;MQ0=1;MQRankSum=-1.650;QD=2.79;ReadPosRankSum=-0.245;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L403F|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,11:68:99:218,0,1758 -chr1 135042 . A G 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.577;DP=75;Dels=0.00;FS=8.931;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=39.96;MQ0=1;MQRankSum=3.045;QD=8.50;ReadPosRankSum=0.420;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aac/Gac|N408D|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,22:75:99:666,0,1347 -chr1 135055 . A G 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.310;DP=84;Dels=0.00;FS=10.873;HaplotypeScore=9.3239;MLEAC=1;MLEAF=0.500;MQ=36.61;MQ0=3;MQRankSum=0.553;QD=3.71;ReadPosRankSum=1.854;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gGa|E412G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:340,0,1652 -chr1 135124 . A G 1965.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.982;DP=84;Dels=0.00;FS=3.513;HaplotypeScore=1.9965;MLEAC=1;MLEAF=0.500;MQ=34.13;MQ0=5;MQRankSum=2.897;QD=23.40;ReadPosRankSum=0.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q435R|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,68:84:99:1994,0,139 -chr1 135152 . T C 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.499;DP=86;Dels=0.00;FS=1.215;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=37.34;MQ0=3;MQRankSum=-0.614;QD=1.25;ReadPosRankSum=0.942;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D444|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,14:86:99:136,0,2271 -chr1 135153 . G A 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.997;DP=87;Dels=0.00;FS=1.186;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=37.69;MQ0=3;MQRankSum=-0.409;QD=1.65;ReadPosRankSum=0.537;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtg/Atg|V445M|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,15:87:99:172,0,2269 -chr1 135160 . C G 200.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.067;DP=80;Dels=0.00;FS=2.719;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=38.64;MQ0=3;MQRankSum=0.297;QD=2.51;ReadPosRankSum=1.116;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tGt|S447C|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,14:80:99:229,0,2067 -chr1 135180 . T A 273.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.230;DP=74;Dels=0.00;FS=21.668;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.55;MQ0=0;MQRankSum=1.094;QD=3.70;ReadPosRankSum=1.690;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ttt/Att|F454I|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,13:74:99:302,0,1980 -chr1 135182 . T C 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=73;Dels=0.00;FS=22.648;HaplotypeScore=16.1489;MLEAC=1;MLEAF=0.500;MQ=42.76;MQ0=0;MQRankSum=-0.479;QD=10.89;ReadPosRankSum=1.077;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F454|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,29:73:99:823,0,1443 -chr1 135209 . A G 937.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.127;DP=78;Dels=0.00;FS=18.781;HaplotypeScore=10.8281;MLEAC=1;MLEAF=0.500;MQ=48.03;MQ0=0;MQRankSum=-2.484;QD=12.02;ReadPosRankSum=0.229;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A463|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:966,0,1557 -chr1 135218 . T C 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.068;DP=76;Dels=0.00;FS=7.732;HaplotypeScore=20.2693;MLEAC=1;MLEAF=0.500;MQ=49.54;MQ0=0;MQRankSum=-1.200;QD=6.59;ReadPosRankSum=-0.624;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S466|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,19:76:99:529,0,1942 -chr1 135220 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.987;DP=77;Dels=0.00;FS=5.434;HaplotypeScore=9.4397;MLEAC=1;MLEAF=0.500;MQ=49.95;MQ0=0;MQRankSum=-0.384;QD=6.30;ReadPosRankSum=-0.821;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E467G|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:58,19:77:99:513,0,1945 -chr1 135242 . G T 897.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.801;DP=84;Dels=0.00;FS=4.355;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=52.91;MQ0=0;MQRankSum=-2.169;QD=10.69;ReadPosRankSum=-0.189;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccT|P474|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,32:84:99:926,0,1735 -chr1 135249 . C A 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=83;Dels=0.00;FS=0.951;HaplotypeScore=23.7688;MLEAC=1;MLEAF=0.500;MQ=53.90;MQ0=0;MQRankSum=3.080;QD=7.48;ReadPosRankSum=1.491;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P477T|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,22:83:99:649,0,2002 -chr1 135260 . G C 1586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=1.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=-0.838;QD=20.61;ReadPosRankSum=0.358;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcC|A480|Cc01g00100|mRNA||GSCOCT00012426001|Exon_chr1_133387_135269),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,50:77:99:1615,0,861 -chr1 135276 . C T 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=78;Dels=0.00;FS=3.392;HaplotypeScore=25.9840;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=0.021;QD=9.15;ReadPosRankSum=0.503;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,25:78:99:742,0,1838 -chr1 135284 . A G 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.412;DP=83;Dels=0.00;FS=0.867;HaplotypeScore=45.6804;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=2.555;QD=10.96;ReadPosRankSum=-0.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,30:83:99:938,0,1841 -chr1 135290 . A G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.543;DP=80;Dels=0.00;FS=3.316;HaplotypeScore=43.6813;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=-0.055;QD=11.50;ReadPosRankSum=-0.730;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:948,0,1404 -chr1 135296 . T A 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.491;DP=77;Dels=0.00;FS=3.797;HaplotypeScore=25.7468;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.051;QD=7.83;ReadPosRankSum=0.366;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,22:77:99:631,0,2017 -chr1 135305 . C A 231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.358;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=18.7849;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.819;QD=2.55;ReadPosRankSum=-4.449;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:77,14:91:99:260,0,2802 -chr1 135319 . A G 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.119;DP=101;Dels=0.00;FS=0.864;HaplotypeScore=3.9995;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.932;QD=7.50;ReadPosRankSum=-0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,27:101:99:786,0,2632 -chr1 135362 . G C 521.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.995;DP=104;Dels=0.00;FS=0.933;HaplotypeScore=3.5999;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=-0.569;QD=5.02;ReadPosRankSum=1.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,21:104:99:550,0,2813 -chr1 135376 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=104;Dels=0.00;FS=0.969;HaplotypeScore=2.8632;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-2.044;QD=4.12;ReadPosRankSum=0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:85,19:104:99:457,0,2999 -chr1 135384 . G A 3914.77 . AC=2;AF=1.00;AN=2;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=22.8484;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;QD=33.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,103:103:99:3943,301,0 -chr1 135391 . T G 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.718;DP=103;Dels=0.00;FS=2.944;HaplotypeScore=27.2496;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-0.169;QD=7.15;ReadPosRankSum=0.641;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:103:99:765,0,2417 -chr1 135400 . G A 1703.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.624;DP=108;Dels=0.00;FS=6.146;HaplotypeScore=26.0389;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-2.758;QD=15.78;ReadPosRankSum=-0.354;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,52:108:99:1732,0,1799 -chr1 135425 . T C 2440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.380;DP=100;Dels=0.00;FS=5.702;HaplotypeScore=37.9722;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-2.038;QD=24.41;ReadPosRankSum=-0.257;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,72:100:99:2469,0,843 -chr1 135428 . G T 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=96;Dels=0.00;FS=3.339;HaplotypeScore=38.9718;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-1.010;QD=4.73;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:482,0,2684 -chr1 135433 . G T 404.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=100;Dels=0.00;FS=5.032;HaplotypeScore=76.9445;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-4.688;QD=4.05;ReadPosRankSum=0.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:82,18:100:99:433,0,2862 -chr1 135440 . A T 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.355;DP=97;Dels=0.00;FS=0.920;HaplotypeScore=61.9081;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.804;QD=5.41;ReadPosRankSum=-0.442;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:553,0,2671 -chr1 135443 . C T 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.451;DP=97;Dels=0.00;FS=2.004;HaplotypeScore=60.8069;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-4.533;QD=5.00;ReadPosRankSum=-0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,21:97:99:513,0,2730 -chr1 135446 . C T 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.176;DP=97;Dels=0.00;FS=2.653;HaplotypeScore=42.8139;MLEAC=1;MLEAF=0.500;MQ=56.90;MQ0=0;MQRankSum=-7.372;QD=12.97;ReadPosRankSum=-0.666;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,42:97:99:1286,0,1882 -chr1 135450 . C T 1233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.600;DP=94;Dels=0.00;FS=2.740;HaplotypeScore=39.6045;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-7.169;QD=13.13;ReadPosRankSum=-0.593;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:54,40:94:99:1262,0,1853 -chr1 135469 . C T 1458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=101;Dels=0.00;FS=3.736;HaplotypeScore=21.2632;MLEAC=1;MLEAF=0.500;MQ=56.64;MQ0=0;MQRankSum=-8.200;QD=14.44;ReadPosRankSum=0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:55,46:101:99:1487,0,1800 -chr1 135483 . A C 2726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.152;DP=96;Dels=0.00;FS=0.981;HaplotypeScore=66.5358;MLEAC=1;MLEAF=0.500;MQ=56.79;MQ0=0;MQRankSum=-3.811;QD=28.40;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,75:96:99:2755,0,482 -chr1 135489 . T G 1566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.993;DP=97;Dels=0.00;FS=12.274;HaplotypeScore=43.2734;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-7.619;QD=16.15;ReadPosRankSum=1.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,47:97:99:1595,0,1719 -chr1 135492 . A G 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.233;DP=97;Dels=0.00;FS=1.972;HaplotypeScore=44.2721;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=-4.134;QD=6.52;ReadPosRankSum=0.715;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:661,0,2654 -chr1 135504 . C T 1475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.723;DP=98;Dels=0.00;FS=21.343;HaplotypeScore=21.9832;MLEAC=1;MLEAF=0.500;MQ=57.14;MQ0=0;MQRankSum=-6.623;QD=15.06;ReadPosRankSum=2.581;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:53,45:98:99:1504,0,1796 -chr1 135514 . T A 652.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.982;DP=97;Dels=0.00;FS=12.661;HaplotypeScore=41.9659;MLEAC=1;MLEAF=0.500;MQ=56.88;MQ0=0;MQRankSum=-5.004;QD=6.73;ReadPosRankSum=0.614;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,24:97:99:681,0,2606 -chr1 135517 . C T 1587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.502;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=21.9725;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=2.170;QD=16.71;ReadPosRankSum=1.418;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,48:95:99:1616,0,1560 -chr1 135526 . T G 3368.77 . AC=2;AF=1.00;AN=2;DP=85;Dels=0.00;FS=0.000;HaplotypeScore=53.9823;MLEAC=2;MLEAF=1.00;MQ=57.70;MQ0=0;QD=26.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,85:85:99:3397,256,0 -chr1 135527 . T C 236.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.045;DP=85;Dels=0.00;FS=8.852;HaplotypeScore=80.9742;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-4.243;QD=2.79;ReadPosRankSum=1.642;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,13:85:99:265,0,2552 -chr1 135535 . G A 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.892;DP=82;Dels=0.00;FS=8.551;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-5.078;QD=3.08;ReadPosRankSum=1.676;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:69,13:82:99:281,0,2484 -chr1 135536 . C T 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=79;Dels=0.00;FS=4.308;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=-1.623;QD=4.20;ReadPosRankSum=1.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:52,14:79:99:360,0,1863 -chr1 135537 . A G 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.307;DP=78;Dels=0.00;FS=9.867;HaplotypeScore=39.9876;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.630;QD=11.14;ReadPosRankSum=1.297;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:50,28:78:99:897,0,1742 -chr1 135551 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.458;DP=91;Dels=0.00;FS=9.889;HaplotypeScore=1.9986;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=-4.719;QD=8.24;ReadPosRankSum=-1.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:63,27:91:99:778,0,2232 -chr1 135557 . A C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.109;DP=92;Dels=0.00;FS=11.651;HaplotypeScore=3.9926;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-3.944;QD=8.20;ReadPosRankSum=-1.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:783,0,2240 -chr1 135582 . G A 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.013;DP=97;Dels=0.00;FS=10.159;HaplotypeScore=29.4167;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-4.142;QD=6.48;ReadPosRankSum=2.534;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,24:97:99:657,0,2497 -chr1 135587 . G C 2286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.678;DP=96;Dels=0.00;FS=0.869;HaplotypeScore=28.5846;MLEAC=1;MLEAF=0.500;MQ=58.98;MQ0=0;MQRankSum=0.144;QD=23.82;ReadPosRankSum=0.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,67:96:99:2315,0,856 -chr1 135606 . C A 458.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.585;DP=96;Dels=0.00;FS=2.045;HaplotypeScore=21.9828;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.629;QD=4.78;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,21:96:99:487,0,2576 -chr1 135609 . C A 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.944;DP=93;Dels=0.00;FS=7.797;HaplotypeScore=83.8468;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=-3.424;QD=7.92;ReadPosRankSum=-0.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,27:93:99:765,0,2259 -chr1 135618 . C T 350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.853;DP=89;Dels=0.00;FS=1.036;HaplotypeScore=65.8507;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.727;QD=3.94;ReadPosRankSum=2.134;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,17:89:99:379,0,2429 -chr1 135632 . G C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.374;DP=89;Dels=0.00;FS=3.725;HaplotypeScore=67.7422;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-1.496;QD=4.58;ReadPosRankSum=-0.189;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,18:89:99:436,0,2397 -chr1 135636 . T C 2955.77 . AC=2;AF=1.00;AN=2;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=82.6805;MLEAC=2;MLEAF=1.00;MQ=58.77;MQ0=0;QD=24.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,78:79:99:2984,226,0 -chr1 135637 . A C 1811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.105;DP=80;Dels=0.00;FS=0.000;HaplotypeScore=83.6799;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-0.341;QD=22.65;ReadPosRankSum=-0.215;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,56:80:99:1840,0,664 -chr1 135639 . T G 364.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.448;DP=83;Dels=0.00;FS=11.996;HaplotypeScore=104.6691;MLEAC=1;MLEAF=0.500;MQ=58.83;MQ0=0;MQRankSum=-0.923;QD=4.39;ReadPosRankSum=0.569;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:65,18:83:99:393,0,2312 -chr1 135641 . C T 573.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.648;QD=6.67;ReadPosRankSum=-0.401;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:602,0,2169 -chr1 135642 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.688;DP=86;Dels=0.00;FS=7.119;HaplotypeScore=129.6566;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=2.954;QD=6.71;ReadPosRankSum=-0.144;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:64,22:86:99:605,0,2180 -chr1 135643 . C T 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=90;Dels=0.00;FS=9.549;HaplotypeScore=115.6735;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-2.215;QD=4.20;ReadPosRankSum=0.801;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,19:90:99:406,0,2519 -chr1 135648 . G C 605.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=94;Dels=0.00;FS=0.939;HaplotypeScore=81.8473;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.363;QD=6.44;ReadPosRankSum=-0.062;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:71,23:94:99:634,0,2439 -chr1 135650 . G A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=98;Dels=0.00;FS=0.925;HaplotypeScore=85.9035;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.805;QD=6.04;ReadPosRankSum=0.553;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,23:98:99:620,0,2541 -chr1 135660 . T G 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.004;DP=101;Dels=0.00;FS=0.897;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.059;QD=6.71;ReadPosRankSum=0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,25:101:99:706,0,2603 -chr1 135662 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=101;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=1.122;QD=6.70;ReadPosRankSum=0.532;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:75,26:101:99:705,0,2524 -chr1 135693 . G A 727.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.518;DP=102;Dels=0.00;FS=1.895;HaplotypeScore=1.7219;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=1;MQRankSum=1.915;QD=7.13;ReadPosRankSum=1.270;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:74,28:102:99:756,0,2603 -chr1 135705 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=103;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=1;MQRankSum=0.990;QD=6.44;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:76,26:103:99:692,0,2558 -chr1 135724 . G A 3782.77 . AC=2;AF=1.00;AN=2;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=2;MLEAF=1.00;MQ=58.30;MQ0=1;QD=35.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,97:97:99:3811,286,0 -chr1 135725 . C A 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=98;Dels=0.00;FS=0.000;HaplotypeScore=12.9950;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=2;MQRankSum=0.224;QD=6.62;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:73,25:98:99:677,0,2539 -chr1 135734 . C T 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.312;DP=84;Dels=0.00;FS=9.368;HaplotypeScore=43.9728;MLEAC=1;MLEAF=0.500;MQ=56.92;MQ0=3;MQRankSum=-0.578;QD=2.59;ReadPosRankSum=1.536;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:72,12:84:99:246,0,2508 -chr1 135736 . C G 2208.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.981;DP=87;Dels=0.00;FS=2.092;HaplotypeScore=32.9825;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=3;MQRankSum=-1.198;QD=25.39;ReadPosRankSum=-0.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,66:87:99:2237,0,546 -chr1 135750 . A G 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.586;DP=76;Dels=0.00;FS=5.360;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.60;MQ0=3;MQRankSum=-1.757;QD=1.50;ReadPosRankSum=2.431;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:66,10:76:99:142,0,2292 -chr1 135758 . G T 393.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.643;DP=79;Dels=0.00;FS=5.453;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.66;MQ0=3;MQRankSum=-3.574;QD=4.98;ReadPosRankSum=-1.937;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,18:79:99:422,0,2063 -chr1 135778 . C T 195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.029;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=-4.222;QD=5.93;ReadPosRankSum=2.331;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,8:33:99:224,0,882 -chr1 135782 . G T 167.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.47;MQ0=0;MQRankSum=-3.992;QD=5.41;ReadPosRankSum=3.567;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,7:31:99:196,0,843 -chr1 135800 . C T 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.440;DP=36;Dels=0.00;FS=3.702;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-4.077;QD=3.97;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,7:36:99:171,0,1061 -chr1 135819 . T C 428.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.242;DP=52;Dels=0.00;FS=6.289;HaplotypeScore=11.8640;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=-1.616;QD=8.25;ReadPosRankSum=-2.282;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:457,0,1294 -chr1 135828 . C T 230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.663;DP=51;Dels=0.00;FS=8.174;HaplotypeScore=22.8565;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.593;QD=4.52;ReadPosRankSum=-0.164;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,11:51:99:259,0,1414 -chr1 135836 . G T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.890;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=12.5980;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=4.353;QD=12.80;ReadPosRankSum=2.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,24:60:99:796,0,1231 -chr1 135848 . G A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.467;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=0.656;QD=13.62;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1249 -chr1 135855 . T G 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.541;DP=69;Dels=0.00;FS=0.917;HaplotypeScore=17.9912;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=1.635;QD=13.33;ReadPosRankSum=-2.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,29:69:99:948,0,1381 -chr1 135865 . T C 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.418;DP=67;Dels=0.00;FS=2.217;HaplotypeScore=55.9758;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.993;QD=8.09;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,20:67:99:570,0,1674 -chr1 135868 . A T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.045;DP=65;Dels=0.00;FS=1.000;HaplotypeScore=20.9924;MLEAC=1;MLEAF=0.500;MQ=58.17;MQ0=0;MQRankSum=1.676;QD=9.50;ReadPosRankSum=1.269;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),UPSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,21:65:99:646,0,1554 -chr1 135874 . T C 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.590;DP=70;Dels=0.00;FS=0.954;HaplotypeScore=19.9927;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-2.097;QD=10.60;ReadPosRankSum=-0.176;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTc/tCc|F2S|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:44,26:70:99:770,0,1499 -chr1 135880 . T G 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.422;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-1.102;QD=10.01;ReadPosRankSum=0.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F4C|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:45,24:69:99:719,0,1540 -chr1 135884 . T C 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.749;DP=70;Dels=0.00;FS=2.105;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=58.22;MQ0=0;MQRankSum=-0.179;QD=10.03;ReadPosRankSum=1.132;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H5|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,24:70:99:730,0,1622 -chr1 135900 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.045;DP=74;Dels=0.00;FS=1.994;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.68;MQ0=0;MQRankSum=-0.685;QD=10.38;ReadPosRankSum=0.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_GAINED(HIGH|NONSENSE|Cga/Tga|R11*|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:47,27:74:99:796,0,1573 -chr1 135922 . T C 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=92;Dels=0.00;FS=1.814;HaplotypeScore=1.8319;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.479;QD=9.52;ReadPosRankSum=0.760;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I18T|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:61,31:92:99:904,0,2103 -chr1 135936 . A G 764.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=84;Dels=0.00;FS=4.645;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=1.810;QD=9.10;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T23A|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:57,27:84:99:793,0,1944 -chr1 135937 . C T 1766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.525;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.487;QD=21.55;ReadPosRankSum=-0.188;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T23I|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1795,0,896 -chr1 135938 . A G 1781.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.486;DP=82;Dels=0.00;FS=0.000;HaplotypeScore=25.8884;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.699;QD=21.73;ReadPosRankSum=-0.255;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T23|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,52:82:99:1810,0,895 -chr1 135950 . G A 807.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.094;DP=83;Dels=0.00;FS=4.423;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=0.851;QD=9.73;ReadPosRankSum=-0.919;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K27|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_135870_135972),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:56,27:83:99:836,0,1943 -chr1 135990 . T G 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.534;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=18.3925;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-0.628;QD=8.58;ReadPosRankSum=0.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:46,21:67:99:603,0,1660 -chr1 135994 . A T 2749.77 . AC=2;AF=1.00;AN=2;DP=70;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.86;MQ0=0;QD=31.63;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,70:70:99:2778,211,0 -chr1 136009 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.369;DP=44;Dels=0.00;FS=6.444;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.106;QD=14.20;ReadPosRankSum=-2.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:653,0,848 -chr1 136065 . A T 567.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=46;Dels=0.00;FS=1.150;HaplotypeScore=1.7675;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.035;QD=12.34;ReadPosRankSum=1.749;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,18:46:99:596,0,963 -chr1 136086 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.177;DP=51;Dels=0.00;FS=2.381;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-1.043;QD=12.07;ReadPosRankSum=0.565;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,21:51:99:644,0,1054 -chr1 136090 . A G 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.098;DP=50;Dels=0.00;FS=2.463;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=-1.042;QD=12.52;ReadPosRankSum=-0.059;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:654,0,1012 -chr1 136102 . G A 1209.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.676;DP=59;Dels=0.00;FS=2.203;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.365;QD=20.50;ReadPosRankSum=0.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,36:59:99:1238,0,690 -chr1 136134 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.488;DP=52;Dels=0.00;FS=11.273;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=1.346;QD=8.28;ReadPosRankSum=1.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,17:52:99:459,0,1143 -chr1 136138 . C T 388.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.276;DP=53;Dels=0.00;FS=12.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.93;MQ0=0;MQRankSum=-0.829;QD=7.34;ReadPosRankSum=1.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:36,17:53:99:417,0,1249 -chr1 136150 . G C 528.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.335;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=17.3638;MLEAC=1;MLEAF=0.500;MQ=58.73;MQ0=0;MQRankSum=-0.945;QD=10.37;ReadPosRankSum=-0.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,19:51:99:557,0,1120 -chr1 136165 . A G 483.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.333;DP=49;Dels=0.00;FS=8.545;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=-0.736;QD=9.87;ReadPosRankSum=0.238;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:512,0,993 -chr1 136178 . C T 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.591;DP=49;Dels=0.00;FS=8.560;HaplotypeScore=1.9248;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.250;QD=9.83;ReadPosRankSum=-0.031;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,18:49:99:510,0,1040 -chr1 136208 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.664;DP=40;Dels=0.00;FS=5.407;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.65;MQ0=0;MQRankSum=-2.022;QD=7.12;ReadPosRankSum=-0.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,12:40:99:313,0,1004 -chr1 136237 . T A 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.248;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.694;QD=3.25;ReadPosRankSum=1.152;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:142,0,1006 -chr1 136238 . T A 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.197;DP=35;Dels=0.03;FS=1.803;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-1.423;QD=3.16;ReadPosRankSum=1.242;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,6:34:99:139,0,998 -chr1 136245 . A G 123.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.130;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.151;QD=3.26;ReadPosRankSum=1.280;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:152,0,1108 -chr1 136246 . G A 128.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.582;DP=38;Dels=0.00;FS=1.534;HaplotypeScore=2.9328;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-1.054;QD=3.39;ReadPosRankSum=1.393;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,7:38:99:157,0,1099 -chr1 136281 . A G 1035.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=2.132;QD=20.72;ReadPosRankSum=1.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,32:50:99:1064,0,533 -chr1 136286 . T A 497.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.044;DP=50;Dels=0.00;FS=1.154;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.74;MQ0=0;MQRankSum=1.147;QD=9.96;ReadPosRankSum=-0.430;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:526,0,1136 -chr1 136296 . T C 498.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.294;DP=57;Dels=0.00;FS=2.395;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.166;QD=8.75;ReadPosRankSum=1.526;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:527,0,1372 -chr1 136297 . A C 501.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=57;Dels=0.00;FS=1.124;HaplotypeScore=1.7870;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.951;QD=8.80;ReadPosRankSum=1.788;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:530,0,1359 -chr1 136349 . A G 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.221;DP=55;Dels=0.00;FS=4.256;HaplotypeScore=2.8244;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.501;QD=7.32;ReadPosRankSum=-2.806;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:40,15:55:99:431,0,1458 -chr1 136355 . G A 2168.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=2.7122;MLEAC=2;MLEAF=1.00;MQ=59.70;MQ0=0;QD=25.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2197,163,0 -chr1 136407 . T A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.022;DP=36;Dels=0.00;FS=1.438;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=55.10;MQ0=0;MQRankSum=-4.739;QD=7.63;ReadPosRankSum=1.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,11:36:99:303,0,897 -chr1 136411 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.363;DP=35;Dels=0.00;FS=3.074;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.96;MQ0=0;MQRankSum=-4.708;QD=7.94;ReadPosRankSum=1.723;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,11:35:99:306,0,864 -chr1 136414 . A G 279.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.761;DP=34;Dels=0.00;FS=1.456;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.80;MQ0=0;MQRankSum=-4.675;QD=8.23;ReadPosRankSum=1.951;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,11:34:99:308,0,808 -chr1 136416 . G A 282.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.470;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=54.63;MQ0=0;MQRankSum=-4.640;QD=8.57;ReadPosRankSum=1.814;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:311,0,783 -chr1 136425 . A G 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.487;DP=37;Dels=0.00;FS=4.887;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-5.166;QD=12.29;ReadPosRankSum=0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:483,0,735 -chr1 136429 . G A 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=39;Dels=0.00;FS=6.978;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.85;MQ0=0;MQRankSum=-5.339;QD=12.84;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),INTRON(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:529,0,713 -chr1 136439 . C T 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=42;Dels=0.00;FS=8.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.51;MQ0=0;MQRankSum=-5.553;QD=13.61;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A37V|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:600,0,750 -chr1 136450 . C G 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.709;DP=44;Dels=0.00;FS=8.887;HaplotypeScore=14.9765;MLEAC=1;MLEAF=0.500;MQ=51.92;MQ0=0;MQRankSum=-5.669;QD=12.77;ReadPosRankSum=0.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Gat|H41D|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:590,0,832 -chr1 136462 . G A 354.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;DP=37;Dels=0.00;FS=5.041;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=51.93;MQ0=0;MQRankSum=-4.995;QD=9.59;ReadPosRankSum=1.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E45K|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:383,0,810 -chr1 136465 . T A 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.278;DP=36;Dels=0.00;FS=5.077;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.37;MQ0=0;MQRankSum=-5.070;QD=11.02;ReadPosRankSum=1.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),STOP_LOST(HIGH|MISSENSE|Tga/Aga|*46R|Cc01g00110|mRNA||GSCOCT00012425001|Exon_chr1_136433_136467),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,15:36:99:425,0,704 -chr1 136487 . G T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.53;ReadPosRankSum=1.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:361,0,895 -chr1 136488 . T C 337.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.143;DP=39;Dels=0.00;FS=7.323;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=53.86;MQ0=0;MQRankSum=-5.050;QD=8.66;ReadPosRankSum=1.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UPSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,13:39:99:366,0,788 -chr1 136547 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.519;DP=52;Dels=0.00;FS=24.103;HaplotypeScore=1.3990;MLEAC=1;MLEAF=0.500;MQ=58.33;MQ0=1;MQRankSum=0.123;QD=15.98;ReadPosRankSum=1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I7M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,28:52:99:859,0,785 -chr1 136596 . A C 975.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.509;DP=52;Dels=0.00;FS=1.083;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.44;MQ0=0;MQRankSum=-0.139;QD=18.76;ReadPosRankSum=-0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aag/Cag|K24Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1004,0,696 -chr1 136655 . T A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.512;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=0.278;QD=15.84;ReadPosRankSum=1.301;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caA|H43Q|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:18,20:38:99:630,0,576 -chr1 136658 . A G 1300.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.42;MQ0=0;QD=31.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I44M|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1329,102,0 -chr1 136742 . C T 829.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.161;DP=48;Dels=0.00;FS=11.641;HaplotypeScore=1.8937;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=0.635;QD=17.29;ReadPosRankSum=-0.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F72|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,27:48:99:858,0,624 -chr1 136752 . C T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=43;Dels=0.00;FS=4.498;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-1.528;QD=15.37;ReadPosRankSum=0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P76S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,24:43:99:689,0,591 -chr1 136754 . T C 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.739;DP=45;Dels=0.00;FS=8.549;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-0.808;QD=15.51;ReadPosRankSum=1.172;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccC|P76|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,24:45:99:726,0,665 -chr1 136841 . A G 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.684;DP=46;Dels=0.00;FS=2.588;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=0.110;QD=17.34;ReadPosRankSum=0.265;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E105|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,25:46:99:826,0,691 -chr1 136898 . A G 1598.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E124|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1627,126,0 -chr1 136902 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.935;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=3.1864;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.194;QD=13.13;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L126|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,20:46:99:632,0,609 -chr1 136996 . A G 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=42;Dels=0.00;FS=1.141;HaplotypeScore=2.5774;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.082;QD=14.73;ReadPosRankSum=0.402;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAa/aGa|K157R|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:647,0,707 -chr1 137035 . T C 801.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.623;QD=14.32;ReadPosRankSum=1.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gCg|V170A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:29,27:56:99:830,0,902 -chr1 137064 . G A 1076.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.151;DP=65;Dels=0.00;FS=3.370;HaplotypeScore=0.9734;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.846;QD=16.57;ReadPosRankSum=0.020;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V180I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,33:65:99:1105,0,993 -chr1 137119 . A G 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=59;Dels=0.00;FS=0.985;HaplotypeScore=3.6004;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-1.388;QD=18.93;ReadPosRankSum=-0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAt/aGt|N198S|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,34:59:99:1145,0,816 -chr1 137153 . A G 972.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.416;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=1;MQRankSum=2.932;QD=17.69;ReadPosRankSum=-0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S209|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,29:55:99:1001,0,825 -chr1 137179 . A G 799.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.118;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=1.7878;MLEAC=1;MLEAF=0.500;MQ=57.41;MQ0=1;MQRankSum=-3.289;QD=13.79;ReadPosRankSum=-0.603;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E218G|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:828,0,1091 -chr1 137275 . G A 1116.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.099;DP=55;Dels=0.00;FS=4.048;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=56.44;MQ0=1;MQRankSum=-2.535;QD=20.30;ReadPosRankSum=0.922;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aAa|R250K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:20,35:55:99:1145,0,643 -chr1 137372 . C T 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-0.028;QD=13.71;ReadPosRankSum=0.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtC/gtT|V282|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1029,0,1332 -chr1 137373 . A G 1056.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=73;Dels=0.00;FS=1.936;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.51;MQ0=0;MQRankSum=-2.632;QD=14.48;ReadPosRankSum=0.272;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T283A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:40,33:73:99:1085,0,1343 -chr1 137483 . G A 453.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.443;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=0;MQRankSum=-0.043;QD=11.64;ReadPosRankSum=-0.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M319I|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,16:39:99:482,0,810 -chr1 137571 . A G 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.393;DP=61;Dels=0.00;FS=1.046;HaplotypeScore=1.9787;MLEAC=1;MLEAF=0.500;MQ=55.97;MQ0=0;MQRankSum=-2.341;QD=13.06;ReadPosRankSum=-0.022;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Gat|N349D|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:35,26:61:99:825,0,1208 -chr1 137613 . C T 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.184;DP=57;Dels=0.00;FS=4.341;HaplotypeScore=3.9492;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-2.620;QD=14.84;ReadPosRankSum=-0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L363F|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:31,26:57:99:874,0,1052 -chr1 137666 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.663;DP=44;Dels=0.00;FS=1.184;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=52.01;MQ0=0;MQRankSum=-0.687;QD=17.20;ReadPosRankSum=1.422;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|tgC/tgT|C380|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:19,25:44:99:785,0,643 -chr1 137873 . T C 798.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.330;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=53.28;MQ0=0;MQRankSum=-1.416;QD=15.98;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V449|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:25,25:50:99:827,0,840 -chr1 137891 . C T 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.155;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.27;MQ0=0;MQRankSum=1.660;QD=16.26;ReadPosRankSum=1.350;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I455|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,26:50:99:841,0,766 -chr1 137927 . A T 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.977;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.120;QD=12.43;ReadPosRankSum=-0.680;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccT|P467|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:32,26:58:99:749,0,1114 -chr1 138034 . T C 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.586;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8939;MLEAC=1;MLEAF=0.500;MQ=53.14;MQ0=0;MQRankSum=0.781;QD=7.54;ReadPosRankSum=-1.513;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gCt|V503A|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:33,13:46:99:375,0,1176 -chr1 138075 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.293;DP=48;Dels=0.00;FS=2.557;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=48.83;MQ0=0;MQRankSum=-4.500;QD=14.02;ReadPosRankSum=-0.466;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|Ctg/Ttg|L517|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,22:48:99:701,0,894 -chr1 138170 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.530;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=54.39;MQ0=0;MQRankSum=-3.956;QD=13.84;ReadPosRankSum=-0.258;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K548|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:22,18:40:99:582,0,750 -chr1 138221 . G A 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.402;DP=49;Dels=0.00;FS=4.125;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=0;MQRankSum=-4.650;QD=14.73;ReadPosRankSum=1.474;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|aaG/aaA|K565|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:24,24:49:99:750,0,740 -chr1 138281 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.653;DP=47;Dels=0.00;FS=8.620;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-4.611;QD=12.82;ReadPosRankSum=0.332;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T585|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,21:47:99:631,0,882 -chr1 138362 . T C 690.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.377;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.11;MQ0=0;MQRankSum=-3.648;QD=16.45;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A612|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:21,21:42:99:719,0,680 -chr1 138386 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.181;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=1.7884;MLEAC=1;MLEAF=0.500;MQ=52.41;MQ0=0;MQRankSum=-3.153;QD=15.48;ReadPosRankSum=0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),SYNONYMOUS_CODING(LOW|SILENT|ttT/ttC|F620|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:23,20:43:99:694,0,739 -chr1 138609 . G A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.214;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=48.15;MQ0=0;MQRankSum=-4.884;QD=12.04;ReadPosRankSum=0.573;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E695K|Cc01g00120|mRNA||GSCOCT00012424001|Exon_chr1_136527_139057) GT:AD:DP:GQ:PL 0/1:26,24:50:99:630,0,897 -chr1 138660 . C A 981.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.11;MQ0=0;MQRankSum=4.417;QD=18.88;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1010,0,467 -chr1 138683 . G T 559.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.363;DP=56;Dels=0.00;FS=2.284;HaplotypeScore=2.8620;MLEAC=1;MLEAF=0.500;MQ=46.57;MQ0=0;MQRankSum=-4.417;QD=10.00;ReadPosRankSum=-2.357;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:588,0,1019 -chr1 138698 . T C 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.649;DP=58;Dels=0.00;FS=2.144;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.13;MQ0=0;MQRankSum=-3.995;QD=10.77;ReadPosRankSum=-1.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:653,0,1080 -chr1 138718 . T C 720.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.205;DP=53;Dels=0.00;FS=5.608;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.57;MQ0=0;MQRankSum=-4.422;QD=13.60;ReadPosRankSum=-0.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:749,0,948 -chr1 138736 . T C 816.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.990;DP=50;Dels=0.00;FS=10.029;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.58;MQ0=0;MQRankSum=-4.540;QD=16.34;ReadPosRankSum=-0.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:845,0,811 -chr1 138777 . T A 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.575;DP=53;Dels=0.00;FS=2.347;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=0;MQRankSum=-4.937;QD=16.24;ReadPosRankSum=-1.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:27,26:53:99:889,0,952 -chr1 138778 . C T 2144.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=2;MLEAF=1.00;MQ=52.94;MQ0=0;QD=33.40;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2173,163,0 -chr1 138820 . A C 2124.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.95;MQ0=0;QD=31.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2153,160,0 -chr1 138922 . A T 728.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.417;DP=57;Dels=0.00;FS=1.039;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=51.61;MQ0=1;MQRankSum=-0.363;QD=12.79;ReadPosRankSum=-1.187;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,26:57:99:757,0,1026 -chr1 138960 . T C 2157.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.52;MQ0=1;QD=28.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2186,172,0 -chr1 138982 . C A 1007.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.642;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=51.16;MQ0=1;MQRankSum=0.793;QD=17.38;ReadPosRankSum=0.248;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,32:58:99:1036,0,849 -chr1 139024 . A T 1024.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=56;Dels=0.00;FS=5.451;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.72;MQ0=0;MQRankSum=-1.928;QD=18.30;ReadPosRankSum=0.478;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,31:56:99:1053,0,858 -chr1 139066 . A G 959.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.30;MQ0=0;MQRankSum=-3.328;QD=16.55;ReadPosRankSum=-0.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:29,29:58:99:988,0,1020 -chr1 139093 . A G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.500;DP=47;Dels=0.00;FS=4.452;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.31;MQ0=0;MQRankSum=-4.267;QD=16.85;ReadPosRankSum=-1.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,24:47:99:820,0,809 -chr1 139143 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.629;DP=38;Dels=0.00;FS=2.742;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.86;MQ0=0;MQRankSum=-4.926;QD=17.57;ReadPosRankSum=1.973;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:696,0,605 -chr1 139149 . A G 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;DP=38;Dels=0.00;FS=2.835;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.61;MQ0=0;MQRankSum=-4.932;QD=18.23;ReadPosRankSum=1.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,21:38:99:721,0,567 -chr1 139163 . C T 557.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=39;Dels=0.00;FS=6.884;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.156;QD=14.30;ReadPosRankSum=1.391;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:586,0,689 -chr1 139224 . A G 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.302;DP=58;Dels=0.00;FS=3.833;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=54.37;MQ0=0;MQRankSum=-5.755;QD=12.22;ReadPosRankSum=0.039;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:737,0,1030 -chr1 139254 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.070;DP=60;Dels=0.00;FS=3.815;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-4.339;QD=14.35;ReadPosRankSum=-0.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,27:60:99:889,0,1036 -chr1 139269 . A G 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.023;DP=58;Dels=0.00;FS=1.019;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.74;MQ0=0;MQRankSum=-4.651;QD=14.17;ReadPosRankSum=0.305;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:850,0,1089 -chr1 139286 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.863;DP=56;Dels=0.00;FS=3.856;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.14;MQ0=0;MQRankSum=-3.836;QD=15.19;ReadPosRankSum=0.222;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:30,26:56:99:879,0,1015 -chr1 139341 . A G 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.17;MQ0=0;MQRankSum=-2.059;QD=15.48;ReadPosRankSum=-0.421;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:725,0,819 -chr1 139358 . A T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.459;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.28;MQ0=0;MQRankSum=-2.238;QD=14.18;ReadPosRankSum=-0.694;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:737,0,962 -chr1 139417 . A C 411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.696;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-5.263;QD=8.24;ReadPosRankSum=-1.884;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:440,0,1164 -chr1 139435 . T G 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.343;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.55;MQ0=0;MQRankSum=-5.052;QD=4.45;ReadPosRankSum=0.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:255,0,1407 -chr1 139441 . G A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.092;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.34;MQ0=0;MQRankSum=-5.283;QD=5.05;ReadPosRankSum=0.845;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:39,13:52:99:291,0,1353 -chr1 139480 . A G 107.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.50;MQ0=0;MQRankSum=-4.475;QD=2.29;ReadPosRankSum=1.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:38,9:47:99:136,0,1324 -chr1 139483 . T C 1251.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.548;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.24;MQ0=0;MQRankSum=5.087;QD=25.04;ReadPosRankSum=0.863;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:13,37:50:99:1280,0,278 -chr1 139488 . T A 312.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.949;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.71;MQ0=0;MQRankSum=-5.373;QD=6.01;ReadPosRankSum=-1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:37,15:52:99:341,0,1293 -chr1 139495 . G T 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.423;DP=50;Dels=0.00;FS=1.248;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=53.45;MQ0=0;MQRankSum=-5.314;QD=6.36;ReadPosRankSum=-1.207;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:346,0,1235 -chr1 139501 . T G 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.434;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.62;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:326,0,1098 -chr1 139502 . A G 294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.066;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9790;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-5.063;QD=6.55;ReadPosRankSum=-0.454;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:31,14:45:99:323,0,1098 -chr1 139534 . T C 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.920;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=51.00;MQ0=0;MQRankSum=-5.026;QD=15.83;ReadPosRankSum=-0.795;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:19,24:43:99:709,0,616 -chr1 139556 . A G 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.516;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.43;MQ0=0;MQRankSum=5.120;QD=12.09;ReadPosRankSum=-2.136;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:560,0,740 -chr1 139563 . T C 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.675;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=51.21;MQ0=0;MQRankSum=-5.014;QD=18.81;ReadPosRankSum=1.928;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:856,0,472 -chr1 139576 . C A 817.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.257;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=19.9086;MLEAC=1;MLEAF=0.500;MQ=51.06;MQ0=1;MQRankSum=-4.247;QD=21.52;ReadPosRankSum=1.511;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:846,0,350 -chr1 139610 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=44;Dels=0.00;FS=11.681;HaplotypeScore=8.3569;MLEAC=1;MLEAF=0.500;MQ=48.86;MQ0=0;MQRankSum=-4.699;QD=13.06;ReadPosRankSum=-1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:603,0,686 -chr1 139650 . C A 691.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.148;DP=45;Dels=0.00;FS=8.659;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.29;MQ0=0;MQRankSum=-3.849;QD=15.37;ReadPosRankSum=0.647;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:720,0,755 -chr1 139666 . T A 1813.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=51.90;MQ0=0;QD=29.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,46:47:99:1842,138,0 -chr1 139700 . T C 657.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.796;DP=42;Dels=0.00;FS=2.709;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=53.09;MQ0=1;MQRankSum=-4.603;QD=15.66;ReadPosRankSum=-0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:686,0,746 -chr1 139730 . T C 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.840;DP=44;Dels=0.00;FS=2.648;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.08;MQ0=1;MQRankSum=-5.150;QD=13.86;ReadPosRankSum=0.037;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:638,0,806 -chr1 139736 . A G 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=47;Dels=0.00;FS=4.288;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.00;MQ0=1;MQRankSum=-4.921;QD=13.97;ReadPosRankSum=-0.637;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:685,0,804 -chr1 139754 . C T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=44;Dels=0.00;FS=9.774;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=49.58;MQ0=1;MQRankSum=-5.101;QD=14.49;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:666,0,663 -chr1 139766 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.920;DP=47;Dels=0.00;FS=19.585;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.61;MQ0=2;MQRankSum=-4.394;QD=11.61;ReadPosRankSum=0.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:574,0,790 -chr1 139816 . T A 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=40;Dels=0.00;FS=36.168;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.74;MQ0=1;MQRankSum=3.812;QD=18.44;ReadPosRankSum=0.871;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:16,24:40:99:766,0,353 -chr1 139888 . A G 186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.061;DP=34;Dels=0.00;FS=8.801;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.98;MQ0=0;MQRankSum=-4.243;QD=5.49;ReadPosRankSum=-1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 0/1:26,8:34:99:215,0,931 -chr1 140035 . C T 1028.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.162;DP=30;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.59;MQ0=0;MQRankSum=1.764;QD=34.29;ReadPosRankSum=-0.387;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:2,27:29:43:1057,43,0 -chr1 140037 . C T 1021.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.347;DP=31;Dels=0.03;FS=0.000;HaplotypeScore=5.5143;MLEAC=2;MLEAF=1.00;MQ=56.70;MQ0=0;MQRankSum=1.271;QD=32.96;ReadPosRankSum=0.924;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:1,29:30:44:1050,44,0 -chr1 140066 . A G 1165.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1194,90,0 -chr1 140150 . A G 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0 -chr1 140265 . A T 876.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.93;MQ0=0;QD=24.94;EFF=DOWNSTREAM(MODIFIER||||Cc01g00100|mRNA||GSCOCT00012426001|),DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:905,69,0 -chr1 140358 . G A 1191.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,31:31:90:1220,90,0 -chr1 140388 . T C 1024.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.11;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),INTRON(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:1053,78,0 -chr1 140546 . T C 430.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:459,36,0 -chr1 140560 . T C 561.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.13;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UTR_3_PRIME(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:590,45,0 -chr1 141091 . G A 812.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.5641;MLEAC=2;MLEAF=1.00;MQ=59.48;MQ0=0;QD=32.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:841,63,0 -chr1 141137 . A G 1166.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:32:90:1195,90,0 -chr1 141143 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1290,96,0 -chr1 141147 . C T 1086.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,31:31:84:1115,84,0 -chr1 141182 . C G 1085.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1114,84,0 -chr1 141263 . G A 1101.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1130,84,0 -chr1 141349 . C T 1090.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9990;MLEAC=2;MLEAF=1.00;MQ=59.61;MQ0=0;QD=30.27;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1119,84,0 -chr1 141378 . T C 1215.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=30.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1244,96,0 -chr1 141387 . C T 1141.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=27.07;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1170,90,0 -chr1 141396 . C T 955.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=32.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:984,75,0 -chr1 141400 . T C 1036.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.36;MQ0=0;QD=27.18;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1065,81,0 -chr1 141412 . T C 854.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=32.36;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:883,66,0 -chr1 141422 . G A 736.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=28.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,19:20:57:765,57,0 -chr1 141455 . G A 804.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.72;MQ0=0;QD=26.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00110|mRNA||GSCOCT00012425001|),DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:833,63,0 -chr1 141471 . C T 759.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:788,60,0 -chr1 141498 . C A 891.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:920,69,0 -chr1 141507 . G C 961.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,25:25:75:990,75,0 -chr1 141536 . A G 1066.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.47;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1095,81,0 -chr1 141614 . A T 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0 -chr1 141636 . C A 434.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:463,39,0 -chr1 141654 . T A 544.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:573,45,0 -chr1 141655 . T A 534.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:563,45,0 -chr1 142437 . C T 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.548;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=-4.440;QD=13.66;ReadPosRankSum=-4.440;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:397,0,497 -chr1 142438 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.383;DP=27;Dels=0.00;FS=27.139;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.77;MQ0=0;MQRankSum=4.392;QD=16.73;ReadPosRankSum=4.392;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:13,14:27:99:480,0,389 -chr1 142481 . A G 1079.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.38;MQ0=0;QD=33.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1108,90,0 -chr1 142494 . T C 884.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.77;MQ0=0;QD=32.77;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,27:27:75:913,75,0 -chr1 142601 . A G 2064.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.05;MQ0=0;QD=31.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2093,165,0 -chr1 142776 . G A 1396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.227;DP=67;Dels=0.00;FS=3.384;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.34;MQ0=0;MQRankSum=-3.183;QD=20.85;ReadPosRankSum=1.355;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,42:67:99:1425,0,774 -chr1 142787 . C T 2578.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.71;MQ0=0;QD=24.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2607,199,0 -chr1 142805 . A G 2382.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=42.75;MQ0=0;QD=29.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2411,184,0 -chr1 142821 . T A 1258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.014;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=43.83;MQ0=0;MQRankSum=-1.966;QD=20.30;ReadPosRankSum=-0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,37:62:99:1287,0,713 -chr1 142863 . G A 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.691;DP=51;Dels=0.00;FS=2.359;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.90;MQ0=0;MQRankSum=-0.161;QD=16.58;ReadPosRankSum=-0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:874,0,753 -chr1 142891 . A T 926.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=3.828;HaplotypeScore=2.9990;MLEAC=1;MLEAF=0.500;MQ=56.01;MQ0=0;MQRankSum=2.468;QD=17.49;ReadPosRankSum=-0.294;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:955,0,777 -chr1 142898 . A G 956.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=0.197;QD=17.09;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,29:56:99:985,0,879 -chr1 142936 . A C 1403.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.302;DP=77;Dels=0.00;FS=0.875;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.936;QD=18.23;ReadPosRankSum=-0.445;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,42:77:99:1432,0,1097 -chr1 142944 . T C 1485.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.608;DP=75;Dels=0.00;FS=1.980;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.683;QD=19.81;ReadPosRankSum=-1.458;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,44:75:99:1514,0,922 -chr1 142972 . C T 1381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=75;Dels=0.00;FS=0.882;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.02;MQ0=0;MQRankSum=1.585;QD=18.42;ReadPosRankSum=1.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,42:75:99:1410,0,1088 -chr1 143047 . G C 845.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.743;DP=57;Dels=0.00;FS=5.471;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.96;MQ0=2;MQRankSum=-0.379;QD=14.84;ReadPosRankSum=0.665;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,29:57:99:874,0,913 -chr1 143077 . G A 615.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=43;Dels=0.00;FS=4.575;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=1;MQRankSum=-1.876;QD=14.32;ReadPosRankSum=-0.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:644,0,718 -chr1 143079 . T A 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.790;DP=44;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=1;MQRankSum=-1.497;QD=13.54;ReadPosRankSum=0.231;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:624,0,799 -chr1 143101 . G A 869.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.221;DP=58;Dels=0.00;FS=5.324;HaplotypeScore=5.2545;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=0;MQRankSum=-0.582;QD=15.00;ReadPosRankSum=-0.123;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,28:58:99:898,0,920 -chr1 143121 . C T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.297;DP=78;Dels=0.00;FS=16.462;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-4.301;QD=1.05;ReadPosRankSum=-3.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:69,9:78:99:110,0,2263 -chr1 143129 . A G 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=82;Dels=0.00;FS=21.866;HaplotypeScore=20.8424;MLEAC=1;MLEAF=0.500;MQ=57.31;MQ0=0;MQRankSum=-4.844;QD=1.53;ReadPosRankSum=-2.748;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,11:82:99:154,0,2388 -chr1 143138 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.733;DP=85;Dels=0.00;FS=19.743;HaplotypeScore=26.7703;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.325;QD=10.00;ReadPosRankSum=1.658;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:51,34:85:99:878,0,1589 -chr1 143140 . C T 264.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=85;Dels=0.00;FS=27.442;HaplotypeScore=15.7969;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-4.591;QD=3.11;ReadPosRankSum=-1.831;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:71,14:85:99:293,0,2284 -chr1 143161 . G A 909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=78;Dels=0.00;FS=0.906;HaplotypeScore=32.9944;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=1.886;QD=11.66;ReadPosRankSum=-0.501;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,32:78:99:938,0,1383 -chr1 143163 . C A 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.670;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=33.0925;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=0;MQRankSum=3.100;QD=10.32;ReadPosRankSum=-0.545;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:46,31:78:99:833,0,1525 -chr1 143164 . G T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.056;DP=79;Dels=0.00;FS=32.060;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-4.706;QD=4.33;ReadPosRankSum=2.731;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:370,0,2093 -chr1 143165 . G A 310.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.444;DP=79;Dels=0.00;FS=28.863;HaplotypeScore=33.8812;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=0;MQRankSum=-3.856;QD=3.93;ReadPosRankSum=2.881;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:64,15:79:99:339,0,2068 -chr1 143178 . C A 314.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.003;DP=76;Dels=0.00;FS=33.120;HaplotypeScore=44.4775;MLEAC=1;MLEAF=0.500;MQ=56.95;MQ0=0;MQRankSum=-4.295;QD=4.14;ReadPosRankSum=3.343;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:62,14:76:99:343,0,1910 -chr1 143221 . A T 81.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.319;DP=63;Dels=0.00;FS=19.029;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=2;MQRankSum=-2.568;QD=1.30;ReadPosRankSum=-0.916;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,9:63:99:110,0,1876 -chr1 143253 . G T 2036.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.62;MQ0=0;QD=42.33;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2065,159,0 -chr1 143376 . C G 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.421;DP=51;Dels=0.00;FS=6.452;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=6;MQRankSum=2.251;QD=20.51;ReadPosRankSum=-0.229;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,30:51:99:1074,0,461 -chr1 143406 . G A 740.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.599;DP=55;Dels=0.00;FS=3.966;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.48;MQ0=2;MQRankSum=-1.903;QD=13.47;ReadPosRankSum=0.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,26:55:99:769,0,1020 -chr1 143414 . A G 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.607;DP=56;Dels=0.00;FS=5.804;HaplotypeScore=0.9979;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=2;MQRankSum=-0.572;QD=12.89;ReadPosRankSum=1.336;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,27:56:99:750,0,1015 -chr1 143459 . G T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.432;DP=56;Dels=0.00;FS=5.668;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.85;MQ0=2;MQRankSum=1.522;QD=11.17;ReadPosRankSum=0.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:654,0,1069 -chr1 143490 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.752;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=-1.155;QD=11.50;ReadPosRankSum=0.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,23:54:99:649,0,1103 -chr1 143531 . G A 1174.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=61;Dels=0.00;FS=2.178;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.591;QD=19.26;ReadPosRankSum=1.087;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,35:61:99:1203,0,835 -chr1 143603 . C T 889.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.678;DP=57;Dels=0.00;FS=3.724;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=-1.269;QD=15.61;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,28:57:99:918,0,950 -chr1 143650 . T C 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.674;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.267;QD=17.93;ReadPosRankSum=1.209;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:871,0,713 -chr1 143705 . G A 755.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.934;DP=50;Dels=0.00;FS=10.323;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=1.538;QD=15.12;ReadPosRankSum=0.097;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,23:50:99:784,0,957 -chr1 143726 . C T 774.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.972;DP=51;Dels=0.00;FS=4.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.74;MQ0=0;MQRankSum=0.349;QD=15.19;ReadPosRankSum=-1.179;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:803,0,907 -chr1 143837 . A G 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.524;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.74;MQ0=0;MQRankSum=-3.207;QD=15.49;ReadPosRankSum=2.365;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,28:55:99:880,0,915 -chr1 143843 . G T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.62;MQ0=0;MQRankSum=-2.653;QD=15.86;ReadPosRankSum=1.953;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:948,0,954 -chr1 143851 . A T 948.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.281;DP=55;Dels=0.00;FS=2.282;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.36;MQ0=0;MQRankSum=-2.639;QD=17.25;ReadPosRankSum=0.789;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,31:55:99:977,0,823 -chr1 143867 . T A 1082.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.451;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=52.98;MQ0=0;MQRankSum=-2.076;QD=17.19;ReadPosRankSum=-0.993;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1111,0,885 -chr1 143879 . A C 1059.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.732;DP=66;Dels=0.00;FS=0.942;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=53.64;MQ0=0;MQRankSum=-1.603;QD=16.06;ReadPosRankSum=-1.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,36:66:99:1088,0,1011 -chr1 143887 . C G 1133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.947;DP=70;Dels=0.00;FS=0.918;HaplotypeScore=4.7286;MLEAC=1;MLEAF=0.500;MQ=54.49;MQ0=0;MQRankSum=-0.633;QD=16.20;ReadPosRankSum=-1.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,38:70:99:1162,0,1037 -chr1 143960 . C T 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.036;DP=49;Dels=0.00;FS=2.555;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.728;QD=12.06;ReadPosRankSum=-0.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),DOWNSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:619,0,1001 -chr1 144130 . G A 1136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.142;DP=62;Dels=0.00;FS=5.270;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.014;QD=18.33;ReadPosRankSum=-1.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,35:62:99:1165,0,864 -chr1 144149 . G A 1000.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.171;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=1.013;QD=17.25;ReadPosRankSum=-1.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_3_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1029,0,881 -chr1 144222 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.156;DP=54;Dels=0.00;FS=5.623;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.87;MQ0=0;MQRankSum=-2.776;QD=15.38;ReadPosRankSum=-0.729;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R143|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,29:54:99:859,0,804 -chr1 144255 . A G 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.055;DP=54;Dels=0.00;FS=10.821;HaplotypeScore=2.7619;MLEAC=1;MLEAF=0.500;MQ=55.54;MQ0=0;MQRankSum=-5.069;QD=15.64;ReadPosRankSum=1.367;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T132|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,27:54:99:873,0,825 -chr1 144286 . C G 684.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.419;DP=45;Dels=0.00;FS=1.238;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.87;MQ0=0;MQRankSum=-5.256;QD=15.22;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gCt|G122A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:713,0,730 -chr1 144294 . T A 757.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=46;Dels=0.00;FS=1.253;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.36;MQ0=0;MQRankSum=-5.317;QD=16.47;ReadPosRankSum=0.330;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaA/gaT|E119D|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:786,0,731 -chr1 144318 . G T 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.548;DP=40;Dels=0.00;FS=5.217;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.65;MQ0=0;MQRankSum=-5.240;QD=14.62;ReadPosRankSum=-1.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgC/cgA|R111|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:613,0,598 -chr1 144319 . C T 586.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=40;Dels=0.00;FS=2.910;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.74;MQ0=0;MQRankSum=-5.180;QD=14.67;ReadPosRankSum=-1.312;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R111H|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:615,0,628 -chr1 144346 . G C 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=45;Dels=0.00;FS=4.291;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.27;MQ0=0;MQRankSum=-4.374;QD=17.19;ReadPosRankSum=0.400;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aGt|T102S|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:802,0,630 -chr1 144351 . A C 735.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.002;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.03;MQ0=0;MQRankSum=-4.499;QD=15.33;ReadPosRankSum=1.692;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|ccT/ccG|P100|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,25:48:99:764,0,687 -chr1 144382 . T G 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.479;DP=53;Dels=0.00;FS=2.371;HaplotypeScore=4.8928;MLEAC=1;MLEAF=0.500;MQ=56.28;MQ0=0;MQRankSum=-2.346;QD=14.58;ReadPosRankSum=2.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gCt|D90A|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:53:99:801,0,829 -chr1 144385 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.198;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=6.8884;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-2.125;QD=15.05;ReadPosRankSum=2.399;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D89G|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:811,0,831 -chr1 144434 . T A 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=55;Dels=0.00;FS=1.039;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-0.232;QD=12.49;ReadPosRankSum=-0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N73Y|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:715,0,1146 -chr1 144525 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.018;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.856;QD=18.21;ReadPosRankSum=-0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgC|R42|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:629,0,394 -chr1 144561 . C G 729.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=39;Dels=0.00;FS=1.238;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.186;QD=18.71;ReadPosRankSum=1.042;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|cgG/cgC|R30|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,23:39:99:758,0,482 -chr1 144564 . C T 706.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.015;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=0.541;QD=19.10;ReadPosRankSum=0.943;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q29|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:735,0,466 -chr1 144576 . C G 1458.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;QD=35.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttC|L25F|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1487,114,0 -chr1 144606 . G C 868.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.165;DP=54;Dels=0.00;FS=2.347;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.276;QD=16.09;ReadPosRankSum=-0.898;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcG|S15|Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,27:54:99:897,0,877 -chr1 144686 . T C 910.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.844;DP=54;Dels=0.00;FS=1.047;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.788;QD=16.87;ReadPosRankSum=-1.169;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:26,28:54:99:939,0,867 -chr1 144759 . C G 541.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.336;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.833;QD=14.26;ReadPosRankSum=1.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:20,18:38:99:570,0,686 -chr1 144778 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.293;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=-1.949;QD=17.02;ReadPosRankSum=-1.535;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),START_GAINED(LOW||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:607,0,531 -chr1 144839 . C T 299.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.6671;MLEAC=1;MLEAF=0.500;MQ=56.40;MQ0=0;MQRankSum=-3.678;QD=8.56;ReadPosRankSum=-2.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UTR_5_PRIME(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|Exon_chr1_144043_144887) GT:AD:DP:GQ:PL 0/1:24,11:35:99:328,0,819 -chr1 144896 . C T 1822.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.76;MQ0=0;QD=33.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1851,138,0 -chr1 144909 . G A 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.494;DP=44;Dels=0.00;FS=4.590;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=0.603;QD=20.77;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,27:44:99:942,0,494 -chr1 144934 . T G 809.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.348;DP=38;Dels=0.00;FS=17.088;HaplotypeScore=0.9983;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.893;QD=21.31;ReadPosRankSum=1.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,24:38:99:838,0,442 -chr1 144950 . G A 844.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.054;DP=38;Dels=0.00;FS=11.386;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.801;QD=22.23;ReadPosRankSum=0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,25:38:99:873,0,375 -chr1 144960 . A G 731.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.762;DP=31;Dels=0.00;FS=13.484;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=0.675;QD=23.61;ReadPosRankSum=-0.762;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,22:31:99:760,0,270 -chr1 144980 . T G 288.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.632;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.879;QD=10.70;ReadPosRankSum=-0.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:317,0,537 -chr1 145002 . C G 240.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=27;Dels=0.00;FS=10.401;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=0.427;QD=8.92;ReadPosRankSum=0.778;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:269,0,580 -chr1 145030 . C T 408.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=27;Dels=0.00;FS=7.832;HaplotypeScore=1.7465;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-0.704;QD=15.14;ReadPosRankSum=0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,13:27:99:437,0,486 -chr1 145051 . C T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.259;DP=26;Dels=0.00;FS=10.770;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.99;MQ0=0;MQRankSum=-0.571;QD=19.38;ReadPosRankSum=-1.038;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:532,0,376 -chr1 145056 . T C 302.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.860;DP=25;Dels=0.00;FS=10.578;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.248;QD=12.11;ReadPosRankSum=1.525;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:331,0,511 -chr1 145062 . C T 1092.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=29.15;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,28:28:84:1121,84,0 -chr1 145137 . A G 151.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.333;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=17.5729;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-3.783;QD=5.84;ReadPosRankSum=-3.420;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,7:26:99:180,0,645 -chr1 145149 . G C 959.1 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.936;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9894;MLEAC=2;MLEAF=1.00;MQ=52.35;MQ0=2;MQRankSum=1.244;QD=29.97;ReadPosRankSum=2.005;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,27:32:11:987,11,0 -chr1 145165 . C A 1164.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=50.22;MQ0=3;QD=33.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,35:35:96:1193,96,0 -chr1 145178 . T A 1075.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.61;MQ0=3;QD=33.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:87:1104,87,0 -chr1 145196 . A T 636.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.445;DP=31;Dels=0.00;FS=4.262;HaplotypeScore=15.6286;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=3;MQRankSum=-2.370;QD=20.54;ReadPosRankSum=1.908;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,19:31:99:665,0,196 -chr1 145230 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=40;Dels=0.00;FS=9.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=2;MQRankSum=1.303;QD=8.29;ReadPosRankSum=2.151;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,13:40:99:360,0,901 -chr1 145381 . T C 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.906;DP=37;Dels=0.03;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=1;MQRankSum=0.283;QD=22.64;ReadPosRankSum=-0.321;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,27:36:99:866,0,203 -chr1 145385 . A T 223.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=9.9562;MLEAC=1;MLEAF=0.500;MQ=56.75;MQ0=1;MQRankSum=-0.159;QD=5.89;ReadPosRankSum=0.619;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,9:38:99:252,0,952 -chr1 145416 . T C 1041.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=23.0537;MLEAC=2;MLEAF=1.00;MQ=54.28;MQ0=1;QD=31.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:87:1070,87,0 -chr1 145429 . C T 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=33;Dels=0.00;FS=4.709;HaplotypeScore=14.4456;MLEAC=1;MLEAF=0.500;MQ=53.98;MQ0=1;MQRankSum=-2.077;QD=14.17;ReadPosRankSum=1.057;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:496,0,578 -chr1 145442 . C T 489.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.854;DP=28;Dels=0.00;FS=4.661;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=1;MQRankSum=2.415;QD=17.49;ReadPosRankSum=-2.025;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,16:28:99:518,0,409 -chr1 145448 . T C 377.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=31.09;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:406,30,0 -chr1 145453 . A G 385.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.88;MQ0=0;QD=26.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:414,30,0 -chr1 145503 . G A,C 789.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.79;MQ0=0;QD=29.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,8:27:99:956,264,207,691,0,667 -chr1 145509 . G A 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=1.970;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=0.472;QD=23.26;ReadPosRankSum=1.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:633,0,240 -chr1 145512 . C T 213.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.259;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=1.711;QD=9.29;ReadPosRankSum=-1.840;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:242,0,524 -chr1 145513 . G A 480.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.226;DP=23;Dels=0.00;FS=1.824;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-1.904;QD=20.90;ReadPosRankSum=1.646;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:509,0,246 -chr1 145515 . G A 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.013;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.126;QD=10.13;ReadPosRankSum=-1.945;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,8:22:99:251,0,503 -chr1 145531 . A G 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.177;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.67;MQ0=0;MQRankSum=-1.288;QD=17.10;ReadPosRankSum=-1.733;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,10:18:99:336,0,240 -chr1 145534 . C T 216.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.280;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=2.518;QD=11.41;ReadPosRankSum=2.106;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,8:19:99:245,0,339 -chr1 145538 . T C 270.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.376;QD=16.92;ReadPosRankSum=-2.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,9:16:99:299,0,219 -chr1 145544 . T C 141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.000;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.50;MQ0=0;MQRankSum=1.134;QD=11.81;ReadPosRankSum=2.793;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:99:170,0,230 -chr1 145555 . A G 127.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-0.470;QD=12.78;ReadPosRankSum=-2.450;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,5:10:99:156,0,173 -chr1 145615 . A C 535.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=1.9330;MLEAC=2;MLEAF=1.00;MQ=55.87;MQ0=0;QD=32.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,14:14:42:564,42,0 -chr1 145642 . A G 1135.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=8.6529;MLEAC=2;MLEAF=1.00;MQ=54.53;MQ0=0;QD=31.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1164,87,0 -chr1 145654 . T C 490.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.083;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.94;MQ0=1;MQRankSum=-2.198;QD=15.83;ReadPosRankSum=0.249;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:519,0,451 -chr1 145666 . G A 452.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.376;DP=33;Dels=0.00;FS=1.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.78;MQ0=2;MQRankSum=-1.364;QD=13.72;ReadPosRankSum=1.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:481,0,521 -chr1 145673 . T C 481.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.099;DP=35;Dels=0.00;FS=1.624;HaplotypeScore=15.4641;MLEAC=1;MLEAF=0.500;MQ=52.28;MQ0=2;MQRankSum=0.955;QD=13.76;ReadPosRankSum=-0.630;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:510,0,570 -chr1 145676 . A G 468.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.570;DP=36;Dels=0.00;FS=1.666;HaplotypeScore=16.4306;MLEAC=1;MLEAF=0.500;MQ=52.51;MQ0=2;MQRankSum=0.707;QD=13.02;ReadPosRankSum=0.224;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:497,0,607 -chr1 145688 . A G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.302;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=-0.944;QD=15.17;ReadPosRankSum=-0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:544,0,419 -chr1 145689 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.642;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=52.23;MQ0=2;MQRankSum=1.171;QD=11.67;ReadPosRankSum=0.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:425,0,541 -chr1 145706 . C T 986.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.77;MQ0=2;QD=32.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:78:1015,78,0 -chr1 145712 . A G 1007.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.65;MQ0=2;QD=32.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00120|mRNA||GSCOCT00012424001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:81:1036,81,0 -chr1 145783 . G A 363.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=19;Dels=0.00;FS=2.199;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.549;QD=19.15;ReadPosRankSum=2.409;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,12:19:99:392,0,216 -chr1 145845 . C T 1598.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.27;MQ0=0;QD=26.69;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1627,120,0 -chr1 145926 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.984;DP=43;Dels=0.00;FS=1.186;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=2.423;QD=15.23;ReadPosRankSum=0.621;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:683,0,719 -chr1 145928 . A T 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=41;Dels=0.00;FS=2.731;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.19;MQ0=0;MQRankSum=-0.745;QD=16.12;ReadPosRankSum=-0.588;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:689,0,634 -chr1 145949 . T C 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.879;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-1.907;QD=16.95;ReadPosRankSum=0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:791,0,650 -chr1 145950 . G C 1750.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=0;QD=26.60;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1779,135,0 -chr1 145957 . T C 913.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-2.937;QD=19.86;ReadPosRankSum=0.461;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,28:46:99:942,0,588 -chr1 145961 . G A 927.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=47;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.44;MQ0=0;MQRankSum=-3.067;QD=19.74;ReadPosRankSum=1.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,28:47:99:956,0,621 -chr1 145971 . T C 1794.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.38;MQ0=0;QD=30.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1823,135,0 -chr1 145982 . C T 1821.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.7334;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=0;QD=35.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1850,138,0 -chr1 145991 . T C 1257.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=40;Dels=0.00;FS=2.157;HaplotypeScore=1.7334;MLEAC=1;MLEAF=0.500;MQ=57.75;MQ0=0;MQRankSum=-0.969;QD=31.44;ReadPosRankSum=2.998;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,36:40:39:1286,0,39 -chr1 145995 . C T 1327.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.079;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.3985;MLEAC=2;MLEAF=1.00;MQ=57.63;MQ0=0;MQRankSum=-0.621;QD=34.94;ReadPosRankSum=2.190;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,36:38:38:1356,38,0 -chr1 146000 . G A 1358.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;QD=22.90;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1387,108,0 -chr1 146028 . T C 1707.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.8730;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;QD=27.76;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1736,135,0 -chr1 146053 . A G 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.384;DP=42;Dels=0.00;FS=1.216;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=0.654;QD=14.85;ReadPosRankSum=-1.484;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:652,0,659 -chr1 146141 . G C 886.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.446;DP=55;Dels=0.00;FS=1.026;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.379;QD=16.12;ReadPosRankSum=0.093;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,27:55:99:915,0,948 -chr1 146183 . C T 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=61;Dels=0.00;FS=13.794;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.91;MQ0=0;MQRankSum=0.166;QD=14.73;ReadPosRankSum=1.165;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:927,0,1096 -chr1 146259 . G A 679.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.772;DP=50;Dels=0.00;FS=1.112;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-2.160;QD=13.60;ReadPosRankSum=0.225;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:708,0,962 -chr1 146273 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.267;DP=47;Dels=0.00;FS=2.512;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=-0.672;QD=14.27;ReadPosRankSum=0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:699,0,859 -chr1 146296 . T C 695.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123;DP=51;Dels=0.00;FS=2.461;HaplotypeScore=1.7074;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.406;QD=13.64;ReadPosRankSum=0.802;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,24:51:99:724,0,886 -chr1 146334 . G A 730.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.744;DP=54;Dels=0.00;FS=15.099;HaplotypeScore=4.3788;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=0.234;QD=13.53;ReadPosRankSum=-0.892;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,28:54:99:759,0,888 -chr1 146352 . A C 847.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.498;DP=51;Dels=0.00;FS=10.821;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=1.008;QD=16.62;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:876,0,875 -chr1 146412 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.096;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-1.487;QD=17.29;ReadPosRankSum=-0.974;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,26:47:99:841,0,718 -chr1 146446 . G T 677.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.410;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.03;MQ0=0;MQRankSum=-3.670;QD=13.83;ReadPosRankSum=-0.730;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:706,0,869 -chr1 146451 . T C 696.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.785;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-1.455;QD=13.94;ReadPosRankSum=-0.796;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:725,0,868 -chr1 146456 . G C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.673;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=3.9978;MLEAC=1;MLEAF=0.500;MQ=56.54;MQ0=0;MQRankSum=-3.167;QD=10.90;ReadPosRankSum=0.452;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:44:99:508,0,846 -chr1 146467 . C T 464.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9988;MLEAC=1;MLEAF=0.500;MQ=55.70;MQ0=0;MQRankSum=-3.722;QD=12.56;ReadPosRankSum=-0.562;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:493,0,671 -chr1 146489 . T A 333.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.236;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=6.7989;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-3.721;QD=8.78;ReadPosRankSum=3.030;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,12:38:99:362,0,945 -chr1 146502 . C T 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.559;DP=40;Dels=0.00;FS=2.861;HaplotypeScore=82.1865;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=-2.486;QD=11.52;ReadPosRankSum=2.989;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:489,0,888 -chr1 146626 . C A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=0.151;QD=9.56;ReadPosRankSum=-0.179;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,14:41:99:420,0,892 -chr1 146707 . A T 748.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.116;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=51.1918;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-0.045;QD=14.13;ReadPosRankSum=-0.846;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:777,0,951 -chr1 146722 . C T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.569;DP=53;Dels=0.00;FS=2.427;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-0.514;QD=12.00;ReadPosRankSum=0.966;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:664,0,1073 -chr1 146734 . G A 460.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.057;QD=8.69;ReadPosRankSum=2.226;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:489,0,1193 -chr1 146736 . C T 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.906;QD=9.05;ReadPosRankSum=2.432;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:508,0,1187 -chr1 146737 . T C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.399;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-2.038;QD=9.15;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:513,0,1186 -chr1 146738 . G A 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.178;DP=53;Dels=0.00;FS=2.739;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.80;MQ0=0;MQRankSum=-1.005;QD=8.94;ReadPosRankSum=2.470;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:502,0,1205 -chr1 146751 . T C 1086.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.546;DP=56;Dels=0.00;FS=8.313;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=1;MQRankSum=2.036;QD=19.41;ReadPosRankSum=-0.424;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,34:56:99:1115,0,613 -chr1 146757 . T C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.536;DP=54;Dels=0.00;FS=8.599;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=1;MQRankSum=-1.537;QD=11.00;ReadPosRankSum=-0.118;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:622,0,1058 -chr1 146765 . T C 455.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.851;DP=50;Dels=0.00;FS=2.814;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=57.67;MQ0=1;MQRankSum=-1.838;QD=9.12;ReadPosRankSum=0.011;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,18:50:99:484,0,1120 -chr1 146805 . C G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.862;DP=39;Dels=0.00;FS=3.130;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=1;MQRankSum=0.738;QD=8.51;ReadPosRankSum=0.585;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:360,0,832 -chr1 146811 . A T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.860;DP=41;Dels=0.00;FS=1.258;HaplotypeScore=1.7306;MLEAC=1;MLEAF=0.500;MQ=58.53;MQ0=1;MQRankSum=-0.246;QD=10.92;ReadPosRankSum=-0.821;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,18:41:99:476,0,771 -chr1 146917 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.342;DP=34;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.919;QD=22.14;ReadPosRankSum=0.523;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,22:34:99:781,0,382 -chr1 146962 . C T 400.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.455;DP=33;Dels=0.00;FS=8.473;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.13;MQ0=0;MQRankSum=0.387;QD=12.14;ReadPosRankSum=-0.387;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,13:33:99:429,0,656 -chr1 147004 . A G 326.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:355,27,0 -chr1 147012 . A G 322.78 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.46;MQ0=0;QD=27.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:27:351,27,0 -chr1 147033 . A G 283.78 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.29;MQ0=0;QD=27.26;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,8:8:24:312,24,0 -chr1 147043 . G A 158.9 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.198;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.14;MQ0=1;MQRankSum=1.495;QD=19.86;ReadPosRankSum=0.922;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,5:8:15:187,15,0 -chr1 147044 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.720;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.27;MQ0=1;MQRankSum=1.380;QD=18.86;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,4:7:12:160,12,0 -chr1 147046 . C T 132.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.638;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=27.75;MQ0=1;MQRankSum=2.017;QD=14.67;ReadPosRankSum=2.017;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,4:9:12:160,12,0 -chr1 147053 . C T 129.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.73;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:157,12,0 -chr1 147055 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.51;MQ0=1;QD=11.46;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:154,12,0 -chr1 147074 . G A 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=4.7802;MLEAC=1;MLEAF=0.500;MQ=29.47;MQ0=1;MQRankSum=2.617;QD=5.25;ReadPosRankSum=-1.880;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,6:23:99:149,0,214 -chr1 147113 . A C 82.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.303;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=27.3842;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=3;MQRankSum=1.937;QD=2.30;ReadPosRankSum=2.310;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,6:36:99:111,0,296 -chr1 147139 . G A 323.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.091;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=16.6145;MLEAC=1;MLEAF=0.500;MQ=25.38;MQ0=11;MQRankSum=2.940;QD=6.11;ReadPosRankSum=1.127;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:53:99:352,0,249 -chr1 147150 . T G 99.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.178;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=10.0978;MLEAC=1;MLEAF=0.500;MQ=26.62;MQ0=11;MQRankSum=-1.429;QD=2.04;ReadPosRankSum=-1.554;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:128,0,456 -chr1 147170 . G A 326.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.347;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=42.8592;MLEAC=1;MLEAF=0.500;MQ=26.42;MQ0=13;MQRankSum=3.898;QD=6.95;ReadPosRankSum=-1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,13:47:99:355,0,181 -chr1 147223 . T C 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=20.60;MQ0=4;MQRankSum=-2.013;QD=3.22;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,18:26:99:112,0,126 -chr1 147226 . G C 57.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.109;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=4.9798;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=1.702;QD=2.41;ReadPosRankSum=1.702;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,8:24:86:86,0,115 -chr1 147227 . C A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.182;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=6.9023;MLEAC=1;MLEAF=0.500;MQ=21.38;MQ0=3;MQRankSum=0.910;QD=0.99;ReadPosRankSum=-0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,5:24:52:52,0,159 -chr1 147238 . A G 178.8 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=5.5670;MLEAC=2;MLEAF=1.00;MQ=23.04;MQ0=2;QD=10.52;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:21:207,21,0 -chr1 147243 . C T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.311;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=22.90;MQ0=2;MQRankSum=0.755;QD=3.39;ReadPosRankSum=1.200;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,8:20:96:96,0,131 -chr1 147246 . A T 53.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.236;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=7.5617;MLEAC=1;MLEAF=0.500;MQ=24.50;MQ0=1;MQRankSum=1.559;QD=2.56;ReadPosRankSum=-2.126;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:17,4:21:82:82,0,176 -chr1 147259 . A G 289.56 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.540;DP=19;Dels=0.00;FS=4.393;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=29.17;MQ0=1;MQRankSum=1.185;QD=15.24;ReadPosRankSum=-1.303;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,16:19:7:317,7,0 -chr1 147272 . C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.709;DP=16;Dels=0.00;FS=3.522;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=31.58;MQ0=1;MQRankSum=2.298;QD=9.11;ReadPosRankSum=-2.062;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,6:16:99:174,0,100 -chr1 147273 . T C 302.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=31.58;MQ0=1;QD=18.92;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,15:16:27:331,27,0 -chr1 147296 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.795;DP=18;Dels=0.00;FS=7.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=40.13;MQ0=0;MQRankSum=3.532;QD=16.93;ReadPosRankSum=-0.530;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:51:333,0,51 -chr1 147357 . A T 143.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.153;DP=30;Dels=0.00;FS=28.709;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.13;MQ0=6;MQRankSum=-3.766;QD=4.79;ReadPosRankSum=-1.133;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,14:30:99:172,0,529 -chr1 147416 . T C 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.937;DP=10;Dels=0.00;FS=15.441;HaplotypeScore=26.0957;MLEAC=1;MLEAF=0.500;MQ=30.35;MQ0=3;MQRankSum=-1.754;QD=3.98;ReadPosRankSum=-1.754;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,4:10:68:68,0,134 -chr1 147424 . A G 110.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.380;DP=8;Dels=0.00;FS=11.761;HaplotypeScore=2.8995;MLEAC=1;MLEAF=0.500;MQ=30.85;MQ0=2;MQRankSum=1.380;QD=13.85;ReadPosRankSum=1.380;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,4:8:31:139,0,31 -chr1 147427 . T C 164.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=23.55;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:193,18,0 -chr1 147428 . T C 173.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.98;MQ0=1;QD=24.83;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:202,18,0 -chr1 147440 . C T 145.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.219;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=30.86;MQ0=2;MQRankSum=2.219;QD=13.27;ReadPosRankSum=-0.876;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,5:11:5:173,0,5 -chr1 147461 . G A 174.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.074;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=8.9694;MLEAC=1;MLEAF=0.500;MQ=32.41;MQ0=2;MQRankSum=3.016;QD=11.65;ReadPosRankSum=-1.493;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,6:15:24:203,0,24 -chr1 147474 . C T 286.9 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.223;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=10.9207;MLEAC=1;MLEAF=0.500;MQ=41.09;MQ0=2;MQRankSum=3.281;QD=15.94;ReadPosRankSum=-2.752;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,9:18:15:315,0,15 -chr1 147490 . G A 297.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.899;DP=23;Dels=0.00;FS=3.834;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=2.760;QD=12.95;ReadPosRankSum=3.318;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:326,0,430 -chr1 147522 . C T 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.004;DP=30;Dels=0.00;FS=1.449;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.65;MQ0=0;MQRankSum=-3.516;QD=17.83;ReadPosRankSum=-0.963;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:563,0,394 -chr1 147528 . A G 1043.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.18;MQ0=0;QD=31.37;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1072,81,0 -chr1 147529 . T C 344.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.492;DP=27;Dels=0.00;FS=1.598;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.18;MQ0=0;MQRankSum=3.380;QD=12.77;ReadPosRankSum=0.962;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,11:27:99:373,0,495 -chr1 147542 . C T 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.567;DP=33;Dels=0.00;FS=5.188;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.17;MQ0=0;MQRankSum=-2.900;QD=17.30;ReadPosRankSum=-0.234;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,17:33:99:599,0,528 -chr1 147543 . C T 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.328;DP=34;Dels=0.00;FS=3.064;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQ0=0;MQRankSum=-1.639;QD=17.52;ReadPosRankSum=-0.535;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:624,0,489 -chr1 147546 . G A 434.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.043;DP=35;Dels=0.00;FS=3.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=3.560;QD=12.42;ReadPosRankSum=0.248;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:463,0,624 -chr1 147575 . G A 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.453;DP=42;Dels=0.00;FS=4.613;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.79;MQ0=0;MQRankSum=-2.836;QD=20.26;ReadPosRankSum=-0.194;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,26:42:99:879,0,470 -chr1 147578 . A C 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.122;DP=41;Dels=0.00;FS=2.845;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.07;MQ0=0;MQRankSum=2.964;QD=10.43;ReadPosRankSum=0.744;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:456,0,851 -chr1 147586 . C T 1415.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=53.48;MQ0=0;QD=32.80;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1444,114,0 -chr1 147591 . C T 640.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.283;DP=35;Dels=0.00;FS=1.344;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-2.317;QD=18.31;ReadPosRankSum=0.850;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:669,0,479 -chr1 147594 . G C,T 1053.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.02;MQ0=0;QD=30.98;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,19,15:34:99:1240,557,500,683,0,638 -chr1 147597 . A G 1257.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=2;MLEAF=1.00;MQ=52.79;MQ0=0;QD=24.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1286,99,0 -chr1 147598 . G A 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.387;DP=33;Dels=0.00;FS=5.093;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=52.79;MQ0=0;MQRankSum=-2.045;QD=19.33;ReadPosRankSum=0.166;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,20:33:99:666,0,407 -chr1 147606 . A C 1323.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.20;MQ0=0;QD=29.38;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1352,105,0 -chr1 147628 . C T 1132.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.90;MQ0=0;QD=33.91;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1161,90,0 -chr1 147635 . A G 947.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=49.40;MQ0=0;QD=28.17;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,26:26:78:976,78,0 -chr1 147636 . C T 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.792;DP=26;Dels=0.00;FS=1.796;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=49.40;MQ0=0;MQRankSum=-2.081;QD=23.18;ReadPosRankSum=1.272;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,19:26:99:631,0,203 -chr1 147641 . T A 609.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.241;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.93;MQ0=0;MQRankSum=-1.623;QD=24.39;ReadPosRankSum=1.241;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,19:25:99:638,0,170 -chr1 147653 . T G 1125.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.44;MQ0=0;QD=36.65;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1154,93,0 -chr1 147665 . C T 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.781;DP=31;Dels=0.00;FS=11.051;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.68;MQ0=0;MQRankSum=2.182;QD=11.86;ReadPosRankSum=-1.741;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,13:31:99:396,0,590 -chr1 147671 . C T 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.104;DP=30;Dels=0.00;FS=8.496;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.13;MQ0=0;MQRankSum=-1.517;QD=15.93;ReadPosRankSum=2.099;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:14,16:30:99:506,0,416 -chr1 147698 . T C 448.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=29;Dels=0.00;FS=11.831;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=58.55;MQ0=0;MQRankSum=-0.240;QD=15.47;ReadPosRankSum=-2.160;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:15,14:29:99:477,0,517 -chr1 147700 . A G 1091.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=2.4530;MLEAC=2;MLEAF=1.00;MQ=58.55;MQ0=0;QD=32.47;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1120,84,0 -chr1 147730 . T C 494.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.074;DP=38;Dels=0.00;FS=24.449;HaplotypeScore=2.5770;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=1.345;QD=13.02;ReadPosRankSum=1.109;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:523,0,753 -chr1 147779 . C T 1482.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.43;MQ0=0;QD=28.95;EFF=UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|),UPSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1511,111,0 -chr1 147815 . G A 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.116;DP=38;Dels=0.00;FS=5.625;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.779;QD=10.52;ReadPosRankSum=1.129;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S6N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:428,0,860 -chr1 147816 . C T 396.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.538;DP=38;Dels=0.00;FS=5.221;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=0.154;QD=10.44;ReadPosRankSum=1.292;EFF=SYNONYMOUS_CODING(LOW|SILENT|agC/agT|S6|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:425,0,850 -chr1 147861 . G A 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.261;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-2.322;QD=18.06;ReadPosRankSum=-0.782;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S21|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:823,0,602 -chr1 147863 . G C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-1.540;QD=18.84;ReadPosRankSum=-0.782;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aCc|S22T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:857,0,597 -chr1 147893 . A C 372.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=28;Dels=0.00;FS=12.411;HaplotypeScore=17.4716;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.534;QD=13.31;ReadPosRankSum=1.694;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAt/tCt|Y32S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:401,0,517 -chr1 147940 . G A 136.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.992;DP=60;Dels=0.00;FS=5.651;HaplotypeScore=4.9890;MLEAC=1;MLEAF=0.500;MQ=51.15;MQ0=1;MQRankSum=2.013;QD=2.28;ReadPosRankSum=0.601;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gaa/Aaa|E48K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,9:60:99:165,0,1548 -chr1 147974 . G T 2172.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=52.02;MQ0=1;QD=32.90;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W59L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2201,172,0 -chr1 147980 . T C 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.561;DP=60;Dels=0.00;FS=2.594;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=53.04;MQ0=1;MQRankSum=-5.013;QD=5.68;ReadPosRankSum=2.921;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTg/tCg|L61S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:42,18:60:99:369,0,1413 -chr1 148008 . T G 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.047;DP=70;Dels=0.00;FS=5.868;HaplotypeScore=1.4679;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-4.821;QD=6.14;ReadPosRankSum=0.000;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T70|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,19:70:99:458,0,1746 -chr1 148023 . G A 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=65;Dels=0.00;FS=8.565;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=57.73;MQ0=0;MQRankSum=-4.083;QD=6.41;ReadPosRankSum=0.082;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V75|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:445,0,1615 -chr1 148028 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.066;DP=60;Dels=0.00;FS=14.560;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.07;MQ0=0;MQRankSum=-4.165;QD=5.43;ReadPosRankSum=0.768;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S77L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,15:60:99:354,0,1522 -chr1 148029 . G A 296.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.097;DP=57;Dels=0.00;FS=9.963;HaplotypeScore=3.3988;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=0;MQRankSum=-2.445;QD=5.21;ReadPosRankSum=1.708;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S77|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:43,13:57:99:325,0,1421 -chr1 148050 . T C 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7172;MLEAC=1;MLEAF=0.500;MQ=58.18;MQ0=0;MQRankSum=2.073;QD=10.00;ReadPosRankSum=-0.265;EFF=SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I84|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,24:65:99:678,0,1415 -chr1 148062 . G A 2262.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=1.3990;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=26.81;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R88|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2291,178,0 -chr1 148077 . T G 374.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.434;DP=53;Dels=0.00;FS=12.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.62;MQ0=0;MQRankSum=-4.267;QD=7.07;ReadPosRankSum=0.313;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caT/caG|H93Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,14:53:99:403,0,1389 -chr1 148078 . C A 356.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.438;DP=54;Dels=0.00;FS=12.716;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=0;MQRankSum=-4.017;QD=6.61;ReadPosRankSum=0.365;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Act|P94T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,14:54:99:385,0,1444 -chr1 148095 . C T 290.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.542;DP=44;Dels=0.00;FS=14.379;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.117;QD=6.61;ReadPosRankSum=1.003;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A99|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:319,0,1163 -chr1 148104 . C T 340.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.046;DP=48;Dels=0.00;FS=16.904;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.38;MQ0=0;MQRankSum=-4.176;QD=7.10;ReadPosRankSum=-0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A102|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,13:48:99:369,0,1201 -chr1 148117 . T C 207.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.521;DP=50;Dels=0.00;FS=18.397;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=-3.965;QD=4.16;ReadPosRankSum=1.152;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S107P|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:40,10:50:99:236,0,1399 -chr1 148124 . C T 182.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.360;DP=49;Dels=0.00;FS=20.451;HaplotypeScore=1.8499;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.155;QD=3.73;ReadPosRankSum=0.409;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T109I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,10:49:99:211,0,1394 -chr1 148128 . T C 178.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.819;DP=48;Dels=0.00;FS=20.451;HaplotypeScore=45.3427;MLEAC=1;MLEAF=0.500;MQ=56.97;MQ0=0;MQRankSum=-4.649;QD=3.72;ReadPosRankSum=0.608;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcC|A110|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:39,9:48:99:207,0,1389 -chr1 148133 . A G 175.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=46;Dels=0.00;FS=20.653;HaplotypeScore=118.8295;MLEAC=1;MLEAF=0.500;MQ=56.83;MQ0=0;MQRankSum=-4.624;QD=3.82;ReadPosRankSum=-0.194;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAc/gGc|D112G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,9:46:99:204,0,1210 -chr1 148165 . C G 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=43;Dels=0.00;FS=1.213;HaplotypeScore=4.9810;MLEAC=1;MLEAF=0.500;MQ=56.32;MQ0=0;MQRankSum=1.859;QD=11.99;ReadPosRankSum=-1.096;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ccc/Gcc|P123A|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,18:43:99:544,0,806 -chr1 148184 . A G 1381.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=2.9827;MLEAC=2;MLEAF=1.00;MQ=56.12;MQ0=0;QD=29.22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K129R|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1410,111,0 -chr1 148218 . T A 561.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.156;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.57;MQ0=0;MQRankSum=0.826;QD=13.38;ReadPosRankSum=0.216;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcT/tcA|S140|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_147799_148243),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:590,0,747 -chr1 148366 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.171;DP=46;Dels=0.00;FS=2.594;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=1;MQRankSum=0.742;QD=18.06;ReadPosRankSum=0.811;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:859,0,635 -chr1 148435 . A C 1097.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=54;Dels=0.00;FS=9.969;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=0.801;QD=20.33;ReadPosRankSum=-0.361;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,32:54:99:1126,0,692 -chr1 148463 . A G 1201.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.268;DP=54;Dels=0.00;FS=1.155;HaplotypeScore=28.9952;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.199;QD=22.25;ReadPosRankSum=0.507;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,35:54:99:1230,0,586 -chr1 148468 . A G 1266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.651;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=15.2316;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.761;QD=23.46;ReadPosRankSum=0.615;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,36:54:99:1295,0,544 -chr1 148595 . C T 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.094;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.341;QD=12.88;ReadPosRankSum=-0.048;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:29,22:51:99:685,0,1002 -chr1 148617 . G A 749.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.242;DP=50;Dels=0.00;FS=1.142;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=1.203;QD=15.00;ReadPosRankSum=-1.901;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:778,0,841 -chr1 148704 . G C 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.689;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.50;MQ0=0;MQRankSum=0.330;QD=17.33;ReadPosRankSum=-0.481;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,798 -chr1 148761 . A T 1165.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.413;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.244;QD=17.66;ReadPosRankSum=0.925;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1194,0,997 -chr1 148794 . T C 1570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.757;DP=84;Dels=0.00;FS=0.829;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.198;QD=18.70;ReadPosRankSum=-0.117;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:37,47:84:99:1599,0,1205 -chr1 148795 . C T 1196.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.725;DP=81;Dels=0.00;FS=0.833;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.043;QD=14.77;ReadPosRankSum=-0.327;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:44,37:81:99:1225,0,1499 -chr1 148840 . T A 1013.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.283;DP=67;Dels=0.00;FS=6.538;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.018;QD=15.13;ReadPosRankSum=0.094;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:36,31:67:99:1042,0,1215 -chr1 148975 . A T 1278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.432;DP=70;Dels=0.00;FS=2.050;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.446;QD=18.27;ReadPosRankSum=-0.383;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:32,38:70:99:1307,0,1024 -chr1 148997 . T C 2678.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.02;MQ0=0;QD=25.77;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2707,205,0 -chr1 149029 . T C 1230.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.008;DP=64;Dels=0.00;FS=7.922;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=49.51;MQ0=4;MQRankSum=-3.991;QD=19.23;ReadPosRankSum=0.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,40:64:99:1259,0,799 -chr1 149049 . C T 841.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=53;Dels=0.00;FS=4.125;HaplotypeScore=3.9326;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.050;QD=15.88;ReadPosRankSum=0.650;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:28,25:53:99:870,0,827 -chr1 149054 . T A 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.693;DP=53;Dels=0.00;FS=1.097;HaplotypeScore=2.9329;MLEAC=1;MLEAF=0.500;MQ=48.44;MQ0=4;MQRankSum=-3.556;QD=14.32;ReadPosRankSum=1.012;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:30,23:53:99:787,0,898 -chr1 149065 . C T 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.127;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=47.38;MQ0=4;MQRankSum=3.705;QD=16.74;ReadPosRankSum=-1.056;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:748,0,583 -chr1 149079 . T A 1585.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.50;MQ0=0;QD=35.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1614,120,0 -chr1 149083 . G A 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.106;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=1.535;QD=16.43;ReadPosRankSum=1.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:636,0,597 -chr1 149099 . C T 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.884;DP=40;Dels=0.00;FS=2.794;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=0;MQRankSum=-0.095;QD=14.47;ReadPosRankSum=-0.340;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,754 -chr1 149136 . A C 1526.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.87;MQ0=0;QD=32.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1555,117,0 -chr1 149156 . G A 46.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.214;DP=52;Dels=0.00;FS=6.760;HaplotypeScore=3.3564;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-0.965;QD=0.90;ReadPosRankSum=-3.566;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R158|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:45,7:52:75:75,0,1569 -chr1 149170 . A G 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.215;DP=58;Dels=0.00;FS=6.984;HaplotypeScore=11.3843;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.167;QD=0.36;ReadPosRankSum=-0.215;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAg/gGg|E163G|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:51,7:58:49:49,0,1750 -chr1 149174 . A G 793.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.409;DP=60;Dels=0.00;FS=14.447;HaplotypeScore=10.5956;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=0;MQRankSum=0.030;QD=13.23;ReadPosRankSum=0.195;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P164|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:35,25:60:99:822,0,1037 -chr1 149224 . T C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.926;DP=47;Dels=0.00;FS=19.146;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.421;QD=14.51;ReadPosRankSum=-0.769;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTc/aCc|I181T|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,21:47:99:710,0,673 -chr1 149225 . C G 72.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.685;DP=47;Dels=0.00;FS=6.565;HaplotypeScore=12.8749;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.526;QD=1.55;ReadPosRankSum=1.164;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atC/atG|I181M|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:41,6:47:99:101,0,1493 -chr1 149237 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.474;DP=43;Dels=0.00;FS=4.406;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=0.284;QD=0.81;ReadPosRankSum=1.118;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctG/ctA|L185|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:38,5:43:63:63,0,1390 -chr1 149253 . C T 1318.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.87;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Tca|P191S|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1347,105,0 -chr1 149279 . G A 504.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.121;DP=34;Dels=0.00;FS=8.198;HaplotypeScore=1.9330;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.052;QD=14.85;ReadPosRankSum=0.155;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S199|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_149142_149360),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:533,0,627 -chr1 149379 . T C 993.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.329;DP=49;Dels=0.00;FS=1.117;HaplotypeScore=2.8936;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.187;QD=20.28;ReadPosRankSum=0.193;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:1022,0,551 -chr1 149421 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.477;DP=43;Dels=0.00;FS=1.218;HaplotypeScore=3.8299;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.086;QD=13.09;ReadPosRankSum=0.037;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:591,0,836 -chr1 149472 . A G 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.173;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.074;QD=12.76;ReadPosRankSum=-0.015;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,16:38:99:513,0,690 -chr1 149514 . C T 435.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.438;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.243;QD=12.10;ReadPosRankSum=1.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:464,0,734 -chr1 149653 . G T 579.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.40;MQ0=1;QD=28.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 1/1:0,16:16:45:608,45,0 -chr1 149713 . T G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.394;DP=42;Dels=0.00;FS=1.480;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.750;QD=12.83;ReadPosRankSum=0.496;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:567,0,822 -chr1 149716 . C T 625.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.591;DP=44;Dels=0.00;FS=3.214;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.78;MQ0=0;MQRankSum=-0.177;QD=14.22;ReadPosRankSum=-0.365;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:654,0,836 -chr1 149737 . A G 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.170;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.238;QD=16.15;ReadPosRankSum=1.192;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:755,0,792 -chr1 149745 . C T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.331;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.697;QD=13.88;ReadPosRankSum=1.519;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:25,20:45:99:653,0,850 -chr1 149746 . A G 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.247;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.420;QD=13.21;ReadPosRankSum=1.732;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:649,0,910 -chr1 149780 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.077;DP=33;Dels=0.00;FS=3.967;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.998;QD=11.84;ReadPosRankSum=-1.803;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00130|mRNA||GSCOCT00012422001|) GT:AD:DP:GQ:PL 0/1:19,13:33:99:419,0,669 -chr1 149946 . T C 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.827;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.80;MQ0=0;MQRankSum=-1.482;QD=12.69;ReadPosRankSum=0.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:701,0,1128 -chr1 149947 . G A 2084.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.80;MQ0=0;QD=27.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2113,157,0 -chr1 149959 . T G 1968.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.79;MQ0=0;QD=31.52;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1997,150,0 -chr1 149962 . T C 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=50;Dels=0.00;FS=1.172;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.553;QD=10.14;ReadPosRankSum=-0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,17:50:99:535,0,1193 -chr1 150069 . A G 699.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=0;MQRankSum=-1.083;QD=17.49;ReadPosRankSum=0.217;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I248V|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:19,21:40:99:728,0,642 -chr1 150083 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.606;DP=42;Dels=0.00;FS=2.885;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=2.679;QD=14.76;ReadPosRankSum=0.859;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtG/gtA|V252|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_150006_150117) GT:AD:DP:GQ:PL 0/1:23,19:42:99:648,0,802 -chr1 150232 . C T 2061.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=59.55;MQ0=0;QD=24.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2090,159,0 -chr1 150236 . G A 666.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.696;DP=55;Dels=0.00;FS=5.672;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.713;QD=12.12;ReadPosRankSum=0.850;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:695,0,1131 -chr1 150249 . C G 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.775;DP=55;Dels=0.00;FS=3.715;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.844;QD=13.76;ReadPosRankSum=2.150;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,24:55:99:785,0,958 -chr1 150265 . C T 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;DP=57;Dels=0.00;FS=2.302;HaplotypeScore=2.8318;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.049;QD=11.47;ReadPosRankSum=2.072;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,22:57:99:682,0,1070 -chr1 150297 . T C 2289.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.46;MQ0=0;QD=28.40;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2318,175,0 -chr1 150375 . T G 713.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.134;DP=48;Dels=0.00;FS=14.013;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=-0.610;QD=14.87;ReadPosRankSum=0.735;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,22:48:99:742,0,881 -chr1 150494 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.680;DP=38;Dels=0.00;FS=1.849;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=0.182;QD=25.63;ReadPosRankSum=1.541;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,28:38:99:1002,0,268 -chr1 150499 . C A 217.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.340;DP=37;Dels=0.00;FS=1.885;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=58.20;MQ0=1;MQRankSum=-0.698;QD=5.89;ReadPosRankSum=-1.378;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,10:37:99:246,0,955 -chr1 150581 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.334;DP=28;Dels=0.00;FS=7.346;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.220;QD=6.46;ReadPosRankSum=-0.318;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:209,0,766 -chr1 150588 . A T 1273.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.05;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1302,96,0 -chr1 150606 . C T 1237.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1266,93,0 -chr1 150717 . T A,G 1153.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.04;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,16,20:36:99:1346,748,699,599,0,539 -chr1 150752 . G A 1457.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1486,114,0 -chr1 150838 . A G 553.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.568;DP=52;Dels=0.00;FS=6.106;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.029;QD=10.65;ReadPosRankSum=1.741;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,18:52:99:582,0,1173 -chr1 150929 . G A 2230.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.19;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2259,172,0 -chr1 150953 . C A 979.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.538;DP=60;Dels=0.00;FS=31.975;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.044;QD=16.33;ReadPosRankSum=-0.680;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,31:60:99:1008,0,1004 -chr1 150957 . T C 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.859;DP=61;Dels=0.00;FS=31.108;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.888;QD=17.03;ReadPosRankSum=-0.744;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,32:61:99:1067,0,979 -chr1 151031 . T A 2189.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=33.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2218,166,0 -chr1 151074 . A T 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.170;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=1.9853;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-0.650;QD=16.10;ReadPosRankSum=-0.550;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,25:49:99:817,0,821 -chr1 151153 . T A 762.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.182;DP=58;Dels=0.00;FS=7.584;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.355;QD=13.15;ReadPosRankSum=-0.087;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:791,0,1148 -chr1 151277 . G C 328.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.054;DP=35;Dels=0.00;FS=8.547;HaplotypeScore=3.9810;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-0.126;QD=9.39;ReadPosRankSum=0.811;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccG/ccC|P284|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_151216_151324) GT:AD:DP:GQ:PL 0/1:22,12:35:99:357,0,750 -chr1 151351 . A G 1121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.257;DP=53;Dels=0.00;FS=5.783;HaplotypeScore=5.9768;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.771;QD=21.17;ReadPosRankSum=-0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,33:53:99:1150,0,663 -chr1 151361 . A G,T 1601.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.03;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,26,24:50:99:1836,882,804,954,0,882 -chr1 151391 . T A 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.522;DP=43;Dels=0.00;FS=1.286;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.140;QD=10.46;ReadPosRankSum=-0.675;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,15:43:99:478,0,965 -chr1 151489 . T C 922.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.223;DP=53;Dels=0.00;FS=1.065;HaplotypeScore=1.9990;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.773;QD=17.41;ReadPosRankSum=-0.401;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,28:53:99:951,0,823 -chr1 151542 . C T 1073.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.309;DP=63;Dels=0.00;FS=30.147;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.313;QD=17.04;ReadPosRankSum=-0.351;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1102,0,1065 -chr1 151610 . C A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.325;DP=59;Dels=0.00;FS=9.684;HaplotypeScore=2.9991;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=0.218;QD=14.40;ReadPosRankSum=1.356;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:878,0,1066 -chr1 151618 . T C 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.238;DP=61;Dels=0.00;FS=5.239;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=59.53;MQ0=0;MQRankSum=0.094;QD=16.44;ReadPosRankSum=0.815;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,31:61:99:1031,0,1031 -chr1 151695 . T G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.206;DP=51;Dels=0.00;FS=1.161;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.688;QD=20.33;ReadPosRankSum=2.209;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1065,0,641 -chr1 151785 . A G 2449.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2478,184,0 -chr1 151923 . T C 530.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.913;DP=42;Dels=0.00;FS=6.816;HaplotypeScore=1.8662;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-0.225;QD=12.64;ReadPosRankSum=-0.225;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,17:42:99:559,0,782 -chr1 151972 . A G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.562;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=0.876;QD=17.48;ReadPosRankSum=-0.614;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:745,0,597 -chr1 152191 . C G 1805.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.9945;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=30.22;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1834,147,0 -chr1 152290 . A G 1160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.627;DP=72;Dels=0.00;FS=4.729;HaplotypeScore=2.7880;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=-1.788;QD=16.12;ReadPosRankSum=1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,35:72:99:1189,0,1208 -chr1 152381 . C A 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.304;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.73;MQ0=0;MQRankSum=-0.235;QD=10.50;ReadPosRankSum=-0.254;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:595,0,1229 -chr1 152382 . C T 533.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.305;DP=53;Dels=0.00;FS=1.147;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=0.873;QD=10.07;ReadPosRankSum=-0.009;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:53:99:562,0,1258 -chr1 152486 . A G 2355.77 . AC=2;AF=1.00;AN=2;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,61:61:99:2384,181,0 -chr1 152515 . T A 2726.77 . AC=2;AF=1.00;AN=2;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,69:69:99:2755,208,0 -chr1 152581 . C A 2660.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2689,202,0 -chr1 152658 . A T 954.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.086;DP=65;Dels=0.00;FS=3.385;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.165;QD=14.69;ReadPosRankSum=-0.574;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:36,29:65:99:983,0,1258 -chr1 152684 . C G 2666.77 . AC=2;AF=1.00;AN=2;DP=68;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.01;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,68:68:99:2695,202,0 -chr1 152720 . A G 1186.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.493;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.563;QD=18.84;ReadPosRankSum=0.826;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,36:63:99:1215,0,861 -chr1 152741 . G T 795.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.082;DP=61;Dels=0.00;FS=3.616;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=0.365;QD=13.05;ReadPosRankSum=-1.096;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:824,0,1171 -chr1 152749 . T C 1986.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.667;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.72;MQ0=1;MQRankSum=-0.360;QD=25.29;ReadPosRankSum=0.033;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,53:54:99:2015,153,0 -chr1 152752 . G C 2005.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=55.46;MQ0=1;QD=30.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2034,153,0 -chr1 152755 . T C 951.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=55;Dels=0.00;FS=3.860;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=55.24;MQ0=1;MQRankSum=2.481;QD=17.30;ReadPosRankSum=1.370;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:980,0,789 -chr1 152892 . T C 96.28 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=23.44;MQ0=4;QD=10.70;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:9:124,9,0 -chr1 152911 . G A 137.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.54;MQ0=4;QD=12.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:165,12,0 -chr1 152938 . C T 136.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.683;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.60;MQ0=4;MQRankSum=1.683;QD=10.46;ReadPosRankSum=1.001;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:6,7:13:12:164,12,0 -chr1 153166 . G A 87.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=5.7547;MLEAC=1;MLEAF=0.500;MQ=18.57;MQ0=5;MQRankSum=1.137;QD=2.93;ReadPosRankSum=1.137;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:20,10:30:92:116,0,92 -chr1 153200 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.078;DP=33;Dels=0.00;FS=3.979;HaplotypeScore=1.7046;MLEAC=1;MLEAF=0.500;MQ=15.76;MQ0=8;MQRankSum=0.670;QD=1.11;ReadPosRankSum=1.136;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,10:33:65:65,0,140 -chr1 153324 . A G 148.31 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.081;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=2.9300;MLEAC=1;MLEAF=0.500;MQ=13.59;MQ0=11;MQRankSum=2.944;QD=4.24;ReadPosRankSum=2.348;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:9,25:35:21:200,21,0 -chr1 153381 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.203;DP=68;Dels=0.00;FS=15.911;HaplotypeScore=21.0001;MLEAC=1;MLEAF=0.500;MQ=12.66;MQ0=25;MQRankSum=0.041;QD=0.61;ReadPosRankSum=0.528;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,13:68:70:70,0,248 -chr1 153430 . T C 161.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.369;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.7356;MLEAC=2;MLEAF=1.00;MQ=10.12;MQ0=25;MQRankSum=0.822;QD=3.68;ReadPosRankSum=-1.734;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,34:44:24:190,24,0 -chr1 153445 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.027;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=-0.451;QD=0.83;ReadPosRankSum=0.239;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:55,12:67:84:84,0,310 -chr1 153446 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.512;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=9.0452;MLEAC=1;MLEAF=0.500;MQ=15.14;MQ0=40;MQRankSum=1.877;QD=0.65;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:59,8:67:72:72,0,323 -chr1 153476 . C T 447.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.346;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=14.6632;MLEAC=1;MLEAF=0.500;MQ=16.01;MQ0=39;MQRankSum=1.279;QD=5.89;ReadPosRankSum=0.316;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,35:76:79:476,0,79 -chr1 153481 . G A 48.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.783;DP=79;Dels=0.00;FS=2.335;HaplotypeScore=14.5114;MLEAC=1;MLEAF=0.500;MQ=15.99;MQ0=39;MQRankSum=0.178;QD=0.62;ReadPosRankSum=-0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:67,12:79:77:77,0,497 -chr1 153516 . G T 31.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.961;DP=86;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=40;MQRankSum=1.294;QD=0.37;ReadPosRankSum=0.222;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,8:86:60:60,0,573 -chr1 153518 . G A 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=84;Dels=0.00;FS=0.000;HaplotypeScore=11.4714;MLEAC=1;MLEAF=0.500;MQ=17.03;MQ0=39;MQRankSum=1.715;QD=0.41;ReadPosRankSum=-1.174;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,12:84:63:63,0,569 -chr1 153554 . T C 71.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.458;DP=51;Dels=0.00;FS=5.129;HaplotypeScore=5.7732;MLEAC=1;MLEAF=0.500;MQ=14.69;MQ0=20;MQRankSum=0.275;QD=1.41;ReadPosRankSum=-1.078;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,19:51:99:100,0,209 -chr1 153590 . T C 124.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.398;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=7.8158;MLEAC=1;MLEAF=0.500;MQ=13.34;MQ0=22;MQRankSum=0.750;QD=1.69;ReadPosRankSum=0.824;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,41:74:99:153,0,172 -chr1 153593 . T A 267.79 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.432;DP=73;Dels=0.00;FS=12.430;HaplotypeScore=16.3870;MLEAC=1;MLEAF=0.500;MQ=13.50;MQ0=20;MQRankSum=-2.002;QD=3.67;ReadPosRankSum=0.471;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:4,65:73:23:296,0,23 -chr1 153603 . C T 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.475;DP=131;Dels=0.00;FS=1.943;HaplotypeScore=7.3720;MLEAC=1;MLEAF=0.500;MQ=19.19;MQ0=28;MQRankSum=1.316;QD=3.97;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:83,47:131:99:548,0,748 -chr1 153634 . C T 189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.160;DP=250;Dels=0.00;FS=8.821;HaplotypeScore=55.7961;MLEAC=1;MLEAF=0.500;MQ=21.90;MQ0=51;MQRankSum=-0.113;QD=0.76;ReadPosRankSum=2.098;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:217,33:250:99:218,0,3652 -chr1 153635 . A T 2861.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.523;DP=250;Dels=0.00;FS=76.787;HaplotypeScore=57.8078;MLEAC=1;MLEAF=0.500;MQ=22.51;MQ0=49;MQRankSum=3.056;QD=11.45;ReadPosRankSum=2.693;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:101,149:250:99:2890,0,1044 -chr1 153682 . C T 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.146;DP=249;Dels=0.00;FS=4.305;HaplotypeScore=56.1815;MLEAC=1;MLEAF=0.500;MQ=24.41;MQ0=45;MQRankSum=2.445;QD=0.69;ReadPosRankSum=1.423;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,20:249:99:200,0,3583 -chr1 153721 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.195;DP=246;Dels=0.00;FS=1.847;HaplotypeScore=63.1880;MLEAC=1;MLEAF=0.500;MQ=23.87;MQ0=46;MQRankSum=3.002;QD=0.06;ReadPosRankSum=-2.172;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:227,14:246:42:42,0,3329 -chr1 153722 . G A 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.376;DP=245;Dels=0.00;FS=1.279;HaplotypeScore=60.2739;MLEAC=1;MLEAF=0.500;MQ=23.89;MQ0=46;MQRankSum=2.339;QD=0.86;ReadPosRankSum=1.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:218,26:245:99:239,0,3144 -chr1 153752 . T C 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.489;DP=115;Dels=0.00;FS=5.126;HaplotypeScore=12.2854;MLEAC=1;MLEAF=0.500;MQ=17.73;MQ0=25;MQRankSum=-2.081;QD=0.17;ReadPosRankSum=-1.203;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:75,40:115:48:48,0,900 -chr1 153768 . A G 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.509;DP=106;Dels=0.00;FS=2.104;HaplotypeScore=3.8507;MLEAC=1;MLEAF=0.500;MQ=16.93;MQ0=30;MQRankSum=-0.643;QD=1.08;ReadPosRankSum=0.595;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:72,30:106:99:143,0,668 -chr1 153796 . G A 1945.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.977;DP=209;Dels=0.00;FS=0.000;HaplotypeScore=23.0694;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=44;MQRankSum=4.401;QD=9.31;ReadPosRankSum=0.585;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:85,120:209:99:1974,0,350 -chr1 153918 . G A 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=231;Dels=0.00;FS=102.092;HaplotypeScore=38.2429;MLEAC=1;MLEAF=0.500;MQ=21.52;MQ0=56;MQRankSum=1.367;QD=0.09;ReadPosRankSum=2.636;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:212,19:231:49:49,0,2890 -chr1 153928 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.721;DP=177;Dels=0.00;FS=70.822;HaplotypeScore=49.5301;MLEAC=1;MLEAF=0.500;MQ=19.80;MQ0=52;MQRankSum=2.469;QD=0.32;ReadPosRankSum=1.151;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:165,11:177:84:84,0,1870 -chr1 153931 . G C 1198.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.672;DP=171;Dels=0.00;FS=63.103;HaplotypeScore=41.3083;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=50;MQRankSum=3.349;QD=7.01;ReadPosRankSum=-0.504;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:103,67:171:99:1227,0,745 -chr1 153947 . A G 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.164;DP=117;Dels=0.00;FS=16.425;HaplotypeScore=22.7832;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=38;MQRankSum=2.093;QD=2.57;ReadPosRankSum=-1.715;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:97,20:117:99:329,0,946 -chr1 153962 . T C 390.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.029;DP=76;Dels=0.00;FS=28.843;HaplotypeScore=13.6296;MLEAC=1;MLEAF=0.500;MQ=17.52;MQ0=25;MQRankSum=3.039;QD=5.14;ReadPosRankSum=-2.479;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,22:76:99:419,0,279 -chr1 153982 . C G 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=27;Dels=0.00;FS=10.000;HaplotypeScore=2.6670;MLEAC=1;MLEAF=0.500;MQ=11.06;MQ0=11;MQRankSum=2.285;QD=1.36;ReadPosRankSum=2.415;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,5:27:29:65,0,29 -chr1 154000 . A C 52.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.44;MQ0=1;QD=8.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:80,9,0 -chr1 154002 . G A 52.28 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.74;MQ0=1;QD=10.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,5:5:9:80,9,0 -chr1 154038 . G A 30.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.736;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=18.18;MQ0=1;MQRankSum=0.736;QD=7.69;ReadPosRankSum=-0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,3:4:6:58,6,0 -chr1 154066 . G A 262.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=23.89;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,10:11:27:291,27,0 -chr1 154073 . A T 236.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=30.80;MQ0=2;QD=21.53;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:11:24:265,24,0 -chr1 154089 . C T 246.1 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.061;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=1.9468;MLEAC=1;MLEAF=0.500;MQ=27.14;MQ0=4;MQRankSum=2.003;QD=16.41;ReadPosRankSum=2.003;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:5,10:15:11:274,0,11 -chr1 154114 . T C 272.41 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.778;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=25.10;MQ0=4;MQRankSum=2.024;QD=15.13;ReadPosRankSum=0.934;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:5,13:18:8:300,8,0 -chr1 154133 . C T 113.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.115;DP=35;Dels=0.00;FS=9.558;HaplotypeScore=3.5584;MLEAC=1;MLEAF=0.500;MQ=18.65;MQ0=14;MQRankSum=2.353;QD=3.25;ReadPosRankSum=1.445;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,7:35:99:142,0,207 -chr1 154140 . G A 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.372;QD=0.88;ReadPosRankSum=0.501;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,368 -chr1 154141 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.501;DP=45;Dels=0.00;FS=11.635;HaplotypeScore=12.4237;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=14;MQRankSum=2.238;QD=0.88;ReadPosRankSum=0.167;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,3:45:68:68,0,372 -chr1 154150 . C T 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.188;DP=52;Dels=0.00;FS=11.840;HaplotypeScore=12.4214;MLEAC=1;MLEAF=0.500;MQ=19.66;MQ0=15;MQRankSum=1.795;QD=3.11;ReadPosRankSum=-1.146;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:41,11:52:99:190,0,332 -chr1 154162 . G A 237.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.044;DP=55;Dels=0.00;FS=11.710;HaplotypeScore=10.1969;MLEAC=1;MLEAF=0.500;MQ=18.76;MQ0=15;MQRankSum=2.642;QD=4.32;ReadPosRankSum=-0.664;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:43,12:55:99:266,0,265 -chr1 154178 . A T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.453;DP=57;Dels=0.00;FS=12.518;HaplotypeScore=35.4325;MLEAC=1;MLEAF=0.500;MQ=19.06;MQ0=14;MQRankSum=0.047;QD=0.65;ReadPosRankSum=0.421;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:49,8:57:65:65,0,554 -chr1 154185 . G A 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.265;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=32.5155;MLEAC=1;MLEAF=0.500;MQ=19.28;MQ0=13;MQRankSum=-1.073;QD=0.29;ReadPosRankSum=-0.593;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:47,8:55:44:44,0,542 -chr1 154186 . C T 307.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.791;DP=56;Dels=0.00;FS=6.576;HaplotypeScore=25.1706;MLEAC=1;MLEAF=0.500;MQ=19.31;MQ0=13;MQRankSum=2.199;QD=5.50;ReadPosRankSum=1.671;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,16:56:99:336,0,269 -chr1 154211 . G T 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.560;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=20.8680;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=-1.269;QD=0.41;ReadPosRankSum=1.843;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,10:58:52:52,0,633 -chr1 154212 . G A 44.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.108;DP=58;Dels=0.00;FS=23.517;HaplotypeScore=19.0376;MLEAC=1;MLEAF=0.500;MQ=19.61;MQ0=12;MQRankSum=0.000;QD=0.77;ReadPosRankSum=-1.855;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:48,10:58:73:73,0,611 -chr1 154215 . A G 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.101;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=11.7095;MLEAC=1;MLEAF=0.500;MQ=19.47;MQ0=12;MQRankSum=-0.934;QD=0.60;ReadPosRankSum=2.084;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:45,10:55:61:61,0,555 -chr1 154233 . T A 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.328;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=4.6866;MLEAC=1;MLEAF=0.500;MQ=22.49;MQ0=0;MQRankSum=-1.708;QD=3.52;ReadPosRankSum=-1.604;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,16:34:99:148,0,338 -chr1 154250 . A G 353.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=2.8562;MLEAC=2;MLEAF=1.00;MQ=21.26;MQ0=0;QD=20.81;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:382,45,0 -chr1 154253 . T G 102.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.637;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=19.93;MQ0=0;MQRankSum=0.174;QD=6.85;ReadPosRankSum=0.637;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:8,7:15:99:131,0,128 -chr1 154292 . T C 33.74 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.69;MQ0=3;QD=4.82;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:2,5:7:6:61,6,0 -chr1 154334 . G A 125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.692;DP=29;Dels=0.00;FS=9.558;HaplotypeScore=2.4530;MLEAC=1;MLEAF=0.500;MQ=23.50;MQ0=4;MQRankSum=-0.028;QD=4.34;ReadPosRankSum=-1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:154,0,227 -chr1 154358 . C A 12.05 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.756;DP=47;Dels=0.00;FS=6.284;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.42;MQ0=3;MQRankSum=-1.018;QD=0.26;ReadPosRankSum=-0.844;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,9:47:40:40,0,642 -chr1 154359 . T G 544.14 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.915;DP=45;Dels=0.00;FS=12.648;HaplotypeScore=26.6661;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=3;MQRankSum=0.678;QD=12.09;ReadPosRankSum=0.265;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,34:45:24:632,24,0 -chr1 154370 . C A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.646;DP=51;Dels=0.00;FS=8.661;HaplotypeScore=31.0665;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=4;MQRankSum=-2.073;QD=0.43;ReadPosRankSum=1.470;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,13:51:50:50,0,714 -chr1 154426 . G A 41.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=49;Dels=0.00;FS=2.566;HaplotypeScore=5.9227;MLEAC=1;MLEAF=0.500;MQ=20.19;MQ0=9;MQRankSum=-0.765;QD=0.85;ReadPosRankSum=-0.359;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,10:49:70:70,0,505 -chr1 154501 . C T 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=30;Dels=0.00;FS=2.793;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=20.43;MQ0=7;MQRankSum=2.328;QD=1.86;ReadPosRankSum=-0.411;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,3:30:84:84,0,237 -chr1 154559 . G A 70.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.761;DP=30;Dels=0.00;FS=8.741;HaplotypeScore=6.7678;MLEAC=1;MLEAF=0.500;MQ=21.74;MQ0=1;MQRankSum=1.761;QD=2.36;ReadPosRankSum=0.953;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,5:30:99:99,0,279 -chr1 154589 . G A 67.03 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=15.06;MQ0=1;QD=7.45;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,9:9:12:95,12,0 -chr1 154697 . A G 47.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=20.50;MQ0=0;QD=15.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:75,9,0 -chr1 154715 . A G 15.88 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.988;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=24.23;MQ0=0;MQRankSum=0.406;QD=2.27;ReadPosRankSum=-0.406;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:7:44:44,0,65 -chr1 154731 . T A 37.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.895;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=3.8976;MLEAC=1;MLEAF=0.500;MQ=22.58;MQ0=0;MQRankSum=1.214;QD=3.78;ReadPosRankSum=-1.214;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,3:10:66:66,0,111 -chr1 154741 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.309;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=3.8993;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=-1.309;QD=1.82;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:7,5:12:50:50,0,124 -chr1 154746 . C T 193.78 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=2;MLEAF=1.00;MQ=21.34;MQ0=0;QD=16.15;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,12:12:24:222,24,0 -chr1 154748 . G C 40.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.185;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=11.7238;MLEAC=1;MLEAF=0.500;MQ=21.34;MQ0=0;MQRankSum=1.664;QD=3.40;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:9,3:12:69:69,0,77 -chr1 154754 . C T 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=7.8245;MLEAC=1;MLEAF=0.500;MQ=21.59;MQ0=0;MQRankSum=1.246;QD=2.34;ReadPosRankSum=0.000;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:11,3:14:61:61,0,161 -chr1 154802 . G A 95.96 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.831;DP=13;Dels=0.00;FS=2.533;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=17.54;MQ0=1;MQRankSum=2.367;QD=7.38;ReadPosRankSum=0.135;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,7:13:5:123,0,5 -chr1 154809 . G T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.768;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=2.9205;MLEAC=1;MLEAF=0.500;MQ=18.22;MQ0=1;MQRankSum=1.296;QD=1.24;ReadPosRankSum=-1.532;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:10,2:12:43:43,0,89 -chr1 154987 . T C 21.77 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.751;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=2;MLEAF=1.00;MQ=9.62;MQ0=4;MQRankSum=0.751;QD=1.67;ReadPosRankSum=0.751;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,12:13:6:49,6,0 -chr1 155087 . G A 13.97 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.736;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=8.76;MQ0=18;MQRankSum=-0.736;QD=0.67;ReadPosRankSum=0.736;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,18:21:23:42,0,23 -chr1 155148 . C T 12.99 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.005;DP=98;Dels=0.00;FS=2.718;HaplotypeScore=13.7215;MLEAC=1;MLEAF=0.500;MQ=23.52;MQ0=36;MQRankSum=0.569;QD=0.13;ReadPosRankSum=-1.756;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:89,8:98:41:41,0,1299 -chr1 155229 . G A 480.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=17.42;MQ0=12;QD=10.93;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:51:509,51,0 -chr1 155280 . G A 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.347;DP=131;Dels=0.00;FS=0.000;HaplotypeScore=11.9766;MLEAC=1;MLEAF=0.500;MQ=30.43;MQ0=12;MQRankSum=3.514;QD=1.38;ReadPosRankSum=-1.410;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:118,13:131:99:209,0,2278 -chr1 155283 . G A 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.499;DP=138;Dels=0.00;FS=1.657;HaplotypeScore=13.9302;MLEAC=1;MLEAF=0.500;MQ=30.63;MQ0=13;MQRankSum=-1.295;QD=0.08;ReadPosRankSum=-0.289;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:125,13:138:39:39,0,2616 -chr1 155314 . T C 2942.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=180;Dels=0.00;FS=0.919;HaplotypeScore=9.2358;MLEAC=1;MLEAF=0.500;MQ=31.00;MQ0=20;MQRankSum=-4.581;QD=16.35;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,153:180:99:2971,0,552 -chr1 155368 . C T 1195.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.080;DP=116;Dels=0.00;FS=10.244;HaplotypeScore=19.2230;MLEAC=1;MLEAF=0.500;MQ=26.70;MQ0=28;MQRankSum=-3.527;QD=10.31;ReadPosRankSum=-0.904;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,89:116:99:1224,0,527 -chr1 155372 . G A 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.818;DP=110;Dels=0.00;FS=21.794;HaplotypeScore=22.7736;MLEAC=1;MLEAF=0.500;MQ=26.51;MQ0=28;MQRankSum=-2.154;QD=5.63;ReadPosRankSum=-1.004;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:54,56:110:99:648,0,967 -chr1 155396 . T C 412.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.969;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=11.0107;MLEAC=1;MLEAF=0.500;MQ=20.74;MQ0=18;MQRankSum=0.787;QD=6.88;ReadPosRankSum=-2.546;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:18,42:60:99:441,0,159 -chr1 155402 . T C 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.238;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=14.3324;MLEAC=1;MLEAF=0.500;MQ=18.93;MQ0=15;MQRankSum=0.120;QD=0.70;ReadPosRankSum=1.919;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:44,7:51:64:64,0,412 -chr1 155404 . G A 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.763;DP=50;Dels=0.00;FS=2.315;HaplotypeScore=14.9975;MLEAC=1;MLEAF=0.500;MQ=18.26;MQ0=14;MQRankSum=-0.535;QD=2.86;ReadPosRankSum=0.049;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:171,0,293 -chr1 155489 . G A 2696.77 . AC=2;AF=1.00;AN=2;DP=145;Dels=0.00;FS=0.000;HaplotypeScore=54.3672;MLEAC=2;MLEAF=1.00;MQ=28.17;MQ0=15;QD=18.60;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,143:145:99:2725,270,0 -chr1 155496 . C T 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.978;DP=159;Dels=0.00;FS=16.800;HaplotypeScore=104.1353;MLEAC=1;MLEAF=0.500;MQ=28.15;MQ0=19;MQRankSum=4.281;QD=1.63;ReadPosRankSum=-1.263;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:142,17:159:99:287,0,2754 -chr1 155542 . G A 286.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=109;Dels=0.00;FS=13.436;HaplotypeScore=10.2277;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=23;MQRankSum=3.323;QD=2.63;ReadPosRankSum=1.718;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:93,16:109:99:315,0,1464 -chr1 155548 . C G 18.82 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.467;DP=104;Dels=0.00;FS=0.000;HaplotypeScore=19.0733;MLEAC=1;MLEAF=0.500;MQ=25.34;MQ0=22;MQRankSum=1.496;QD=0.18;ReadPosRankSum=0.594;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:92,9:104:47:47,0,1624 -chr1 155558 . G A 539.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.354;DP=83;Dels=0.00;FS=2.807;HaplotypeScore=16.4098;MLEAC=1;MLEAF=0.500;MQ=23.92;MQ0=22;MQRankSum=-3.424;QD=6.50;ReadPosRankSum=-1.063;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,48:83:99:568,0,598 -chr1 155561 . G A 244.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.883;DP=74;Dels=0.00;FS=6.505;HaplotypeScore=10.4277;MLEAC=1;MLEAF=0.500;MQ=24.10;MQ0=19;MQRankSum=3.377;QD=3.31;ReadPosRankSum=0.558;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:63,11:74:99:273,0,780 -chr1 155586 . T A 23.79 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.592;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=3.4598;MLEAC=1;MLEAF=0.500;MQ=17.41;MQ0=15;MQRankSum=1.659;QD=0.72;ReadPosRankSum=-0.829;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,3:33:52:52,0,180 -chr1 155593 . G A 101.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.635;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=1.8664;MLEAC=2;MLEAF=1.00;MQ=13.93;MQ0=11;MQRankSum=0.529;QD=4.39;ReadPosRankSum=-1.134;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:10,13:23:12:129,12,0 -chr1 155655 . A G 941.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.704;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=3.7914;MLEAC=2;MLEAF=1.00;MQ=23.15;MQ0=4;MQRankSum=1.320;QD=18.11;ReadPosRankSum=-1.065;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,48:52:74:970,74,0 -chr1 155704 . T C 886.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.9933;MLEAC=2;MLEAF=1.00;MQ=23.78;MQ0=5;QD=18.47;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,48:48:87:915,87,0 -chr1 155711 . T C 319.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.006;DP=48;Dels=0.00;FS=10.017;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=23.78;MQ0=5;MQRankSum=-2.049;QD=6.66;ReadPosRankSum=2.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,27:48:99:348,0,395 -chr1 155748 . G T 107.9 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.97;MQ0=2;QD=6.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:15:136,15,0 -chr1 155814 . G A 37.28 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=12.84;MQ0=1;QD=6.21;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,6:6:9:65,9,0 -chr1 155851 . A T 60.03 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=11.42;MQ0=4;QD=5.46;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,11:11:12:88,12,0 -chr1 155852 . C T 60.03 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=10.93;MQ0=5;QD=5.00;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:1,11:12:12:88,12,0 -chr1 155921 . C T 563.77 . AC=2;AF=1.00;AN=2;DP=81;Dels=0.00;FS=0.000;HaplotypeScore=2.8662;MLEAC=2;MLEAF=1.00;MQ=13.15;MQ0=40;QD=6.96;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,81:81:69:592,69,0 -chr1 156028 . T C 2144.77 . AC=2;AF=1.00;AN=2;DP=128;Dels=0.00;FS=0.000;HaplotypeScore=3.6927;MLEAC=2;MLEAF=1.00;MQ=20.13;MQ0=19;QD=16.76;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:3,124:128:99:2173,231,0 -chr1 156056 . G A 1257.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.469;DP=97;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=18.35;MQ0=26;MQRankSum=0.191;QD=12.97;ReadPosRankSum=0.052;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:12,85:97:99:1286,109,0 -chr1 156246 . G A 1190.77 . AC=2;AF=1.00;AN=2;DP=78;Dels=0.00;FS=0.000;HaplotypeScore=2.8995;MLEAC=2;MLEAF=1.00;MQ=20.38;MQ0=6;QD=15.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,77:78:99:1219,129,0 -chr1 156279 . C A 10.9 LowQual AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=16.91;MQ0=4;QD=1.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,10:10:3:37,3,0 -chr1 156526 . A G 48.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 -chr1 156547 . A G 811.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.837;DP=56;Dels=0.00;FS=5.379;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=55.83;MQ0=1;MQRankSum=0.887;QD=14.50;ReadPosRankSum=1.631;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:840,0,999 -chr1 156554 . T G 920.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.004;DP=67;Dels=0.00;FS=4.974;HaplotypeScore=1.7313;MLEAC=1;MLEAF=0.500;MQ=56.53;MQ0=1;MQRankSum=-1.187;QD=13.74;ReadPosRankSum=2.549;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:949,0,1225 -chr1 156595 . T C 2518.77 . AC=2;AF=1.00;AN=2;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;QD=29.54;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,64:64:99:2547,190,0 -chr1 156606 . A C 1350.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.290;DP=67;Dels=0.00;FS=6.694;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=0.388;QD=20.16;ReadPosRankSum=2.689;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,39:67:99:1379,0,939 -chr1 156782 . C T 914.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.833;DP=67;Dels=0.00;FS=3.401;HaplotypeScore=3.7879;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=0;MQRankSum=1.087;QD=13.65;ReadPosRankSum=-1.036;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:39,28:67:99:943,0,1345 -chr1 156846 . T A 1011.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.628;DP=63;Dels=0.00;FS=3.924;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.21;MQ0=2;MQRankSum=0.166;QD=16.06;ReadPosRankSum=2.460;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:31,32:63:99:1040,0,959 -chr1 156855 . T C 1152.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.634;DP=65;Dels=0.00;FS=9.722;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=2;MQRankSum=-0.848;QD=17.73;ReadPosRankSum=1.937;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,35:65:99:1181,0,930 -chr1 156873 . C A 440.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.088;DP=54;Dels=0.00;FS=4.462;HaplotypeScore=1.7781;MLEAC=1;MLEAF=0.500;MQ=57.51;MQ0=2;MQRankSum=-0.709;QD=8.16;ReadPosRankSum=0.210;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,18:54:99:469,0,1228 -chr1 156909 . G C 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.429;DP=59;Dels=0.00;FS=5.572;HaplotypeScore=1.6553;MLEAC=1;MLEAF=0.500;MQ=56.17;MQ0=4;MQRankSum=0.042;QD=13.79;ReadPosRankSum=-0.951;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:842,0,823 -chr1 156944 . G A 1215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.313;DP=65;Dels=0.00;FS=0.962;HaplotypeScore=1.8316;MLEAC=1;MLEAF=0.500;MQ=58.32;MQ0=2;MQRankSum=-0.243;QD=18.70;ReadPosRankSum=1.160;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,37:65:99:1244,0,895 -chr1 157008 . C T 1261.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.015;DP=79;Dels=0.00;FS=7.743;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.24;MQ0=0;MQRankSum=1.211;QD=15.97;ReadPosRankSum=-0.240;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,39:79:99:1290,0,1323 -chr1 157051 . C T 2830.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=28.67;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I320|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2859,217,0 -chr1 157058 . G A 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.588;DP=69;Dels=0.00;FS=2.053;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.597;QD=14.53;ReadPosRankSum=0.814;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gag/Aag|E323K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_157049_157117) GT:AD:DP:GQ:PL 0/1:38,31:69:99:1031,0,1223 -chr1 157169 . C T 769.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.476;DP=58;Dels=0.00;FS=2.379;HaplotypeScore=1.9994;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=0.173;QD=13.27;ReadPosRankSum=0.973;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,25:58:99:798,0,1053 -chr1 157239 . C T 856.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.399;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.039;QD=14.77;ReadPosRankSum=1.165;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:885,0,1106 -chr1 157240 . T A 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.274;DP=58;Dels=0.00;FS=11.764;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.086;QD=14.63;ReadPosRankSum=1.196;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:877,0,1125 -chr1 157275 . G A 1900.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.20;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1929,147,0 -chr1 157331 . G A 1541.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1570,117,0 -chr1 157449 . C G 1036.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.059;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.95;MQ0=0;MQRankSum=0.040;QD=18.19;ReadPosRankSum=-0.929;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,33:57:99:1065,0,774 -chr1 157515 . T A 1070.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.511;DP=64;Dels=0.00;FS=5.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.17;MQ0=0;MQRankSum=-0.839;QD=16.73;ReadPosRankSum=0.879;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,32:64:99:1099,0,1080 -chr1 157636 . T G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.591;QD=13.12;ReadPosRankSum=0.988;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,29:71:99:960,0,1393 -chr1 157678 . C T 2841.77 . AC=2;AF=1.00;AN=2;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.8273;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=30.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,72:72:99:2870,214,0 -chr1 157733 . T G 2546.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.75;MQ0=1;QD=32.27;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2575,190,0 -chr1 157895 . A G 2244.77 . AC=2;AF=1.00;AN=2;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.96;MQ0=2;QD=30.24;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,58:58:99:2273,169,0 -chr1 157961 . G A 784.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.614;DP=56;Dels=0.00;FS=2.293;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.124;QD=14.01;ReadPosRankSum=0.654;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:813,0,1117 -chr1 158098 . C T 10.9 LowQual AC=2;AF=1.00;AN=2;DP=1;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=33.00;MQ0=0;QD=10.90;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 -chr1 158261 . T A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.358;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=23.67;MQ0=3;MQRankSum=1.231;QD=5.72;ReadPosRankSum=-1.231;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,2:8:28:74,0,28 -chr1 158283 . C T 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=1.1567;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.77;ReadPosRankSum=-1.733;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:62:62,0,105 -chr1 158288 . C T 35.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.898;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=2.3135;MLEAC=1;MLEAF=0.500;MQ=14.13;MQ0=34;MQRankSum=1.733;QD=0.81;ReadPosRankSum=-0.898;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:42,2:44:64:64,0,104 -chr1 158368 . A G 424.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.21;MQ0=0;QD=32.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,13:13:36:453,36,0 -chr1 158427 . G A 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.660;DP=16;Dels=0.00;FS=17.404;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=31.30;MQ0=1;MQRankSum=0.505;QD=1.36;ReadPosRankSum=2.093;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:13,3:16:50:50,0,292 -chr1 158461 . C A 13.95 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=16;Dels=0.00;FS=11.139;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=39.10;MQ0=1;MQRankSum=-1.083;QD=0.87;ReadPosRankSum=-0.505;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:12,4:16:42:42,0,369 -chr1 158596 . T C 606.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.058;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.36;MQ0=5;MQRankSum=1.809;QD=18.96;ReadPosRankSum=0.444;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:4,28:32:32:635,32,0 -chr1 158745 . A G 347.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=28.00;MQ0=3;QD=21.74;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:376,33,0 -chr1 159147 . A G 38.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=19.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:66,6,0 -chr1 159238 . C T 2056.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=60.21;MQ0=0;QD=32.71;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2085,157,0 -chr1 159252 . G A 1542.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.28;MQ0=0;QD=33.84;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1571,117,0 -chr1 159421 . C A 2132.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=26.0957;MLEAC=2;MLEAF=1.00;MQ=60.29;MQ0=0;QD=24.99;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2161,163,0 -chr1 159489 . A C 349.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.295;DP=35;Dels=0.00;FS=5.503;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=-0.782;QD=9.99;ReadPosRankSum=0.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,12:35:99:378,0,778 -chr1 159490 . G C 316.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.923;DP=36;Dels=0.00;FS=5.305;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.017;QD=8.80;ReadPosRankSum=0.285;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,12:36:99:345,0,811 -chr1 159582 . A C 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=64;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-0.531;QD=16.89;ReadPosRankSum=0.155;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:30,34:64:99:1109,0,986 -chr1 159628 . G A 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.490;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=1.246;QD=12.01;ReadPosRankSum=1.624;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:33,22:55:99:689,0,1123 -chr1 159661 . T C 1693.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1722,132,0 -chr1 159721 . T G 1542.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=1;QD=30.48;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1571,120,0 -chr1 159818 . G C 2039.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=58.07;MQ0=1;QD=29.67;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2068,157,0 -chr1 159860 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.581;DP=31;Dels=0.00;FS=1.455;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=1;MQRankSum=1.161;QD=15.99;ReadPosRankSum=-0.581;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:16,15:31:99:524,0,479 -chr1 159991 . T A 2027.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.38;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2056,154,0 -chr1 160001 . G A 1962.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1991,147,0 -chr1 160043 . A G 1679.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1708,126,0 -chr1 160064 . A G 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.648;DP=44;Dels=0.00;FS=4.575;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.662;QD=13.65;ReadPosRankSum=2.440;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,20:44:99:629,0,815 -chr1 160171 . C A 1993.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.78;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gAt|A363D|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160110_160217) GT:AD:DP:GQ:PL 1/1:0,53:53:99:2022,156,0 -chr1 160220 . A G 973.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.049;DP=63;Dels=0.00;FS=8.766;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=1;MQRankSum=0.585;QD=15.46;ReadPosRankSum=0.275;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1002,0,1082 -chr1 160223 . T C 2397.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=1;QD=28.87;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,62:63:99:2426,184,0 -chr1 160312 . T C 966.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.919;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=1;MQRankSum=0.460;QD=18.96;ReadPosRankSum=0.700;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,32:51:99:995,0,618 -chr1 160344 . G T 996.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.378;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=59.67;MQ0=1;MQRankSum=-0.844;QD=17.19;ReadPosRankSum=-1.600;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,33:58:99:1025,0,815 -chr1 160346 . C T 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.698;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.68;MQ0=1;MQRankSum=-1.756;QD=18.01;ReadPosRankSum=-2.002;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1109,0,813 -chr1 160403 . C T 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.418;DP=47;Dels=0.00;FS=2.597;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=1;MQRankSum=0.187;QD=15.87;ReadPosRankSum=1.792;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:774,0,801 -chr1 160457 . T C 752.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.631;DP=50;Dels=0.00;FS=6.171;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=1;MQRankSum=-1.072;QD=15.06;ReadPosRankSum=-0.691;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:781,0,825 -chr1 160628 . A G 1125.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.790;DP=56;Dels=0.00;FS=3.920;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.486;QD=20.10;ReadPosRankSum=0.964;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1154,0,734 -chr1 160653 . T C 936.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.121;DP=49;Dels=0.00;FS=2.547;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.131;QD=19.12;ReadPosRankSum=1.337;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:965,0,743 -chr1 160771 . A G 413.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.517;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=0.483;QD=11.82;ReadPosRankSum=0.983;EFF=SYNONYMOUS_CODING(LOW|SILENT|agA/agG|R393|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_160727_160819) GT:AD:DP:GQ:PL 0/1:20,15:35:99:442,0,684 -chr1 160830 . T C 1740.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.72;MQ0=0;QD=32.09;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1769,129,0 -chr1 160855 . T G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=49;Dels=0.00;FS=2.463;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.510;QD=16.59;ReadPosRankSum=0.790;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:841,0,789 -chr1 160924 . A T 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.068;DP=45;Dels=0.00;FS=4.461;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=1;MQRankSum=0.305;QD=15.66;ReadPosRankSum=2.608;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:733,0,738 -chr1 161085 . T C 995.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.826;DP=50;Dels=0.00;FS=4.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.708;QD=19.92;ReadPosRankSum=0.314;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,29:50:99:1024,0,658 -chr1 161127 . C T 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.700;DP=43;Dels=0.00;FS=2.692;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.281;QD=14.51;ReadPosRankSum=0.159;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:24,19:43:99:652,0,837 -chr1 161227 . G A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.349;DP=54;Dels=0.00;FS=1.054;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.588;QD=17.01;ReadPosRankSum=1.522;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atG/atA|M421I|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161192_161296) GT:AD:DP:GQ:PL 0/1:27,27:54:99:947,0,859 -chr1 161350 . A G 760.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.657;DP=58;Dels=0.00;FS=2.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=1;MQRankSum=-1.366;QD=13.12;ReadPosRankSum=0.024;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:34,24:58:99:789,0,1101 -chr1 161518 . G T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.065;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.343;QD=20.21;ReadPosRankSum=0.639;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1079,0,713 -chr1 161550 . T G 2153.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2182,163,0 -chr1 161583 . T C 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.314;DP=48;Dels=0.00;FS=1.275;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.066;QD=17.70;ReadPosRankSum=-0.672;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,26:48:99:878,0,744 -chr1 161598 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.153;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.505;QD=16.36;ReadPosRankSum=-0.176;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:748,0,762 -chr1 161607 . G A 761.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.483;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=2.8660;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.527;QD=16.56;ReadPosRankSum=0.154;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:790,0,787 -chr1 161743 . A C 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.492;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=1.6643;MLEAC=1;MLEAF=0.500;MQ=57.06;MQ0=1;MQRankSum=0.379;QD=15.60;ReadPosRankSum=-1.327;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K479Q|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,22:41:99:668,0,538 -chr1 161769 . A T 896.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.793;DP=46;Dels=0.00;FS=9.187;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=57.39;MQ0=1;MQRankSum=0.471;QD=19.49;ReadPosRankSum=0.172;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaA/aaT|K487N|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:19,27:46:99:925,0,511 -chr1 161794 . A C 607.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.236;DP=52;Dels=0.00;FS=10.280;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.58;MQ0=1;MQRankSum=-0.009;QD=11.69;ReadPosRankSum=-2.236;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Cta|I496L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,25:52:99:636,0,971 -chr1 161795 . T A 649.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.758;DP=53;Dels=0.00;FS=10.399;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=1;MQRankSum=-0.513;QD=12.26;ReadPosRankSum=-2.363;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTa/aAa|I496K|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:27,26:53:99:678,0,963 -chr1 161822 . C T 899.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.364;DP=66;Dels=0.00;FS=11.007;HaplotypeScore=3.5506;MLEAC=1;MLEAF=0.500;MQ=58.70;MQ0=1;MQRankSum=-1.119;QD=13.63;ReadPosRankSum=1.484;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P505L|Cc01g00140|mRNA||GSCOCT00012421001|Exon_chr1_161641_161847) GT:AD:DP:GQ:PL 0/1:35,30:66:99:928,0,1200 -chr1 161928 . A G 1788.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=2;MLEAF=1.00;MQ=59.37;MQ0=0;QD=29.28;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1817,138,0 -chr1 162022 . A G 715.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.438;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=0.169;QD=11.01;ReadPosRankSum=1.409;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:40,25:65:99:744,0,1397 -chr1 162207 . G A 2798.77 . AC=2;AF=1.00;AN=2;DP=71;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.29;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,71:71:99:2827,214,0 -chr1 162353 . G C 1411.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.839;QD=20.46;ReadPosRankSum=0.322;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,42:69:99:1440,0,796 -chr1 162433 . T G 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.759;DP=62;Dels=0.00;FS=3.875;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=2.175;QD=11.56;ReadPosRankSum=0.455;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:38,24:62:99:745,0,1353 -chr1 162531 . C T 1811.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1840,141,0 -chr1 162535 . G T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.412;DP=48;Dels=0.00;FS=1.450;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.094;QD=13.18;ReadPosRankSum=0.596;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,20:48:99:661,0,948 -chr1 162542 . A C,T 1553.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;QD=32.36;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/2:0,28,20:48:99:1782,749,665,1033,0,973 -chr1 162739 . G T 67.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.537;DP=6;Dels=0.00;FS=10.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.04;MQ0=0;MQRankSum=0.406;QD=11.29;ReadPosRankSum=-1.537;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,3:6:45:96,0,45 -chr1 162750 . G T 119.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.322;DP=8;Dels=0.00;FS=7.068;HaplotypeScore=2.9939;MLEAC=1;MLEAF=0.500;MQ=59.28;MQ0=0;MQRankSum=1.517;QD=14.97;ReadPosRankSum=-1.920;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:3,5:8:77:148,0,77 -chr1 162805 . C T 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.349;DP=24;Dels=0.00;FS=6.214;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.920;QD=0.91;ReadPosRankSum=0.611;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,3:24:50:50,0,779 -chr1 162820 . T C 161.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.584;DP=28;Dels=0.00;FS=7.181;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.539;QD=5.78;ReadPosRankSum=-2.122;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:190,0,773 -chr1 162833 . A G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.944;DP=31;Dels=0.00;FS=12.129;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.218;QD=26.80;ReadPosRankSum=0.130;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:6,24:31:99:859,0,157 -chr1 163107 . T C 1577.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.40;MQ0=1;QD=30.33;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1606,117,0 -chr1 163152 . G C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=54;Dels=0.00;FS=5.807;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.98;MQ0=0;MQRankSum=0.996;QD=10.96;ReadPosRankSum=-0.127;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1162 -chr1 163218 . T G 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=50;Dels=0.00;FS=3.842;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.806;QD=15.84;ReadPosRankSum=-0.456;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:26,24:50:99:820,0,917 -chr1 163281 . T A 1020.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.585;DP=49;Dels=0.00;FS=5.959;HaplotypeScore=1.9995;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.365;QD=20.83;ReadPosRankSum=-0.133;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:19,30:49:99:1049,0,617 -chr1 163602 . A T 1204.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.050;DP=60;Dels=0.00;FS=1.004;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.135;QD=20.08;ReadPosRankSum=-1.080;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1233,0,823 -chr1 163615 . A C 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=61;Dels=0.00;FS=0.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.905;QD=15.06;ReadPosRankSum=0.485;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,28:61:99:947,0,1113 -chr1 163628 . T C 1045.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.228;DP=65;Dels=0.00;FS=0.942;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.992;QD=16.09;ReadPosRankSum=0.046;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,31:65:99:1074,0,1122 -chr1 163725 . C T 998.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=1;MQRankSum=1.996;QD=17.52;ReadPosRankSum=-0.090;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,30:57:99:1027,0,891 -chr1 163736 . G C 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.072;DP=58;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=1;MQRankSum=-0.360;QD=17.74;ReadPosRankSum=-0.280;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1057,0,874 -chr1 163748 . T G 2436.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.15;MQ0=1;QD=33.58;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:1,62:63:99:2465,187,0 -chr1 163777 . C A 1052.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.340;DP=58;Dels=0.00;FS=2.434;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=2;MQRankSum=0.445;QD=18.15;ReadPosRankSum=0.330;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1081,0,777 -chr1 163806 . C T 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=52;Dels=0.00;FS=4.176;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=1;MQRankSum=0.386;QD=15.90;ReadPosRankSum=0.763;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:855,0,885 -chr1 163808 . A G 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.176;DP=49;Dels=0.00;FS=2.654;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=1;MQRankSum=-2.064;QD=17.10;ReadPosRankSum=0.186;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:866,0,770 -chr1 163854 . A G 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=1;MQRankSum=-1.274;QD=13.14;ReadPosRankSum=0.742;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:646,0,892 -chr1 163894 . A C 659.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.057;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.626;QD=14.66;ReadPosRankSum=0.011;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:688,0,813 -chr1 163957 . T A 957.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.166;DP=61;Dels=0.00;FS=3.596;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.570;QD=15.70;ReadPosRankSum=-1.105;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,29:61:99:986,0,1103 -chr1 163980 . A G 1028.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.148;DP=63;Dels=0.00;FS=3.778;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.763;QD=16.33;ReadPosRankSum=-1.010;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,31:63:99:1057,0,1126 -chr1 164145 . A T 2835.77 . AC=2;AF=1.00;AN=2;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.01;MQ0=0;QD=32.13;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2864,220,0 -chr1 164203 . T G 1012.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.489;DP=77;Dels=0.00;FS=0.917;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=0.110;QD=13.15;ReadPosRankSum=1.352;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:44,33:77:99:1041,0,1470 -chr1 164252 . A C 1239.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.049;DP=65;Dels=0.00;FS=3.361;HaplotypeScore=3.6644;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.297;QD=19.07;ReadPosRankSum=-0.284;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,36:65:99:1268,0,967 -chr1 164282 . T G 1111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.437;DP=64;Dels=0.00;FS=8.767;HaplotypeScore=1.7886;MLEAC=1;MLEAF=0.500;MQ=59.69;MQ0=0;MQRankSum=-0.443;QD=17.37;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,33:64:99:1140,0,1007 -chr1 164379 . G A 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.789;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=1.7845;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.487;QD=17.46;ReadPosRankSum=0.834;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,37:72:99:1285,0,1107 -chr1 164466 . A T 2375.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.56;MQ0=0;QD=28.88;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2404,181,0 -chr1 164494 . T C 612.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.288;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9829;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.082;QD=11.78;ReadPosRankSum=2.323;EFF=INTRON(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,20:52:99:641,0,1102 -chr1 164861 . T C 1256.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.530;DP=68;Dels=0.00;FS=4.986;HaplotypeScore=1.9732;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-0.679;QD=18.48;ReadPosRankSum=-1.576;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:28,40:68:99:1285,0,918 -chr1 164906 . A G 2110.77 . AC=2;AF=1.00;AN=2;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=27.84;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 1/1:0,55:55:99:2139,163,0 -chr1 164958 . A G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.907;DP=50;Dels=0.00;FS=1.129;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.295;QD=12.86;ReadPosRankSum=-1.081;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:671,0,981 -chr1 165095 . G A 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.403;DP=52;Dels=0.00;FS=2.379;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.531;QD=16.03;ReadPosRankSum=-0.751;EFF=UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|) GT:AD:DP:GQ:PL 0/1:27,25:52:99:862,0,944 -chr1 165389 . T G 915.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.072;DP=62;Dels=0.00;FS=5.213;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=0;MQRankSum=-2.850;QD=14.77;ReadPosRankSum=-1.735;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,29:62:99:944,0,1149 -chr1 165407 . C A 871.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.847;DP=64;Dels=0.00;FS=2.112;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.97;MQ0=0;MQRankSum=-5.528;QD=13.62;ReadPosRankSum=-1.455;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,28:64:99:900,0,1192 -chr1 165447 . A G 873.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.256;DP=49;Dels=0.00;FS=5.913;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=48.96;MQ0=0;MQRankSum=4.271;QD=17.83;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,27:49:99:902,0,692 -chr1 165482 . G T 565.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.083;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-0.596;QD=13.47;ReadPosRankSum=0.190;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:42:99:594,0,720 -chr1 165483 . G T 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.222;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=3.1091;MLEAC=1;MLEAF=0.500;MQ=54.70;MQ0=0;MQRankSum=-1.082;QD=15.12;ReadPosRankSum=0.196;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,21:41:99:648,0,635 -chr1 165526 . C T 1019.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.764;QD=21.70;ReadPosRankSum=0.631;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,30:47:99:1048,0,485 -chr1 165678 . C T 989.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.733;DP=56;Dels=0.00;FS=5.297;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.10;MQ0=0;MQRankSum=-3.048;QD=17.67;ReadPosRankSum=0.468;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,30:56:99:1018,0,833 -chr1 165701 . T A 1032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.604;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9992;MLEAC=1;MLEAF=0.500;MQ=55.17;MQ0=0;MQRankSum=-1.305;QD=19.86;ReadPosRankSum=0.839;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,31:52:99:1061,0,610 -chr1 165957 . G A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.556;DP=42;Dels=0.00;FS=6.343;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.657;QD=17.66;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:770,0,629 -chr1 165982 . T G 534.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.314;DP=35;Dels=0.00;FS=1.320;HaplotypeScore=2.6981;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-1.007;QD=15.28;ReadPosRankSum=-0.677;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,18:35:99:563,0,552 -chr1 166129 . A T 583.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.425;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.719;QD=14.24;ReadPosRankSum=2.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:612,0,716 -chr1 166135 . T G 604.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=40;Dels=0.00;FS=4.837;HaplotypeScore=2.7214;MLEAC=1;MLEAF=0.500;MQ=58.41;MQ0=0;MQRankSum=-1.300;QD=15.12;ReadPosRankSum=1.625;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:633,0,714 -chr1 166157 . C T 309.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.204;DP=19;Dels=0.00;FS=17.041;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=1.592;QD=16.30;ReadPosRankSum=-0.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:9,10:19:99:338,0,285 -chr1 166165 . G A 819.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=59.74;MQ0=0;QD=35.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:848,66,0 -chr1 166187 . T C 745.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.71;MQ0=0;QD=23.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:774,60,0 -chr1 166200 . C T 1299.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=13.5158;MLEAC=2;MLEAF=1.00;MQ=55.26;MQ0=0;QD=30.02;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1328,99,0 -chr1 166214 . C T 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.550;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=54.69;MQ0=0;MQRankSum=-5.017;QD=10.28;ReadPosRankSum=-1.750;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:388,0,673 -chr1 166219 . A G 469.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.058;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.67;MQ0=0;MQRankSum=-5.166;QD=12.70;ReadPosRankSum=-0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:498,0,722 -chr1 166226 . G A 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.613;DP=35;Dels=0.00;FS=1.330;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.35;MQ0=0;MQRankSum=-5.050;QD=14.16;ReadPosRankSum=1.043;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:524,0,649 -chr1 166233 . G A 527.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.763;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=54.82;MQ0=0;MQRankSum=-4.961;QD=13.89;ReadPosRankSum=2.701;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:556,0,691 -chr1 166248 . G A 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.442;DP=37;Dels=0.00;FS=2.870;HaplotypeScore=1.7333;MLEAC=1;MLEAF=0.500;MQ=56.38;MQ0=0;MQRankSum=-3.398;QD=13.51;ReadPosRankSum=2.423;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,645 -chr1 166255 . A C 437.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.555;DP=34;Dels=0.00;FS=3.155;HaplotypeScore=13.4643;MLEAC=1;MLEAF=0.500;MQ=56.99;MQ0=0;MQRankSum=-3.919;QD=12.88;ReadPosRankSum=2.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:466,0,539 -chr1 166256 . C T 475.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=35;Dels=0.00;FS=2.984;HaplotypeScore=14.4309;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=0;MQRankSum=-3.394;QD=13.59;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,16:35:99:504,0,583 -chr1 166297 . G A 1027.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.528;DP=52;Dels=0.00;FS=1.203;HaplotypeScore=4.3119;MLEAC=1;MLEAF=0.500;MQ=57.74;MQ0=0;MQRankSum=-0.194;QD=19.76;ReadPosRankSum=0.843;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,30:52:99:1056,0,614 -chr1 166322 . T A 1149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.604;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=1.305;QD=19.16;ReadPosRankSum=0.500;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,34:60:99:1178,0,786 -chr1 166453 . A G 939.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.040;DP=55;Dels=0.00;FS=9.665;HaplotypeScore=2.6999;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=-0.583;QD=17.09;ReadPosRankSum=-2.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:25,30:55:99:968,0,816 -chr1 166585 . G A 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.313;DP=56;Dels=0.00;FS=2.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.945;QD=13.09;ReadPosRankSum=0.923;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,25:56:99:761,0,1060 -chr1 166654 . A T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.786;DP=46;Dels=0.00;FS=4.286;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=1;MQRankSum=-1.445;QD=16.45;ReadPosRankSum=0.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:785,0,700 -chr1 166658 . T G 701.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.864;DP=44;Dels=0.00;FS=9.040;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=1;MQRankSum=-2.277;QD=15.95;ReadPosRankSum=0.572;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:730,0,641 -chr1 166669 . G C 742.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.834;DP=42;Dels=0.00;FS=15.562;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=1;MQRankSum=-0.595;QD=17.68;ReadPosRankSum=-0.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:17,25:42:99:771,0,549 -chr1 166716 . A G 732.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.762;DP=46;Dels=0.00;FS=4.124;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.93;MQ0=2;MQRankSum=-1.715;QD=15.93;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,25:46:99:761,0,715 -chr1 166733 . T G 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.886;DP=52;Dels=0.00;FS=5.964;HaplotypeScore=1.7337;MLEAC=1;MLEAF=0.500;MQ=56.36;MQ0=2;MQRankSum=-1.925;QD=13.15;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:712,0,936 -chr1 166734 . G T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.213;DP=54;Dels=0.00;FS=5.816;HaplotypeScore=3.7324;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=2;MQRankSum=-2.232;QD=12.46;ReadPosRankSum=0.732;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,24:54:99:701,0,1010 -chr1 166737 . T C 665.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.734;DP=56;Dels=0.00;FS=5.681;HaplotypeScore=4.7320;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=2;MQRankSum=-1.928;QD=11.89;ReadPosRankSum=1.083;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,24:56:99:694,0,1084 -chr1 166751 . A C 821.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=57;Dels=0.00;FS=2.274;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.45;MQ0=1;MQRankSum=-0.813;QD=14.42;ReadPosRankSum=0.550;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:850,0,1009 -chr1 166834 . G A 582.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.137;DP=38;Dels=0.00;FS=25.349;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=0.410;QD=15.34;ReadPosRankSum=0.167;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:611,0,646 -chr1 166877 . T A 439.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.197;DP=32;Dels=0.00;FS=21.686;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.083;QD=13.74;ReadPosRankSum=1.273;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:18,14:32:99:468,0,592 -chr1 166961 . T C 287.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.053;DP=32;Dels=0.00;FS=15.187;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.468;QD=8.99;ReadPosRankSum=1.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:316,0,780 -chr1 167041 . T A 743.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=16.8441;MLEAC=2;MLEAF=1.00;MQ=57.88;MQ0=0;QD=34.22;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,21:21:63:772,63,0 -chr1 167090 . C T 1469.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.69;MQ0=0;QD=28.97;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1498,114,0 -chr1 167165 . C T 1575.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=31.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1604,120,0 -chr1 167170 . A C 1602.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;QD=33.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,42:42:99:1631,123,0 -chr1 167208 . G A 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.357;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.870;QD=12.28;ReadPosRankSum=1.405;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:27,19:46:99:593,0,944 -chr1 167228 . C G 835.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=45;Dels=0.00;FS=2.529;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.633;QD=18.57;ReadPosRankSum=1.519;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:20,25:45:99:864,0,666 -chr1 167283 . A G 824.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.416;DP=47;Dels=0.00;FS=13.823;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.906;QD=17.55;ReadPosRankSum=1.333;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:22,25:47:99:853,0,735 -chr1 167363 . T A 1954.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1983,153,0 -chr1 167371 . G A 883.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.085;DP=51;Dels=0.00;FS=2.387;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.897;QD=17.33;ReadPosRankSum=0.066;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:912,0,760 -chr1 167399 . G T 890.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.694;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.632;QD=16.20;ReadPosRankSum=-0.531;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,29:55:99:919,0,873 -chr1 167568 . C T 700.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.692;DP=47;Dels=0.00;FS=4.301;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.926;QD=14.91;ReadPosRankSum=-1.266;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:729,0,770 -chr1 167574 . G T 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=45;Dels=0.00;FS=4.485;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.580;QD=14.26;ReadPosRankSum=-1.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:670,0,813 -chr1 167656 . G A 1543.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.41;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1572,123,0 -chr1 167672 . C G 467.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.198;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.97;MQ0=0;MQRankSum=-2.527;QD=11.41;ReadPosRankSum=-0.834;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:496,0,851 -chr1 167681 . A T 620.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.107;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.34;MQ0=0;MQRankSum=-0.635;QD=12.42;ReadPosRankSum=-1.397;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:28,22:50:99:649,0,985 -chr1 168087 . G A 685.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=2.7985;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=0.503;QD=14.59;ReadPosRankSum=0.781;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:714,0,900 -chr1 168095 . G C 862.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.150;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-1.112;QD=17.61;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:23,26:49:99:891,0,777 -chr1 168096 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.232;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=-0.551;QD=14.46;ReadPosRankSum=-0.851;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,23:49:99:737,0,907 -chr1 168153 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.248;DP=44;Dels=0.00;FS=6.747;HaplotypeScore=3.9991;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=1.608;QD=15.79;ReadPosRankSum=-0.065;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,22:44:99:723,0,628 -chr1 168196 . G A 445.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.243;DP=34;Dels=0.00;FS=3.353;HaplotypeScore=0.9469;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=0.659;QD=13.11;ReadPosRankSum=-0.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:474,0,581 -chr1 168202 . G T 1401.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.28;MQ0=0;QD=39.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1430,108,0 -chr1 168341 . T C 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=58;Dels=0.00;FS=1.012;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.993;QD=13.50;ReadPosRankSum=-0.649;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:811,0,1056 -chr1 168360 . G T 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.648;DP=55;Dels=0.00;FS=2.266;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.955;QD=12.69;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,25:55:99:726,0,991 -chr1 168533 . C T 429.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.077;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.4538;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=0;MQRankSum=0.230;QD=11.62;ReadPosRankSum=-1.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P42L|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:21,16:37:99:458,0,718 -chr1 168548 . A T 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.299;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=58.68;MQ0=0;MQRankSum=0.239;QD=11.20;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tAc/tTc|Y47F|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:23,15:38:99:454,0,793 -chr1 168693 . T C 454.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.458;DP=42;Dels=0.00;FS=4.987;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=2;MQRankSum=-0.505;QD=10.83;ReadPosRankSum=2.382;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|tcT/tcC|S95|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:26,15:42:99:483,0,823 -chr1 168747 . A T 674.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.500;DP=48;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=1;MQRankSum=0.649;QD=14.06;ReadPosRankSum=-0.309;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggT|G113|Cc01g00150|mRNA||GSCOCT00012419001|Exon_chr1_168361_168782) GT:AD:DP:GQ:PL 0/1:25,23:48:99:703,0,783 -chr1 168840 . T C 808.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.320;DP=52;Dels=0.00;FS=5.785;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=58.50;MQ0=0;MQRankSum=1.858;QD=15.55;ReadPosRankSum=0.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,26:52:99:837,0,857 -chr1 168897 . T C 843.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.871;DP=57;Dels=0.00;FS=5.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.07;MQ0=0;MQRankSum=0.583;QD=14.80;ReadPosRankSum=0.120;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,27:57:99:872,0,987 -chr1 168928 . C T 2404.77 . AC=2;AF=1.00;AN=2;DP=63;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=2;MLEAF=1.00;MQ=62.12;MQ0=0;QD=31.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,63:63:99:2433,184,0 -chr1 168963 . A C 1092.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.126;DP=70;Dels=0.00;FS=0.909;HaplotypeScore=4.3674;MLEAC=1;MLEAF=0.500;MQ=61.66;MQ0=1;MQRankSum=1.602;QD=15.61;ReadPosRankSum=0.462;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,35:70:99:1121,0,1161 -chr1 168974 . T C 245.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.577;DP=49;Dels=0.00;FS=5.429;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-4.252;QD=5.02;ReadPosRankSum=2.424;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,11:49:99:274,0,1377 -chr1 168984 . G A 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.339;DP=50;Dels=0.00;FS=1.222;HaplotypeScore=2.6583;MLEAC=1;MLEAF=0.500;MQ=58.95;MQ0=1;MQRankSum=-3.464;QD=8.06;ReadPosRankSum=1.051;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,15:50:99:431,0,1261 -chr1 169015 . C G 1930.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=1;QD=24.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:1959,147,0 -chr1 169059 . T C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.424;DP=48;Dels=0.00;FS=1.206;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.445;QD=9.25;ReadPosRankSum=2.069;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,15:48:99:472,0,1188 -chr1 169061 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.010;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.503;QD=10.74;ReadPosRankSum=0.995;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:33,18:51:99:576,0,1182 -chr1 169185 . G A 596.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.050;DP=50;Dels=0.00;FS=4.235;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.29;MQ0=0;MQRankSum=0.980;QD=11.94;ReadPosRankSum=-1.594;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:30,20:50:99:625,0,1008 -chr1 169348 . G T 2385.77 . AC=2;AF=1.00;AN=2;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.35;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 1/1:0,60:60:99:2414,181,0 -chr1 169423 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.535;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.324;QD=14.74;ReadPosRankSum=-0.211;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:21,19:40:99:618,0,620 -chr1 169424 . C T 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.169;DP=40;Dels=0.00;FS=4.763;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=58.49;MQ0=1;MQRankSum=0.690;QD=14.42;ReadPosRankSum=0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:605,0,616 -chr1 169456 . C G 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.543;DP=47;Dels=0.00;FS=13.725;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=1;MQRankSum=-1.163;QD=13.68;ReadPosRankSum=0.388;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:26,21:47:99:671,0,799 -chr1 169607 . G A 825.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.477;DP=58;Dels=0.00;FS=3.625;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.227;QD=14.24;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,26:58:99:854,0,1075 -chr1 169642 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.356;DP=58;Dels=0.00;FS=3.717;HaplotypeScore=0.9832;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=-0.639;QD=14.27;ReadPosRankSum=-0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:58:99:856,0,1091 -chr1 169648 . A G 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.575;DP=59;Dels=0.00;FS=5.223;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=0.312;QD=14.28;ReadPosRankSum=-0.616;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:871,0,1059 -chr1 169705 . C T 813.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=63;Dels=0.00;FS=0.971;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=58.48;MQ0=0;MQRankSum=-0.354;QD=12.92;ReadPosRankSum=0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:36,27:63:99:842,0,1216 -chr1 169719 . G A 827.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.216;DP=60;Dels=0.00;FS=0.971;HaplotypeScore=1.9997;MLEAC=1;MLEAF=0.500;MQ=58.91;MQ0=0;MQRankSum=1.529;QD=13.80;ReadPosRankSum=1.290;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:856,0,1191 -chr1 169815 . T C 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.744;DP=85;Dels=0.00;FS=5.036;HaplotypeScore=1.7339;MLEAC=1;MLEAF=0.500;MQ=57.77;MQ0=1;MQRankSum=-0.413;QD=6.71;ReadPosRankSum=-0.785;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:63,22:85:99:599,0,2148 -chr1 169830 . T G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.067;DP=82;Dels=0.00;FS=5.065;HaplotypeScore=4.3793;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=1;MQRankSum=0.781;QD=7.48;ReadPosRankSum=-0.522;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:58,24:82:99:642,0,1903 -chr1 169867 . A T 1602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.283;DP=92;Dels=0.00;FS=3.988;HaplotypeScore=1.7331;MLEAC=1;MLEAF=0.500;MQ=57.78;MQ0=0;MQRankSum=0.596;QD=17.42;ReadPosRankSum=0.004;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,51:92:99:1631,0,1086 -chr1 169896 . A G 763.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.532;DP=92;Dels=0.00;FS=1.896;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=-1.080;QD=8.30;ReadPosRankSum=0.557;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,27:92:99:792,0,2212 -chr1 169909 . A G 1909.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=89;Dels=0.00;FS=2.916;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.306;QD=21.46;ReadPosRankSum=-1.499;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,54:89:99:1938,0,1053 -chr1 169968 . C T 618.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.404;DP=95;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.734;QD=6.51;ReadPosRankSum=1.116;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,23:95:99:647,0,2530 -chr1 169972 . T C 2032.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.409;DP=99;Dels=0.00;FS=0.000;HaplotypeScore=24.7819;MLEAC=1;MLEAF=0.500;MQ=58.87;MQ0=0;MQRankSum=-1.407;QD=20.53;ReadPosRankSum=0.611;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,62:99:99:2061,0,1189 -chr1 169997 . G T 668.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.396;DP=92;Dels=0.00;FS=3.217;HaplotypeScore=46.8443;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=1.054;QD=7.27;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:68,24:92:99:697,0,2342 -chr1 170001 . A C 590.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.420;DP=93;Dels=0.00;FS=3.202;HaplotypeScore=65.8412;MLEAC=1;MLEAF=0.500;MQ=58.80;MQ0=0;MQRankSum=0.583;QD=6.35;ReadPosRankSum=-0.298;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:70,23:93:99:619,0,2321 -chr1 170005 . T A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=91;Dels=0.00;FS=0.000;HaplotypeScore=62.8400;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=0.339;QD=9.09;ReadPosRankSum=1.319;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:60,31:91:99:855,0,2167 -chr1 170011 . T A 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.010;DP=90;Dels=0.00;FS=3.403;HaplotypeScore=40.8458;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=0.801;QD=6.26;ReadPosRankSum=0.496;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,21:90:99:592,0,2430 -chr1 170043 . G T 514.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.393;DP=92;Dels=0.00;FS=6.914;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.42;MQ0=0;MQRankSum=-0.005;QD=5.60;ReadPosRankSum=0.648;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:72,20:92:99:543,0,2449 -chr1 170079 . C T 325.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.269;DP=84;Dels=0.00;FS=36.316;HaplotypeScore=155.6412;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.479;QD=3.88;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:69,15:84:99:354,0,2529 -chr1 170134 . C T 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.806;DP=84;Dels=0.00;FS=25.920;HaplotypeScore=2.3987;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.915;QD=2.15;ReadPosRankSum=1.360;EFF=DOWNSTREAM(MODIFIER||||Cc01g00140|mRNA||GSCOCT00012421001|),DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:71,13:84:99:209,0,2556 -chr1 170169 . T A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.068;DP=75;Dels=0.00;FS=22.598;HaplotypeScore=2.7329;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.239;QD=2.08;ReadPosRankSum=1.348;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:65,10:75:99:184,0,2327 -chr1 170210 . A C 885.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.379;DP=80;Dels=0.00;FS=12.034;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=1;MQRankSum=-0.591;QD=11.07;ReadPosRankSum=-0.955;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:50,30:80:99:914,0,1744 -chr1 170224 . G A 865.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.075;DP=77;Dels=0.00;FS=12.005;HaplotypeScore=3.7332;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=1;MQRankSum=-0.353;QD=11.24;ReadPosRankSum=-0.225;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,29:77:99:894,0,1620 -chr1 170239 . C A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.912;DP=71;Dels=0.00;FS=8.610;HaplotypeScore=2.7334;MLEAC=1;MLEAF=0.500;MQ=59.58;MQ0=1;MQRankSum=-0.098;QD=11.11;ReadPosRankSum=1.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:45,26:71:99:817,0,1578 -chr1 170266 . C T 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.026;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=4.0879;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.051;QD=9.33;ReadPosRankSum=0.076;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:49,24:73:99:709,0,1696 -chr1 170289 . A G 766.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.276;DP=77;Dels=0.00;FS=2.006;HaplotypeScore=1.7803;MLEAC=1;MLEAF=0.500;MQ=59.66;MQ0=0;MQRankSum=-0.339;QD=9.96;ReadPosRankSum=-2.375;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:51,26:77:99:795,0,1734 -chr1 170303 . G A 352.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=63;Dels=0.00;FS=33.610;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.166;QD=5.60;ReadPosRankSum=2.598;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:381,0,1693 -chr1 170304 . A G 425.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.845;DP=63;Dels=0.00;FS=8.306;HaplotypeScore=17.9844;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.545;QD=6.76;ReadPosRankSum=0.497;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:454,0,1606 -chr1 170360 . C T 818.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.394;DP=63;Dels=0.00;FS=0.955;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-0.256;QD=13.00;ReadPosRankSum=0.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:847,0,1189 -chr1 170364 . C G 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.042;DP=59;Dels=0.00;FS=2.175;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=0.510;QD=14.08;ReadPosRankSum=0.936;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:859,0,1076 -chr1 170366 . C T 848.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.811;DP=59;Dels=0.00;FS=1.010;HaplotypeScore=2.5184;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.234;QD=14.39;ReadPosRankSum=0.842;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,27:59:99:877,0,1076 -chr1 170381 . C T 648.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.037;DP=59;Dels=0.00;FS=9.493;HaplotypeScore=9.7866;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.356;QD=11.00;ReadPosRankSum=-0.214;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:38,21:59:99:677,0,1290 -chr1 170382 . G A 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.535;DP=59;Dels=0.00;FS=7.433;HaplotypeScore=10.7863;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=0;MQRankSum=-0.341;QD=3.44;ReadPosRankSum=0.302;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,11:59:99:231,0,1765 -chr1 170393 . T A 852.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.295;DP=67;Dels=0.00;FS=1.050;HaplotypeScore=21.7756;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.059;QD=12.73;ReadPosRankSum=0.008;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:29,26:67:99:881,0,961 -chr1 170403 . C A 345.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.760;DP=68;Dels=0.00;FS=2.482;HaplotypeScore=25.9777;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-0.799;QD=5.08;ReadPosRankSum=0.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:53,15:68:99:374,0,1880 -chr1 170482 . T C 486.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.358;DP=57;Dels=0.00;FS=11.052;HaplotypeScore=19.8261;MLEAC=1;MLEAF=0.500;MQ=59.27;MQ0=0;MQRankSum=-0.166;QD=8.54;ReadPosRankSum=0.166;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:40,17:57:99:515,0,1440 -chr1 170483 . C T 496.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.764;DP=54;Dels=0.00;FS=14.133;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=-1.397;QD=9.20;ReadPosRankSum=-0.317;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:37,17:54:99:525,0,1294 -chr1 170487 . A G 170.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.205;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=21.8256;MLEAC=1;MLEAF=0.500;MQ=59.26;MQ0=0;MQRankSum=0.892;QD=3.05;ReadPosRankSum=-0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,9:56:99:199,0,1721 -chr1 170502 . T C 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.810;DP=57;Dels=0.00;FS=1.273;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.23;MQ0=0;MQRankSum=0.354;QD=4.54;ReadPosRankSum=-1.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,11:57:99:287,0,1595 -chr1 170515 . G C 394.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.903;DP=63;Dels=0.00;FS=10.967;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.21;MQ0=0;MQRankSum=-2.124;QD=6.27;ReadPosRankSum=1.540;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:47,16:63:99:423,0,1617 -chr1 170578 . C G 538.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.209;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=1.493;QD=8.29;ReadPosRankSum=-0.627;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:46,19:65:99:567,0,1665 -chr1 170582 . C T 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.246;DP=65;Dels=0.00;FS=12.918;HaplotypeScore=32.9738;MLEAC=1;MLEAF=0.500;MQ=59.82;MQ0=0;MQRankSum=-0.097;QD=7.18;ReadPosRankSum=2.829;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:48,17:65:99:495,0,1695 -chr1 170584 . C T 1141.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.424;DP=66;Dels=0.00;FS=3.389;HaplotypeScore=31.9744;MLEAC=1;MLEAF=0.500;MQ=59.51;MQ0=0;MQRankSum=-0.899;QD=17.30;ReadPosRankSum=2.390;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:31,35:66:99:1170,0,1057 -chr1 170628 . C T 912.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.299;DP=67;Dels=0.00;FS=2.101;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.26;MQ0=0;MQRankSum=0.483;QD=13.62;ReadPosRankSum=0.659;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:35,32:67:99:941,0,1173 -chr1 170648 . G A 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=67;Dels=0.00;FS=6.632;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.90;MQ0=0;MQRankSum=-1.055;QD=1.77;ReadPosRankSum=1.823;EFF=DOWNSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),INTRON(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|) GT:AD:DP:GQ:PL 0/1:55,12:67:99:147,0,1992 -chr1 170807 . C G 863.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.270;DP=63;Dels=0.00;FS=8.737;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=0.906;QD=13.71;ReadPosRankSum=-0.546;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,28:63:99:892,0,1101 -chr1 170817 . G A 791.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.267;DP=59;Dels=0.00;FS=3.720;HaplotypeScore=21.9878;MLEAC=1;MLEAF=0.500;MQ=59.33;MQ0=0;MQRankSum=0.618;QD=13.42;ReadPosRankSum=0.206;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,26:59:99:820,0,1062 -chr1 170849 . A T 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.123;DP=51;Dels=0.00;FS=13.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.123;QD=15.02;ReadPosRankSum=0.426;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:28,23:51:99:794,0,925 -chr1 170873 . A T 1038.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.666;DP=58;Dels=0.00;FS=17.770;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=0.826;QD=17.91;ReadPosRankSum=-1.590;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,31:58:99:1067,0,865 -chr1 170879 . G A 987.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.614;DP=59;Dels=0.00;FS=14.005;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.493;QD=16.74;ReadPosRankSum=-0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,30:59:99:1016,0,929 -chr1 170937 . C G 931.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.022;DP=60;Dels=0.00;FS=5.062;HaplotypeScore=3.7392;MLEAC=1;MLEAF=0.500;MQ=59.90;MQ0=0;MQRankSum=1.504;QD=15.53;ReadPosRankSum=-1.652;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,28:60:99:960,0,1076 -chr1 170995 . G T 921.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.784;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=58.94;MQ0=0;MQRankSum=-1.752;QD=18.44;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,27:50:99:950,0,694 -chr1 171012 . A G 1169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.147;DP=55;Dels=0.00;FS=2.354;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-2.330;QD=21.27;ReadPosRankSum=1.308;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,34:55:99:1198,0,645 -chr1 171029 . C T 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.183;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.183;QD=20.21;ReadPosRankSum=2.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,34:52:99:1079,0,514 -chr1 171034 . A G 1294.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.637;DP=55;Dels=0.00;FS=0.000;HaplotypeScore=1.9467;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=-1.803;QD=23.54;ReadPosRankSum=1.874;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,37:55:99:1323,0,554 -chr1 171062 . A G 1228.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.366;DP=52;Dels=0.00;FS=2.506;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=58.75;MQ0=0;MQRankSum=-3.024;QD=23.63;ReadPosRankSum=-0.527;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,35:52:99:1257,0,545 -chr1 171065 . C A 1210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.009;DP=51;Dels=0.00;FS=2.449;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.72;MQ0=0;MQRankSum=-1.908;QD=23.74;ReadPosRankSum=-0.689;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,34:51:99:1239,0,544 -chr1 171068 . G T 1269.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.744;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-1.725;QD=23.96;ReadPosRankSum=-1.153;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,36:53:99:1298,0,506 -chr1 171215 . C T 1231.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.054;DP=66;Dels=0.00;FS=2.128;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.155;QD=18.66;ReadPosRankSum=1.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:29,37:66:99:1260,0,877 -chr1 171376 . A G 2221.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.05;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2250,169,0 -chr1 171546 . A T 929.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.055;DP=52;Dels=0.00;FS=1.174;HaplotypeScore=1.6208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.350;QD=17.88;ReadPosRankSum=-1.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,29:52:99:958,0,752 -chr1 171611 . A G 719.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.465;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=15.99;ReadPosRankSum=-0.148;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:748,0,784 -chr1 171683 . C T 1678.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1707,132,0 -chr1 171685 . A G 660.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.679;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.182;QD=15.73;ReadPosRankSum=1.811;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,21:42:99:689,0,730 -chr1 171706 . C G 707.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.897;DP=45;Dels=0.00;FS=1.174;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.351;QD=15.73;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:736,0,753 -chr1 171990 . G T 2282.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2311,172,0 -chr1 172009 . G A 788.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.720;DP=61;Dels=0.00;FS=11.177;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.109;QD=12.93;ReadPosRankSum=-0.605;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:35,26:61:99:817,0,1209 -chr1 172061 . A G 812.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.707;DP=51;Dels=0.00;FS=18.810;HaplotypeScore=2.4678;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.159;QD=15.94;ReadPosRankSum=1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:841,0,812 -chr1 172078 . G A 1642.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.98;MQ0=0;QD=30.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1671,129,0 -chr1 172093 . C T 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=35;Dels=0.00;FS=3.303;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=0.728;QD=22.02;ReadPosRankSum=0.444;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,24:35:99:799,0,305 -chr1 172108 . C T 56.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.397;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=32.9713;MLEAC=1;MLEAF=0.500;MQ=57.87;MQ0=0;MQRankSum=-1.397;QD=2.10;ReadPosRankSum=-0.826;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UTR_3_PRIME(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,7:27:85:85,0,539 -chr1 172146 . G C 1035.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aGg|T826R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,29:29:84:1064,84,0 -chr1 172150 . T C 1050.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=25.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I825V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1079,87,0 -chr1 172178 . T C 1336.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.42;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P815|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1365,114,0 -chr1 172179 . G C 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.629;DP=38;Dels=0.00;FS=9.942;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.716;QD=12.55;ReadPosRankSum=1.798;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cGa|P815R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:505,0,656 -chr1 172203 . G A 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.094;DP=46;Dels=0.00;FS=11.390;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.76;MQ0=0;MQRankSum=-2.028;QD=12.73;ReadPosRankSum=0.233;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCg/tTg|S807L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:614,0,792 -chr1 172283 . C T 303.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.164;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-0.747;QD=9.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G780|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,14:33:99:332,0,598 -chr1 172319 . A G 758.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.142;DP=33;Dels=0.00;FS=1.475;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.46;MQ0=1;MQRankSum=0.833;QD=22.99;ReadPosRankSum=0.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agT/agC|S768|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,23:33:99:787,0,281 -chr1 172364 . T C 828.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.018;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.16;MQ0=1;MQRankSum=0.201;QD=23.02;ReadPosRankSum=-0.128;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccA/ccG|P753|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:10,26:36:99:857,0,295 -chr1 172459 . T C 898.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.971;DP=43;Dels=0.00;FS=14.539;HaplotypeScore=0.9992;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=1;MQRankSum=0.000;QD=20.90;ReadPosRankSum=0.289;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I722V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:16,27:43:99:927,0,470 -chr1 172499 . A G 1675.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.64;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L708|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1704,129,0 -chr1 172613 . G C 2055.77 . AC=2;AF=1.00;AN=2;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=57.02;MQ0=0;QD=34.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L670|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,59:59:99:2084,162,0 -chr1 172721 . A G 739.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.419;DP=52;Dels=0.00;FS=10.166;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.56;MQ0=0;MQRankSum=0.276;QD=14.23;ReadPosRankSum=-0.958;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D634|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,23:52:99:768,0,1005 -chr1 172810 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.584;DP=54;Dels=0.00;FS=5.733;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=0.733;QD=10.96;ReadPosRankSum=0.362;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Ggt|S605G|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:35,19:54:99:620,0,1125 -chr1 173004 . G A 692.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.902;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.007;QD=16.90;ReadPosRankSum=0.693;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T540I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:19,22:41:99:721,0,631 -chr1 173180 . C T 566.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.132;QD=14.91;ReadPosRankSum=1.155;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S481|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,18:38:99:595,0,656 -chr1 173273 . A C 1050.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.237;DP=55;Dels=0.00;FS=3.786;HaplotypeScore=1.8320;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.026;QD=19.10;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|cgT/cgG|R450|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1079,0,685 -chr1 173338 . C G 770.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.117;DP=53;Dels=0.00;FS=1.043;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.759;QD=14.54;ReadPosRankSum=-1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Ctt|V429L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,24:53:99:799,0,968 -chr1 173346 . C T 721.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.557;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.210;QD=13.37;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGg/gAg|G426E|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,23:54:99:750,0,981 -chr1 173348 . A G 680.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.312;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.467;QD=12.61;ReadPosRankSum=-0.220;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N425|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:32,22:54:99:709,0,1099 -chr1 173405 . A G 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.617;DP=42;Dels=0.00;FS=9.292;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.43;MQ0=0;MQRankSum=-1.162;QD=12.76;ReadPosRankSum=-0.177;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L406|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,19:42:99:564,0,777 -chr1 173410 . C T 823.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.566;DP=46;Dels=0.00;FS=8.606;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.794;QD=17.91;ReadPosRankSum=0.243;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V405I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,25:46:99:852,0,607 -chr1 173421 . C A 601.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.194;DP=45;Dels=0.00;FS=11.272;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=59.47;MQ0=0;MQRankSum=0.582;QD=13.37;ReadPosRankSum=-0.377;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W401L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,20:45:99:630,0,843 -chr1 173444 . G A 516.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=48;Dels=0.00;FS=1.134;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.88;MQ0=0;MQRankSum=-0.970;QD=10.77;ReadPosRankSum=0.696;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I393|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,19:48:99:545,0,1014 -chr1 173446 . T C 585.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.885;DP=49;Dels=0.00;FS=2.535;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.90;MQ0=0;MQRankSum=-1.190;QD=11.95;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I393V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,20:49:99:614,0,949 -chr1 173456 . G C 1836.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=2;MLEAF=1.00;MQ=58.90;MQ0=0;QD=29.53;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L389|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1865,141,0 -chr1 173462 . A G 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.354;DP=52;Dels=0.00;FS=5.860;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.97;MQ0=0;MQRankSum=-0.951;QD=11.80;ReadPosRankSum=0.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaT/aaC|N387|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,21:52:99:642,0,1078 -chr1 173510 . C T 500.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.000;DP=53;Dels=0.00;FS=1.110;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=2;MQRankSum=-0.086;QD=9.45;ReadPosRankSum=-0.699;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ccG/ccA|P371|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,23:53:99:529,0,994 -chr1 173561 . T C 786.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.704;DP=55;Dels=0.00;FS=1.072;HaplotypeScore=1.7885;MLEAC=1;MLEAF=0.500;MQ=57.65;MQ0=2;MQRankSum=0.864;QD=14.30;ReadPosRankSum=0.027;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|aaA/aaG|K354|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:28,27:55:99:815,0,864 -chr1 173585 . G A 614.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.075;DP=52;Dels=0.00;FS=2.386;HaplotypeScore=2.7882;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-1.379;QD=11.82;ReadPosRankSum=0.561;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I346|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:30,22:52:99:643,0,934 -chr1 173596 . C A 918.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.149;DP=52;Dels=0.00;FS=1.065;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.69;MQ0=1;MQRankSum=-0.331;QD=17.67;ReadPosRankSum=0.407;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A343S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:947,0,721 -chr1 173627 . A G 875.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.524;DP=52;Dels=0.00;FS=1.082;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.71;MQ0=1;MQRankSum=0.180;QD=16.84;ReadPosRankSum=-0.218;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L332|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,29:52:99:904,0,775 -chr1 173642 . A T 635.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.002;DP=46;Dels=0.00;FS=6.250;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-0.935;QD=13.82;ReadPosRankSum=0.143;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A327|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:24,22:46:99:664,0,819 -chr1 173687 . T C 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.329;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.658;QD=14.97;ReadPosRankSum=0.094;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggA/ggG|G312|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,21:44:99:687,0,788 -chr1 173717 . A G 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.077;DP=36;Dels=0.00;FS=4.925;HaplotypeScore=1.7323;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.982;QD=17.52;ReadPosRankSum=0.982;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D302|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:17,19:36:99:659,0,518 -chr1 173759 . C T 664.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.765;DP=43;Dels=0.00;FS=6.309;HaplotypeScore=1.8237;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-1.154;QD=15.46;ReadPosRankSum=-0.158;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaG/gaA|E288|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:22,21:43:99:693,0,696 -chr1 173818 . C A 796.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.603;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=-1.032;QD=15.94;ReadPosRankSum=-1.071;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A269S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,27:50:99:825,0,741 -chr1 173846 . G A 1783.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.38;MQ0=0;QD=28.29;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S259|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,48:48:99:1812,141,0 -chr1 173921 . G A 1387.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L234|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1416,105,0 -chr1 173942 . C T 1229.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=37.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S227|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1258,93,0 -chr1 173991 . T A 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.583;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=-1.550;QD=13.08;ReadPosRankSum=0.583;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAg/cTg|Q211L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:20,15:35:99:486,0,659 -chr1 174026 . G T 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.138;DP=42;Dels=0.00;FS=2.755;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.579;QD=14.71;ReadPosRankSum=1.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agC/agA|S199R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,21:42:99:646,0,703 -chr1 174172 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.056;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.22;MQ0=0;MQRankSum=-1.622;QD=1.68;ReadPosRankSum=-3.635;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Tgc|S151C|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:43,7:50:99:112,0,1507 -chr1 174192 . G A 157.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.321;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.05;MQ0=0;MQRankSum=-1.855;QD=3.51;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T144M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,8:45:99:186,0,1296 -chr1 174204 . T C 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.410;DP=46;Dels=0.00;FS=1.159;HaplotypeScore=5.9821;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=1.606;QD=12.86;ReadPosRankSum=-1.451;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAt/cGt|H140R|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,20:46:99:620,0,865 -chr1 174214 . T G 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.366;DP=37;Dels=0.00;FS=1.982;HaplotypeScore=7.7151;MLEAC=1;MLEAF=0.500;MQ=59.61;MQ0=0;MQRankSum=-0.595;QD=1.37;ReadPosRankSum=2.653;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aaa/Caa|K137Q|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:31,5:37:79:79,0,1105 -chr1 174232 . C T 133.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.406;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-1.789;QD=3.93;ReadPosRankSum=0.000;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Agc|G131S|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,7:34:99:162,0,947 -chr1 174240 . G A 95.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.038;DP=32;Dels=0.00;FS=1.814;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.28;MQ0=0;MQRankSum=-2.100;QD=2.99;ReadPosRankSum=0.941;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P128L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,6:32:99:124,0,917 -chr1 174248 . G A 32.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.044;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.93;MQ0=0;MQRankSum=-3.194;QD=1.13;ReadPosRankSum=0.917;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggT|G125|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:25,4:29:61:61,0,891 -chr1 174251 . C T 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.214;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=-3.203;QD=0.99;ReadPosRankSum=0.885;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caG/caA|Q124|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,4:30:58:58,0,916 -chr1 174253 . G T 50.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.194;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.35;MQ0=0;MQRankSum=-3.037;QD=1.88;ReadPosRankSum=0.853;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q124K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:79:79,0,826 -chr1 174257 . G A 47.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.91;MQ0=0;MQRankSum=-3.037;QD=1.77;ReadPosRankSum=1.263;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|caC/caT|H122|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:23,4:27:76:76,0,816 -chr1 174272 . G A 78.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.316;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.55;MQ0=0;MQRankSum=-3.196;QD=2.54;ReadPosRankSum=1.370;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D117|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:107,0,934 -chr1 174280 . G T 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.297;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.63;MQ0=0;MQRankSum=-3.218;QD=2.37;ReadPosRankSum=1.090;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Atg|L115M|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:27,5:32:99:104,0,957 -chr1 174286 . G C 75.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.671;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=56.45;MQ0=0;MQRankSum=-3.303;QD=2.44;ReadPosRankSum=0.510;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctg/Gtg|L113V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:26,5:31:99:104,0,936 -chr1 174310 . C T 675.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.871;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.07;MQ0=0;MQRankSum=-2.399;QD=19.31;ReadPosRankSum=-1.013;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A105T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:11,24:35:99:704,0,322 -chr1 174313 . G C 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.709;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.6555;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.59;ReadPosRankSum=-0.024;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Gtc|L104V|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:50:50,0,1107 -chr1 174316 . C T 20.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.660;DP=37;Dels=0.00;FS=2.191;HaplotypeScore=9.9900;MLEAC=1;MLEAF=0.500;MQ=55.34;MQ0=0;MQRankSum=-2.812;QD=0.56;ReadPosRankSum=-0.416;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtc/Atc|V103I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:33,4:37:49:49,0,1123 -chr1 174328 . C T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.240;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=56.03;MQ0=0;MQRankSum=-2.863;QD=0.42;ReadPosRankSum=-0.113;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V99I|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:36,4:40:45:45,0,1148 -chr1 174343 . C T 49.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.041;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=0;MQRankSum=-3.088;QD=1.11;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D94N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:40,5:45:78:78,0,1238 -chr1 174344 . A C 449.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.079;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=7.9983;MLEAC=1;MLEAF=0.500;MQ=56.47;MQ0=0;MQRankSum=3.308;QD=9.99;ReadPosRankSum=-2.122;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|acT/acG|T93|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:29,16:45:99:478,0,949 -chr1 174366 . A G 149.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-4.432;QD=2.63;ReadPosRankSum=-0.077;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTt/cCt|L86P|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:178,0,1581 -chr1 174384 . G A 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.258;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=12.0923;MLEAC=1;MLEAF=0.500;MQ=57.82;MQ0=0;MQRankSum=-4.975;QD=3.53;ReadPosRankSum=0.848;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P80L|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,11:62:99:247,0,1745 -chr1 174411 . C T 121.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.558;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=-4.738;QD=2.14;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C71Y|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:48,9:57:99:150,0,1746 -chr1 174419 . C T 104.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.538;DP=59;Dels=0.00;FS=0.000;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-4.754;QD=1.78;ReadPosRankSum=1.634;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R68|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:50,9:59:99:133,0,1748 -chr1 174420 . C T 672.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.019;DP=60;Dels=0.00;FS=1.030;HaplotypeScore=17.8235;MLEAC=1;MLEAF=0.500;MQ=58.46;MQ0=0;MQRankSum=2.493;QD=11.21;ReadPosRankSum=-0.030;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R68K|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:37,23:60:99:701,0,1219 -chr1 174440 . G A 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.576;DP=60;Dels=0.00;FS=3.855;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.81;MQ0=0;MQRankSum=-4.283;QD=0.50;ReadPosRankSum=-0.299;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcC/tcT|S61|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:53,7:60:58:58,0,1883 -chr1 174476 . C T 1633.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.230;DP=51;Dels=0.00;FS=10.504;HaplotypeScore=2.3300;MLEAC=2;MLEAF=1.00;MQ=59.01;MQ0=0;MQRankSum=2.857;QD=32.03;ReadPosRankSum=-0.813;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S49|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:3,48:51:40:1662,40,0 -chr1 174490 . C T 112.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.255;DP=53;Dels=0.00;FS=8.491;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.84;MQ0=0;MQRankSum=-3.764;QD=2.13;ReadPosRankSum=-0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gac/Aac|D45N|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:45,8:53:99:141,0,1535 -chr1 174501 . C T 150.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.101;DP=50;Dels=0.00;FS=5.507;HaplotypeScore=2.3724;MLEAC=1;MLEAF=0.500;MQ=58.77;MQ0=0;MQRankSum=-3.283;QD=3.02;ReadPosRankSum=-0.808;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGc/cAc|R41H|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:41,9:50:99:179,0,1448 -chr1 174533 . C G 2385.77 . AC=2;AF=1.00;AN=2;DP=62;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=2;MLEAF=1.00;MQ=56.66;MQ0=0;QD=25.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),SYNONYMOUS_CODING(LOW|SILENT|ctG/ctC|L30|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 1/1:0,62:62:99:2414,184,0 -chr1 174565 . T C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;DP=66;Dels=0.00;FS=2.875;HaplotypeScore=1.6281;MLEAC=1;MLEAF=0.500;MQ=57.27;MQ0=0;MQRankSum=-1.776;QD=3.19;ReadPosRankSum=0.604;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T20A|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:54,11:66:99:239,0,1827 -chr1 174590 . C A 69.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.835;DP=58;Dels=0.00;FS=6.430;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.01;MQ0=0;MQRankSum=-2.077;QD=1.20;ReadPosRankSum=-0.979;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|ttG/ttT|L11F|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:51,7:58:98:98,0,1786 -chr1 174616 . C T 904.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.798;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=3.4534;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-0.293;QD=18.46;ReadPosRankSum=0.434;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gcg/Acg|A3T|Cc01g00160|mRNA||GSCOCT00012418001|Exon_chr1_170781_174622) GT:AD:DP:GQ:PL 0/1:21,28:49:99:933,0,662 -chr1 174675 . G A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=42;Dels=0.00;FS=11.439;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.088;QD=15.57;ReadPosRankSum=0.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:682,0,737 -chr1 174689 . G A 661.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.132;DP=47;Dels=0.00;FS=8.283;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.96;MQ0=0;MQRankSum=-0.221;QD=14.08;ReadPosRankSum=0.485;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,21:47:99:690,0,836 -chr1 174766 . G A 164.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.016;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=2.107;QD=3.74;ReadPosRankSum=-1.264;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:193,0,1204 -chr1 174767 . G A 160.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.047;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=25.9922;MLEAC=1;MLEAF=0.500;MQ=58.92;MQ0=1;MQRankSum=-1.576;QD=3.65;ReadPosRankSum=-0.702;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,8:44:99:189,0,1253 -chr1 174776 . G T 513.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.083;DP=30;Dels=0.00;FS=12.809;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=58.31;MQ0=1;MQRankSum=-0.811;QD=17.13;ReadPosRankSum=0.417;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:542,0,441 -chr1 174825 . T C 563.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.264;DP=30;Dels=0.00;FS=5.710;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.260;QD=18.79;ReadPosRankSum=0.711;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,17:30:99:592,0,412 -chr1 174849 . C T 503.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=9.9864;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.85;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:532,39,0 -chr1 174856 . T C 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.124;DP=31;Dels=0.00;FS=1.862;HaplotypeScore=9.9864;MLEAC=1;MLEAF=0.500;MQ=56.35;MQ0=1;MQRankSum=-3.069;QD=13.77;ReadPosRankSum=-2.821;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:455,0,505 -chr1 174866 . G T 639.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.717;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=56.78;MQ0=1;MQRankSum=-2.467;QD=18.28;ReadPosRankSum=-2.747;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,21:35:99:668,0,443 -chr1 174893 . G C 1410.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.79;MQ0=0;QD=27.44;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1439,108,0 -chr1 174896 . A G 670.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.059;DP=36;Dels=0.00;FS=7.563;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=-1.893;QD=18.63;ReadPosRankSum=2.054;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,21:36:99:699,0,483 -chr1 174908 . G A 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.143;DP=36;Dels=0.00;FS=7.479;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.525;QD=14.19;ReadPosRankSum=-1.480;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:539,0,683 -chr1 174931 . A T 503.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.783;DP=33;Dels=0.00;FS=7.712;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-0.630;QD=15.27;ReadPosRankSum=0.486;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,16:33:99:532,0,597 -chr1 174937 . T C 474.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.813;DP=33;Dels=0.00;FS=7.702;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.00;MQ0=0;MQRankSum=-1.284;QD=14.39;ReadPosRankSum=0.524;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:503,0,630 -chr1 174940 . C A 1210.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.94;MQ0=0;QD=29.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1239,93,0 -chr1 174946 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.250;DP=35;Dels=0.00;FS=10.992;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.150;QD=13.19;ReadPosRankSum=0.150;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,15:35:99:490,0,676 -chr1 174949 . A T 495.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.150;DP=37;Dels=0.00;FS=16.331;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=59.11;MQ0=0;MQRankSum=-0.751;QD=13.40;ReadPosRankSum=-0.291;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:524,0,731 -chr1 174959 . A C 416.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.957;DP=36;Dels=0.00;FS=23.979;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.535;QD=11.58;ReadPosRankSum=0.016;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:445,0,733 -chr1 174960 . G C 1421.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.9996;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1450,108,0 -chr1 174965 . A G 598.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.564;DP=38;Dels=0.00;FS=25.258;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.14;MQ0=0;MQRankSum=0.777;QD=15.76;ReadPosRankSum=1.173;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:38:99:627,0,565 -chr1 175000 . T C 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.494;DP=31;Dels=0.00;FS=19.167;HaplotypeScore=3.5778;MLEAC=1;MLEAF=0.500;MQ=58.00;MQ0=0;MQRankSum=1.048;QD=16.86;ReadPosRankSum=0.217;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:551,0,513 -chr1 175050 . C T 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.635;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.01;MQ0=0;MQRankSum=-3.633;QD=11.15;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:307,0,488 -chr1 175051 . G A 272.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.191;DP=25;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.08;MQ0=0;MQRankSum=-4.077;QD=10.91;ReadPosRankSum=2.247;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,10:25:99:301,0,523 -chr1 175057 . G A 277.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.016;DP=23;Dels=0.00;FS=1.713;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=-3.752;QD=12.08;ReadPosRankSum=1.830;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:306,0,446 -chr1 175058 . T C 814.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.04;MQ0=0;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:843,63,0 -chr1 175059 . A G 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.796;DP=24;Dels=0.00;FS=3.741;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.91;MQ0=0;MQRankSum=3.766;QD=15.28;ReadPosRankSum=-1.622;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,13:24:99:395,0,347 -chr1 175061 . C T 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=26;Dels=0.00;FS=1.685;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.16;MQ0=0;MQRankSum=-3.944;QD=10.22;ReadPosRankSum=1.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,11:26:99:294,0,532 -chr1 175067 . T C 487.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.392;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=4.465;QD=14.78;ReadPosRankSum=1.067;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:516,0,577 -chr1 175070 . T C 562.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.850;DP=33;Dels=0.00;FS=1.428;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=-4.501;QD=17.05;ReadPosRankSum=-1.284;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:591,0,501 -chr1 175078 . G T 637.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.051;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.709;QD=17.24;ReadPosRankSum=-1.021;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:666,0,570 -chr1 175079 . G A 641.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=-4.800;QD=17.35;ReadPosRankSum=-1.204;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:670,0,560 -chr1 175082 . T C 545.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.533;DP=37;Dels=0.00;FS=1.331;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.23;MQ0=0;MQRankSum=4.587;QD=14.75;ReadPosRankSum=1.082;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:574,0,663 -chr1 175088 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.728;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.59;MQ0=0;MQRankSum=-4.931;QD=16.17;ReadPosRankSum=-0.267;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:659,0,646 -chr1 175118 . A G 626.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.220;DP=33;Dels=0.00;FS=1.402;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.45;MQ0=0;MQRankSum=4.681;QD=18.99;ReadPosRankSum=-2.131;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:14,19:33:99:655,0,376 -chr1 175131 . T C 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.927;DP=32;Dels=0.00;FS=1.440;HaplotypeScore=18.3970;MLEAC=1;MLEAF=0.500;MQ=54.29;MQ0=0;MQRankSum=-4.457;QD=11.06;ReadPosRankSum=1.226;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:20,12:32:99:382,0,689 -chr1 175148 . T G 21.8 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.711;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=55.44;MQ0=0;MQRankSum=-2.725;QD=1.21;ReadPosRankSum=-0.237;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:15,3:18:50:50,0,556 -chr1 175149 . T C 617.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.9789;MLEAC=2;MLEAF=1.00;MQ=55.44;MQ0=0;QD=34.32;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,17:18:48:646,48,0 -chr1 175157 . T C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=1.9788;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.94;ReadPosRankSum=-1.174;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:46:46,0,572 -chr1 175160 . C T 14.91 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.509;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=55.69;MQ0=0;MQRankSum=-2.739;QD=0.78;ReadPosRankSum=-1.398;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:16,3:19:43:43,0,598 -chr1 175191 . T C 33.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.635;DP=24;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-3.412;QD=1.41;ReadPosRankSum=-1.208;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,5:24:62:62,0,696 -chr1 175195 . A G 669.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.355;DP=24;Dels=0.00;FS=2.682;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=3.341;QD=27.91;ReadPosRankSum=0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:5,19:24:71:698,0,71 -chr1 175196 . C T 43.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.932;DP=23;Dels=0.00;FS=2.671;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.391;QD=1.90;ReadPosRankSum=-0.261;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,5:23:72:72,0,661 -chr1 175215 . A C 172.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=26;Dels=0.00;FS=15.740;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.78;MQ0=0;MQRankSum=-4.028;QD=6.64;ReadPosRankSum=-0.028;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:201,0,652 -chr1 175251 . C T 1564.77 . AC=2;AF=1.00;AN=2;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.50;MQ0=0;QD=35.86;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,39:39:99:1593,117,0 -chr1 175255 . C A 1746.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.74;MQ0=0;QD=28.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1775,132,0 -chr1 175270 . T G 698.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.924;DP=54;Dels=0.00;FS=2.436;HaplotypeScore=0.9973;MLEAC=1;MLEAF=0.500;MQ=54.07;MQ0=0;MQRankSum=-5.061;QD=12.94;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:727,0,1094 -chr1 175316 . G A 645.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.625;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=52.26;MQ0=0;MQRankSum=-3.991;QD=13.74;ReadPosRankSum=1.775;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:674,0,909 -chr1 175333 . A G 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=41;Dels=0.00;FS=1.298;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=51.98;MQ0=0;MQRankSum=-4.353;QD=11.17;ReadPosRankSum=0.675;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:486,0,819 -chr1 175342 . C T 387.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.626;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.71;MQ0=0;MQRankSum=-4.498;QD=9.69;ReadPosRankSum=0.475;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,15:40:99:416,0,840 -chr1 175343 . A G 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.450;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.90;MQ0=0;MQRankSum=-4.561;QD=9.21;ReadPosRankSum=0.528;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:26,15:41:99:406,0,870 -chr1 175351 . C T 341.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.893;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.10;MQ0=0;MQRankSum=-4.553;QD=8.76;ReadPosRankSum=-0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,14:39:99:370,0,874 -chr1 175354 . T A 300.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.428;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=52.75;MQ0=0;MQRankSum=-4.347;QD=8.35;ReadPosRankSum=-0.626;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,13:36:99:329,0,790 -chr1 175364 . T A 147.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.351;DP=34;Dels=0.00;FS=1.879;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=53.40;MQ0=0;MQRankSum=-4.021;QD=4.35;ReadPosRankSum=-0.859;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:25,9:34:99:176,0,882 -chr1 175395 . C T 1069.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.59;MQ0=0;QD=29.50;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,29:29:81:1098,81,0 -chr1 175462 . C T 381.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.111;DP=54;Dels=0.00;FS=9.949;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=51.04;MQ0=2;MQRankSum=-4.141;QD=7.07;ReadPosRankSum=-0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:39,15:54:99:410,0,1172 -chr1 175465 . G A 391.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.799;DP=52;Dels=0.00;FS=7.479;HaplotypeScore=6.9505;MLEAC=1;MLEAF=0.500;MQ=50.66;MQ0=2;MQRankSum=-4.022;QD=7.53;ReadPosRankSum=-0.931;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:36,15:52:99:420,0,1104 -chr1 175476 . A G 399.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.975;DP=49;Dels=0.00;FS=9.035;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-4.277;QD=8.16;ReadPosRankSum=2.099;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:33,16:49:99:428,0,984 -chr1 175478 . A G 424.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.647;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=4.6337;MLEAC=1;MLEAF=0.500;MQ=50.04;MQ0=2;MQRankSum=-5.820;QD=8.67;ReadPosRankSum=4.142;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:453,0,901 -chr1 175489 . G A 426.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.045;DP=42;Dels=0.00;FS=4.393;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=48.18;MQ0=2;MQRankSum=-3.213;QD=10.16;ReadPosRankSum=4.079;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:27,15:42:99:455,0,695 -chr1 175502 . C T 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=37;Dels=0.00;FS=3.650;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=1;MQRankSum=-5.014;QD=10.10;ReadPosRankSum=3.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:23,14:37:99:402,0,770 -chr1 175510 . G A 255.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.695;DP=29;Dels=0.00;FS=4.386;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=-4.339;QD=8.82;ReadPosRankSum=1.942;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:284,0,642 -chr1 175518 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.414;DP=29;Dels=0.00;FS=2.032;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.46;MQ0=1;MQRankSum=4.291;QD=21.16;ReadPosRankSum=-0.791;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:642,0,280 -chr1 175519 . T C 180.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.728;DP=26;Dels=0.00;FS=1.927;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.53;MQ0=1;MQRankSum=-3.990;QD=6.95;ReadPosRankSum=0.903;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:209,0,614 -chr1 175550 . T C 868.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.84;MQ0=0;QD=29.72;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:897,69,0 -chr1 175583 . C G 185.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.905;DP=43;Dels=0.00;FS=3.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.67;MQ0=0;MQRankSum=-4.384;QD=4.32;ReadPosRankSum=-4.607;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,11:43:99:214,0,1136 -chr1 175588 . A T 214.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.168;DP=44;Dels=0.00;FS=1.379;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.85;MQ0=0;MQRankSum=-4.418;QD=4.88;ReadPosRankSum=-2.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:243,0,1139 -chr1 175611 . A C 222.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.250;DP=48;Dels=0.00;FS=1.311;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=52.65;MQ0=0;MQRankSum=-4.679;QD=4.64;ReadPosRankSum=1.869;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,12:48:99:251,0,1281 -chr1 175625 . A C 1275.77 . AC=2;AF=1.00;AN=2;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.57;MQ0=0;QD=28.48;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,35:35:99:1304,99,0 -chr1 175674 . T C 812.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.22;MQ0=0;QD=33.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:63:841,63,0 -chr1 175724 . C T 657.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.67;MQ0=0;QD=29.62;EFF=DOWNSTREAM(MODIFIER||||Cc01g00150|mRNA||GSCOCT00012419001|),UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:686,54,0 -chr1 175730 . G A 621.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=31.41;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:650,51,0 -chr1 175731 . A G 612.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.11;MQ0=0;QD=26.71;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:641,51,0 -chr1 175771 . A G 825.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=25.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,21:22:63:854,63,0 -chr1 175776 . G A 814.77 . AC=2;AF=1.00;AN=2;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.18;MQ0=0;QD=27.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,22:22:66:843,66,0 -chr1 175784 . T C 738.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.94;MQ0=0;QD=33.97;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:767,57,0 -chr1 175787 . G A 702.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;QD=30.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:731,54,0 -chr1 175809 . C T 591.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.30;MQ0=0;QD=29.59;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:620,45,0 -chr1 175815 . G T 11.12 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=0.594;QD=0.74;ReadPosRankSum=2.123;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,2:15:39:39,0,491 -chr1 175833 . C A 177.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.203;QD=19.75;ReadPosRankSum=-1.203;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:3,6:9:88:206,0,88 -chr1 175887 . T A 491.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=31;Dels=0.00;FS=11.982;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.42;MQ0=1;MQRankSum=-0.104;QD=15.86;ReadPosRankSum=0.894;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,16:31:99:520,0,468 -chr1 175892 . C T 465.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.327;DP=30;Dels=0.00;FS=11.831;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=0.240;QD=15.53;ReadPosRankSum=2.859;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:494,0,466 -chr1 175895 . T A 442.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=30;Dels=0.00;FS=8.557;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=1;MQRankSum=-0.982;QD=14.76;ReadPosRankSum=2.990;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,15:30:99:471,0,475 -chr1 175993 . C A 385.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.200;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.85;MQ0=0;MQRankSum=-0.646;QD=16.77;ReadPosRankSum=0.031;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,12:23:99:414,0,304 -chr1 176009 . T C 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.368;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=53.56;MQ0=0;MQRankSum=0.380;QD=16.09;ReadPosRankSum=2.507;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,11:20:99:350,0,229 -chr1 176036 . A T 405.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.485;DP=21;Dels=0.00;FS=4.419;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=0.187;QD=19.32;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:7,14:21:99:434,0,213 -chr1 176049 . C T 718.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=2;MLEAF=1.00;MQ=58.65;MQ0=0;QD=21.77;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:747,60,0 -chr1 176097 . T G 339.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:368,30,0 -chr1 176139 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.97;MQ0=0;QD=32.45;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:912,69,0 -chr1 176158 . C G 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=26;Dels=0.00;FS=24.095;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=1.397;QD=10.95;ReadPosRankSum=-0.079;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:313,0,559 -chr1 176165 . T C 291.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.778;DP=27;Dels=0.00;FS=25.156;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.04;MQ0=0;MQRankSum=0.979;QD=10.81;ReadPosRankSum=-0.226;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,10:27:99:320,0,588 -chr1 176174 . T C 169.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=24;Dels=0.00;FS=23.395;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.43;MQ0=0;MQRankSum=-0.381;QD=7.07;ReadPosRankSum=-0.064;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,7:24:99:198,0,602 -chr1 176177 . G A 905.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.96;MQ0=0;QD=29.06;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:69:934,69,0 -chr1 176195 . C T 1025.77 . AC=2;AF=1.00;AN=2;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.45;MQ0=0;QD=32.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,28:28:78:1054,78,0 -chr1 176207 . C T 870.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.28;MQ0=0;QD=26.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:66:899,66,0 -chr1 176233 . C T 725.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.85;MQ0=0;QD=26.02;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:754,57,0 -chr1 176286 . G A 535.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=31.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:564,45,0 -chr1 176290 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.9992;MLEAC=2;MLEAF=1.00;MQ=50.55;MQ0=0;QD=32.99;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:48:589,48,0 -chr1 176293 . G A 373.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.510;DP=17;Dels=0.00;FS=6.117;HaplotypeScore=12.9225;MLEAC=1;MLEAF=0.500;MQ=49.38;MQ0=0;MQRankSum=1.642;QD=21.99;ReadPosRankSum=2.774;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:4,13:17:99:402,0,106 -chr1 176307 . T A 463.28 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.868;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=2;MLEAF=1.00;MQ=48.64;MQ0=0;MQRankSum=-1.519;QD=28.96;ReadPosRankSum=1.519;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,15:16:9:491,9,0 -chr1 176308 . T A 420.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.556;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=15.9189;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-2.302;QD=26.30;ReadPosRankSum=1.826;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:2,14:16:32:449,0,32 -chr1 176309 . T A 83.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.031;DP=16;Dels=0.00;FS=6.317;HaplotypeScore=14.9199;MLEAC=1;MLEAF=0.500;MQ=48.64;MQ0=0;MQRankSum=-1.637;QD=5.24;ReadPosRankSum=0.667;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,4:16:99:112,0,330 -chr1 176346 . T A 108.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.960;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.11;MQ0=0;MQRankSum=-1.920;QD=5.44;ReadPosRankSum=-0.175;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,5:20:99:137,0,516 -chr1 176350 . T C 479.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.440;DP=21;Dels=0.00;FS=7.501;HaplotypeScore=6.9981;MLEAC=1;MLEAF=0.500;MQ=49.68;MQ0=0;MQRankSum=0.662;QD=22.85;ReadPosRankSum=-0.117;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:6,15:21:99:508,0,178 -chr1 176353 . T C 739.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=5.9978;MLEAC=2;MLEAF=1.00;MQ=49.68;MQ0=0;QD=24.14;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,20:21:60:768,60,0 -chr1 176364 . G A 278.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.154;DP=30;Dels=0.00;FS=6.914;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.99;MQ0=0;MQRankSum=-0.110;QD=9.29;ReadPosRankSum=-0.374;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,10:30:99:307,0,694 -chr1 176371 . A G 304.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.936;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.66;MQ0=0;MQRankSum=0.363;QD=9.24;ReadPosRankSum=-0.325;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,11:33:99:333,0,777 -chr1 176377 . G A 1335.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.86;MQ0=0;QD=32.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1364,102,0 -chr1 176389 . G C 1302.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=55.23;MQ0=0;QD=22.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1331,99,0 -chr1 176391 . A G 265.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.646;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.568;QD=8.05;ReadPosRankSum=-1.273;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:294,0,820 -chr1 176394 . G A 276.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.255;DP=33;Dels=0.00;FS=9.645;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=55.23;MQ0=0;MQRankSum=0.333;QD=8.39;ReadPosRankSum=-0.842;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,10:33:99:305,0,820 -chr1 176397 . C T 259.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.338;DP=32;Dels=0.00;FS=9.755;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=0.427;QD=8.12;ReadPosRankSum=-1.037;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,10:32:99:288,0,782 -chr1 176400 . G A 1117.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=1.9993;MLEAC=2;MLEAF=1.00;MQ=56.80;MQ0=0;QD=27.50;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:87:1146,87,0 -chr1 176402 . T A 653.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.647;DP=34;Dels=0.00;FS=11.168;HaplotypeScore=1.9993;MLEAC=1;MLEAF=0.500;MQ=57.36;MQ0=0;MQRankSum=0.472;QD=19.23;ReadPosRankSum=0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,20:34:99:682,0,440 -chr1 176422 . C T 430.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.143;DP=43;Dels=0.00;FS=10.456;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=-0.013;QD=10.02;ReadPosRankSum=0.716;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:459,0,874 -chr1 176432 . G T 846.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.659;DP=44;Dels=0.00;FS=10.793;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.87;MQ0=0;MQRankSum=0.275;QD=19.24;ReadPosRankSum=-0.131;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,26:44:99:875,0,599 -chr1 176471 . G C 623.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.307;DP=39;Dels=0.00;FS=2.886;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.520;QD=15.99;ReadPosRankSum=-0.239;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:652,0,620 -chr1 176483 . T G 746.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.208;DP=46;Dels=0.00;FS=2.660;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.714;QD=16.23;ReadPosRankSum=-0.022;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:775,0,731 -chr1 176494 . G A 777.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.467;DP=44;Dels=0.00;FS=4.658;HaplotypeScore=1.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.705;QD=17.68;ReadPosRankSum=1.292;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:806,0,667 -chr1 176561 . T C 1205.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.346;DP=45;Dels=0.00;FS=7.565;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.578;QD=26.79;ReadPosRankSum=-1.424;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,33:45:99:1234,0,358 -chr1 176568 . G C 285.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.949;DP=44;Dels=0.00;FS=5.029;HaplotypeScore=20.3301;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.488;QD=6.49;ReadPosRankSum=1.464;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,11:44:99:314,0,1180 -chr1 176599 . G C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.485;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.076;QD=0.94;ReadPosRankSum=-0.227;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:32,4:37:63:63,0,1130 -chr1 176618 . C T 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.231;DP=49;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.553;QD=14.46;ReadPosRankSum=-2.864;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:737,0,944 -chr1 176635 . C T 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.787;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.075;QD=13.67;ReadPosRankSum=1.784;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,20:46:99:657,0,863 -chr1 176661 . A T 1847.77 . AC=2;AF=1.00;AN=2;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.95;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,47:47:99:1876,141,0 -chr1 176688 . T C 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.618;DP=44;Dels=0.00;FS=5.897;HaplotypeScore=0.9332;MLEAC=1;MLEAF=0.500;MQ=58.64;MQ0=1;MQRankSum=-0.962;QD=18.13;ReadPosRankSum=0.110;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,24:44:99:826,0,625 -chr1 176698 . C T 1695.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=2;MLEAF=1.00;MQ=57.62;MQ0=1;QD=32.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1724,129,0 -chr1 176733 . G A 903.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.44;MQ0=1;QD=32.93;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:932,69,0 -chr1 176761 . A T 38.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.205;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.97;MQ0=1;MQRankSum=1.449;QD=2.15;ReadPosRankSum=-2.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,3:18:67:67,0,485 -chr1 176800 . G A 390.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.42;MQ0=0;QD=30.63;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:419,33,0 -chr1 176848 . G T 11.83 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.90;MQ0=0;MQRankSum=0.804;QD=5.91;ReadPosRankSum=0.804;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,1:2:3:38,3,0 -chr1 177059 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.067;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=12.03;MQ0=24;MQRankSum=-1.333;QD=1.47;ReadPosRankSum=2.933;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,11:38:84:84,0,91 -chr1 177070 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.788;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=11.58;MQ0=27;MQRankSum=-0.689;QD=1.43;ReadPosRankSum=-2.793;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,9:39:84:84,0,91 -chr1 177088 . A C 29.77 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.599;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=10.40;MQ0=30;MQRankSum=0.825;QD=0.71;ReadPosRankSum=-0.600;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,6:42:58:58,0,94 -chr1 177252 . G A 55.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.667;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.9665;MLEAC=1;MLEAF=0.500;MQ=10.59;MQ0=35;MQRankSum=-1.333;QD=1.14;ReadPosRankSum=-1.867;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:36,13:49:84:84,0,91 -chr1 177401 . A C 299.78 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.64;MQ0=0;QD=18.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:24:328,24,0 -chr1 177522 . A C 484.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.083;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.77;MQ0=0;MQRankSum=-1.692;QD=19.39;ReadPosRankSum=-0.971;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,15:25:99:513,0,327 -chr1 177533 . A C 443.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.661;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=56.89;MQ0=0;MQRankSum=-1.713;QD=17.07;ReadPosRankSum=-0.415;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,15:26:99:472,0,360 -chr1 177599 . C T 1453.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1482,111,0 -chr1 177668 . A G 401.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.681;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=-0.893;QD=10.57;ReadPosRankSum=0.741;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,14:38:99:430,0,785 -chr1 177672 . C G 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.827;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.730;QD=11.08;ReadPosRankSum=0.438;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:427,0,755 -chr1 177673 . T C 407.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.730;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.23;MQ0=0;MQRankSum=-0.990;QD=11.33;ReadPosRankSum=0.406;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,14:36:99:436,0,759 -chr1 177685 . C T 1270.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=40.5933;MLEAC=2;MLEAF=1.00;MQ=57.82;MQ0=0;QD=30.38;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1299,96,0 -chr1 177713 . T C 676.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.250;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.12;MQ0=0;MQRankSum=4.183;QD=19.34;ReadPosRankSum=0.383;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,20:35:99:705,0,508 -chr1 177736 . T G 409.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.22;MQ0=0;MQRankSum=-4.078;QD=12.81;ReadPosRankSum=0.906;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,15:32:99:438,0,601 -chr1 177753 . T A 1468.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.25;MQ0=0;QD=28.29;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,38:38:99:1497,114,0 -chr1 177771 . C T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.27;MQ0=0;MQRankSum=-4.477;QD=16.37;ReadPosRankSum=0.663;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,20:40:99:683,0,691 -chr1 177787 . T C 1629.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=56.90;MQ0=0;QD=33.13;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1658,123,0 -chr1 177789 . A G 619.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.560;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.25;MQ0=0;MQRankSum=4.009;QD=13.47;ReadPosRankSum=1.245;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,20:46:99:648,0,869 -chr1 177795 . G T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.622;DP=44;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.29;MQ0=0;MQRankSum=-1.983;QD=16.77;ReadPosRankSum=-0.270;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:766,0,709 -chr1 177797 . C T 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.081;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.23;MQ0=0;MQRankSum=-2.636;QD=17.06;ReadPosRankSum=-0.595;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:762,0,706 -chr1 177814 . C T 711.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.198;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=58.25;MQ0=0;MQRankSum=-2.138;QD=16.18;ReadPosRankSum=-0.047;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,21:44:99:740,0,797 -chr1 177863 . C A 826.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.327;DP=44;Dels=0.00;FS=2.649;HaplotypeScore=0.9987;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.900;QD=18.79;ReadPosRankSum=0.237;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,25:44:99:855,0,637 -chr1 177874 . C T 686.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.014;DP=46;Dels=0.00;FS=2.569;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.40;MQ0=0;MQRankSum=-0.816;QD=14.93;ReadPosRankSum=-0.860;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,21:46:99:715,0,849 -chr1 177924 . T G 554.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.175;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=58.82;MQ0=0;MQRankSum=0.467;QD=14.22;ReadPosRankSum=0.014;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:583,0,741 -chr1 177937 . A G 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.034;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=1.402;QD=13.92;ReadPosRankSum=-1.034;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:571,0,787 -chr1 177938 . T C 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.869;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=0.327;QD=14.73;ReadPosRankSum=-1.556;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:632,0,783 -chr1 177940 . C T 783.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.961;DP=44;Dels=0.00;FS=2.498;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-1.786;QD=17.81;ReadPosRankSum=1.645;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,23:44:99:812,0,687 -chr1 177955 . T C 962.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.952;DP=48;Dels=0.00;FS=1.129;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=1.014;QD=20.06;ReadPosRankSum=0.178;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,28:48:99:991,0,659 -chr1 177959 . T G 595.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.975;DP=49;Dels=0.00;FS=1.137;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.37;MQ0=0;MQRankSum=-0.359;QD=12.16;ReadPosRankSum=0.544;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,19:49:99:624,0,1063 -chr1 177983 . A G 1899.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=2.4892;MLEAC=2;MLEAF=1.00;MQ=59.77;MQ0=0;QD=26.52;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1928,144,0 -chr1 177992 . G A 849.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.582;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=0.388;QD=17.00;ReadPosRankSum=0.466;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,25:50:99:878,0,780 -chr1 178064 . C T 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.594;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.34;MQ0=0;MQRankSum=-0.137;QD=14.80;ReadPosRankSum=-0.229;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,17:37:99:576,0,654 -chr1 178089 . G C 602.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.777;DP=34;Dels=0.00;FS=3.270;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.72;MQ0=1;MQRankSum=-0.777;QD=17.73;ReadPosRankSum=0.235;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,19:34:99:631,0,457 -chr1 178121 . C A 797.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.759;DP=41;Dels=0.00;FS=1.294;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=57.54;MQ0=1;MQRankSum=-1.035;QD=19.46;ReadPosRankSum=0.676;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,25:41:99:826,0,488 -chr1 178255 . T C 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.918;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3123;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.153;QD=11.21;ReadPosRankSum=1.458;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,13:32:99:387,0,613 -chr1 178259 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.469;DP=29;Dels=0.00;FS=1.449;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.329;QD=13.89;ReadPosRankSum=1.206;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:431,0,537 -chr1 178261 . T A 359.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.066;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.460;QD=12.41;ReadPosRankSum=1.250;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,13:29:99:388,0,533 -chr1 178263 . T C 398.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.963;DP=30;Dels=0.00;FS=1.484;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.879;QD=13.29;ReadPosRankSum=1.549;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,13:30:99:427,0,582 -chr1 178287 . G A 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.739;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.465;QD=12.47;ReadPosRankSum=-0.575;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,11:25:99:340,0,480 -chr1 178289 . G C 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.381;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.6651;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.205;QD=11.87;ReadPosRankSum=-0.263;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,481 -chr1 178299 . A T 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.271;DP=23;Dels=0.00;FS=1.674;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.403;QD=11.42;ReadPosRankSum=-0.465;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,10:23:99:291,0,437 -chr1 178322 . G A 377.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.414;DP=26;Dels=0.00;FS=5.734;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.723;QD=14.53;ReadPosRankSum=-0.283;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,12:26:99:406,0,467 -chr1 178360 . A G 519.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.944;DP=39;Dels=0.00;FS=9.536;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=59.06;MQ0=0;MQRankSum=-1.169;QD=13.33;ReadPosRankSum=0.070;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,18:39:99:548,0,674 -chr1 178364 . T A 546.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.080;DP=42;Dels=0.00;FS=6.822;HaplotypeScore=1.9946;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.639;QD=13.02;ReadPosRankSum=0.928;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,18:42:99:575,0,786 -chr1 178390 . A G 1140.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=43.1047;MLEAC=2;MLEAF=1.00;MQ=58.29;MQ0=0;QD=36.62;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1169,87,0 -chr1 178393 . A G 1175.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=32.4731;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=34.88;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1204,90,0 -chr1 178400 . G A 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=57.96;MQ0=0;QD=26.43;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:93:1209,93,0 -chr1 178402 . A C 1294.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.3670;MLEAC=2;MLEAF=1.00;MQ=58.02;MQ0=0;QD=27.35;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1323,99,0 -chr1 178406 . A G 608.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.24;MQ0=0;MQRankSum=3.905;QD=16.45;ReadPosRankSum=0.228;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,19:37:99:637,0,616 -chr1 178418 . C T 1535.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.98;MQ0=0;QD=29.23;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1564,117,0 -chr1 178431 . A G 1627.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.75;MQ0=0;QD=31.86;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1656,123,0 -chr1 178470 . C T 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.086;DP=34;Dels=0.00;FS=2.928;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.34;MQ0=0;MQRankSum=-2.467;QD=17.46;ReadPosRankSum=-1.570;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,18:34:99:622,0,545 -chr1 178476 . G T 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.612;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=57.56;MQ0=0;MQRankSum=-2.884;QD=8.63;ReadPosRankSum=1.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,611 -chr1 178477 . A G 254.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.269;DP=26;Dels=0.00;FS=1.596;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.66;MQ0=0;MQRankSum=-2.910;QD=9.80;ReadPosRankSum=0.701;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,9:26:99:283,0,607 -chr1 178478 . C T 202.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.777;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=1.9951;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.466;QD=8.11;ReadPosRankSum=1.311;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:231,0,607 -chr1 178481 . A G 215.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.087;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=1;MLEAF=0.500;MQ=57.76;MQ0=0;MQRankSum=-3.408;QD=8.63;ReadPosRankSum=1.486;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:244,0,606 -chr1 178485 . T C 322.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.141;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.540;QD=11.53;ReadPosRankSum=0.329;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,11:28:99:351,0,575 -chr1 178493 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.291;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-2.900;QD=12.23;ReadPosRankSum=1.207;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,593 -chr1 178499 . T C 366.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.953;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.14;MQ0=0;MQRankSum=-1.630;QD=12.23;ReadPosRankSum=1.503;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,12:30:99:395,0,603 -chr1 178504 . A G 368.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.255;DP=28;Dels=0.00;FS=1.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=58.01;MQ0=0;MQRankSum=-2.019;QD=13.17;ReadPosRankSum=0.998;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,12:28:99:397,0,533 -chr1 178548 . T C 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.026;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=57.92;MQ0=0;MQRankSum=-2.451;QD=11.14;ReadPosRankSum=-0.975;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,10:26:99:318,0,550 -chr1 178628 . A G 367.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.831;DP=38;Dels=0.00;FS=1.378;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=46.44;MQ0=0;MQRankSum=-1.015;QD=9.68;ReadPosRankSum=0.708;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,13:38:99:396,0,801 -chr1 178641 . T C 1162.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.07;MQ0=0;QD=31.81;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1191,93,0 -chr1 178645 . G T 233.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.239;DP=31;Dels=0.00;FS=1.525;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.35;MQ0=0;MQRankSum=-0.152;QD=7.54;ReadPosRankSum=-0.457;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,9:31:99:262,0,672 -chr1 178672 . T C 271.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=27.18;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:300,24,0 -chr1 178673 . T C 269.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.82;MQ0=0;QD=26.98;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:298,24,0 -chr1 178709 . G A 304.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=25.04;MQ0=3;QD=19.05;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,16:16:30:333,30,0 -chr1 178719 . T C 176.84 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=22.41;MQ0=3;QD=14.74;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,12:12:18:205,18,0 -chr1 178740 . C T 36.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.796;DP=26;Dels=0.00;FS=6.166;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=24.19;MQ0=11;MQRankSum=-1.408;QD=1.41;ReadPosRankSum=-0.674;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,8:26:65:65,0,324 -chr1 178796 . T C 52.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.153;DP=25;Dels=0.00;FS=6.726;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=33.15;MQ0=9;MQRankSum=0.404;QD=2.11;ReadPosRankSum=2.153;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,10:25:81:81,0,383 -chr1 178979 . T C 232.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.041;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.40;MQ0=0;MQRankSum=-0.286;QD=12.25;ReadPosRankSum=-0.041;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:10,9:19:99:261,0,334 -chr1 179063 . T A 690.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=35.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:719,54,0 -chr1 179198 . A G 517.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.885;DP=40;Dels=0.00;FS=9.838;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.25;MQ0=3;MQRankSum=4.522;QD=12.94;ReadPosRankSum=2.437;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,16:40:99:546,0,642 -chr1 179200 . A T 1439.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.25;MQ0=3;QD=28.36;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1468,108,0 -chr1 179320 . C T 756.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DP=48;Dels=0.00;FS=4.336;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=-0.475;QD=15.77;ReadPosRankSum=0.578;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:785,0,835 -chr1 179364 . T G 1002.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.428;DP=58;Dels=0.00;FS=7.156;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=1.284;QD=17.29;ReadPosRankSum=0.801;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:28,30:58:99:1031,0,933 -chr1 179397 . G T 2003.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.90;MQ0=0;QD=29.19;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:2032,147,0 -chr1 179511 . C T 782.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.212;DP=55;Dels=0.00;FS=1.064;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.61;MQ0=0;MQRankSum=1.179;QD=14.23;ReadPosRankSum=1.655;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:31,24:55:99:811,0,1053 -chr1 179518 . C T 289.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.344;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=11.7849;MLEAC=1;MLEAF=0.500;MQ=58.38;MQ0=0;MQRankSum=0.855;QD=5.68;ReadPosRankSum=-0.078;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:39,12:51:99:318,0,1406 -chr1 179542 . C T 332.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.582;DP=59;Dels=0.00;FS=2.644;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.05;MQ0=0;MQRankSum=2.112;QD=5.64;ReadPosRankSum=-0.814;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:46,13:59:99:361,0,1612 -chr1 179564 . C T 1118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.408;DP=67;Dels=0.00;FS=6.477;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.831;QD=16.70;ReadPosRankSum=-0.332;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:33,34:67:99:1147,0,1135 -chr1 179583 . T C 2571.77 . AC=2;AF=1.00;AN=2;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=52.03;MQ0=0;QD=33.16;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,66:66:99:2600,193,0 -chr1 179617 . A T 2299.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.562;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.19;MQ0=0;MQRankSum=1.392;QD=28.69;ReadPosRankSum=0.085;EFF=UPSTREAM(MODIFIER||||Cc01g00160|mRNA||GSCOCT00012418001|),UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:1,60:61:99:2328,144,0 -chr1 179762 . G A 933.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.767;DP=51;Dels=0.00;FS=1.114;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.21;MQ0=0;MQRankSum=-1.618;QD=18.31;ReadPosRankSum=-0.407;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:23,28:51:99:962,0,770 -chr1 179884 . G C 308.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.415;DP=28;Dels=0.00;FS=4.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.47;MQ0=0;MQRankSum=-1.658;QD=11.03;ReadPosRankSum=0.184;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,13:28:99:337,0,516 -chr1 179951 . C T 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.506;DP=48;Dels=0.00;FS=2.471;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=61.42;MQ0=0;MQRankSum=-2.488;QD=11.47;ReadPosRankSum=-0.021;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:29,19:48:99:579,0,987 -chr1 180063 . G T 1117.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.357;DP=60;Dels=0.00;FS=0.000;HaplotypeScore=2.5225;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.238;QD=18.63;ReadPosRankSum=-0.015;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,33:60:99:1146,0,891 -chr1 180136 . T A 725.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=58.59;MQ0=0;MQRankSum=-2.350;QD=16.88;ReadPosRankSum=-0.012;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:754,0,646 -chr1 180164 . C T 658.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.143;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=59.59;MQ0=0;MQRankSum=0.075;QD=14.02;ReadPosRankSum=1.546;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:687,0,853 -chr1 180372 . A C 617.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.314;DP=38;Dels=0.00;FS=4.887;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.28;MQ0=0;MQRankSum=-1.285;QD=16.26;ReadPosRankSum=0.671;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:646,0,633 -chr1 180419 . G T 1311.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=8.9974;MLEAC=2;MLEAF=1.00;MQ=58.26;MQ0=0;QD=32.14;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:99:1340,102,0 -chr1 180460 . G A 1379.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9995;MLEAC=2;MLEAF=1.00;MQ=57.15;MQ0=1;QD=29.16;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1408,105,0 -chr1 180463 . T A 537.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.550;DP=35;Dels=0.00;FS=1.423;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.07;MQ0=1;MQRankSum=2.273;QD=15.36;ReadPosRankSum=-0.517;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:566,0,578 -chr1 180470 . G C 584.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.224;DP=36;Dels=0.00;FS=1.373;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=3.571;QD=16.24;ReadPosRankSum=-1.604;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,18:36:99:613,0,506 -chr1 180531 . A C 550.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.306;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.99;MQ0=1;MQRankSum=0.486;QD=16.20;ReadPosRankSum=-0.847;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,17:34:99:579,0,522 -chr1 180557 . C G 1180.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=1;QD=32.27;EFF=UPSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:90:1209,90,0 -chr1 180708 . G A 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=24;Dels=0.00;FS=4.269;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.223;QD=24.12;ReadPosRankSum=0.953;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aAt|S43N|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:7,17:24:99:607,0,206 -chr1 180728 . A G 258.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.774;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=59.93;MQ0=0;MQRankSum=-0.437;QD=9.58;ReadPosRankSum=-0.489;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agg/Ggg|R50G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:18,9:27:99:287,0,626 -chr1 180746 . C T 1097.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=31.29;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P56S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1126,90,0 -chr1 180749 . T C 1103.77 . AC=2;AF=1.00;AN=2;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.93;MQ0=0;QD=26.57;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C57R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 1/1:0,29:29:87:1132,87,0 -chr1 180758 . C T 321.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.356;DP=25;Dels=0.00;FS=13.757;HaplotypeScore=0.8321;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=-0.027;QD=12.87;ReadPosRankSum=1.068;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L60F|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_180581_180872) GT:AD:DP:GQ:PL 0/1:14,11:25:99:350,0,458 -chr1 181012 . A G 667.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.249;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.6617;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.626;QD=23.03;ReadPosRankSum=-0.542;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,20:29:99:696,0,216 -chr1 181024 . C A 591.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.337;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=1.9989;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.742;QD=20.41;ReadPosRankSum=1.506;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,18:29:99:620,0,319 -chr1 181102 . T G 569.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.886;DP=33;Dels=0.00;FS=3.837;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.862;QD=17.27;ReadPosRankSum=0.560;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,18:33:99:598,0,487 -chr1 181156 . G A 274.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.099;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=0.560;QD=12.49;ReadPosRankSum=-0.429;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:12,10:22:99:303,0,376 -chr1 181173 . A C 171.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.766;DP=15;Dels=0.00;FS=3.256;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=57.59;MQ0=0;MQRankSum=0.884;QD=11.45;ReadPosRankSum=-0.648;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:9,6:15:99:200,0,268 -chr1 181194 . A G 142.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.535;DP=19;Dels=0.00;FS=2.017;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=2.149;QD=7.51;ReadPosRankSum=-2.850;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:171,0,426 -chr1 181230 . T A 1286.77 . AC=2;AF=1.00;AN=2;DP=32;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.67;MQ0=0;QD=31.97;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1315,96,0 -chr1 181244 . G T 1304.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.89;MQ0=0;QD=27.50;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1333,99,0 -chr1 181276 . T C 402.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.427;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=59.54;MQ0=0;MQRankSum=-0.632;QD=11.19;ReadPosRankSum=-0.905;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,13:36:99:431,0,793 -chr1 181325 . G C 210.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=2.299;HaplotypeScore=1.8279;MLEAC=1;MLEAF=0.500;MQ=56.80;MQ0=0;MQRankSum=-1.711;QD=9.16;ReadPosRankSum=0.678;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:239,0,509 -chr1 181330 . A G 904.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.8279;MLEAC=2;MLEAF=1.00;MQ=56.57;MQ0=0;QD=31.12;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:933,72,0 -chr1 181337 . A G 906.77 . AC=2;AF=1.00;AN=2;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.8321;MLEAC=2;MLEAF=1.00;MQ=56.47;MQ0=0;QD=29.13;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,25:25:72:935,72,0 -chr1 181340 . G A 284.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.025;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=1.5661;MLEAC=1;MLEAF=0.500;MQ=56.31;MQ0=0;MQRankSum=-1.259;QD=11.87;ReadPosRankSum=-0.205;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:14,10:24:99:313,0,471 -chr1 181363 . C T 211.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.002;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.743;QD=9.21;ReadPosRankSum=0.936;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:240,0,515 -chr1 181373 . C G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.033;DP=23;Dels=0.00;FS=3.982;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.15;MQ0=0;MQRankSum=-2.033;QD=8.99;ReadPosRankSum=0.484;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:15,8:23:99:235,0,521 -chr1 181378 . A G 451.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.646;DP=23;Dels=0.00;FS=4.200;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.88;MQ0=0;MQRankSum=3.647;QD=19.64;ReadPosRankSum=-1.130;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:480,0,235 -chr1 181389 . T G 653.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.19;MQ0=0;QD=30.52;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:682,54,0 -chr1 181394 . T C 708.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=29.42;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:737,57,0 -chr1 181400 . T C 686.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.03;MQ0=0;QD=29.72;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:715,54,0 -chr1 181432 . C T 663.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.63;MQ0=0;QD=28.65;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,17:17:51:692,51,0 -chr1 181520 . C T 266.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.692;DP=35;Dels=0.00;FS=3.290;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=44.29;MQ0=2;MQRankSum=-3.125;QD=7.62;ReadPosRankSum=1.141;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,14:35:99:295,0,721 -chr1 181569 . C T 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.437;DP=41;Dels=0.00;FS=11.992;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=54.50;MQ0=0;MQRankSum=-0.807;QD=11.26;ReadPosRankSum=0.463;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:24,17:41:99:490,0,840 -chr1 181583 . T C 477.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.827;DP=39;Dels=0.00;FS=8.484;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=54.83;MQ0=0;MQRankSum=-1.317;QD=12.25;ReadPosRankSum=1.827;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:22,17:39:99:506,0,762 -chr1 181595 . G A 522.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.137;DP=37;Dels=0.00;FS=9.049;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.78;MQ0=0;MQRankSum=-1.322;QD=14.13;ReadPosRankSum=0.319;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:551,0,655 -chr1 181616 . A G 1243.77 . AC=2;AF=1.00;AN=2;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.37;MQ0=0;QD=26.17;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,34:34:96:1272,96,0 -chr1 181649 . A G 871.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.28;MQ0=0;QD=28.35;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:900,72,0 -chr1 181678 . C A 59.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.180;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=11.4067;MLEAC=1;MLEAF=0.500;MQ=54.06;MQ0=0;MQRankSum=-0.467;QD=4.27;ReadPosRankSum=2.335;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:11,3:14:88:88,0,315 -chr1 181750 . T C 1735.77 . AC=2;AF=1.00;AN=2;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.6208;MLEAC=2;MLEAF=1.00;MQ=61.04;MQ0=0;QD=29.40;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTa/tCa|L98S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,46:46:99:1764,132,0 -chr1 181932 . T C 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.890;DP=42;Dels=0.00;FS=2.883;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.09;MQ0=0;MQRankSum=-0.630;QD=20.26;ReadPosRankSum=0.577;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgt/Cgt|C159R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:15,27:42:99:879,0,440 -chr1 182026 . T G 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.046;DP=37;Dels=0.00;FS=2.884;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.39;MQ0=0;MQRankSum=1.966;QD=13.51;ReadPosRankSum=0.625;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cTc/cGc|L190R|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:20,17:37:99:528,0,608 -chr1 182058 . G C 1193.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=58.19;MQ0=0;QD=29.48;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gta/Cta|V201L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:93:1222,93,0 -chr1 182100 . A G 750.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.141;DP=37;Dels=0.00;FS=16.118;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.13;MQ0=0;MQRankSum=2.302;QD=20.29;ReadPosRankSum=-0.955;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R215G|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:14,23:37:99:779,0,366 -chr1 182108 . G A 386.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.361;DP=39;Dels=0.00;FS=10.673;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.96;MQ0=0;MQRankSum=-0.794;QD=9.92;ReadPosRankSum=0.188;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S217|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:24,15:39:99:415,0,775 -chr1 182195 . C A 1439.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;QD=30.91;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atA|I246|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,37:37:99:1468,111,0 -chr1 182198 . G A 616.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.546;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.182;QD=17.62;ReadPosRankSum=0.348;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L247|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:16,19:35:99:645,0,523 -chr1 182199 . A T 624.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=1.5226;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-0.475;QD=17.35;ReadPosRankSum=0.792;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Ttg|M248L|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:17,19:36:99:653,0,531 -chr1 182231 . G A 1226.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.83;MQ0=0;QD=29.57;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A258|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 1/1:0,33:33:96:1255,96,0 -chr1 182291 . A G 423.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.930;DP=43;Dels=0.00;FS=26.079;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.032;QD=9.86;ReadPosRankSum=-0.828;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V278|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_181750_182298) GT:AD:DP:GQ:PL 0/1:28,15:43:99:452,0,940 -chr1 182317 . C T 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.746;DP=43;Dels=0.00;FS=22.687;HaplotypeScore=0.9958;MLEAC=1;MLEAF=0.500;MQ=58.56;MQ0=0;MQRankSum=-0.239;QD=11.09;ReadPosRankSum=1.018;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:27,16:43:99:505,0,912 -chr1 182395 . C T 499.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.875;DP=36;Dels=0.00;FS=3.014;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.11;MQ0=0;MQRankSum=0.462;QD=13.88;ReadPosRankSum=-2.786;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:20,16:36:99:528,0,655 -chr1 182404 . G A 717.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.278;DP=42;Dels=0.00;FS=1.218;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=57.53;MQ0=0;MQRankSum=0.834;QD=17.09;ReadPosRankSum=0.430;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),SPLICE_SITE_ACCEPTOR(HIGH||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,23:42:99:746,0,627 -chr1 182424 . G A 837.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.760;DP=47;Dels=0.00;FS=1.150;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.78;MQ0=0;MQRankSum=0.738;QD=17.82;ReadPosRankSum=0.952;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A287|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:21,26:47:99:866,0,703 -chr1 182545 . G A 427.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.911;DP=38;Dels=0.00;FS=1.257;HaplotypeScore=0.9989;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=0.986;QD=11.26;ReadPosRankSum=-1.015;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V328I|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182405_182607) GT:AD:DP:GQ:PL 0/1:23,15:38:99:456,0,764 -chr1 182610 . A G 353.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.208;DP=34;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-2.012;QD=10.40;ReadPosRankSum=1.873;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,15:34:99:382,0,506 -chr1 182637 . T C 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.289;DP=36;Dels=0.00;FS=8.730;HaplotypeScore=2.3122;MLEAC=1;MLEAF=0.500;MQ=56.37;MQ0=0;MQRankSum=-2.372;QD=17.99;ReadPosRankSum=1.735;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:16,20:36:99:676,0,448 -chr1 182641 . T C 564.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.109;DP=38;Dels=0.00;FS=13.898;HaplotypeScore=1.7338;MLEAC=1;MLEAF=0.500;MQ=56.24;MQ0=0;MQRankSum=-2.511;QD=14.86;ReadPosRankSum=2.365;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:593,0,579 -chr1 182646 . A G,T 974.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=56.03;MQ0=0;QD=27.06;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/2:0,18,18:36:99:1162,642,594,520,0,465 -chr1 182648 . A T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.525;DP=35;Dels=0.00;FS=17.460;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.91;MQ0=0;MQRankSum=-2.723;QD=15.34;ReadPosRankSum=2.228;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:565,0,436 -chr1 182657 . T C 830.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;DP=46;Dels=0.00;FS=7.638;HaplotypeScore=0.5784;MLEAC=1;MLEAF=0.500;MQ=54.60;MQ0=0;MQRankSum=-3.778;QD=18.06;ReadPosRankSum=-1.934;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:17,29:46:99:859,0,438 -chr1 182668 . T C 745.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.640;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=5.9516;MLEAC=1;MLEAF=0.500;MQ=54.15;MQ0=0;MQRankSum=-3.805;QD=14.92;ReadPosRankSum=-0.685;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:19,31:50:99:774,0,262 -chr1 182674 . A T 726.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.564;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=30.8083;MLEAC=1;MLEAF=0.500;MQ=54.48;MQ0=0;MQRankSum=-4.923;QD=15.46;ReadPosRankSum=-1.147;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:18,27:47:99:755,0,282 -chr1 182714 . G A 2208.77 . AC=2;AF=1.00;AN=2;DP=57;Dels=0.00;FS=0.000;HaplotypeScore=18.3637;MLEAC=2;MLEAF=1.00;MQ=56.43;MQ0=0;QD=25.68;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 1/1:0,57:57:99:2237,172,0 -chr1 182756 . A G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=40;Dels=0.00;FS=6.474;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-0.783;QD=5.17;ReadPosRankSum=0.817;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,9:40:99:235,0,1016 -chr1 182758 . G A 226.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.359;DP=40;Dels=0.00;FS=9.072;HaplotypeScore=0.9997;MLEAC=1;MLEAF=0.500;MQ=58.85;MQ0=0;MQRankSum=-1.078;QD=5.67;ReadPosRankSum=0.672;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:30,10:40:99:255,0,986 -chr1 182775 . T G 510.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.370;DP=44;Dels=0.00;FS=3.185;HaplotypeScore=2.9961;MLEAC=1;MLEAF=0.500;MQ=59.57;MQ0=0;MQRankSum=0.227;QD=11.61;ReadPosRankSum=-2.232;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:539,0,817 -chr1 182800 . A T 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.456;DP=41;Dels=0.00;FS=1.435;HaplotypeScore=1.6650;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=1.552;QD=14.73;ReadPosRankSum=0.039;EFF=INTRON(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|) GT:AD:DP:GQ:PL 0/1:21,20:41:99:632,0,657 -chr1 182818 . G T 536.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.524;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.464;QD=16.27;ReadPosRankSum=1.320;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Tct|A353S|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:565,0,472 -chr1 182821 . T G 524.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.271;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.4440;MLEAC=1;MLEAF=0.500;MQ=59.32;MQ0=0;MQRankSum=-1.284;QD=15.90;ReadPosRankSum=1.392;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Gct|S354A|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:15,18:33:99:553,0,504 -chr1 182977 . A G 833.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.152;DP=61;Dels=0.00;FS=1.012;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.01;MQ0=0;MQRankSum=-0.470;QD=13.67;ReadPosRankSum=1.411;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I406V|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:33,28:61:99:862,0,1096 -chr1 183001 . T C 880.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.024;DP=56;Dels=0.00;FS=2.198;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.46;MQ0=0;MQRankSum=1.958;QD=15.73;ReadPosRankSum=0.156;EFF=SYNONYMOUS_CODING(LOW|SILENT|Ttg/Ctg|L414|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123) GT:AD:DP:GQ:PL 0/1:28,28:56:99:909,0,927 -chr1 183099 . A G 694.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.275;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=59.83;MQ0=0;MQRankSum=-1.462;QD=15.10;ReadPosRankSum=-1.154;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttA/ttG|L446|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,24:46:99:723,0,679 -chr1 183112 . A T 654.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.800;DP=47;Dels=0.00;FS=2.546;HaplotypeScore=0.7887;MLEAC=1;MLEAF=0.500;MQ=59.84;MQ0=0;MQRankSum=-1.631;QD=13.93;ReadPosRankSum=-1.738;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Tgt|S451C|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,22:47:99:683,0,847 -chr1 183122 . A G 702.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.754;DP=49;Dels=0.00;FS=6.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.72;MQ0=0;MQRankSum=-0.010;QD=14.34;ReadPosRankSum=-1.538;EFF=SYNONYMOUS_STOP(LOW|SILENT|tAa/tGa|*454|Cc01g00170|mRNA||GSCOCT00012417001|Exon_chr1_182806_183123),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:731,0,933 -chr1 183134 . G C 1853.77 . AC=2;AF=1.00;AN=2;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=19.9966;MLEAC=2;MLEAF=1.00;MQ=59.84;MQ0=0;QD=28.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,47:48:99:1882,141,0 -chr1 183164 . G A 1985.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=23.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2014,153,0 -chr1 183180 . A T 737.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.116;DP=53;Dels=0.00;FS=2.623;HaplotypeScore=2.7335;MLEAC=1;MLEAF=0.500;MQ=59.89;MQ0=0;MQRankSum=-0.670;QD=13.92;ReadPosRankSum=0.045;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,24:53:99:766,0,944 -chr1 183192 . C T 1829.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=4.4532;MLEAC=2;MLEAF=1.00;MQ=59.89;MQ0=0;QD=33.88;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:1858,150,0 -chr1 183206 . C T 577.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=47;Dels=0.00;FS=2.919;HaplotypeScore=3.7882;MLEAC=1;MLEAF=0.500;MQ=59.92;MQ0=0;MQRankSum=0.613;QD=12.29;ReadPosRankSum=0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:606,0,947 -chr1 183210 . C A 1916.77 . AC=2;AF=1.00;AN=2;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=1.7885;MLEAC=2;MLEAF=1.00;MQ=59.92;MQ0=0;QD=30.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,49:49:99:1945,147,0 -chr1 183264 . C G 587.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.804;DP=38;Dels=0.00;FS=1.237;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=-2.646;QD=15.47;ReadPosRankSum=0.073;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:616,0,690 -chr1 183410 . C A 155.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.198;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=2.9453;MLEAC=1;MLEAF=0.500;MQ=55.82;MQ0=0;MQRankSum=-1.739;QD=4.72;ReadPosRankSum=-2.268;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,7:33:99:184,0,765 -chr1 183443 . G A 1009.77 . AC=2;AF=1.00;AN=2;DP=27;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.08;MQ0=0;QD=27.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,27:27:81:1038,81,0 -chr1 183460 . C T 838.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=35.23;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:867,69,0 -chr1 183464 . G A 858.77 . AC=2;AF=1.00;AN=2;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.48;MQ0=0;QD=29.99;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,23:23:69:887,69,0 -chr1 183493 . C A 473.77 . AC=2;AF=1.00;AN=2;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.39;MQ0=0;QD=26.98;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,13:13:39:502,39,0 -chr1 183509 . A G 339.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.00;MQ0=1;QD=28.31;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:30:368,30,0 -chr1 183531 . G A 267.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=39.51;MQ0=1;QD=26.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:296,24,0 -chr1 183542 . T C 237.8 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=6.6549;MLEAC=2;MLEAF=1.00;MQ=39.61;MQ0=1;QD=23.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:21:266,21,0 -chr1 183564 . G A 265.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.16;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:294,24,0 -chr1 183568 . A G 273.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:302,24,0 -chr1 183569 . C T 272.78 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.61;MQ0=1;QD=24.80;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:24:301,24,0 -chr1 183580 . G T 378.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.45;MQ0=1;QD=23.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:33:407,33,0 -chr1 183601 . C T 413.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.58;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:442,36,0 -chr1 183602 . G C 414.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.9832;MLEAC=2;MLEAF=1.00;MQ=36.53;MQ0=0;QD=27.65;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:36:443,36,0 -chr1 183606 . C T 458.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.57;MQ0=0;QD=25.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:39:487,39,0 -chr1 183618 . C T 490.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.82;MQ0=0;QD=25.83;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:42:519,42,0 -chr1 183623 . A G 484.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.91;MQ0=1;QD=24.24;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:42:513,42,0 -chr1 183645 . A G 560.77 . AC=2;AF=1.00;AN=2;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=36.51;MQ0=1;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,21:21:48:589,48,0 -chr1 183881 . T C 84.03 . AC=2;AF=1.00;AN=2;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=19.25;MQ0=1;QD=14.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,6:6:12:112,12,0 -chr1 184039 . C T 65.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=17;Dels=0.00;FS=11.761;HaplotypeScore=0.9947;MLEAC=1;MLEAF=0.500;MQ=14.06;MQ0=10;MQRankSum=1.300;QD=3.87;ReadPosRankSum=1.754;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:12,5:17:39:94,0,39 -chr1 184048 . G A 68.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.380;DP=14;Dels=0.00;FS=6.990;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=15.98;MQ0=8;MQRankSum=0.000;QD=4.91;ReadPosRankSum=1.380;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,6:14:25:97,0,25 -chr1 184262 . G A 35.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=32.39;MQ0=0;QD=17.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:63,6,0 -chr1 184325 . T A 368.77 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=36.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:30:397,30,0 -chr1 184366 . G T 16.86 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=1.495;DP=7;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.95;MQ0=0;MQRankSum=-1.495;QD=2.41;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,2:7:45:45,0,172 -chr1 184384 . T A 250.8 . AC=2;AF=1.00;AN=2;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.83;MQ0=0;QD=27.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,9:9:21:279,21,0 -chr1 184401 . T C 297.78 . AC=2;AF=1.00;AN=2;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=29.78;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,10:10:24:326,24,0 -chr1 184419 . C T 459.77 . AC=2;AF=1.00;AN=2;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.09;MQ0=0;QD=32.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,14:14:36:488,36,0 -chr1 184437 . A C 589.77 . AC=2;AF=1.00;AN=2;DP=17;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=54.37;MQ0=0;QD=34.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,17:17:45:618,45,0 -chr1 184457 . T A 615.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.8941;MLEAC=2;MLEAF=1.00;MQ=57.14;MQ0=0;QD=33.68;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:644,48,0 -chr1 184511 . A G 177.9 . AC=2;AF=1.00;AN=2;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=32.08;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,5:5:15:206,15,0 -chr1 184520 . T C 126.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:154,12,0 -chr1 184712 . A G 14.68 LowQual AC=2;AF=1.00;AN=2;BaseQRankSum=0.804;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=14.76;MQ0=5;MQRankSum=0.804;QD=2.10;ReadPosRankSum=0.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:6,1:7:3:41,3,0 -chr1 184812 . C T 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.740;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=1.849;QD=22.60;ReadPosRankSum=-2.589;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,9:13:24:322,24,0 -chr1 184813 . G A 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.382;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-2.262;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:4,8:13:24:322,24,0 -chr1 184816 . T C 293.78 . AC=2;AF=1.00;AN=2;BaseQRankSum=1.106;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=2.2460;MLEAC=2;MLEAF=1.00;MQ=38.19;MQ0=1;MQRankSum=2.262;QD=22.60;ReadPosRankSum=-0.978;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:3,8:13:24:322,24,0 -chr1 184870 . C G 77.28 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=34.27;MQ0=0;QD=25.76;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:9:105,9,0 -chr1 184877 . A C 110.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=35.51;MQ0=0;QD=27.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:138,12,0 -chr1 184924 . T C 381.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=47.07;MQ0=0;QD=34.71;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:410,33,0 -chr1 184928 . A G 414.77 . AC=2;AF=1.00;AN=2;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.28;MQ0=0;QD=34.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,12:12:36:443,36,0 -chr1 184947 . T C 553.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.40;MQ0=0;QD=29.19;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:582,45,0 -chr1 184967 . G A 179.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.750;DP=26;Dels=0.00;FS=4.435;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.68;MQ0=0;MQRankSum=-3.139;QD=6.91;ReadPosRankSum=-2.639;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,8:26:99:208,0,643 -chr1 184971 . G C 238.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.026;DP=27;Dels=0.00;FS=6.965;HaplotypeScore=2.6549;MLEAC=1;MLEAF=0.500;MQ=52.77;MQ0=0;MQRankSum=-3.060;QD=8.84;ReadPosRankSum=-1.672;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,9:27:99:267,0,627 -chr1 184992 . C A 317.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.420;DP=30;Dels=0.00;FS=3.779;HaplotypeScore=7.2988;MLEAC=1;MLEAF=0.500;MQ=55.33;MQ0=0;MQRankSum=-3.443;QD=10.59;ReadPosRankSum=0.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,11:30:99:346,0,566 -chr1 184999 . G A 589.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.172;DP=36;Dels=0.00;FS=2.798;HaplotypeScore=2.3001;MLEAC=1;MLEAF=0.500;MQ=57.43;MQ0=0;MQRankSum=-2.789;QD=16.38;ReadPosRankSum=-2.345;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,19:36:99:618,0,532 -chr1 185038 . A T 714.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.418;DP=37;Dels=0.00;FS=5.015;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.31;MQ0=0;MQRankSum=-0.820;QD=19.32;ReadPosRankSum=2.088;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,22:37:99:743,0,477 -chr1 185039 . T A 446.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.072;DP=39;Dels=0.00;FS=4.649;HaplotypeScore=1.9983;MLEAC=1;MLEAF=0.500;MQ=59.35;MQ0=0;MQRankSum=0.736;QD=11.46;ReadPosRankSum=-1.833;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,15:39:99:475,0,785 -chr1 185068 . A T 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.341;DP=40;Dels=0.00;FS=6.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=1.559;QD=19.29;ReadPosRankSum=0.657;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,23:40:99:800,0,540 -chr1 185070 . C G 765.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.143;DP=41;Dels=0.00;FS=9.282;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.801;QD=18.68;ReadPosRankSum=0.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,23:41:99:794,0,571 -chr1 185084 . C A 776.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=41;Dels=0.00;FS=6.934;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.86;MQ0=0;MQRankSum=0.781;QD=18.95;ReadPosRankSum=-0.966;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,24:41:99:805,0,519 -chr1 185087 . G A 1558.77 . AC=2;AF=1.00;AN=2;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=59.86;MQ0=0;QD=32.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,41:41:99:1587,120,0 -chr1 185096 . A G 492.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.414;DP=37;Dels=0.00;FS=5.209;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=59.85;MQ0=0;MQRankSum=0.383;QD=13.32;ReadPosRankSum=1.364;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,16:37:99:521,0,697 -chr1 185113 . T C 1279.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.47;MQ0=0;QD=28.25;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1308,99,0 -chr1 185114 . G A 1207.77 . AC=2;AF=1.00;AN=2;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.44;MQ0=0;QD=33.43;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,31:31:93:1236,93,0 -chr1 185129 . C A 571.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.123;DP=36;Dels=0.00;FS=2.788;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.52;MQ0=0;MQRankSum=0.459;QD=15.88;ReadPosRankSum=0.111;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,18:36:99:600,0,584 -chr1 185138 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.656;DP=37;Dels=0.00;FS=1.289;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.17;MQ0=0;MQRankSum=1.595;QD=14.70;ReadPosRankSum=-0.228;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,18:37:99:572,0,645 -chr1 185141 . G A 535.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.601;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=14.8277;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=-1.139;QD=15.31;ReadPosRankSum=0.347;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,17:35:99:564,0,590 -chr1 185145 . G T 473.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.115;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.07;MQ0=0;MQRankSum=-1.139;QD=14.36;ReadPosRankSum=0.886;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,15:33:99:502,0,598 -chr1 185186 . C T 606.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.484;DP=37;Dels=0.00;FS=1.280;HaplotypeScore=19.3302;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.960;QD=16.40;ReadPosRankSum=0.137;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,20:37:99:635,0,578 -chr1 185222 . T A 741.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.397;DP=45;Dels=0.00;FS=1.154;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.13;MQ0=0;MQRankSum=-1.101;QD=16.48;ReadPosRankSum=1.828;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,23:45:99:770,0,755 -chr1 185241 . A G 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.630;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.103;QD=15.31;ReadPosRankSum=0.227;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:763,0,865 -chr1 185245 . G A 733.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.011;DP=48;Dels=0.00;FS=2.415;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.19;MQ0=0;MQRankSum=-0.619;QD=15.29;ReadPosRankSum=-0.433;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,23:48:99:762,0,868 -chr1 185259 . C T 683.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.633;DP=49;Dels=0.00;FS=2.460;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.136;QD=13.95;ReadPosRankSum=-0.915;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,22:49:99:712,0,900 -chr1 185264 . T C 754.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.367;DP=52;Dels=0.00;FS=1.072;HaplotypeScore=1.8665;MLEAC=1;MLEAF=0.500;MQ=59.25;MQ0=0;MQRankSum=-1.606;QD=14.51;ReadPosRankSum=-1.404;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,24:52:99:783,0,962 -chr1 185289 . C T 594.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.904;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=1.8940;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-1.022;QD=12.65;ReadPosRankSum=-0.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,20:47:99:623,0,933 -chr1 185299 . A T 506.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.800;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=16.4921;MLEAC=1;MLEAF=0.500;MQ=58.05;MQ0=0;MQRankSum=-2.184;QD=11.52;ReadPosRankSum=0.752;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,18:44:99:535,0,917 -chr1 185346 . C T 311.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.206;DP=33;Dels=0.00;FS=8.695;HaplotypeScore=0.9967;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-3.050;QD=9.45;ReadPosRankSum=1.815;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:340,0,747 -chr1 185347 . A G 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.318;DP=33;Dels=0.00;FS=11.504;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.55;MQ0=0;MQRankSum=-2.826;QD=10.57;ReadPosRankSum=1.890;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,12:33:99:377,0,759 -chr1 185372 . T C 246.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.574;DP=29;Dels=0.00;FS=17.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.21;MQ0=0;MQRankSum=-4.382;QD=8.51;ReadPosRankSum=0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,10:29:99:275,0,692 -chr1 185376 . C G 153.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.478;DP=28;Dels=0.00;FS=21.622;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=5.49;ReadPosRankSum=1.804;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:182,0,778 -chr1 185383 . C T 118.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.318;DP=28;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.24;ReadPosRankSum=0.584;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:147,0,783 -chr1 185387 . A G 134.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.478;DP=28;Dels=0.00;FS=19.859;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.57;MQ0=0;MQRankSum=-3.926;QD=4.81;ReadPosRankSum=0.212;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,7:28:99:163,0,736 -chr1 185394 . A C 114.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.146;DP=27;Dels=0.00;FS=16.983;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.70;MQ0=0;MQRankSum=-3.703;QD=4.25;ReadPosRankSum=-0.846;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,6:27:99:143,0,783 -chr1 185401 . T A 111.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.242;DP=29;Dels=0.00;FS=15.529;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.86;MQ0=0;MQRankSum=-3.742;QD=3.85;ReadPosRankSum=-0.673;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,6:29:99:140,0,846 -chr1 185407 . C T 19.81 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-0.867;DP=23;Dels=0.00;FS=6.628;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.03;MQ0=0;MQRankSum=-2.784;QD=0.86;ReadPosRankSum=-2.784;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,3:23:48:48,0,737 -chr1 185480 . G A 732.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=30.74;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:57:761,57,0 -chr1 185486 . C T 684.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.24;MQ0=0;QD=29.12;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:713,54,0 -chr1 185509 . T C 606.77 . AC=2;AF=1.00;AN=2;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=62.65;MQ0=0;QD=28.82;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,16:16:48:635,48,0 -chr1 185547 . C T 637.94 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.964;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.91;MQ0=0;MQRankSum=-1.156;QD=24.50;ReadPosRankSum=1.349;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,17:18:14:666,14,0 -chr1 185642 . A T 574.77 . AC=2;AF=1.00;AN=2;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.69;MQ0=0;QD=28.90;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,15:15:45:603,45,0 -chr1 185689 . A C 173.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.167;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.58;MQ0=1;MQRankSum=-2.906;QD=7.24;ReadPosRankSum=-1.837;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,8:24:99:202,0,578 -chr1 185691 . T G 889.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.58;MQ0=1;QD=27.49;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:69:918,69,0 -chr1 185717 . A G 346.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.307;DP=33;Dels=0.00;FS=3.365;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.82;MQ0=1;MQRankSum=-1.880;QD=10.51;ReadPosRankSum=0.998;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,14:33:99:375,0,665 -chr1 185726 . G C 593.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=39;Dels=0.00;FS=4.887;HaplotypeScore=0.9894;MLEAC=1;MLEAF=0.500;MQ=57.32;MQ0=1;MQRankSum=-2.190;QD=15.22;ReadPosRankSum=0.234;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:622,0,634 -chr1 185747 . A T 894.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.281;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=55.36;MQ0=1;MQRankSum=-1.881;QD=20.81;ReadPosRankSum=-0.894;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:14,29:43:99:923,0,453 -chr1 185776 . A G 872.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.350;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=52.87;MQ0=1;MQRankSum=-1.287;QD=22.38;ReadPosRankSum=2.961;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,28:39:99:901,0,314 -chr1 185800 . C T 709.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.468;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=4.9825;MLEAC=1;MLEAF=0.500;MQ=50.92;MQ0=1;MQRankSum=-0.406;QD=25.35;ReadPosRankSum=1.529;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:5,23:28:89:738,0,89 -chr1 185804 . T G 590.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.175;DP=28;Dels=0.00;FS=8.073;HaplotypeScore=5.6476;MLEAC=1;MLEAF=0.500;MQ=49.66;MQ0=1;MQRankSum=1.135;QD=21.10;ReadPosRankSum=0.436;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:3,22:28:16:690,0,16 -chr1 185818 . T G 576.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.771;DP=24;Dels=0.00;FS=2.570;HaplotypeScore=2.9824;MLEAC=1;MLEAF=0.500;MQ=47.71;MQ0=1;MQRankSum=1.176;QD=24.03;ReadPosRankSum=-0.852;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:4,20:24:53:605,0,53 -chr1 186025 . A C 17.84 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=1.9066;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.026;QD=4.46;ReadPosRankSum=1.026;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,2:4:46:46,0,47 -chr1 186043 . A G 570.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;DP=38;Dels=0.00;FS=3.067;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=53.26;MQ0=5;MQRankSum=-1.963;QD=15.02;ReadPosRankSum=-2.900;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,19:38:99:599,0,549 -chr1 186058 . T A 1383.77 . AC=2;AF=1.00;AN=2;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=53.62;MQ0=5;QD=34.59;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,40:40:99:1412,105,0 -chr1 186081 . A G 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.401;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.30;MQ0=0;MQRankSum=-0.474;QD=15.86;ReadPosRankSum=2.879;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:710,0,742 -chr1 186083 . T A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.085;DP=43;Dels=0.00;FS=1.177;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.54;MQ0=0;MQRankSum=2.928;QD=16.48;ReadPosRankSum=-2.126;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:737,0,714 -chr1 186128 . C G 476.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.528;DP=39;Dels=0.00;FS=1.390;HaplotypeScore=19.8272;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.043;QD=12.22;ReadPosRankSum=-0.757;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,16:39:99:505,0,805 -chr1 186204 . A T 1634.77 . AC=2;AF=1.00;AN=2;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.5774;MLEAC=2;MLEAF=1.00;MQ=52.86;MQ0=7;QD=30.84;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,53:53:99:1663,126,0 -chr1 186205 . G C 444.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DP=52;Dels=0.00;FS=2.716;HaplotypeScore=1.5774;MLEAC=1;MLEAF=0.500;MQ=52.72;MQ0=7;MQRankSum=0.198;QD=8.55;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,19:52:99:473,0,903 -chr1 186248 . C T 542.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.117;DP=39;Dels=0.00;FS=2.991;HaplotypeScore=12.5646;MLEAC=1;MLEAF=0.500;MQ=51.44;MQ0=4;MQRankSum=-0.750;QD=13.92;ReadPosRankSum=0.283;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,20:39:99:571,0,491 -chr1 186252 . T C 547.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.617;DP=38;Dels=0.00;FS=1.412;HaplotypeScore=14.4976;MLEAC=1;MLEAF=0.500;MQ=52.11;MQ0=3;MQRankSum=-1.250;QD=14.41;ReadPosRankSum=0.383;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,20:38:99:576,0,472 -chr1 186263 . T C 466.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.915;DP=45;Dels=0.00;FS=1.264;HaplotypeScore=23.4286;MLEAC=1;MLEAF=0.500;MQ=54.89;MQ0=1;MQRankSum=2.794;QD=10.37;ReadPosRankSum=-0.061;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:28,17:45:99:495,0,824 -chr1 186273 . C T 630.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.092;DP=50;Dels=0.00;FS=8.671;HaplotypeScore=22.6968;MLEAC=1;MLEAF=0.500;MQ=55.43;MQ0=1;MQRankSum=3.184;QD=12.62;ReadPosRankSum=1.495;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:29,21:50:99:659,0,894 -chr1 186302 . T C 961.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.434;DP=49;Dels=0.00;FS=5.993;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=58.86;MQ0=0;MQRankSum=-0.254;QD=19.63;ReadPosRankSum=0.315;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,29:49:99:990,0,585 -chr1 186305 . G A 842.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.336;DP=45;Dels=0.00;FS=2.751;HaplotypeScore=2.8649;MLEAC=1;MLEAF=0.500;MQ=59.20;MQ0=0;MQRankSum=-1.332;QD=18.73;ReadPosRankSum=-0.081;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,27:45:99:871,0,521 -chr1 186318 . T C 531.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.825;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=56.94;MQ0=0;MQRankSum=2.087;QD=10.03;ReadPosRankSum=-0.213;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,19:53:99:560,0,1118 -chr1 186366 . G A 683.77 . AC=2;AF=1.00;AN=2;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.40;MQ0=0;QD=32.01;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,18:18:54:712,54,0 -chr1 186382 . G A 56.74 . AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.17;MQ0=0;QD=28.37;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,2:2:6:84,6,0 -chr1 186396 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.37;MQ0=0;MQRankSum=-1.756;QD=22.10;ReadPosRankSum=-2.318;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,16:18:34:426,0,34 -chr1 186407 . T C 557.81 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.691;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=35.89;MQ0=0;MQRankSum=-1.909;QD=24.25;ReadPosRankSum=-2.346;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:2,21:23:20:586,0,20 -chr1 186440 . C A 45.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.795;DP=31;Dels=0.00;FS=19.193;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=41.71;MQ0=0;MQRankSum=3.153;QD=1.48;ReadPosRankSum=-2.740;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,4:31:74:74,0,835 -chr1 186449 . C A 1104.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=44.29;MQ0=0;QD=28.17;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1133,90,0 -chr1 186454 . C T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.649;DP=34;Dels=0.00;FS=22.252;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.56;MQ0=0;MQRankSum=-3.817;QD=27.05;ReadPosRankSum=2.372;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,28:34:99:948,0,144 -chr1 186460 . C T 860.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.748;DP=32;Dels=0.00;FS=17.527;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.19;MQ0=0;MQRankSum=-3.790;QD=26.90;ReadPosRankSum=2.245;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,26:32:99:889,0,146 -chr1 186464 . T C 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.469;DP=34;Dels=0.00;FS=19.762;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=46.63;MQ0=0;MQRankSum=-4.046;QD=25.85;ReadPosRankSum=1.704;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:7,27:34:99:907,0,182 -chr1 186478 . T C 525.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.252;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=-3.990;QD=21.03;ReadPosRankSum=-0.379;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,17:25:99:554,0,243 -chr1 186480 . A C 212.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.087;DP=25;Dels=0.00;FS=15.830;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=49.25;MQ0=0;MQRankSum=3.932;QD=8.51;ReadPosRankSum=1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:17,8:25:99:241,0,553 -chr1 186483 . C T 883.77 . AC=2;AF=1.00;AN=2;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.9916;MLEAC=2;MLEAF=1.00;MQ=50.06;MQ0=0;QD=31.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,24:24:72:912,72,0 -chr1 186485 . A G 470.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.452;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.47;ReadPosRankSum=-1.517;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:499,0,249 -chr1 186488 . C T 450.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.290;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=19.60;ReadPosRankSum=-1.194;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:479,0,255 -chr1 186496 . G T 463.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.613;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.9916;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.16;ReadPosRankSum=-1.130;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:492,0,235 -chr1 186499 . T C 462.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.065;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.12;ReadPosRankSum=-0.484;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:491,0,247 -chr1 186500 . T C 461.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.807;DP=23;Dels=0.00;FS=12.352;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=50.31;MQ0=0;MQRankSum=-3.905;QD=20.08;ReadPosRankSum=-0.549;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,15:23:99:490,0,245 -chr1 186522 . A G 162.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.798;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.47;MQ0=0;MQRankSum=3.201;QD=8.57;ReadPosRankSum=0.307;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:13,6:19:99:191,0,365 -chr1 186527 . T A 262.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.452;DP=18;Dels=0.00;FS=2.762;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=47.08;MQ0=0;MQRankSum=-3.138;QD=14.60;ReadPosRankSum=0.140;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:6,12:18:99:291,0,198 -chr1 186553 . C T 134.03 . AC=2;AF=1.00;AN=2;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=58.05;MQ0=0;QD=33.51;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,4:4:12:162,12,0 -chr1 186562 . C T 97.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.600;DP=12;Dels=0.00;FS=6.818;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=45.72;MQ0=0;MQRankSum=2.637;QD=8.15;ReadPosRankSum=0.825;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:8,4:12:99:126,0,256 -chr1 186565 . C T 383.77 . AC=2;AF=1.00;AN=2;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=42.26;MQ0=0;QD=34.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,11:11:33:412,33,0 -chr1 186581 . C T 24.78 LowQual AC=1;AF=0.500;AN=2;BaseQRankSum=-1.296;DP=11;Dels=0.00;FS=3.310;HaplotypeScore=1.7987;MLEAC=1;MLEAF=0.500;MQ=42.26;MQ0=0;MQRankSum=2.003;QD=2.25;ReadPosRankSum=2.003;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:9,2:11:53:53,0,266 -chr1 186587 . A G 52.74 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=17.58;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:1,2:3:6:80,6,0 -chr1 186588 . T C 53.74 . AC=2;AF=1.00;AN=2;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=43.02;MQ0=0;QD=17.91;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,3:3:6:81,6,0 -chr1 186590 . T C 44.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=43.02;MQ0=0;MQRankSum=0.736;QD=14.93;ReadPosRankSum=0.736;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:1,2:3:26:73,0,26 -chr1 186605 . C T 574.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.941;DP=28;Dels=0.00;FS=12.091;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=3.575;QD=20.53;ReadPosRankSum=-3.810;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:11,17:28:99:603,0,347 -chr1 186611 . A G 331.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.292;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.843;QD=11.44;ReadPosRankSum=2.854;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:360,0,648 -chr1 186614 . C T 339.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.067;DP=29;Dels=0.00;FS=8.572;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.96;MQ0=0;MQRankSum=-3.798;QD=11.72;ReadPosRankSum=2.944;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:18,11:29:99:368,0,655 -chr1 186624 . C T 384.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.559;DP=34;Dels=0.00;FS=11.031;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.15;MQ0=0;MQRankSum=-4.146;QD=11.32;ReadPosRankSum=2.055;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,13:34:99:413,0,758 -chr1 186629 . C T 767.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.439;DP=38;Dels=0.00;FS=8.924;HaplotypeScore=0.9789;MLEAC=1;MLEAF=0.500;MQ=57.33;MQ0=0;MQRankSum=4.390;QD=20.20;ReadPosRankSum=-0.695;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:16,22:38:99:796,0,505 -chr1 186638 . G A 1706.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=57.64;MQ0=0;QD=24.81;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1735,129,0 -chr1 186658 . C T 632.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.573;DP=53;Dels=0.00;FS=6.435;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=57.98;MQ0=0;MQRankSum=-3.592;QD=11.94;ReadPosRankSum=-1.373;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,21:53:99:661,0,1102 -chr1 186661 . C T 663.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.611;DP=54;Dels=0.00;FS=6.487;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.27;MQ0=0;MQRankSum=-3.283;QD=12.29;ReadPosRankSum=-1.276;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,22:54:99:692,0,1121 -chr1 186663 . C T 1074.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.185;DP=57;Dels=0.00;FS=8.033;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=58.36;MQ0=0;MQRankSum=3.964;QD=18.86;ReadPosRankSum=1.552;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,32:57:99:1103,0,821 -chr1 186666 . G A 1080.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.687;DP=56;Dels=0.00;FS=6.180;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=58.79;MQ0=0;MQRankSum=3.767;QD=19.30;ReadPosRankSum=0.538;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,32:56:99:1109,0,798 -chr1 186683 . A C 681.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.388;DP=53;Dels=0.00;FS=1.158;HaplotypeScore=2.9993;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=-3.312;QD=12.86;ReadPosRankSum=1.200;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,22:53:99:710,0,1078 -chr1 186694 . T C 1666.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=2;MLEAF=1.00;MQ=59.08;MQ0=0;QD=30.93;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1695,126,0 -chr1 186695 . C T 736.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.467;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=4.002;QD=16.74;ReadPosRankSum=0.786;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,22:44:99:765,0,705 -chr1 186696 . C T 738.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.300;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.15;MQ0=0;MQRankSum=3.924;QD=17.18;ReadPosRankSum=0.668;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:767,0,660 -chr1 186702 . C T 600.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.286;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.080;QD=13.35;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,21:45:99:629,0,825 -chr1 186707 . G A 708.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.442;DP=45;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.29;MQ0=0;MQRankSum=-0.738;QD=15.75;ReadPosRankSum=0.034;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,22:45:99:737,0,782 -chr1 186723 . G A 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.815;DP=40;Dels=0.00;FS=2.843;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=-0.650;QD=16.19;ReadPosRankSum=-1.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,21:40:99:676,0,656 -chr1 186725 . G A 682.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.320;DP=41;Dels=0.00;FS=4.533;HaplotypeScore=5.9981;MLEAC=1;MLEAF=0.500;MQ=59.70;MQ0=0;MQRankSum=-0.588;QD=16.65;ReadPosRankSum=-1.216;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:19,22:41:99:711,0,635 -chr1 186730 . C T 120.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.280;DP=43;Dels=0.00;FS=6.398;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.477;QD=2.81;ReadPosRankSum=0.609;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:36,7:43:99:149,0,1300 -chr1 186735 . T C 628.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.621;DP=43;Dels=0.00;FS=4.425;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=-1.278;QD=14.62;ReadPosRankSum=-0.110;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,23:43:99:657,0,661 -chr1 186738 . C T 642.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.029;DP=43;Dels=0.00;FS=1.242;HaplotypeScore=7.8644;MLEAC=1;MLEAF=0.500;MQ=59.71;MQ0=0;MQRankSum=0.109;QD=14.95;ReadPosRankSum=-0.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,21:43:99:671,0,692 -chr1 186794 . C A 2054.77 . AC=2;AF=1.00;AN=2;DP=52;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.40;MQ0=0;QD=32.28;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,52:52:99:2083,157,0 -chr1 186799 . A C 2004.77 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.39;MQ0=0;QD=29.67;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,51:51:99:2033,154,0 -chr1 186800 . T C 892.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.425;DP=51;Dels=0.00;FS=3.975;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQ0=0;MQRankSum=0.519;QD=17.51;ReadPosRankSum=0.047;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,27:51:99:921,0,810 -chr1 186804 . C T 2108.77 . AC=2;AF=1.00;AN=2;DP=56;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.45;MQ0=0;QD=28.56;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,56:56:99:2137,166,0 -chr1 186814 . G A 2540.77 . AC=2;AF=1.00;AN=2;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;QD=29.41;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,65:65:99:2569,196,0 -chr1 186823 . T C 2655.77 . AC=2;AF=1.00;AN=2;DP=67;Dels=0.00;FS=0.000;HaplotypeScore=1.7339;MLEAC=2;MLEAF=1.00;MQ=59.54;MQ0=0;QD=27.89;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,67:67:99:2684,202,0 -chr1 186853 . A G 794.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.007;DP=60;Dels=0.00;FS=1.028;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.48;MQ0=0;MQRankSum=0.037;QD=13.25;ReadPosRankSum=-1.052;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:34,26:60:99:823,0,1142 -chr1 186856 . A G 1066.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.908;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.49;MQ0=0;MQRankSum=1.735;QD=17.49;ReadPosRankSum=1.096;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:27,34:61:99:1095,0,816 -chr1 186871 . C T 2064.77 . AC=2;AF=1.00;AN=2;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.64;MQ0=0;QD=34.20;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,54:54:99:2093,160,0 -chr1 186897 . A G 1641.77 . AC=2;AF=1.00;AN=2;DP=44;Dels=0.00;FS=0.000;HaplotypeScore=0.7340;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.39;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,44:44:99:1670,129,0 -chr1 186922 . C T 613.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.042;DP=39;Dels=0.00;FS=10.184;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.363;QD=15.74;ReadPosRankSum=0.576;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,19:39:99:642,0,675 -chr1 186958 . T G 603.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.769;DP=38;Dels=0.00;FS=9.513;HaplotypeScore=2.7878;MLEAC=1;MLEAF=0.500;MQ=59.77;MQ0=0;MQRankSum=-0.015;QD=15.89;ReadPosRankSum=-0.482;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:20,18:38:99:632,0,693 -chr1 186977 . T C 1690.77 . AC=2;AF=1.00;AN=2;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=59.26;MQ0=0;QD=33.69;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,43:43:99:1719,129,0 -chr1 186990 . T A 716.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.733;DP=43;Dels=0.00;FS=1.194;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=1.494;QD=16.67;ReadPosRankSum=-0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,22:43:99:745,0,730 -chr1 186991 . G A 656.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.624;DP=42;Dels=0.00;FS=1.170;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.10;MQ0=0;MQRankSum=-2.632;QD=15.64;ReadPosRankSum=0.743;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,20:42:99:685,0,742 -chr1 186992 . C T 627.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.654;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9999;MLEAC=1;MLEAF=0.500;MQ=59.08;MQ0=0;MQRankSum=-1.503;QD=15.31;ReadPosRankSum=0.980;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:22,19:41:99:656,0,735 -chr1 187055 . G A 772.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.270;DP=49;Dels=0.00;FS=6.133;HaplotypeScore=0.9995;MLEAC=1;MLEAF=0.500;MQ=59.30;MQ0=0;MQRankSum=-1.990;QD=15.77;ReadPosRankSum=-0.770;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,24:49:99:801,0,876 -chr1 187064 . A G 771.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.160;DP=47;Dels=0.00;FS=6.439;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.64;MQ0=0;MQRankSum=-1.075;QD=16.42;ReadPosRankSum=-0.990;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,23:47:99:800,0,846 -chr1 187065 . G A 768.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.120;DP=46;Dels=0.00;FS=6.548;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.63;MQ0=0;MQRankSum=-0.923;QD=16.71;ReadPosRankSum=-1.186;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:797,0,815 -chr1 187147 . C T 647.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.158;DP=43;Dels=0.00;FS=1.192;HaplotypeScore=1.8664;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.400;QD=15.06;ReadPosRankSum=-0.718;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,20:43:99:676,0,759 -chr1 187173 . A T 804.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.160;DP=51;Dels=0.00;FS=1.128;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.970;QD=15.78;ReadPosRankSum=-0.688;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:26,25:51:99:833,0,844 -chr1 187185 . A T 919.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.328;DP=59;Dels=0.00;FS=1.046;HaplotypeScore=0.8941;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-2.148;QD=15.59;ReadPosRankSum=1.192;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:31,28:59:99:948,0,1051 -chr1 187200 . T C 218.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.286;DP=70;Dels=0.00;FS=12.081;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.69;MQ0=0;MQRankSum=-5.431;QD=3.13;ReadPosRankSum=-3.935;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:58,12:70:99:247,0,2146 -chr1 187208 . T G 206.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.365;DP=73;Dels=0.00;FS=9.609;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=-5.455;QD=2.83;ReadPosRankSum=-2.746;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:61,12:73:99:235,0,2122 -chr1 187209 . A C 990.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.151;DP=73;Dels=0.00;FS=1.959;HaplotypeScore=23.9717;MLEAC=1;MLEAF=0.500;MQ=56.50;MQ0=0;MQRankSum=2.896;QD=13.57;ReadPosRankSum=1.981;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:42,31:73:99:1019,0,1427 -chr1 187247 . G A 1055.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.510;DP=55;Dels=0.00;FS=2.329;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.33;MQ0=0;MQRankSum=-1.357;QD=19.20;ReadPosRankSum=-1.118;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,32:55:99:1084,0,781 -chr1 187248 . G T 963.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.193;DP=53;Dels=0.00;FS=3.850;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.19;MQ0=0;MQRankSum=-1.911;QD=18.18;ReadPosRankSum=-0.763;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,30:53:99:992,0,786 -chr1 187270 . C G 518.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=38;Dels=0.00;FS=2.937;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=54.61;MQ0=0;MQRankSum=-5.255;QD=13.65;ReadPosRankSum=3.582;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:21,17:38:99:547,0,742 -chr1 187298 . C T 1101.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.354;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.65;MQ0=0;MQRankSum=0.258;QD=21.60;ReadPosRankSum=1.685;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,36:51:99:1130,0,459 -chr1 187302 . A G 1787.77 . AC=2;AF=1.00;AN=2;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=56.82;MQ0=0;QD=32.03;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,50:50:99:1816,135,0 -chr1 187346 . C T 972.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=-1.918;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=52.31;MQ0=3;MQRankSum=2.275;QD=31.38;ReadPosRankSum=1.918;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:5,26:31:78:1001,78,0 -chr1 187362 . T C 348.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.168;DP=38;Dels=0.00;FS=1.434;HaplotypeScore=0.9998;MLEAC=1;MLEAF=0.500;MQ=52.20;MQ0=4;MQRankSum=-2.189;QD=9.18;ReadPosRankSum=0.655;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:24,13:38:99:377,0,655 -chr1 187385 . C T 1261.77 . AC=2;AF=1.00;AN=2;DP=37;Dels=0.00;FS=0.000;HaplotypeScore=0.9993;MLEAC=2;MLEAF=1.00;MQ=54.34;MQ0=3;QD=34.10;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,35:37:99:1290,99,0 -chr1 187414 . C A 1254.77 . AC=2;AF=1.00;AN=2;DP=33;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=55.94;MQ0=0;QD=26.70;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,33:33:99:1283,99,0 -chr1 187461 . C A 765.77 . AC=2;AF=1.00;AN=2;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=51.91;MQ0=0;QD=29.87;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,20:20:60:794,60,0 -chr1 187503 . G A 696.77 . AC=2;AF=1.00;AN=2;DP=19;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=40.86;MQ0=0;QD=34.21;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,19:19:54:725,54,0 -chr1 187522 . A T 1152.77 . AC=2;AF=1.00;AN=2;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.33;MQ0=0;QD=31.26;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,30:30:90:1181,90,0 -chr1 187574 . T A 1364.77 . AC=2;AF=1.00;AN=2;DP=38;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=45.88;MQ0=2;QD=28.79;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:2,36:38:99:1393,108,0 -chr1 187614 . A G 872.77 . AC=2;AF=1.00;AN=2;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=48.29;MQ0=2;QD=33.57;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,25:26:69:901,69,0 -chr1 187714 . G C 1203.77 . AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=46.78;MQ0=2;QD=28.66;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 1/1:0,42:42:96:1232,96,0 -chr1 187753 . T C 851.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.068;DP=59;Dels=0.00;FS=1.104;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=56.49;MQ0=0;MQRankSum=0.555;QD=14.44;ReadPosRankSum=-5.759;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:32,27:59:99:880,0,1099 -chr1 187793 . T C 1189.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.870;DP=60;Dels=0.00;FS=1.043;HaplotypeScore=15.7240;MLEAC=1;MLEAF=0.500;MQ=59.38;MQ0=0;MQRankSum=0.945;QD=19.83;ReadPosRankSum=3.344;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,35:60:99:1218,0,816 -chr1 187844 . T C 876.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.394;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=0.9578;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.259;QD=21.38;ReadPosRankSum=-0.014;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:15,26:41:99:905,0,488 -chr1 187894 . G A 734.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.395;DP=46;Dels=0.00;FS=4.031;HaplotypeScore=0.8667;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=1.055;QD=15.97;ReadPosRankSum=-0.483;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:763,0,746 -chr1 187903 . C T 775.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.417;DP=46;Dels=0.00;FS=6.439;HaplotypeScore=4.0994;MLEAC=1;MLEAF=0.500;MQ=59.18;MQ0=0;MQRankSum=0.791;QD=16.86;ReadPosRankSum=-0.769;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:23,23:46:99:804,0,717 -chr1 188013 . T A 834.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.499;DP=51;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.291;QD=16.37;ReadPosRankSum=0.725;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UPSTREAM(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|) GT:AD:DP:GQ:PL 0/1:25,26:51:99:863,0,808 -chr1 188103 . G A 773.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.073;DP=55;Dels=0.00;FS=4.032;HaplotypeScore=2.6641;MLEAC=1;MLEAF=0.500;MQ=59.75;MQ0=0;MQRankSum=0.347;QD=14.07;ReadPosRankSum=0.566;EFF=DOWNSTREAM(MODIFIER||||Cc01g00170|mRNA||GSCOCT00012417001|),DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:30,25:55:99:802,0,993 -chr1 188173 . G A 697.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.617;DP=42;Dels=0.00;FS=2.786;HaplotypeScore=1.9991;MLEAC=1;MLEAF=0.500;MQ=59.09;MQ0=0;MQRankSum=-0.013;QD=16.61;ReadPosRankSum=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:20,22:42:99:726,0,669 -chr1 188266 . A G 878.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:28,27:56:99:907,0,965 -chr1 188270 . A G 850.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,27:54:99:879,0,898 -chr1 188311 . T G 901.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,28:53:99:930,0,831 -chr1 188357 . C T 1327.77 . AC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1356,105,0 -chr1 188364 . G C 578.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:22,18:40:99:607,0,770 -chr1 188393 . T C 515.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:24,18:42:99:544,0,828 -chr1 188395 . C G 543.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:23,18:41:99:572,0,791 -chr1 188416 . T C 397.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:25,14:39:99:426,0,821 -chr1 188438 . C A 930.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:21,29:50:99:959,0,659 -chr1 188621 . G A 704.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856) GT:AD:DP:GQ:PL 0/1:27,22:49:99:733,0,926
--- a/VCFToolsStats/vcfToolsStats.sh Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) - -filein=$1 -fileout_label=$2 -fileout_annot=$3 -fileout_het=$4 -fileout_imiss=$5 -fileout_sum=$6 -filelog=$7 - - - -perl $tool_path/VCFToolsStats.pl --input $filein --out $fileout_label - -cp $fileout_label.annotation $fileout_annot ; rm $fileout_label.annotation -cp $fileout_label.het $fileout_het ; rm $fileout_label.het -cp $fileout_label.imiss $fileout_imiss ; rm $fileout_label.imiss -cp $fileout_label.TsTv.summary $fileout_sum ; rm $fileout_label.TsTv.summary - -cp vcftools.log $filelog -rm vcftools.log
--- a/VCFToolsStats/vcfToolsStats.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,214 +0,0 @@ -<tool id="sniplay_vcftoolsstats" name="VCF tools Stats" version="1.0.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Various statistics from VCF using VCFtools</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - <requirement type="package" version="0.1.13">VCFtools</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="perl"> - vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> - <param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" /> - <data name="fileout_het" format="txt" label="${fileout_label}.het" /> - <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> - <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> - <data name="filelog" format="txt" label="${fileout_label}.log" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> - <param name="filein" value="sample.vcf" /> - <output name="fileout_annot" file="result.annotation" /> - <output name="fileout_het" file="result.het" /> - <output name="fileout_imiss" file="result.imiss" /> - <output name="fileout_sum" file="result.TsTv.summary" /> - <output name="filelog" file="result.log" /> - </test> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** - ---------------------------------------------------- - -.. class:: infomark - -**Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep. - ---------------------------------------------------- - -================ -VCF tools filter -================ - ------------ -Description ------------ - - Compute statistics on VCF file - ------------------ -Workflow position ------------------ - -**Upstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= - - -**Downstream tools** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -=========== ========================== ======= - - ----------- -Input file ----------- - -VCF file - VCF file with all SNPs - ----------- -Parameters ----------- - -Output file basename - Prefix for the output VCF file - ------------- -Output files ------------- - -.annotation file - Statistics on annotation/location along genome - -.het file - Statistics on heterozygosity of the individuals - -.imiss - Statistics on missing data of the inidividuals -.TsTv.summary - Statistics on mutation types and transition/transvertion number - -.log file - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -VCF file ---------- - -:: - - #fileformat=VCFv4.1 - #FILTER=<ID=LowQual,Description="Low quality"> - #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> - [...] - CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 - chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 - - -Parameters -========== - -Output name -> vcf_stat - - -Output files -============ - -.annotation file ----------------- - -:: - - Genic 4489 - Intergenic 466 - ======== - Intron 960 - Exon 3248 - UTR 281 - ======== - Non-syn 226 - Synonym 3022 - -.het file ---------- - -:: - - INDV O(HOM) E(HOM) N_SITES F - CATB1 0 0.0 3616 0.00000 - -.imiss file ------------ - -:: - - INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS - CATB1 4813 0 0 0 - -.TsTv.summary file ------------------- - -:: - - MODEL COUNT - AC 371 - AG 1467 - AT 562 - CG 330 - CT 1659 - GT 397 - Ts 3126 - Tv 1660 - - - </help> - -</tool>
--- a/admixture/Admixture.pl Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,159 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <input HAPMAP> - -o, --output <output> - -k, --kmin <K min. int> - -m, --maxK <K max. int> - -d, --directory <temporary directory> - -p, --path <path to executables> -~; -$usage .= "\n"; - -my ($input,$output,$kmin,$kmax,$directory,$path); - - -GetOptions( - "input=s" => \$input, - "output=s" => \$output, - "kmin=s" => \$kmin, - "maxK=s" => \$kmax, - "directory=s" => \$directory, - "path=s" => \$path -); - - -die $usage - if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path); - -if ($kmin =~/^(\d+)\s*$/){ - $kmin = $1; -} -else{ - die "Error: kmin must be an integer\n"; -} -if ($kmax =~/^(\d+)\s*$/){ - $kmax = $1; -} -else{ - die "Error: kmax must be an integer\n"; -} - - -###################### -# create map file -###################### -open(my $M,">$directory/input.map"); -open(my $H,$input); -<$H>; -while(<$H>) -{ - my @infos = split(/\t/,$_); - print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n"; -} -close($H); -close($M); - -###################### -# create ped file -###################### -system("$path/transpose.awk $input >$directory/input.ped.2"); - -open(my $P,">$directory/input.ped"); -open(my $P2,"$directory/input.ped.2"); -my $n = 0; -my $ind_num = 0; -my @individus; -while(<$P2>) -{ - $n++; - if ($n > 11) - { - my $line = $_; - $line =~s/N/0/g; - if (/^([^\s]+)\s+(.*)$/) - { - $ind_num++; - my $ind = $1; - push(@individus,$ind); - my $genoyping_line = $2; - print $P "$ind $ind_num 0 0 1 2"; - my @genotypes = split(/\s/,$genoyping_line); - foreach my $genotype(@genotypes) - { - $genotype =~s/N/0/g; - my @alleles = split("",$genotype); - print $P " " . join(" ",@alleles); - } - - print $P "\n"; - } - } -} -close($P2); -close($P); - -unlink("$directory/input.ped.2"); - -system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1"); - - -################################### -# launch admixture for different K -################################### -my %errors; -for (my $k = $kmin; $k <= $kmax; $k++) -{ - system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1"); - my $cv_error_line = `grep -h CV $directory/log.$k`; - if ($cv_error_line =~/: (\d+\.*\d*)$/) - { - $errors{$1} = $k; - } - system("cat $directory/log.$k >>$directory/logs"); - system("echo '\n\n====================================\n\n' >>$directory/logs"); - system("cat out.$k.Q >>$directory/outputs.Q"); - system("echo '\n\n====================================\n\n' >>$directory/outputs.Q"); - system("cat out.$k.P >>$directory/outputs.P"); - system("echo '\n\n====================================\n\n' >>$directory/outputs.P"); -} - -my @sorted_errors = sort {$a<=>$b} keys(%errors); -my $best_K = $errors{@sorted_errors[0]}; - - -#system("cp -rf out.$best_K.Q $directory/output"); - -open(BEST1,"out.$best_K.Q"); -open(BEST2,">$directory/output"); -print BEST2 "<Covariate>\n"; -print BEST2 "<Trait>"; -for (my $j=1;$j<=$best_K;$j++) -{ - print BEST2 " Q" . $j; -} -print BEST2 "\n"; -my $i = 0; -while(<BEST1>) -{ - my $line = $_; - $line =~s/ /\t/g; - my $ind = $individus[$i]; - print BEST2 "$ind "; - print BEST2 $line; - $i++; -} -close(BEST1); -close(BEST2); - -system("cp -rf $directory/log.$best_K $directory/log"); - - - -
--- a/admixture/admixture.sh Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -#!/bin/bash -input=$1 -outputs=$2 -logs=$3 -best_k_output=$4 -best_k_logfile=$5 -kmin=$6 -kmax=$7 - -directory=`dirname $0` -mkdir tmpdir$$ -cp -rf $input tmpdir$$/input - -/usr/bin/perl $directory/Admixture.pl -i $input -o $outputs -k $kmin -m $kmax -d tmpdir$$ -p $directory - -mv tmpdir$$/output $best_k_output -mv tmpdir$$/log $best_k_logfile -mv tmpdir$$/outputs.Q $outputs -mv tmpdir$$/logs $logs - -
--- a/admixture/admixture.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -<tool id="admixture" name="Admixture" version="1.23"> - <description>a population structure from large SNP genotype datasets</description> - <requirements> - <requirement type="package" version="1.07">plink</requirement> - <requirement type="package" version="1.23">admixture</requirement> - </requirements> - <command interpreter="bash">./admixture.sh $input $outputs $logs $best_k_output $best_k_logfile $kmin $kmax - </command> - <inputs> - <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> - <param type="text" name="kmin" label="K min" value="1"/> - <param type="text" name="kmax" label="K max" value="5"/> - </inputs> - <outputs> - <data format="txt" name="best_k_output" label="Best K Output"/> - <data format="txt" name="best_k_logfile" label="Best K Logfile"/> - <data format="txt" name="outputs" label="All Outputs"/> - <data format="txt" name="logs" label="All Logs"/> - </outputs> - <help> - - -.. class:: infomark - -**Program encapsulated in Galaxy by Southgreen** - -.. class:: infomark - -**Admixture version 1.23** - ------ - -============== - Please cite: -============== - -"Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. - ------ - -=========== - Overview: -=========== - -ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). - ------ - -For further informations, please visite the Admixture_ website. - - -.. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html - </help> - -</tool>
--- a/admixture/transpose.awk Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#!/usr/bin/gawk -f - -BEGIN { - max_x =0; - max_y =0; -} - -{ - max_y++; - for( i=1; i<=NF; i++ ) - { - if (i>max_x) max_x=i; - A[i,max_y] = $i; - } -} - -END { - for ( x=1; x<=max_x; x++ ) - { - for ( y=1; y<=max_y; y++ ) - { - if ( (x,y) in A ) printf "%s",A[x,y]; - if ( y!=max_y ) printf " "; - } - printf "\n"; - } -}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_gwas_inputs/CheckGWASInputs.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,184 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -h, --hapmap <Hapmap input file> + -t, --trait <Trait input file> + -o, --out <Output base name> +~; +$usage .= "\n"; + +my ($hapmap,$trait,$out); + + +GetOptions( + "trait=s" => \$trait, + "out=s" => \$out, + "hapmap=s" => \$hapmap +); + + +die $usage + if ( !$trait || !$out || !$hapmap); + +my %inds; + +####################################### +# get individuals in trait file +####################################### +my %traits; +my $head_trait = `head -1 $trait`; +open(my $T,$trait); +<$T>; +while(<$T>) +{ + my @infos = split(/\t/,$_); + my $ind = $infos[0]; + $inds{$ind}++; + $traits{$ind} = $_; +} +close($T); +my $nb_ind_trait = scalar keys(%traits); + +####################################### +# get individuals in hapmap file +####################################### +my $line_ind = `head -1 $hapmap`; +chomp($line_ind); +my @infos = split(/\t/,$line_ind); +for (my $i = 11; $i <= $#infos; $i++) +{ + my $ind = $infos[$i]; + $inds{$ind}++; +} +my $nb_ind_hapmap = scalar @infos - 11; + +################################################################# +# create trait output by keeping individuals found in both files +################################################################# +open(my $O,">$out.trait"); +print $O $head_trait; +my $nb_common = 0; +foreach my $ind(keys(%inds)) +{ + my $nb_found = $inds{$ind}; + if ($nb_found == 2) + { + $nb_common++; + print $O $traits{$ind}; + } +} +close($O); + + +##################################################################### +# create hapmap output after keeping individuals found in both files +# and removing monomorphic positions +##################################################################### +open(my $O2,">$out.hapmap"); +my $numline = 0; +my %genotypes; +my %columns_to_keep; +my $nb_monomorphic = 0; +my $not_biallelic = 0; +my $diff_variation = 0; +open(my $H,$hapmap); +while(<$H>) +{ + $numline++; + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @infos = split(/\t/,$line); + if ($numline == 1) + { + my @titles; + for (my $i = 0; $i <= 10; $i++) + { + my $title = $infos[$i]; + push(@titles,$title); + } + print $O2 join("\t",@titles); + for (my $i = 11; $i <= $#infos; $i++) + { + my $ind = $infos[$i]; + my $nb_found = $inds{$ind}; + if ($nb_found == 2) + { + print $O2 " $ind"; + $columns_to_keep{$i} = 1; + } + } + print $O2 "\n"; + } + else + { + my $to_be_printed = ""; + my $variation = $infos[1]; + for (my $i = 0; $i <= 10; $i++) + { + my $title = $infos[$i]; + $to_be_printed .= "$title "; + } + my %letters; + for (my $i = 11; $i <= $#infos; $i++) + { + if ($columns_to_keep{$i}) + { + my $genotype = $infos[$i]; + if ($genotype ne 'NN') + { + my ($allele1,$allele2) = split(//,$genotype); + $letters{$allele1}=1; + $letters{$allele2}=1; + } + $to_be_printed .= "$genotype "; + } + } + chop($to_be_printed); + + my $variation_obs = join("/",sort keys(%letters)); + + # print only if polymorphic + if (scalar keys(%letters) < 2) + { + $nb_monomorphic++; + } + elsif (scalar keys(%letters) > 2) + { + $not_biallelic++; + } + else + { + if ($variation ne $variation_obs) + { + $to_be_printed =~s/$variation/$variation_obs/; + $diff_variation++; + } + + print $O2 $to_be_printed . "\n"; + } + } +} +close($H); +close($O2); + +print "==============================================\n"; +print "Individuals\n"; +print "==============================================\n"; +print "Individuals in hapmap file: $nb_ind_hapmap\n"; +print "Individuals in trait file: $nb_ind_trait\n"; +print "Individuals found in both files: $nb_common\n"; +print "==============================================\n"; +print "Markers\n"; +print "==============================================\n"; +print "Discarded markers:\n"; +print "Monomorphic: $nb_monomorphic\n"; +print "Not biallelic: $not_biallelic\n"; +print "Modified markers:\n"; +print "Difference in variation: $diff_variation\n"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_gwas_inputs/CheckGWASInputs.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,17 @@ +#!/bin/bash +hapmap=$1 +trait=$2 +out_hapmap=$3 +out_trait=$4 +stats=$5 + +directory=`dirname $0` +mkdir tmpdir$$ +#cp -rf $input tmpdir$$/input + +perl $directory/CheckGWASInputs.pl -h $hapmap -t $trait -o tmpdir$$/out >>$stats 2>&1 + +mv tmpdir$$/out.hapmap $out_hapmap +mv tmpdir$$/out.trait $out_trait + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_gwas_inputs/CheckGWASInputs.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,184 @@ +<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0"> + <description>checks concordance between input files for GWAS analysis</description> + <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats + </command> + <inputs> + <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> + <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/> + </inputs> + <outputs> + <data format="txt" name="out_hapmap" label="Hapmap output"/> + <data format="txt" name="out_trait" label="Trait output"/> + <data format="txt" name="stats" label="Logfile and statistics"/> + </outputs> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + <![CDATA[ + + +.. class:: infomark + +**Authors** South Green + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** South Green. + +--------------------------------------------------- + + +=============== +CheckGWASInputs +=============== + +----------- +Description +----------- + + | CheckGWASInputs checks concordance between input files for GWAS analysis. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Hapmap file hapmap +=============== ====================== =========== + + + + +---------- +Input file +---------- + +Hapmap file + Allelic file in Hapmap format + +Trait file + Phenotypic file + +------------ +Output files +------------ + +Hapmap output + +Trait output + +Logfile and statistics + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA + +Trait file +---------- + +:: + + <Trait> Test + Ind1 -2.9985936006411 + Ind2 -2.68669426456267 + +Output files +============ + +Hapmap output +------------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT + + +Trait output +------------ + +:: + + <Trait> Test + Ind429 -26.2142525264157 + Ind373 12.0306115988504 + Ind81 1.98118654229534 + +Logfile and statistics +---------------------- + +:: + + + ============================================== + Individuals + ============================================== + Individuals in hapmap file: 500 + Individuals in trait file: 500 + Individuals found in both files: 500 + ============================================== + Markers + ============================================== + Discarded markers: + Monomorphic: 0 + Not biallelic: 0 + Modified markers: + Difference in variation: 0 + + ]]> + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/CalculateDiversityIndexes.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,81 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; +use Bio::SeqIO; + + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <FASTA input> + -o, --output <output filename> + -d, --directory <directory of egglib package> +~; +$usage .= "\n"; + +my ($infile,$outfile,$dir_exe); + + +GetOptions( + "input=s" => \$infile, + "output=s" => \$outfile, + "directory=s"=> \$dir_exe +); + + +die $usage + if ( !$infile || !$outfile || !$dir_exe); + + +my $EGGSTATS_EXE = "$dir_exe/egglib-2.1.5/bin/eggstats"; + +my %gene_alignments; +my $in = Bio::SeqIO->new(-file => $infile , '-format' => 'Fasta'); +while ( my $seq = $in->next_seq() ) +{ + my $id = $seq -> id(); + my $sequence = $seq -> seq(); + my ($gene,$ind,$num_allele) = split("_",$id); + $gene_alignments{$gene}.= ">$id\n$sequence\n"; +} + +open(OUT,">$outfile"); +foreach my $gene(keys(%gene_alignments)) +{ + open(F,">$gene.egglib_input.fa"); + print F $gene_alignments{$gene}; + close(F); + + my $results_egglib = `$EGGSTATS_EXE $gene.egglib_input.fa`; + + # parse Seqlib output + if ($results_egglib) + { + my %egglig_stats; + my @eggstats = split(/^/,$results_egglib); + foreach my $eggstat(@eggstats) + { + my ($desc,$value) = split(/: /,$eggstat); + chomp($value); + $egglig_stats{$desc} = $value; + } + print OUT "$gene;"; + print OUT $egglig_stats{"Total number of sequences"} . ";"; + print OUT $egglig_stats{"Total number of sites"} . ";"; + print OUT $egglig_stats{"Number of analyzed sites"} . ";"; + print OUT $egglig_stats{"S"} . ";"; + print OUT $egglig_stats{"thetaW"} . ";"; + print OUT $egglig_stats{"Pi"} . ";"; + print OUT $egglig_stats{"D"} . ";"; + print OUT $egglig_stats{"number of haplotypes"} . ";"; + print OUT $egglig_stats{"haplotypes diversity"} . ";"; + print OUT $egglig_stats{"Fay and Wu H"} . ";"; + print OUT $egglig_stats{"Fst"} . ";"; + print OUT $egglig_stats{"Snn"} . ";"; + print OUT "\n"; + unlink("$gene.egglib_input.fa"); + } +} +close(OUT); +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/CalculateDiversityIndexes.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,11 @@ +#!/bin/bash +input=$1 +output=$2 +log=$3 + +directory=`dirname $0` + +perl $directory/CalculateDiversityIndexes.pl -i $input -o $output -d $directory >>$log 2>&1 + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/CalculateDiversityIndexes.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,175 @@ +<tool id="calculate_diversity" name="Diversity by gene" version="2.1.6"> + <description>calculates various diversity indexes with EggLib.</description> + <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/> + </inputs> + <outputs> + <data format="txt" name="output" label="Diversity"/> + <data format="txt" name="log" label="Logfile"/> + </outputs> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + + +.. class:: infomark + +**Authors** EggLib_ + +.. _EggLib: http://egglib.sourceforge.net/ + + | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27. + +.. class:: infomark + +**Galaxy integration** South Green. + +.. class:: infomark + +**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +--------------------------------------------------- + + + +================== +Diversity by genes +================== + +----------- +Description +----------- + + | Provides various diversity indexes using EggLib library. + | For further informations, please visite the EggLib website_. + +.. _website: http://egglib.sourceforge.net/ + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Fasta alignment fasta +=============== ====================== =========== + + + +---------- +Input file +---------- + +Fasta file + Fasta alignment + + + +------------ +Output files +------------ + +Diversity + +Log file + + +------------ +Dependencies +------------ +EggLib + version 2.1.5 + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Fasta file +---------- + +:: + + >LOCOs11g09160_AZUCENA_1 + ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA + CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG + GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT + GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA + TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC + >LOCOs11g09160_AZUCENA_2 + ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA + CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG + GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT + GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA + TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC + >LOCOs11g09160_BULUPANDAK_1 + ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA + CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG + GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT + GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA + TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC + >LOCOs11g09160_BULUPANDAK_2 + ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA + CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG + GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT + GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA + TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC + >LOCOs07g23169_AZUCENA_1 + ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA + GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA + TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC + +Output files +============ + +Diversity +--------- + +:: + + LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1; + LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1; + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,378 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_ALIGN_HPP +#define EGGLIB_ALIGN_HPP + +#include "Container.hpp" +#include "CharMatrix.hpp" +#include <vector> + +/** \mainpage Summary + * + * This is the automatically-generated reference manual of the C++ + * egglib-cpp library. The library is presented as several modules, but + * note that they are only used to structure the documentation. + * + * There is a single namespace (egglib) in which all classes are + * defined. See an example of programming with egglib-cpp in the + * EggLib package main documentation. Use "Modules" or "Classes" above + * to navigate in the library reference manual. + * + */ + + +/** \defgroup core core + * + * \brief Central core of the C++ library of Egglib + * + * Data storage classes, parsers/formatters and tools, plus exception + * types. + * + */ + +namespace egglib { + + + /** \brief Handles a sequence alignment + * + * \ingroup core + * + * Creation from a file or string stream should be performed using + * the class Fasta. Align objects can be created by deep copy from + * both Align and Container type. In the latter case, the length are + * artificially equalized by "?" characters. Align objects can be + * created from a DataMatrix object (and all the way arround) using + * the specific class DMAConverter. + * + * Sequences are represented by two strings (name and sequence) and + * an integer (group) that can be accessed or modified by index.The + * order of sequences is guaranteed to be conserved, as if Align was + * a list of triplets (name, sequence, group). + * + * The data matrix is implemented as continuous array (char**) and + * allows efficient access and modification of data. For very large + * data matrices you might claim immediately the required memory + * using the constructor Align(unsigned int, char**). + * + */ + class Align : public Container, public CharMatrix { + public: + + /** \brief Creates an empty alignment + * + */ + Align(); + + + /** \brief Creates an alignment from a data matrix. + * + * Allows you to create an object from data stored in a char* + * array. The array's dimensions must be passed to the + * constructor, and as a result there is not need to + * terminate each sequence by a NULL character. + * + * \param number_of_sequences the number of sequences (the + * length of the first dimension of the array). + * + * \param alignment_length the length of sequences (the + * length of all lines of the array). + * + * \param cstring_array the pointer to the data matrix. + * + */ + Align(unsigned int number_of_sequences, unsigned int alignment_length, char const * const * const cstring_array); + + + /** \brief Creates an alignment with given dimensions + * + * Allows you to allocate directly a data matrix of a given + * size. Names are empty strings, groups 0, and all + * characters are ?. + * + * \param number_of_sequences the number of sequences (the + * length of the first dimension of the array). + * + * \param alignment_length the length of sequences (the + * length of all lines of the array). + * + */ + Align(unsigned int number_of_sequences, unsigned int alignment_length); + + + /** \brief Copy constructor + * + */ + Align(const Align& align); + + + /** \brief Copy constructor accepting a Container object + * + * All but the longest sequences are padded with ? to match + * the longest sequence's length. + * + */ + Align(const Container& container); + + + /** \brief Copy operator + * + */ + Align& operator=(const Align& align); + + + /** \brief Copy operator accepting a Container object + * + * All but the longest sequences are padded with ? to match + * the longest sequence's length. + * + */ + Align& operator=(const Container& container); + + + /** \brief Destructor + * + */ + virtual ~Align(); + + + /** \brief Adds a sequence + * + * If the object already contains at least one sequence, the + * new sequence must have the same length. Otherwise, a + * EggUnalignedError is raised. + * + * \param name the name of the sequence. + * \param sequence the sequence string. + * \param group the group index of the sequence. + * \return The new number of sequences. + * + */ + virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0); + + + /** \brief Removes a position (column) of the alignment + * + * \param pos the position to remove in the alignment. + * \return The new length of the alignment. + * + */ + virtual unsigned int removePosition(unsigned int pos); + + + /** \brief Removes a sequence from the alignment + * + * \param pos the index of the sequence to remove. + * \return The new number of sequences. + * + */ + virtual unsigned int remove(unsigned int pos); + + + /** \brief Replace a sequence string + * + * The new sequence must have the same length than the + * alignment. Otherwise, a EggUnalignedError is raised. + * + * \param seq the index of the sequence to change. + * \param sequence the new sequence. + * + */ + virtual void sequence(unsigned int seq, const char* sequence); + + + /** \brief Gets the name of a given sequence + * + * \param pos the index of the sequence. + * + * \return The sequence string for that particular sequence. + * + */ + virtual inline const char* sequence(unsigned int pos) const { return Container::sequence(pos); } + + + /** \brief Alignment length + * + * Returns 0 if the alignment is empty. + * + */ + virtual unsigned int ls() const; + + + /** \brief Length of a given sequence + * + * Calling this function is exactly the same as calling ls() + * (without arguments), regardless of the index provided, + * except that an exception is thrown if the index is out of + * bounds. Provided for compatibility with Container. + * + * \param pos the index of the sequence. + * \return the length of the alignment. + * + */ + virtual unsigned int ls(unsigned int pos) const; + + + /** \brief Fast and unsecure accessor + * + * This accessor doesn't perform out-of-bound checking! + * + * \param s the index of the sequence (line). + * \param p the position in the alignment (column). + * \return The character at the given position. + * + */ + inline char character(unsigned int s, unsigned int p) const { return sequences[s][p]; } + + + /** \brief Gets a nucleotide + * + * This modifier does perform out-of-bound checking. + * The specified position must exist. + * + * \param sequence the index of the sequence (line). + * \param position the position in the alignment (column). + * \return the character at the given position. + * + */ + virtual char get(unsigned int sequence, unsigned int position) const; + + + /** \brief Sets a matrix position to a new character + * + * This modifier does perform out-of-bound checking. + * The specified position must exist. + * + * \param sequence the index of the sequence (line). + * \param position the position in the alignment (column). + * \param ch the new character value. + */ + virtual void set(unsigned int sequence, unsigned position, char ch); + + + /** \brief Reverse a given column in binary data + * + * The specified column must contain only "0" ans "1" characters. + * "0" is replaced by "1" and all the way around + * + */ + void binSwitch(unsigned int pos); + + + /** \brief Extracts specified positions (columns) of the alignment + * + * All the specified sites are extracted in the specified + * order. This function is suitable for bootstrap (resample + * allowing redrawing the same site) and permutations. + * + * This function doesn't perform out-of-bound checking. + * + * \param list_of_sites a vector containing alignment + * positions. + * + * \return A copy of the object containing the specified + * set of positions. + * + */ + Align vslice(std::vector<unsigned int> list_of_sites); + + + /** \brief Extracts a range of positions (columns) + * + * \param a the first position. + * + * \param b the index immediately passed the last sequence to + * extract. + * + * \return A copy of the object containing the specified + * range of sequences. + * + * Positions a to b-1 are extracted, provided that the + * indices fit in the current length of sequences. To extract + * all sequences, use align.vslice(0, align.ls()). + * + * Note: invalid ranges will be silently supported. If + * a>=ls or b<=a, an empty object is returned. If b>ns, + * ls will be substituted to a. + */ + Align vslice(unsigned int a, unsigned int b); + + + /** \brief Deletes all the content of the object + * + */ + virtual void clear(); + + + /** \brief Same as ns() + * + */ + inline unsigned int numberOfSequences() const { + return _ns; + } + + + /** \brief Same as ls() + * + */ + inline unsigned int numberOfSites() const { + return _ls; + } + + + /** \brief Gets a group label (insecure) + * + */ + inline unsigned int populationLabel(unsigned int sequenceIndex) const { + return groups[sequenceIndex]; + } + + + /** \brief Just return the passed value + * + */ + inline double sitePosition(unsigned int position) const { + return (double) position; + } + + + protected: + + /// This function is not available for alignments + virtual void appendSequence(unsigned int pos, const char* sequence) {} + + // Initializer (creates a valid empty alignment) + virtual void init(); + + // Makes a deep copy of the specified data matrix - if cstring_array is NULL, then ignores it and pads with ?'s + virtual void setFromSource(unsigned int number_of_sequences, unsigned int alignment_length, const char* const * const cstring_array); + + // Copies from a Container + virtual void copyObject(const Container&); + + // Copies from an Align + virtual void copyObject(const Align&); + + // Alignment length + unsigned int _ls; + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,300 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_ARG_HPP +#define EGGLIB_ARG_HPP + + +#include "Current.hpp" +#include "Edge.hpp" +#include <string> + + +/** \defgroup coalesce coalesce + * + * \brief Coalescent simulator + * + * The set of classes implements a three-scale coalescent simulator with + * recombination, and a flexible mutation model. The main classes are + * Controller (the starting point for generating genealogies), ParamSet + * (that centralizes parameter specification), the Change hierarchy + * (that implements demographic change specifications), Arg (ancestral + * recombination graph; the result of generation a genealogy) and + * Mutator (that generates genotype data from an ARG). + * + */ + + +namespace egglib { + + class Random; + + /** \brief Ancestral recombination graph + * + * \ingroup coalesce + * + * This class stores the ARG (genealogical information). It is + * progressively built by appropriate (especially regarding to the + * timing) calls to coal() and recomb() methods. Then it can be + * used by a mutator class to generates data, or it can also + * generate newick trees (one tree by non-recombining segment). + * + */ + class Arg { + + public: + + /** \brief Default constructor + * + * Creates a null, useless, object. + * + */ + Arg(); + + + /** \brief Object initialization + * + * \param current address of the Current instance used by + * the simulator. + * + * \param numberOfSegments number of recombining segments. + * + */ + void set(Current* current, unsigned int numberOfSegments); + + + /** \brief Object reset method + * + * This method doesn't reset all parameters (the number of + * segments and associated tables are retained, as well as + * the Edge object pool). + * + * \param current address of the Current instance used by + * the simulator. + * + */ + void reset(Current* current); + + + /** \brief Standard constructor + * + * \param current address of the Current instance used by + * the simulator. + * + * \param numberOfSegments number of recombining segments + * + */ + Arg(Current* current, unsigned int numberOfSegments); + + + /** \brief Destructor + * + * Clears all Edge instances referenced in the object. + * + */ + virtual ~Arg(); + + + /** \brief Gets the current value of the time counter + * + */ + double time() const; + + + /** \brief Increments the time counter + * + */ + void addTime(double increment); + + + /** \brief Performs a coalescence event + * + * For this version, the two lineages to coalesce are + * predefined. + * + * \param incr increment of the time counter. + * \param pop index of the population. + * \param index1 first lineage to coalesce. + * \param index2 second lineage to coalesce. + * + */ + void coalescence(double incr, unsigned int pop, unsigned int index1, unsigned int index2); + + + /** \brief Performs a coalescence event + * + * For this version, the two lineages to coalesce are + * randomly picked in the given population + * + * \param incr increment of the time counter. + * \param pop index of the population. + * \param random pointer to simulator's random generator + * instance. + * + */ + void coalescence(double incr, unsigned int pop, Random* random); + + + /** \brief Performs a recombination event + * + * \param incr increment of the time counter. + * \param random pointer to simulator's random generator + * instance. + * + */ + void recombination(double incr, Random* random); + + + /** \brief Places a mutation + * + * \param segment index of the segment affected. + * + * \param treePosition a random number placed on the + * interval defined by the tree length at this position. + * + * \return the concerned Edge's address. + * + * \todo why this is not encapsulated? + * + * Another nerve-taking point: calling this method assume + * that all Edge of have previously undergone a call of + * branchLength(position) with intervalPosition - what + * should be done by the called (that is, Mutator) through + * my (Arg's) treeLength of something. BEWARE WHEN MODIFYING + * (enhancements should be directed to Edge in my view) + * + */ + Edge* mute(unsigned int segment, double treePosition); + + + /** \brief Age of the uMRCA + * + * The uMRCA is the ultimate Most Recent Common Ancestor, + * that is the point where the last segment finds its most + * recent common ancestor. This member will have a meaningful + * value only if the coalescent process is completed. + * + */ + inline double ageUltimateMRCA() const { + return _time; + } + + + /** \brief Age of the MRCA for a given segment + * + * The MRCA is the Most Recent Common Ancestor, that is the + * point where the coalescent process is over (all lineages + * have coalesced). This member will have a meaningful + * value only if the coalescent process is completed. + * + * Note that the value is cached; it is computed only one + * upon first call and no again, even if the Arg is modified< + * + */ + inline double ageMRCA(unsigned int segmentIndex) { + return _MRCA[segmentIndex]->bottom; + } + + /** \brief MRCA for each segment + * + * The MRCA is the Most Recent Common Ancestor, that is the + * point where the coalescent process is over (all lineages + * have coalesced). This member will have a meaningful + * value only if the coalescent process is completed. + * + * Note that the value is cached; it is computed only one + * upon first call and no again, even if the Arg is modified + * + */ + inline const Edge* MRCA(unsigned int segmentIndex) { + return _MRCA[segmentIndex]; + } + + /// Ultimate MRCA + + inline const Edge* uMRCA() { + return edges[numberOfEdges-1]; + } + + + /// the number of recombining segments + unsigned int numberOfSegments; + + /** \brief Formats the newick-formatted tree for a segment + * + */ + std::string newick(unsigned int segment); + + + /// Number of initial lineages + unsigned int numberOfSamples; + + + /** \brief Total tree length (summed over all segments) + * + */ + double totalLength; + + /** \brief Segment-specific tree length + * + */ + double* segmentLengths; + + /// Current number of Edges in the tree (including the MRCA node) + unsigned int numberOfEdges; + + /// Total number of recombination events that occurred + unsigned int numberOfRecombinationEvents; + + /// Set the number of actual sites in all branches + void set_actualNumberOfSites(unsigned int actualNumberOfSites); + + + private: + + /// Copy constructor not available + Arg(const Arg&) { } + + /// Assignment operator not available + Arg& operator=(const Arg&) { return *this; } + + void init_stable_parameters(); + void init_variable_parameters(); + void clear(); + void addEdge(Edge*); + std::string rnewick(Edge* edge, unsigned int segment, double cache); + + Current* current; + double _time; + Edge** edges; + + void findMRCA(unsigned int segmentIndex); + void computeTotalLength(); + void computeSegmentLength(unsigned int segmentIndex); + + unsigned int* numberOfEdgesPerSegment; + Edge** _MRCA; + + EdgePool edgePool; + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/BaseDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,169 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_BASEDIVERSITY_HPP +#define EGGLIB_BASEDIVERSITY_HPP + +#include "CharMatrix.hpp" +#include "SitePolymorphism.hpp" +#include <string> + +/** \defgroup polymorphism polymorphism + * + * \brief Diversity analyses + * + * Two classes are contained in this module: NucleotideDiversity, that + * performs site-centered polymorphism analyses, and HaplotypeDiversity, + * that performs haplotype-centered analyses. The detection of + * polymorphic sites is common to both, through the base class + * BaseDiversity. However this phase must be repeated when stats from + * the two classes are needed. To reduce the computational burden, the + * function reserve() can be use, that directly allocates needed memory + * when the eventual number of polymorphic sites is known prior to + * analysis (even if not precisely). For both classes, a set of + * statistics are computed immediately upon load of a data set. For + * NucleotideDiversity, additional statistics are computed per group + * upon use of the corresponding accessors. This number of operations + * performed several times is strictly limited. This is particularly + * useful when different statistics are needed for a given alignment. + * However, this system allows not computing unnecessary statistics to + * a certain extend. + * + */ + +namespace egglib { + + /** \brief Base class of diversity classes + * + * Mutualizes the analysis of polymorphic sites through the method + * importSites() and related accessors. + * + * \ingroup polymorphism + * + */ + class BaseDiversity { + + public: + + /** \brief Constructor + * + */ + BaseDiversity(); + + /** \brief Destructor + * + */ + virtual ~BaseDiversity(); + + /** \brief Reserve sufficient memory for a given number of + * polymorphic sites. + * + * This method makes importSite function faster when you + * already know how many polymorphic sites to expect, since + * the necessary memory will be allocated prior the screening + * of data. It is possible to use reserve() even if with a + * number of sites that is not matching what importSites() + * will find. + * + * \param numberOfSites a strictly positive integer. + * + */ + virtual void reserve(unsigned int numberOfSites); + + /// Gets a site + const SitePolymorphism* get_site(unsigned int index) const; + + /// Gets a site position + unsigned int get_position(unsigned int index) const; + + /** \brief Predefined mapping string for DNA data + * + */ + static const std::string dnaMapping; + + + /** \brief Predefined mapping string for RNA data + * + */ + static const std::string rnaMapping; + + + /** \brief Predefined mapping string for amino acid data + * + */ + static const std::string aaMapping; + + + /// Clears and re-initializes object + virtual void reset(); + + + protected: + + virtual void init(); + virtual void clear(); + + // + void importSites(CharMatrix& data, bool allowMultipleMutations, + double minimumExploitableData, unsigned int ignoreFrequency, + std::string characterMapping, bool useZeroAsAncestral, + bool ignoreOutgroup); + + // + void analyzeSite(CharMatrix& data, unsigned int index, double maxMissingData, bool ignoreOutgroup); // analyzes a site, adds a Site to the Site container if the site is polymorphic + unsigned int getPopIndex(unsigned int label) const; // returns v_npop if not found + + SitePolymorphism** v_sites; // holder of polymorphic site addresses + bool* v_orientables; // stores whether the sites are orientable or not + unsigned int* v_sitePositions; // stores position of sites + + unsigned int v_reserved; + unsigned int v_ns; // maximum number of sequences analyzed (max of sites' ns) + unsigned int v_S; // number of polymorphic sites + unsigned int v_So; // number of orientable sites + unsigned int v_eta; // number of mutation (whatever multiple) + double v_nseff; // average number of analyzed sequence + unsigned int v_lseff; // number of analyzed sites + double v_nseffo; // average number of analyzed sequences for analyzes with outgroup + unsigned int v_lseffo; // number of analyzed sites for analyzes with outgroup + unsigned int v_npop; // number of populations + unsigned int *v_popLabel; // label of each pop + + // options + bool p_allowMultipleMutations; + double p_minimumExploitableData; + std::string p_characterMapping; + unsigned int p_pos_sep_mapping; + bool p_useZeroAsAncestral; + unsigned int p_ignoreFrequency; + + + + private: + + BaseDiversity(const BaseDiversity& source) { } + + BaseDiversity& operator=(const BaseDiversity& source) { + return *this; + } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,428 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_CHANGETYPES_HPP +#define EGGLIB_CHANGETYPES_HPP + +#include "ParamSet.hpp" +#include "Controller.hpp" + +namespace egglib { + +/**********************************************************************/ + + /** \brief Pure virtual base class for parameter changes + * + * \ingroup coalesce + * + */ + class Change { + public: + + /** \brief Default constructor + * + * The default date is 0. + * + */ + Change(); + + /** \brief Standard constructor + * + * \param date the event date. + * + */ + Change(double date); + + /// Gets the event date value + double date() const; + + /// Sets the event date value + void date(double value); + + /** \brief Applies the event + * + * \param paramSet the ParamSet instance to which the Change + * instance is attached. + * \param controller the Controller instance of the + * simulation. + * + */ + virtual void apply(ParamSet* paramSet, Controller* controller) const = 0; + + protected: + double _date; + + }; + +/**********************************************************************/ + + /** \brief Pure virtual base class for single parameter changes + * + * \ingroup coalesce + * + */ + class SingleParamChange : public Change { + public: + + /** \brief Default constructor + * + * The default date is 0., the default parameter value is 0. + * + */ + SingleParamChange(); + + /** \brief Standard constructor + * + * \param date the event date. + * \param value the parameter value. + * + */ + SingleParamChange(double date, double value); + + /// Gets the parameter value + double value() const; + + /// Sets the parameter value + void value(double value); + + protected: + double _value; + + }; + +/**********************************************************************/ + + /** \brief Single parameter changes applied to a single population + * + * \ingroup coalesce + * + */ + class PopulationParamChange : public SingleParamChange { + public: + + /** \brief Default constructor + * + * The default date is 0., the default parameter value is 0., + * the default population is 0 + * + */ + PopulationParamChange(); + + /** \brief Standard constructor + * + * \param date the event date. + * \param population the population index. + * \param value the parameter value. + * + */ + PopulationParamChange(double date, unsigned int population, double value); + + /// Gets the population index + unsigned int population() const; + + /// Sets the population index + void population(unsigned int value); + + protected: + + unsigned int _population; + + }; + + +/**********************************************************************/ + + /** \brief Bottleneck event + * + * \ingroup coalesce + * + * The bottleneck parameter is its strength, corresponding to an + * amount of time where time is locked and only coalescences are + * allowed (resulting in a given - and random - number of + * instantaneous coalescence with branches). + * + */ + class Bottleneck : public SingleParamChange { + public: + Bottleneck(double date, double param) : SingleParamChange(date, param) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + +/**********************************************************************/ + + /** \brief Population-specific bottleneck event + * + * \ingroup coalesce + * + */ + class PopulationBottleneck : public PopulationParamChange { + public: + PopulationBottleneck(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + + +/**********************************************************************/ + + /** \brief Change of the size of all populations + * + * The parameter is the new size (applied to all populations) + * + * \ingroup coalesce + * + */ + class AllPopulationSizeChange : public SingleParamChange { + public: + AllPopulationSizeChange(double date, double value) : SingleParamChange(date, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + + +/**********************************************************************/ + + /** \brief Change of a single population size + * + * \ingroup coalesce + * + */ + class SinglePopulationSizeChange : public PopulationParamChange { + public: + SinglePopulationSizeChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + + + +/**********************************************************************/ + + /** \brief Change of the growth rate of all populations + * + * The parameter is the new rate (applied to all populations) + * + * \ingroup coalesce + * + */ + class GrowthRateChange : public SingleParamChange { + public: + GrowthRateChange(double date, double value) : SingleParamChange(date, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + + +/**********************************************************************/ + + /** \brief Change of a single population's growth rate + * + * \ingroup coalesce + * + */ + class PopulationGrowthRateChange : public PopulationParamChange { + public: + PopulationGrowthRateChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + +/**********************************************************************/ + + /** \brief Change of the selfing rate + * + * The parameter is the new rate + * + * \ingroup coalesce + * + */ + class SelfingRateChange : public SingleParamChange { + public: + SelfingRateChange(double date, double value) : SingleParamChange(date, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + +/**********************************************************************/ + + /** \brief Fusion of two populations + * + * \ingroup coalesce + * + */ + class PopulationFusion : public Change { + public: + /** \brief Default constructor + * + * The default date is 0., the default mother is 0, the + * default daughter is 0. + * + */ + PopulationFusion(); + + /** \brief Standard constructor + * + * \param date the date of the event. + * \param mother first population to merge. + * \param daughter second population to merge. + * + * A time date, all the lineages from the daughter population + * are moved to the mother population and all mutation rates + * to the daughter population are cancelled. This functions + * emulates a population split (forward in time). + * + */ + PopulationFusion(double date, unsigned int mother, unsigned int daughter); + + void apply(ParamSet* paramSet, Controller* controller) const; + + /// Sets the daughter population + void daughter(unsigned int); + + /// Gets the daughter population + unsigned int daughter() const; + + /// Sets the mother population + void mother(unsigned int); + + /// Gets the mother population + unsigned int mother() const; + + protected: + unsigned int _mother; + unsigned int _daughter; + }; + + +/**********************************************************************/ + + /** \brief Split of a population + * + * \ingroup coalesce + * + */ + class PopulationSplit : public Change { + public: + /** \brief Default constructor + * + * The default date is 0., the default population is 0, the + * default probability is 0.5. + * + */ + PopulationSplit(); + + /** \brief Standard constructor + * + * A the time given by date, the specified population is + * split in two. An additional population (whose index is + * incremented from the current total number of population) + * is created and lineages are randomly picked and moved to + * the new population. The parameter proba gives the + * probability that a lineage from the population number pop + * moves instantly to the new population. If proba is 0, + * the program emulates the creation of an empty population + * (thinking forward in time, this is a population + * extinction). In general, forward in time, this is a + * population fusion. + * + * \param date the date of the event. + * \param pop population index. + * \param proba the probability that lineages move to the + * new population. + * + */ + PopulationSplit(double date, unsigned int pop, double proba); + + void apply(ParamSet* paramSet, Controller* controller) const; + + /// Gets the population index + unsigned int population() const; + + /// Sets the population index + void population(unsigned int); + + /// Gets the probability of instant migration + double probability() const; + + /// Sets the probability of instant migration + void probability(double); + + protected: + unsigned int _population; + double _probability; + }; + +/**********************************************************************/ + + /** \brief Change of the migration rate of all population pairs + * + * The parameter is the new rate (applied to all population pairs) + * + * \ingroup coalesce + * + */ + class AllMigrationRateChange : public SingleParamChange { + public: + AllMigrationRateChange(double date, double value) : SingleParamChange(date, value) {} + void apply(ParamSet* paramSet, Controller* controller) const; + }; + +/**********************************************************************/ + + /** \brief Change of a single migration rate + * + * \ingroup coalesce + * + */ + class SingleMigrationRateChange : public SingleParamChange { + public: + /** \brief Default constructor + * + * The default date is 0., the default parameter value is 0., + * the default source population is 0, the default + * destination population 1. + * + */ + SingleMigrationRateChange(); + + /** \brief Standard constructor + * + * \param date the date of the event. + * \param source index of the source population. + * \param dest index of the destination population. + * \param migr new value of the pairwise migration rate. + * + */ + SingleMigrationRateChange(double date, unsigned int source, unsigned int dest, double migr); + + /// Gets the source population index + unsigned source() const; + + /// Sets the source population index + void source(unsigned int); + + /// Gets the dest population index + unsigned dest() const; + + /// Sets the dest population index + void dest(unsigned int); + + void apply(ParamSet* paramSet, Controller* controller) const; + + protected: + unsigned int _source; + unsigned int _dest; + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,70 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_CHARMATRIX_HPP +#define EGGLIB_CHARMATRIX_HPP + + +namespace egglib { + + /** \brief Interface for classes usable as a square matrix of characters + * + * \ingroup core + * + */ + class CharMatrix { + + public: + + /** \brief Gets number of rows or sequences + * + */ + virtual unsigned int numberOfSequences() const = 0; + + + /** \brief Gets number of columns or sites + * + */ + virtual unsigned int numberOfSites() const = 0; + + + /** \brief Gets the character at a given position + * + * The accessor should be "fast" and does not guarantee to + * perform out-of-bounds checks + * + */ + virtual char character(unsigned int sequence, unsigned int site) const = 0; + + + /** \brief Gets population index + * + */ + virtual unsigned int populationLabel(unsigned int row) const = 0; + + + /** \brief Get site position + * + */ + virtual double sitePosition(unsigned int column) const = 0; + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Consensus.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,421 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_CONSENSUS_HPP +#define EGGLIB_CONSENSUS_HPP + +#include "Align.hpp" +#include <sstream> +#include <string> +#include <vector> + +namespace egglib { + + /** \brief Generates consensus sequences + * + * \ingroup polymorphism + * + * + * A consensus is generated when two sequences have the same name, + * ignoring everything after the first separator character (by + * default, "_"). Hence, the names "foo", "foo_goo" and "foo_third" + * will be treated as identical and the root will be "foo". The root + * will be used to name the resulting sequence. Note that the + * class works only for DNA sequences. + * + * Symbol convention: + * - A: adenosine + * - C: cytosine + * - G: guanine + * - T: thymine + * - M: A or C + * - R: A or G + * - W: A or T (weak) + * - S: C or G (strong) + * - Y: C or T + * - K: G or T + * - B: C or G or T(not A) + * - D: A or G or T (not C) + * - H: A or C or T (not G) + * - V: A or C or G (not T) + * - N: A or C or G or T + * - ?: nonsequenced position + * + * Other symbols will be treated as ? (lowercase are supported). + * + * Rigorous (alias liberal or strong) mode: + * - If two characters are the same, it is retained whatever it is + * (A + A = A) + * - Otherwise: + * - If one is the missing character (?) the other is retained + * whatever it is (A + ? = A). + * - If characters are consistent, that is one contains + * more information, that one is retained (A + M = A). + * - If characters are not consistent, the closest + * generic symbol is retained (A + C = M). + * . + * Note that the feedback of inconsistent characters in the + * outcome is not garanteed. + * In fact, (A + A + G) will result in R (as expected) but (A + + * G + A) will result in A, masking the problem. + * However, the position will indeed be counted as inconsistent. + * + * Not rigorous (conservative/weak) mode: + * - If two characters are the same, it is retained whatever it + * is (A + A = A). + * - Otherwise: + * - If one is ? the other is retained whatever it is (A + ? + * = A). + * - Otherwise an inconsistent character (by default, Z) is + * retained (A + C = Z). + * + * Iterative process of consensus: + * - Each sequence is taken in turn. + * - Each pair involving the focus sequence is processed and a + * consensus is generated. + * - When all pair have been processsed, the consensus already + * generated are themselves iteratively processed until only one + * remains. + * - Note that at each time the last two are taken first. + * + * A transparent interface gives access to the data for all steps of + * the consensus process, as vectors that covers all pairs (including + * intermediate steps of the iterative procedure described above) as + * well as singleton sequences. For the latter, the second name is + * not filled and all counts are set to 0. Note also that the name of + * such singleton sequence is shortened to the separator as well. + * + */ + class Consensus { + public: + /** \brief Constructor + * + */ + Consensus(); + + /** \brief Destructor + * + */ + virtual ~Consensus() {} + + /// Sets the character interpreted as missing (default: ?) + void setMissing(char); + + /// Sets the character used to point to disagreements (default: Z) + void setDisagreement(char); + + /// Checks all the characters + bool check_sequences(Align& align); + + /** \brief Reduces the sequence alignment by making consensus sequences + * + * \param align the original alignment. + * + * \param separator the character used to separated the root + * name of sequences to the variable part, as in (for the + * default value: "sequence_read1". + * + * \param rigorous consensus mode. + * + * \return An Align instance with duplicated sequences consensed. + * + */ + Align consensus(Align& align, char separator='_', bool rigorous=true); + + /// First name of consensed pairs + const std::vector<std::string>& firstSequenceNames(); + + /// Second names of consensed pairs + const std::vector<std::string>& secondSequenceNames(); + + /// Root names of consensed pairs + const std::vector<std::string>& roots(); + + /// Number of consistent positions for all consensed pairs + const std::vector<int>& consistentPositions(); + + /// Number of complementary positions for all consensed pairs + const std::vector<int>& complementaryPositions(); + + /// Number of uninformative positions for all consensed pairs + const std::vector<int>& uninformativePositions(); + + /// Number of ambiguous positions for all consensed pairs + const std::vector<int>& ambiguousPositions(); + + /// Number of at least partially resolved ambiguities for all consensed pairs + const std::vector<int>& atLeastPartiallyResolvedAmbiguities(); + + /// Vector of inconsistent positions ofr all consensed pairs + const std::vector<std::vector<int> >& inconsistentPositions(); + + + private: + + /** \brief Copying this class is not allowed + * + */ + Consensus(const Consensus& source) { } + + /** \brief Copying this class is not allowed + * + */ + Consensus& operator=(const Consensus& source) { return *this; } + + // A private helper + class PairwiseConsensus; + + // report data + std::vector<std::string> t_firstSequenceNames; + std::vector<std::string> t_secondSequenceNames; + std::vector<std::string> t_roots; + std::vector<int> t_consistentPositions; + std::vector<int> t_complementaryPositions; + std::vector<int> t_uninformativePositions; + std::vector<int> t_ambiguousPositions; + std::vector<int> t_atLeastPartiallyResolvedAmbiguities; + std::vector<std::vector<int> > t_inconsistentPositions; + + // Code for missing data (usually ?) + char MISSING; + + // Code for disgrement + char DISAGREEMENT; + + // Helper class managing a single pair + class PairwiseConsensus { + public: + // Default object creation + PairwiseConsensus(); + + // Object destruction + virtual ~PairwiseConsensus() {} + + // Usual object creation + PairwiseConsensus(std::string, std::string); + + // Fills an object created with the default constructor + void load(std::string,std::string); + + // Changes the MISSING character + void setUndeterminedCharacter(char); + + // Changes the DISAGREEMENT character + void setDisagreementCharacter(char); + + /* Uses the conservative mode of consensus + * + * Tries to avoid to make decisions, and adds the + * character set by DISAGREEMENT upon inconsistencies + * + * return The number of inconsistencies. + */ + int generateSoftConsensus(); + + /* Strict mode of consensus + * + * The number of inconsistencies. + */ + int generateHardConsensus(); + + // Two fully resolved (including gap) and identical characters + int getConsistentPositions(); + + // One informative (including gap) and one missing + int getComplementaryPositions(); + + // None missing, but different and incompatible + int getInconsistentPositions(); + + // Both are missing + int getUninformativePositions(); + + // Both identical or one missing, but not fully resolved + int getAmbiguousPositions(); + + // Different, not missing, complementary. + int getAtLeastPartiallyResolvedAmbiguities(); + + // Accessor + int getThisInconsistentPosition(unsigned int); + + // Generates the consensus sequence + std::string getConsensus(); + + private: + + inline bool isValid(char c) { + switch (c) { + case 'A': case 'a': + case 'C': case 'c': + case 'G': case 'g': + case 'T': case 't': + return true; + default: + return false; + } + } + + // This initiates a series of embedded objects + void setCharacterContainers(); + + // The first sequence + std::string seqA; + + // The second sequence + std::string seqB; + + // The resulting consensus + std::string cons; + + // The vecotr storing the inconsistent positions + std::vector<int> posIncons; + + // The length of the sequences + unsigned int ls; + + // Counter + int cntConsistentPositions; + + // Counter + int cntComplementaryPositions; + + // Counter + int cntAmbiguousPositions; + + // Counter + int cntInconsistentPositions; + + // Counter + int cntUninformativePositions; + + // Counter + int cntAtLeastPartiallyResolvedAmbiguities; + + // Code for missing data (usually ?) + char MISSING; + + // Code for disgrement + char DISAGREEMENT; + + public: + // This class manages relationships different symbols + class CharacterContainer { + public: + // Default value: @ + CharacterContainer(); + + // Initiates to a given symbol + CharacterContainer(const char&); + + // Assignment operator + CharacterContainer& operator=(const char&); + + // Sets the symbol + void setValue(char); + + // Set the descendants + void setSons(std::vector<CharacterContainer>); + + // Tests whether the symbol is the same + bool is(CharacterContainer); + + // Tests if the query is contained amongst the sons + bool has(CharacterContainer); + + // Tests if the query is contained amongst the sons + bool has(char); + + /* Tests whether the left character has the left one + * Should be called on the N object only. + */ + char lhas(CharacterContainer,CharacterContainer); + + /* Creates the object with the proper sons + * Should be called on the N object only. + */ + CharacterContainer init(char); + + // The symbol + char value; + + // The descendants + std::vector<CharacterContainer> sons; + }; + + private: + // Symbol ? + CharacterContainer ccQ; + + // Symbol A + CharacterContainer ccA; + + // Symbol C + CharacterContainer ccC; + + // Symbol G + CharacterContainer ccG; + + // Symbol T + CharacterContainer ccT; + + // Symbol U + CharacterContainer ccU; + + // Symbol M + CharacterContainer ccM; + + // Symbol R + CharacterContainer ccR; + + // Symbol W + CharacterContainer ccW; + + // Symbol S + CharacterContainer ccS; + + // Symbol Y + CharacterContainer ccY; + + // Symbol K + CharacterContainer ccK; + + // Symbol B + CharacterContainer ccB; + + // Symbol D + CharacterContainer ccD; + + // Symbol H + CharacterContainer ccH; + + // Symbol V + CharacterContainer ccV; + + // Symbol N + CharacterContainer ccN; + + // Symbol - + CharacterContainer ccGAP; + }; + }; +} + +#endif +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,326 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_CONTAINER_HPP +#define EGGLIB_CONTAINER_HPP + + +namespace egglib { + + /** \brief Handles a set of sequence alignment (aligned or not) + * + * \ingroup core + * + * Creation from a file or string stream should be performed using + * the class Fasta. + * + * Sequences are represented by two strings (name and sequence) and + * an integer (group) that can be accessed or modified by index.The + * order of sequences is guaranteed to be conserved, as if Container + * was a list of triplets (name, sequence, group). + * + * The data matrix is implemented as continuous arrays (char**) and + * allows efficient access and modification of data. For very large + * data matrices you might claim immediately the required memory + * using the constructor Container(unsigned int, char**). + * + */ + class Container { + + public: + + /** \brief Creates an empty object + * + */ + Container(); + + + /** \brief Copy constructor + * + */ + Container(const Container& source); + + + /** \brief Assignment operator + * + */ + Container& operator= (const Container& source); + + + /** \brief Creates an object from a data matrix + * + * Allows you to create an object from data stored in a char* + * array. The array's size must be passed to the constructor. + * Since sequences can have different lengths, you need to + * terminate each sequence by a NULL character. This constructor + * is dedicated to very performance-critical tasks. For usual + * tasks, using the default constructor and subsequently adding + * sequences with addSeq should be enough. + * + * \param number_of_sequences the number of sequences (the length + * of the first dimension of the array). + * + * \param cstring_array the pointer to the data matrix. + * + */ + Container(unsigned int number_of_sequences, char const* const* const cstring_array); + + + /** \brief Destructor + * + */ + virtual ~Container(); + + + /** \brief Clears all content of the object + * + */ + virtual void clear(); + + + /** \brief Adds a sequence to the object + * + * \param name the name of the sequence, as a c-string. + * \param sequence the sequence string, as a c-string. + * \param group the group index of the sequence. + * + * \return The new number of sequences. + * + */ + virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0); + + + /** \brief Removes a sequence from the object + * + * \param pos the index of the sequence to remove. + * + * \return The new number of sequences. + */ + virtual unsigned int remove(unsigned int pos); + + + /** \brief Changes the name of a given sequence + * + * \param pos the sequence index. + * \param name the new name as a C-like string. + * + */ + virtual void name(unsigned int pos, const char* name); + + + /** \brief Changes the sequence string of a given sequence + * + * \param pos the sequence index. + * \param sequence the new sequence as a C-like string. + * + */ + virtual void sequence(unsigned int pos, const char* sequence); + + + /** \brief Appends a string to the a given sequence + * + * \param pos the sequence index. + * \param sequence the sequence to append at the end of the + * current one. + * + */ + virtual void appendSequence(unsigned int pos, const char* sequence); + + + /** \brief Changes a character + * + * \param sequence the sequence index. + * \param position the character index. + * \param ch the new character value. + * + * The positions must fit in the current ranges. + * + */ + virtual void set(unsigned int sequence, unsigned position, char ch); + + + /** \brief Gets a given character + * + * \param s the sequence index. + * \param p the character index. + * + * \return the character value. + * + * The positions must fit in the current ranges. + * + */ + virtual char get(unsigned int s, unsigned int p) const; + + + /** \brief Changes the group index of a given sequence + * + * \param pos the sequence index. + * \param group the new group index value. + * + */ + virtual void group(unsigned int pos, unsigned int group); + + + /** \brief Extracts a range of sequences + * + * \param a the index of the first sequence. + * + * \param b the index immediately passed the last sequence to + * extract. + * + * \return A copy of the object containing the specified + * range of sequences. + * + * Sequences a to b-1 are extracted, provided that the + * indices fit in the current number of sequences. To extract + * all sequences, use container.hslice(0, container.ns()). + * + * Note: invalid ranges will be silently supported. If + * a>=ls or b<=a, an empty object is returned. If b>ns, + * ls will be substituted to a. + * + */ + Container hslice(unsigned int a, unsigned int b) const; + + + /** \brief Gets the number of sequences + * + */ + unsigned int ns() const; + + + /** \brief Gets the length of a given sequence + * + * \param pos the index of the sequence. + * + * \return The length of that particular sequence. + * + */ + virtual unsigned int ls(unsigned int pos) const ; + + + /** \brief Gets the name of the a given sequence + * + * \param pos the index of the sequence. + * + * \return The name of that particular sequence. + * + */ + virtual const char* name(unsigned int pos) const; + + + /** \brief Gets the name of a given sequence + * + * \param pos the index of the sequence. + * + * \return The sequence string for that particular sequence. + * + */ + virtual const char* sequence(unsigned int pos) const; + + + + /** \brief Gets the group index of a given sequence + * + * \param pos the index of the sequence. + * + * \return The group index of that particular sequence. + * + */ + virtual unsigned int group(unsigned int pos) const; + + + /** \brief Checks if all lengths are equal + * + * Returns true if the length of all sequences are equal or + * if there is less thant two sequences. + * + */ + bool isEqual() const; + + + /** \brief Equalizes sequence lengths + * + * Extends sequences as need to ensure that all sequences + * have the same length. + * + * \param ch the character to use for padding. + * + * \return The final length obtained, which is the length of + * the longest sequence before the operation. + * + */ + unsigned int equalize(char ch='?'); + + + /** \brief Finds a sequence by its name + * + * Gets the position of the first sequence with the specified + * name. + * + * \param string a sequence name. + * + * \param strict if true, seeks an exact match. If false, + * compares only until the end of the requested name (for + * example: ATCFF will match ATCFF_01 if strict is false). + * + * \return The lowest index where the name matches, -1 if no + * sequence has such name. + * + */ + int find(const char* string, bool strict=true) const; + + + protected: + // The number of sequences + unsigned int _ns; + + // The array of name lengths + unsigned int* lnames; + + // The array of names + char** names; + + // The array of sequences (as c-strings) + char** sequences; + + // The array of groups + unsigned int* groups; + + // Imports an array of c-strings + virtual void setFromSource(unsigned int number_of_sequences, const char* const* const cstring_array); + + // Constructor helper + virtual void copyObject(const Container&); + + // Constructor partial helper + virtual void getNamesAndGroups(const Container&); + + private: + + // The array of sequence lengths + unsigned int* lsequences; + + // Setup a valid empty object + virtual void init(); + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,156 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_CONTROLLER_HPP +#define EGGLIB_CONTROLLER_HPP + +#include "Current.hpp" +#include "Arg.hpp" +#include "ParamSet.hpp" + +namespace egglib { + + class Random; + + /** \brief Controls a coalescent simulation + * + * \ingroup coalesce + * + * This class generates the gene genealogy, based on the parameters + * stocked in a ParamSet object. + * + */ + class Controller { + + public: + + /** \brief Default constructor + * + * Uses a default ParamSet object that will not allow + * performing simulations. + * + */ + Controller(); + + /** \brief Destructor + * + */ + ~Controller(); + + /** \brief Standard constructor + * + * \param paramSet a ParamSet object containing run + * parameters (it is taken as a reference and stored as this + * so it must not be modified during simulations). + * + * \param random the address of the random number generator. + * + */ + Controller(const ParamSet* paramSet, Random* random); + + /** \brief Reset for a new simulation + * + * Object is reinitiliazed for a new simulation. + * + */ + void reset(); + + /** \brief Increments the coalescent model + * + * \return The number of lineages. + * + */ + unsigned int step(); + + /** \brief Gets the Ancestral Recombination Graph + * + * \return The address of the ARG contained in the object. + * + */ + Arg* getArg(); + + /** \brief Applies a bottleneck to a given population + * + * The bottleneck is applied following Galtier, Depaulis and + * Barton (Genetics, 2000): the general time counter is + * stopped, and coalescence events are performed during a + * time (of normal coalescent process) given by the parameter + * strength. All coalescent events are instantaneous. + * + * \param populationIndex index of the population concerned + * by the event. + * + * \param strength strength of the bottleneck given by a + * number of time units (2N generations times the size of + * the population). + * + */ + void bottleneck(unsigned int populationIndex, double strength); + + /** \brief Migrate a complete population + * + * Takes all the lineages currently present in the population + * source to the population dest. + * + */ + void moveAllLineages(unsigned int source, unsigned int dest); + + /** \brief Migrate a complete population + * + * Takes all the lineages currently present in the population + * source to the population dest. + * + * \param source source population. + * \param dest destination population. + * \param probability the probability that a lineage of + * source migrates to dest. + * + */ + void moveSomeLineages(unsigned int source, unsigned int dest, double probability); + + /// Adds an empty population + void addPopulation(); + + private: + + /// The copy constructor is disabled + Controller(const Controller& source) {} + + /// The assignment operator is disabled + Controller& operator=(const Controller& source) {return *this;} + + void diploids(); + double getMigrationTime(double& migrationParameterDestination); + void getCoalescenceTime(double& destTime, unsigned int& destPopIndex); + double getCoalescenceTimeForPopulation(unsigned int populationIndex); + double getRecombinationTime() const; + void migrate(double migrationParameter); + + const ParamSet* initialParamSet; + ParamSet paramSet; + Current current; + Arg arg; + + Random* random; + + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Convert.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,234 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_CONVERT_HPP +#define EGGLIB_CONVERT_HPP + + +#include "DataMatrix.hpp" +#include "Align.hpp" +#include "EggException.hpp" +#include "Random.hpp" +#include <string> + +#include "config.h" + +#ifdef HAVE_LIBBPP_SEQ +#include <Bpp/Seq/Alphabet.all> +#include <Bpp/Seq/Sequence.h> +#include <Bpp/Seq/Container.all> +#endif + + + +namespace egglib { + + + /** \brief Performs conversion between sequence holder types + * + * \ingroup core + * + * Static methods of this class allows conversion between sequence + * holder types implying parametrizable modifications. + * + */ + class Convert { + + public: + + /** \brief DataMatrix to Align conversion + * + * By defaut, this method generates an Align instance + * containing only the polymorphic sites. The integers of + * the DataMatrix will be converted as follow: 0 to A, 1 to + * C, 2 to G and 3 to T. This behaviour can be largely + * modified using options. + * + * \param dataMatrix DataMatrix instance. + * + * \param length length of the desired alignment. Non-varying + * stretches of data will be introduced to reach the + * specified length. By default the positions of segregating + * sites will be determined from the positions given by the + * DataMatrix object. Those positions are expressed in a + * continuous range, and will be discretized. Mutations + * falling on the same site will be moved of one position + * left or right (always preserving the order of mutation + * sites). If positions are all zero (the default of the + * DataMatrix class) and if length is larger than the number + * of segregating sites, then all segregating sites will + * cluster on the left-hand side of the alignment. + * + * \param random the address to a Random object allowing to + * draw random numbers (for randomizing positions and/or + * non-varying states). If an address is provided but no + * random numbers are required, it is ignored. If no address + * if provided and random numbers are required, a Random + * instance is built internally. + * + * \param randomizePositions if true, the positions specified + * in the DataMatrix objects are ignored and the positions of + * mutations are drawn randomly along the interval (only if + * the specified length is larger than the number of + * segregating sites). If randomizePositions and false and + * positions are not + * + * \param enforceLength specify whether a + * EggRuntimeError should be thrown when the number of + * polymorphic sites is larger than the specified length. If + * false (the default) and in cases where the specified + * length is too short to harbor all polymorphic sites, the + * alignment length will be increased as needed. + * + * \param randomizeNonVaryingStates if true, the stretches of + * conserved positions (between segregating sites) will be + * randomly drawn from the current symbol mapping. Otherwise, + * the symbol given by fixed will be used. + * + * \param randomizeAlleles if true, alleles will be drawn + * randomly from the mapped characters. Note that if a + * genotype value is larger than the size of the mapping, it + * will be replaced by the character given by unknown, + * without randomization. In other words, with the mapping + * "ACGT", alleles 0, 1, 2 and 3 will be randomly assigned + * to these four characters, but larger and negative alleles + * will be assigned to the unknown character. + * + * \param mapping a string given the character to assign to + * different character values read from the DataMatrix. If + * the read value is 0, the first character of the string + * will used, the the value is 1, the second character will + * be used, and so on. If the integer read is out of range + * (in particular, for any negative value), then the + * character given by unknown will be used. An empty string + * will always lead to alignments containing only the + * character given by unknown. The string "01" is suitable + * for binary data. + * + * \param unknown the character to use if an integer genotype + * value is not mapped in the mapping string (that is, if + * the mapping string is too short). + * + * \param nonVaryingState character to use for conserved + * stretches of data. It doesn't have to be included in the + * mapping. If randomizeNonVaryingState is true, this + * argument is ignored. + * + * \return The resulting Align object. + * + */ + static Align align( + DataMatrix& dataMatrix, + unsigned int length=0, + Random* random=NULL, + bool randomizePositions=false, + bool randomizeNonVaryingStates=false, + bool randomizeAlleles=false, + bool enforceLength=false, + std::string mapping="ACGT", + char unknown='?', + char nonVaryingState='A' + ); + + +#ifdef HAVE_LIBBPP_SEQ + + /** \brief Converts an alignment to the equivalent Bio++ type + * + * During conversion, name information is lost (arbitrary + * names are generated in order toprevent duplicate names). + * The object is attached to an alphabet matching the passed + * integer. The names are bare rank integers (starting at the + * value giving by *offset*). + * + * \param align the source alignment object. + * + * \param alphabetID an integer indicating which alphabet to + * use: + * - 1 for DNA + * - 2 for RNA + * - 3 for proteins + * - 4 for standard codon + * - 5 for vertebrate mitochondrial codon + * - 6 for invertebrate mitochondrial codon + * - 7 for echinoderm mitochondrial codon + * . + * Other values will result in an exception. + * + * \param outgroupFlag an integer indicating whether to + * include outgroup sequences: + * - 0 use all sequences + * - 1 use only sequences without 999 label (ingroup) + * - 2 use only sequences with 999 label (outgroup) + * . + * Other values will result in an exception. + * + * \param offset enter an integer to shift the names of the + * resulting alignment (useful to merge alignment and ensure + * that names are not duplicated). + * + * \return A Bio++ alignment. + * + */ + static bpp::AlignedSequenceContainer egglib2bpp(Align& align, unsigned int alphabetID, unsigned int outgroupFlag, unsigned int offset=0); + +#endif + + + + protected: + + /** \brief This class cannot be instantiated + * + */ + Convert() { } + + + /** \brief This class cannot be instantiated + * + */ + Convert(const Convert& source) { } + + + /** \brief This class cannot be instantiated + * + */ + Convert& operator=(const Convert& source) { return *this; } + + + /** \brief This class cannot be instantiated + * + */ + virtual ~Convert() { } + +#ifdef HAVE_LIBBPP_SEQ + static bpp::DNA dnaAlphabet; + static bpp::RNA rnaAlphabet; + static bpp::ProteicAlphabet proteicAlphabet; + static bpp::StandardCodonAlphabet standardCodonAlphabet; + static bpp::VertebrateMitochondrialCodonAlphabet vertebrateMitochondrialCodonAlphabet; + static bpp::InvertebrateMitochondrialCodonAlphabet invertebrateMitochondrialCodonAlphabet; + static bpp::EchinodermMitochondrialCodonAlphabet echinodermMitochondrialCodonAlphabet; +#endif + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,128 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_CURRENT_HPP +#define EGGLIB_CURRENT_HPP + + +namespace egglib { + + class Population; + class ParamSet; + + /** \brief Represents the current set of populations + * + * \ingroup coalesce + * + */ + class Current { + + public: + + /** \brief Default constructor + * + */ + Current(); + + /** \brief Standard constructor + * + * \param paramSet allows to initiate the correct structure + * of populations. + * + */ + Current(ParamSet* paramSet); + + /** \brief Rebuilds the object + * + * \param paramSet allows to initiate the correct structure + * of populations. + * + */ + void reset(ParamSet* paramSet); + + /** \brief Destructor + * + */ + virtual ~Current(); + + /** \brief Copy constructor + * + */ + Current(const Current&); + + /** \brief Assignment operator + * + */ + Current& operator=(const Current&); + + /** \brief Gets the current number of populations + * + */ + unsigned int numberOfPopulations() const; + + + /** \brief Adds an empty population to the system + * + */ + void addPopulation(); + + + /** \brief Gets the number of lineages contained by a given + * population + * + */ + unsigned int populationNumberOfLineages(unsigned int populationIndex) const; + + + /** \brief Provides access to a given population + * + * The returned pointer can be used to modify the object. + * + */ + Population* population(unsigned int populationIndex); + + + /** \brief Total number of lineages + * + */ + unsigned int totalNumberOfLineages() const; + + + /** \brief Efficient number of lineages + * + * This sums the number of covered segments of each lineage. + * + */ + unsigned int efficientNumberOfLineages() const; + + + private: + + void setPopulationArray(); + void copy(const Current&); + void clear(); + + unsigned int _numberOfPopulations; + unsigned int _numberOfSegments; + Population** populations; + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,219 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_DATAMATRIX_HPP +#define EGGLIB_DATAMATRIX_HPP + + +#include "CharMatrix.hpp" + + +namespace egglib { + + /** \brief Data table + * + * \ingroup core + * + * Holds a data matrix representing genotype data from simulations. + * Data are stored as integers, to each site is associated a + * position, and to each sequence is associated a group index (any + * integer labelling, for example, a subpopulation). Supports the + * CharMatrix interface with the condition that allele genotype + * datum is >=0 and <=9. + * + */ + class DataMatrix : public CharMatrix { + + public: + + /** \brief Default constructor + * + * The data table default dimensions are {0,0} + * + */ + DataMatrix(); + + + /** \brief Standard constructor + * + * The data table dimensions must be given. + * Each cell default default is 0, and each site position is 0.. + * + * \param numberOfSequences number of lines of the data table. + * \param numberOfSites number of columns of the data table. + * + */ + DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites); + + + /** \brief Copy constructor + * + */ + DataMatrix(const DataMatrix&); + + + /** \brief Copy constructor + * + */ + DataMatrix(const CharMatrix&); + + + /** \brief Assignment operator + * + */ + virtual DataMatrix& operator=(const DataMatrix&); + + + /** \brief Assignment operator + * + */ + virtual DataMatrix& operator=(const CharMatrix&); + + + /** \brief Destructor + * + */ + virtual ~DataMatrix(); + + + /** \brief Gets number of sites + * + */ + unsigned int numberOfSites() const; + + + /** \brief Gets number of sequences + * + */ + unsigned int numberOfSequences() const; + + + /** \brief Sets a value of the data table + * + */ + void set(unsigned int sequence, unsigned int site, int value); + + + /** \brief Gets a value from the data table + * + */ + int get(unsigned int sequence, unsigned int site) const; + + + /** \brief Faster and unsecure version of get + * + */ + inline int fget(unsigned int sequence, unsigned int site) const { + return dataMatrix[sequence][site]; + } + + + /** \brief Sets the position of a site + * + */ + void sitePosition(unsigned int site, double value); + + + /** \brief Gets the position of a site + * + */ + double sitePosition(unsigned int site) const; + + + /** \brief Sets the group label of a sequence + * + */ + void populationLabel(unsigned int sequence, unsigned int value); + + + /** \brief Gets the group label of a sequence + * + */ + unsigned int populationLabel(unsigned int sequence) const; + + + /** \brief Removes all information from the object + * + */ + void clear(); + + + /** \brief Resizes the data matrix + * + * \param newNumberOfSequences number of sequences (rows) + * \param newNumberOfSites number of sites (columns) + * + * If new values are larger, data already set is left unchanged. + * New data are set to zero. + * + */ + void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites); + + + /** \brief Shifts allele value + * + * \param minimum the minimum allele value. + * + * Shifts all alleles at all sites to ensure that alleles alleles + * are equal to or larger than minimum. The shifting is specific + * to each site. + * + */ + void shift(int minimum); + + /** \brief Gets the character at a given position + * + * An exception is generated if the allele value at this + * position is not >=0 and <=9. Not out-of-bound check is + * performed. + * + */ + char character(unsigned int sequence, unsigned int site) const; + + + + private: + + // Initializes to default values (for empty object) + void init(); + + // Copies from a source object + virtual void copy(const CharMatrix&); + + // Copies from a source object + virtual void copy(const DataMatrix&); + + // Number of lines of the data matrix + unsigned int _numberOfSequences; + + // Number of columns of the data matrix + unsigned int _numberOfSites; + + // Data matrix + int **dataMatrix; + + // Vector of site positions + double *positions; + + // Vector of group indices + unsigned int *groups; + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Edge.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,331 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_EDGE_HPP +#define EGGLIB_EDGE_HPP + +#include <vector> +#include <climits> +#include "EggException.hpp" + +namespace egglib { + + class Random; + + /** \brief Edge of the ancestral recombination graph + * + * \ingroup coalesce + * + * Each Edge instance provides access to its 0, 1 or 2 descendants + * (the former holds for a terminal node, the middle for the parent + * of a recombined node and the latter for the parent of a coalesced + * node (most classical node in the coalescent).The Edge also + * provides to the edge length. Note that the Edge instance must be + * understood as an ARG node and the branch above it (latter in the + * coalescence process). Edge instances also keep track of the list + * of descendants descending from this node (which may differ along + * recombining segment). Edge instances *must* be created through one + * of the "default" and "coalescence" constructors or through the + * recombination method. Edge instances should never be copied but + * manipulated by references. + * + */ + class Edge { + + public: + + /// Destructor + virtual ~Edge(); + + /** \brief Constructor + * + * \param numberOfSegments the number of recombining segments + * (one for a non-recombining region). + * + * Use the Pool, instead. Objects are delivered with a + * complete coverage. + * + */ + Edge(unsigned int numberOfSegments); + + + /// Restore object to `factory` state + void reset(); + + + /** \brief Builds for internal node + * + * \param date the date of creation of the edge. + * \param son1 first edge descending from this edge. + * \param son2 second edge descending from this edge. + * \param edgesPerSegments counts the current number of + * (non-coalesced lineages for each lineages); must have the + * appropriate size and will be updated. + * \param MRCA the list where to place the address of segment + * MRCA, if it occurs. + * \param totalLength the total length of the tree. + * \param segmentLengths the table of tree lengths per + * segment. + * + * Assumes the current object has the correct number of + * segments. + * + */ + void coalescence(double date, Edge* son1, Edge* son2, + unsigned int* edgesPerSegments, Edge** MRCA, + double& totalLength, double* segmentLengths); + + + /** \brief Generates a recombination event + * + * \param date the date of the event. + * \param dest1 destination for the first resulting edge. + * \param dest2 destination for the second resulting edge. + * \param random pointer to the Random instance used by the + * simulator. + * \param totalLength the total length of the tree. + * \param segmentLengths the table of tree lengths per + * segment. + * + * dest1 and dest2 must be Edge address initialized with the + * appropriate number of segments. + * + */ + void recombination(double date, + Edge* dest1, Edge* dest2, Random* random, + double& totalLength, double* segmentLengths); + + + /** \brief Define this edge to be terminal + * + * The edge have only non-covered segments + * + */ + void set_terminal(unsigned int leaf_index); + + /// Branch's raw length (doesn't take account segment coverage) + double length; + + /// Number of covered segments + unsigned int coverage; + + /// Time position of the branch's bottom + double bottom; + + /// Time position of the branch's top + double top; + + /// Address of the first son + Edge* son1; + + /// Address of the second son + Edge* son2; + + /// Number of sons (0, 1 or 2) + unsigned int numberOfSons; + + /// Checks if a given segment is covered + inline bool segment(unsigned int segmentIndex) const { + //while(segments[segmentIndex]==0) segmentIndex--; + if (segments[segmentIndex]==0) return false; + if (segments[segmentIndex]==UINT_MAX) return true; + return segbools[segmentIndex]; + } + + /// leaf index (0 for internal nodes) + inline unsigned int label() const { + return _label; + } + + /// Number of mutations per segment + unsigned int* numberOfMutationsPerActualSite; + + /// Sets the actual number of sites + void set_actualNumberOfSites(unsigned int actualNumberOfSites); + + + private: + + unsigned int _label; + + /// Default constructor is not available + Edge(); + + /// Copy constructor is not available + Edge(const Edge& edge) {} + + /// Assignment operator is not available + Edge& operator=(const Edge& edge) { return *this; } + + void init(unsigned int numberOfSegments); + + unsigned int numberOfSegments; + unsigned int* segments; + bool* segbools; + + /// complete the covered ranges with UINT_MAX's and the non-covered by 0's + inline void fill() { + coverage=0.; + unsigned int i=0,j; + while (i<numberOfSegments) { + if (segbools[i]==true) { + coverage += segments[i]; + for (j=1; j<segments[i]; j++) { + segments[i+j] = UINT_MAX; + } + } + i+=segments[i]; + } + } + + + + /// update containing Arg's branch lengths + inline void update_lengths(double& totalLength, double* segmentLengths) { + unsigned int i=0,j; + while (i<numberOfSegments) { + if (segbools[i]==true) { + totalLength += segments[i]*length; + for (j=0; j<segments[i]; j++) { + segmentLengths[i+j] += length; + } + } + i+=segments[i]; + } + } + + + }; + + + + + + + + + + + + + /** \brief Pool of Edge objects + * + * \ingroup coalesce + * + * Holds a pool of Edge objects that can be recycled to spare the + * building burden. A construction time, a number of Edge objects + * equals to the predicted number of needed instances should be + * requested. The Edge's will be prebuilt immediately and delivered + * upon request. After use, the Edge's should be released. It is only + * possible to release the last issued Edge instance or all of them + * at once. + * + */ + class EdgePool { + + public: + + /// Default constructor (nothing allocated) + EdgePool(); + + + /// Destructor + virtual ~EdgePool(); + + + /** \brief Configure pool + * + * Pre-allocates a given number of Edge objects. The objects + * will be immediately available. + * + * Data previously allocated (by a previous call of this + * function or by the deliver() method) will be lost so it + * can be required to use clear() before. + * + * \param numberOfSegments the number of segments of the + * simulation; all Edge instances will use this value. + * + * \param numberOfPreAllocated the number of Edge that should + * be kept ready for immediate use. + * + */ + void set(unsigned int numberOfSegments, unsigned numberOfPreAllocated); + + + /** \brief Frees internally stored memory + * + * This invalidate all points that have been delivered + * previously. However, any previously set number of segments + * (0, by default) is retained. + * + */ + void clear(); + + + /** \brief Deliver an Edge + * + * The object must not be freed by the client! This object is + * allocated on the heap if the cache is not large enough, + * only reset if it was previously released, or just delivered + * if it is one of the initially allocated instances. + * + */ + Edge* deliver(); + + + /** \brief Release an Edge + * + * Release the last delivered Edge. The instance is only + * cached for a potential future use; it is not freed nor + * reset immediately. If no Edge's are in use, nothing is + * done. + * + */ + void releaseLast(); + + + /** \brief Release all Edge's + * + * Release all delivered Edges. The instances are only + * cached for a potential future use; they are not freed nor + * reset immediately. If no Edge's are in use, nothing is + * done. + * + */ + void releaseAll(); + + private: + + /// Not available + EdgePool(const EdgePool& ep) {} + + /// Not available + EdgePool& operator=(const EdgePool& ep) { return *this; } + + unsigned int numberOfSegments; + unsigned int used; + unsigned int released; + unsigned int ready; + Edge** cache; + + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/EggException.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,173 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_EGGEXCEPTION_HPP +#define EGGLIB_EGGEXCEPTION_HPP + +#include <string> +#include <exception> + +namespace egglib { + + /** \brief Base exception type for errors occurring in this library + * + * \ingroup core + * + */ + class EggException : public std::exception { + public: + /// Constructor with empty error message + EggException(); + /// Creates the exception + EggException(const char* message); + /// Destructor + ~EggException() throw() {} + /// Gets error message + virtual const char* what() const throw(); + + protected: + std::string message; + + }; + + + /** \brief Exception type for memory errors + * + * \ingroup core + * + */ + class EggMemoryError : public EggException { + public: + /// Creates the exception + EggMemoryError(); + /// Destructor + ~EggMemoryError() throw() {} + }; + + + /** \brief Exception type for argument value errors + * + * \ingroup core + * + */ + class EggArgumentValueError : public EggException { + public: + /// Creates the exception + EggArgumentValueError(const char* m ); + /// Destructor + ~EggArgumentValueError() throw() {} + }; + + + /** \brief Exception type for runtime errors + * + * Runtime error definition is rather large. Includes bugs as well + * as logical errors. + * + * \ingroup core + * + */ + class EggRuntimeError : public EggException { + public: + /// Creates the exception + EggRuntimeError(const char* m ); + /// Destructor + ~EggRuntimeError() throw() {} + }; + + + /** \brief Exception type for file/string formatting errors + * + * \ingroup core + * + */ + class EggFormatError : public EggException { + public: + /// Creates the exception + EggFormatError(const char* fileName, const char* expectedFormat, const char* m); + /// Destructor + ~EggFormatError() throw() {} + /// Gets the file name + std::string fileName() const; + /// Gets the expected format + std::string expectedFormat() const; + /// Formats a longer string + virtual const char* what_more() const; + + protected: + std::string fname; + std::string eformat; + }; + + + /** \brief Exception type for errors while opening a file + * + * \ingroup core + * + */ + class EggOpenFileError : public EggException { + public: + /// Creates the exception + EggOpenFileError(const char* fileName ); + /// Destructor + ~EggOpenFileError() throw() {} + }; + + + /** \brief Exception type for unaligned sequences + * + * \ingroup core + * + */ + class EggUnalignedError : public EggException { + public: + /** \brief Creates the exception + * + */ + EggUnalignedError(); + + /** \brief Destructor + * + */ + ~EggUnalignedError() throw() {} + }; + + /** \brief Exception type for invalid character + * + * \ingroup core + * + */ + class EggInvalidCharacterError : public EggException { + public: + /** \brief Creates the exception + * + */ + EggInvalidCharacterError(char c, unsigned int seqIndex, unsigned int posIndex); + + /** \brief Destructor + * + */ + ~EggInvalidCharacterError() throw() {} + }; + +} + + + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/FStatistics.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,288 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_FSTATISTICS_HPP +#define EGGLIB_FSTATISTICS_HPP + + + +namespace egglib { + + + /** \brief Computes Fis, Fst and Fit from diploid data + * + * The class requires loading data. Data are loaded by individual + * (two genotypes per individual). The analyses are cached: they are + * performed upon the first call to statistics accessors. The cache + * is emptied whenever a datum is loaded. + * + * The computations are performed after Weir and Cockerham. The + * statistics F, theta and f are generalized for multiple alleles. + * To allow computation of multi-locus statistics, variance + * components are also available. The three components of the + * variance are Vpopulation (between-population), Vindividual + * (within-population, between-individual) and Vallele (within- + * individual). The formulas to compute the F-statistics are as + * follows: + * - 1-F = Vallele/(Vpopulation+Vindividual+Vallele) + * - theta = Vpopulation/(Vpopulation+Vindividual+Vallele) + * - 1-f = Vallele/(Vindividual+Vallele). + * + * \ingroup polymorphism + * + */ + class FStatistics { + + public: + + /** \brief Constructor + * + */ + FStatistics(); + + + /** \brief Destructor + * + */ + virtual ~FStatistics(); + + + /** \brief Reserve sufficient memory for a given number of + * individuals. + * + * This method makes the load function faster by allocating + * all required memory at once. + * + * \param numberOfIndividuals a strictly positive integer. + * + */ + void reserve(unsigned int numberOfIndividuals); + + + /** \brief Loads the data for one individual + * + * \param genotype1 an integer giving the first allele. + * \param genotype2 an integer giving the second allele. + * \param populationLabel an integer indication belonging to + * a population. + * + * Genotypes and population labels are not required to be + * consecutive (both are labels, not indices). They are + * internally mapped to indices (the mapping can be obtained + * by accessors populationLabel and allele). + * + * All genotypes are considered to be valid (no missing data). + * If statistics were computed previous to call to this + * function, all data will be erase. + * + */ + void loadIndividual(unsigned int genotype1, + unsigned int genotype2, unsigned int populationLabel); + + + /** \brief Label of a population + * + * The index corresponds to the local mapping of populations + * regardless of the ranking of population labels. (No out + * of bound checking.) + * + */ + unsigned int populationLabel(unsigned int populationIndex); + + + /** \brief Value of an allele + * + * The index corresponds to the local mapping of alleles + * regardless of the ranking of allele values. (No out of + * bound checking.) + * + */ + unsigned int alleleValue(unsigned int alleleIndex); + + + /// First allele of a given individual (no checking) + unsigned int firstAllele(unsigned int individualIndex) const; + + /// Second allele of a given individual (no checking) + unsigned int secondAllele(unsigned int individualIndex) const; + + /// Population label of a given individual (no checking) + unsigned int individualLabel(unsigned int individualIndex) const; + + + /** \brief Number of alleles + * + */ + unsigned int numberOfAlleles(); + + + /** \brief Number of populations + * + */ + unsigned int numberOfPopulations(); + + + /** \brief Number of loaded genotypes + * + */ + unsigned int numberOfGenotypes() const; + + + /** \brief Absolute total allele frequency + * + */ + unsigned int alleleFrequencyTotal(unsigned int alleleIndex); + + + /** \brief Absolute allele frequency in a population + * + */ + unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex); + + + /** \brief Absolute genotype frequency + * + * Note that allele AB is considered different to BA (this + * means that values can be accessed both sides of the + * diagonal. + * + */ + unsigned int genotypeFrequencyTotal(unsigned int alleleIndex1, unsigned int alleleIndex2); + + + /** \brief Absolute genotype frequency in a population + * + * Note that allele AB is considered different to BA (this + * means that values can be accessed both sides of the + * diagonal. + * + */ + unsigned int genotypeFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex1, unsigned int alleleIndex2); + + + /** \brief Sample size of a population + * + */ + unsigned int populationFrequency(unsigned int populationIndex); + + + /** \brief Weir-Cockerham F-statistic + * + * Note: equivalent to Fit. + * + */ + double F(); + + + /** \brief Weir-Cockerham theta-statistic + * + * Note: equivalent to Fst. + * + */ + double theta(); + + + /** \brief Weir-Cockerham f-statistic + * + * Note: equivalent to Fis. + * + */ + double f(); + + + /** \brief Between-population component of variance + * + */ + double Vpopulation(); + + + /** \brief Within-population, between-individual component of variance + * + */ + double Vindividual(); + + + /** \brief Within-individual component of variance + * + */ + double Vallele(); + + + protected: + + bool d_flag; + void d_init(); + void d_clear(); + unsigned int d_reserved; + unsigned int d_numberOfGenotypes; + unsigned int *d_genotypes; + unsigned int *d_populationLabels; + + bool s_flag; + void s_init(); + void s_clear(); + void s_compute(); + void processPopulations(); + void processAlleles(); + unsigned int getPopulationIndex(unsigned int) const; + unsigned int getAlleleIndex(unsigned int) const; + unsigned int s_numberOfAlleles; + unsigned int *s_alleleValueMapping; + unsigned int s_numberOfPopulations; + unsigned int *s_populationLabelMapping; + unsigned int *s_populationFrequencies; + unsigned int *s_alleleFrequenciesTotal; + unsigned int **s_alleleFrequenciesPerPopulation; + unsigned int **s_genotypeFrequenciesTotal; + unsigned int ***s_genotypeFrequenciesPerPopulation; + + bool w_flag; + void w_init(); + void w_clear(); + void w_compute(); + double w_F; + double w_T; + double w_f; + double *w_a; + double *w_b; + double *w_c; + double w_nbar; + double w_nc; + double *w_pbar; + double *w_ssquare; + double *w_hbar; + double w_sum_a; + double w_sum_b; + double w_sum_c; + double w_sum_abc; + double w_sum_bc; + + + private: + + FStatistics(const FStatistics& source) { } + + FStatistics& operator=(const FStatistics& source) { + return *this; + } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Fasta.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,278 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_FASTA_HPP +#define EGGLIB_FASTA_HPP + +#include <istream> +#include <iostream> +#include <string> +#include "Container.hpp" + +namespace egglib { + + /** \brief Fasta parser/formatted + * + * \ingroup core + * + * Reads a multifasta sequence file from a string, a stream or a file + * and returns a Container. See the description of the format below. + * Formats a fasta string from a sequence container object and places + * it in a string, a stream of a file. All methods are static and the + * class cannot be instantiated. The methods parsef and formatf will + * open the file for you while the others will read/write directly + * in a string. + * + * Specifications of the fasta format: + * + * - The number of sequences is not limited. + * + * - Each sequence is preceded by a header limited to a single + * line and starting by a ">" character. + * + * - The header length is not limited and all characters are + * allowed but white spaces and special characters are + * discouraged. + * + * - Group indices are specified by \@0, \@1, \@2... strings + * appearing at the end of the header string (just before the + * carriage return). Note that group labels are ignored by + * default. + * + * - Group indices are ignored unless specifically specified in a + * parser's options. + * + * - The sequence itself continues on following lines until the + * next ">" character or the end of the file. + * + * - White spaces, tab and carriage returns are allowed at any + * position There is no limitation in length and different + * sequences can have different lengths. + * + * - Although the standard is lower case characters, Fasta + * assumes upper case characters and only supports lower case + * characters (and converts them to upper case characters). + * Information coded by change in case is lost. + * + */ + class Fasta { + + public: + + /** \brief Imports a fasta file + * + * Imports the content of the file as is. Calls the method + * pase(std::istream*, bool) by creating its own istream. + * + * \param fname the name of a fasta file. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return A Container object containing the sequences. + * + */ + static Container parsef(const char* fname, bool importGroupLabels=false); + + + /** \brief Imports a fasta file + * + * Imports the content of the file as is. Calls the method + * pase(std::istream*, bool) by creating its own istream. This + * method expects a reference to a Container to which the + * sequences will be appended. + * + * \param fname the name of a fasta file. + * + * \param container a Container instance, empty or not. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return Nothings: the new sequences are appended to the + * Container passed as argument. + * + */ + static void parsef(const char* fname, Container& container, bool importGroupLabels=false); + + + /** \brief Imports a fasta file + * + * Imports the content of the file as is. Calls the method + * pase(std::istream*, bool) by creating its own istream. + * + * \param str a string containing the data. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return A Container object containing the sequences. + * + */ + static Container parse(const std::string& str, bool importGroupLabels=false); + + + /** \brief Imports a fasta file + * + * Imports the content of the file as is. Calls the method + * pase(std::istream*, bool) by creating its own istream. This + * method expects a reference to a Container to which the + * sequences will be appended. + * + * \param str a string containing the data. + * + * \param container a Container instance, empty or not. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return Nothing: new sequences are appended to the Container + * passed as argument. + * + */ + static void parse(const std::string& str, Container& container, bool importGroupLabels=false); + + + /** \brief Imports a fasta file from an open stream + * + * Imports the content of the file as is. + * + * \param stream an open stream (file or string) containing the + * data. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return A Container object containing the sequences. + * + */ + static Container parse(std::istream& stream, bool importGroupLabels=false); + + + /** \brief Imports a fasta file from an open stream + * + * Imports the content of the file as is. This + * method expects a reference to a Container to which the + * sequences will be appended. + * + * \param stream an open stream (file or string) containing the + * data. + * + * \param container a Container instance, empty or not. + * + * \param importGroupLabels if set to true, scan automatically + * for groups. The format is @ followed by an integer, placed + * at the end of the header string(sequences without labels + * will be treated as \@0). + * + * \return Nothing: the new sequences are appended to the + * Container passed as argument. + * + */ + static void parse(std::istream& stream, Container& container, bool importGroupLabels=false); + + + /** \brief Export sequences as fasta + * + * \param fname the name of the file where to place the result. + * + * \param container Container object to export. + * + * \param exportGroupLabels if set to true, exports group + * indices as a \@x at the end of the sequence name, where x is + * the group index. Otherwise, this information is discarded. + * + * \param lineLength the number of characters to place on a + * single line. If zero, no newlines are inserted within + * sequences. + * + */ + static void formatf(const char* fname, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); + + + /** \brief Export sequences as fasta + * + * \param file an open stream. + * + * \param container Container object to export. + * + * \param exportGroupLabels if set to true, exports group + * indices as a \@x at the end of the sequence name, where x is + * the group index. Otherwise, this information is discarded. + * + * \param lineLength the number of characters to place on a + * single line. If zero, no newlines are inserted within + * sequences. + * + */ + static void format(std::ostream& file, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); + + + /** \brief Export sequences as fasta + * + * This medod creates internally an ostringstream, calls the + * method format(ostream, container, bool) and returns the + * resulting string. + * + * \param container Container object to export. + * + * \param exportGroupLabels if set to true, exports group + * indices as a \@x at the end of the sequence name, where x is + * the group index. Otherwise, this information is discarded. + * + * \param lineLength the number of characters to place on a + * single line. If zero, no newlines are inserted within + * sequences. + * + * \return The formatted string. + * + */ + static std::string format(const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); + + + + protected: + + /// This class cannot be instantiated + Fasta() { } + + /// This class cannot be instantiated + Fasta(const Fasta& source) { } + + /// This class cannot be or copied + Fasta& operator=(const Fasta& source) { return *this; } + + /// This class cannot be instantiated + virtual ~Fasta() { } + + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/HFStatistics.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,227 @@ +/* + Copyright 2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_HFSTATISTICS_HPP +#define EGGLIB_HFSTATISTICS_HPP + + + +namespace egglib { + + + /** \brief Computes Fst and Fit from haploid data + * + * The class requires loading data. Data are loaded by haploid + * (one genotype per individual). The analyses are cached: they are + * performed upon the first call to statistics accessors. The cache + * is emptied whenever a datum is loaded. + * + * The computations are performed after Weir and Cockerham. The + * statistic theta is generalized for multiple alleles. To allow + * computation of multi-locus statistics, variance components are + * also available. The two components of the variance are T1 and T2 + * and theta is T1/T2 (from Weir 1996 "Genetic Data Analysis II", + * Sinauer associates, Sunderland MA). + * + * \ingroup polymorphism + * + */ + class HFStatistics { + + public: + + /** \brief Constructor + * + */ + HFStatistics(); + + + /** \brief Destructor + * + */ + virtual ~HFStatistics(); + + + /** \brief Reserve sufficient memory for a given number of + * individuals. + * + * This method makes the load function faster by allocating + * all required memory at once. + * + * \param numberOfIndividuals a strictly positive integer. + * + */ + void reserve(unsigned int numberOfIndividuals); + + + /** \brief Loads the data for one individual + * + * \param genotype an integer giving the allele. + * \param populationLabel an integer indication belonging to + * a population. + * + * Genotypes and population labels are not required to be + * consecutive (both are labels, not indices). They are + * internally mapped to indices (the mapping can be obtained + * by accessors populationLabel and allele). + * + * All genotypes are considered to be valid (no missing data). + * If statistics were computed previous to call to this + * function, all data will be erased. + * + */ + void loadIndividual(unsigned int genotype, unsigned int populationLabel); + + + /** \brief Label of a population + * + * The index corresponds to the local mapping of populations + * regardless of the ranking of population labels. (No out + * of bound checking.) + * + */ + unsigned int populationLabel(unsigned int populationIndex); + + + /** \brief Value of an allele + * + * The index corresponds to the local mapping of alleles + * regardless of the ranking of allele values. (No out of + * bound checking.) + * + */ + unsigned int alleleValue(unsigned int alleleIndex); + + + /// Allele of a given individual (no checking) + unsigned int allele(unsigned int individualIndex) const; + + /// Population label of a given individual (no checking) + unsigned int individualLabel(unsigned int individualIndex) const; + + + /** \brief Number of alleles + * + */ + unsigned int numberOfAlleles(); + + + /** \brief Number of populations + * + */ + unsigned int numberOfPopulations(); + + + /** \brief Number of loaded genotypes + * + */ + unsigned int numberOfGenotypes() const; + + + /** \brief Absolute total allele frequency + * + */ + unsigned int alleleFrequencyTotal(unsigned int alleleIndex); + + + /** \brief Absolute allele frequency in a population + * + */ + unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex); + + + /** \brief Sample size of a population + * + */ + unsigned int populationFrequency(unsigned int populationIndex); + + + /** \brief Weir-Cockerham theta-statistic + * + * Note: equivalent to Fst. + * + */ + double theta(); + + + /** \brief Between-population component of variance + * + */ + double T1(); + + + /** \brief Total variance + * + */ + double T2(); + + + protected: + + bool d_flag; + void d_init(); + void d_clear(); + unsigned int d_reserved; + unsigned int d_numberOfGenotypes; + unsigned int *d_genotypes; + unsigned int *d_populationLabels; + + bool s_flag; + void s_init(); + void s_clear(); + void s_compute(); + void processPopulations(); + void processAlleles(); + unsigned int getPopulationIndex(unsigned int) const; + unsigned int getAlleleIndex(unsigned int) const; + unsigned int s_numberOfAlleles; + unsigned int *s_alleleValueMapping; + unsigned int s_numberOfPopulations; + unsigned int *s_populationLabelMapping; + unsigned int *s_populationFrequencies; + unsigned int *s_alleleFrequenciesTotal; + unsigned int **s_alleleFrequenciesPerPopulation; + + bool w_flag; + void w_init(); + void w_clear(); + void w_compute(); + double w_T; + double *w_T1; + double *w_T2; + double w_nbar; + double w_nc; + double *w_pbar; + double *w_ssquare; + double w_sum_T1; + double w_sum_T2; + + + private: + + HFStatistics(const HFStatistics& source) { } + + HFStatistics& operator=(const HFStatistics& source) { + return *this; + } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/HaplotypeDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,176 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_HAPLOTYPEDIVERSITY_HPP +#define EGGLIB_HAPLOTYPEDIVERSITY_HPP + +#include "BaseDiversity.hpp" + +namespace egglib { + + + /** \brief Computes diversity based on haplotype analysis + * + * \ingroup polymorphism + * + * This class relies on detection of polymorphic sites, as does + * NucleotideDiversity, with the exception that sites with missing + * data cannot be processed (minimumExploitableData is enforced to + * 1.). + * + * Like NucleotideDiversity, the same object can be used to analyze + * different data sets. Only the call to load() is required before + * accessing the data. + * + * Hst, Gst and Kst are between population differenciation indices. + * They are respectively defined in equations 2, 5-6 and 9 of Hudson + * et al. 1992a (Molecular Biology and Evolution 9:138-151). Also, + * Fst is defined in equation 3 of Hudson et al. 1992b (Genetics + * 132:583-589). Finally, Snn is from Hudson 2000 Genetics. It is + * computed as the average of Xi for all sequences. Where Xi is the + * ratio of nearest neighbours from the same group to the number of + * nearest neighbours. Nearest neigbours are all the sequences with + * the lowest number of differences to the focal sequence. NOTE: + * Gst/Hst are quite similar, but Fst and Kst are more different. Snn + * is a different statistic. Gst and Hst are two ways to estimate the + * between-population fraction of haplotypic diversity. + * + */ + class HaplotypeDiversity : public BaseDiversity { + + public: + + /** \brief Constructor + * + */ + HaplotypeDiversity(); + + /** \brief Destructor + * + */ + virtual ~HaplotypeDiversity(); + + /** \brief Identifies polymorphic sites and computes basis + * statistics + * + * \param data an alignment object (subclass of CharMatrix). + * The presence of outgroup or of different populations will + * be detected based on the populationLabel members of the + * passed object. The populationLabel 999 will be interpreted + * as outgroups. If several outgroups are passed, sites were + * the outgroups are not consistent will be treated as "non- + * orientable". + * + * \param allowMultipleMutations if true, sites with more + * than two alleles will not be ignored. The sum of the + * frequencies of all alleles not matching the outgroup will + * treated as the derived allele frequency (for orientable + * sites). + * + * \param ignoreFrequency removes sites that are polymorph + * because of an allele at absolute frequency smaller than or + * equal to this value. If ignoreFrequency=1, no sites are + * removed, if ignoreFrequency=1, singleton sites are + * ignored. Such sites are completely removed from the + * analysis (not counted in lseff). Note that if more than + * one mutation is allowed, the site is removed only if all + * the alleles but one are smaller than or equal to this + * value. For example, an alignment column AAAAAAGAAT is + * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is + * conserved (including the third allele T which is a + * singleton). + * + * \param characterMapping a string giving the list of + * characters that should be considered as valid data. If a + * space is present in the string, the characters left of the + * space will be treated as valid data and the characters + * right of the space will be treated as missing data, that + * is tolerated but ignored. All characters not in the string + * will cause an EggInvalidCharacterError to be raised. + * + */ + void load(CharMatrix& data, + bool allowMultipleMutations=false, + unsigned int ignoreFrequency=0, + std::string characterMapping=dnaMapping + ); + + /// Number of distinct haplotypes + unsigned int K() const; + + /// Haplotype diversity (unbiased) + double He() const; + + /** \brief Returns the allele number of a given sequence + * + * The passed index must be given ignoring any outgroup + * sequence. + * + */ + unsigned int haplotypeIndex(unsigned int) const; + + /// Population differenciation, based on nucleotides (Hudson 1992a) + double Kst() const; + + /// Population differenciation, based on nucleotides (Hudson 1992b) + double Fst() const; + + /// Population differenciation, based on haplotypes (Nei version) + double Gst() const; + + /// Population differenciation, based on haplotypes (Hudson et al. version) + double Hst() const; + + /// Hudson's Snn (nearest neighbor statistics) + double Snn() const; + + + protected: + + void init(); + void clear(); + + inline unsigned int diff(CharMatrix& data, unsigned int ind1, unsigned int ind2) const; + + bool m_loaded; + unsigned int m_K; + double m_He; + double m_Kst; + double m_Fst; + double m_Gst; + double m_Hst; + double m_Snn; + unsigned int *m_haplotypeIndex; + + + private: + + HaplotypeDiversity(const HaplotypeDiversity& source) { + + } + + HaplotypeDiversity& operator=(const HaplotypeDiversity& source) { + return *this; + } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/LinkageDisequilibrium.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,233 @@ +/* + Copyright 2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_LINKAGEDISEQUILIBRUM_HPP +#define EGGLIB_LINKAGEDISEQUILIBRUM_HPP + + +#include "BaseDiversity.hpp" +#include "EggException.hpp" + + +namespace egglib { + + /** \brief Analyzes linkage disequilibrium per pair of polymorphic sites + * + * \ingroup polymorphism + * + * The class considers an alignment and detects polymorphic sites + * using the BaseDiversity functionality (shared with other classes + * of the module). Only sites with exactly two alleles are + * considered. Statistics of pairwise linkage disequilibrium can + * be accessed by pair index (note that out-of-range errors are not + * checked). Population labels are ignored (but outgroups are + * excluded from the analysis). + * + */ + class LinkageDisequilibrium : public BaseDiversity { + + public: + + /// Default constructor + LinkageDisequilibrium(); + + /// Destructor + virtual ~LinkageDisequilibrium(); + + /** \brief Analyzes polymorphic sites of an alignment + * + * \param data an alignment object (subclass of CharMatrix). + * The presence of outgroup or of different populations will + * be detected based on the populationLabel members of the + * passed object. The populationLabel 999 will be interpreted + * as outgroups. If several outgroups are passed, sites were + * the outgroups are not consistent will be treated as "non- + * orientable". + * + * \param minimumExploitableData site where the non-missing + * data (as defined by characterMapping) are at a frequency + * larger than this value will be removed from the analysis. + * Use 1. to take only 'complete' sites into account and 0. + * to use all sites. + * + * \param ignoreFrequency removes sites that are polymorphic + * because of an allele at absolute frequency smaller than or + * equal to this value. If ignoreFrequency=1, no sites are + * removed, if ignoreFrequency=1, singleton sites are + * ignored. Such sites are completely removed from the + * analysis (not counted in lseff). Note that if more than + * one mutation is allowed, the site is removed only if all + * the alleles but one are smaller than or equal to this + * value. For example, an alignment column AAAAAAGAAT is + * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is + * conserved (including the third allele T which is a + * singleton). + * + * \param characterMapping a string giving the list of + * characters that should be considered as valid data. If a + * space is present in the string, the characters left of the + * space will be treated as valid data and the characters + * right of the space will be treated as missing data, that + * is tolerated but ignored. All characters not in the string + * will cause an EggInvalidCharacterError to be raised. + */ + void load(CharMatrix& data, + double minimumExploitableData=1., + unsigned int ignoreFrequency=0, + std::string characterMapping=dnaMapping); + + + /// Number of pairs contained in the instance + unsigned int numberOfPairs() const; + + /// Alignment distance between a given pair + int d(unsigned int pair_index); + + /// D statistic for a given pair + double D(unsigned int pair_index); + + /// D' statistic for a given pair + double Dp(unsigned int pair_index); + + /// r statistic for a given pair + double r(unsigned int pair_index); + + /// r2 statistic for a given pair + double r2(unsigned int pair_index); + + /// position of the first site for a given pair + unsigned int site1(unsigned int pair_index); + + /// position of the second site for a given pair + unsigned int site2(unsigned int pair_index); + + /// correlation coefficient between r2 and distance + double correl() const; + + /** \brief Computes the minimal number of recombination events + * + * The computation is performed as described in Hudson, RR and + * NL Kaplan. 1985. Statistical properties of the number of + * recombination events in the history of a sample of DNA + * sequences. Genetics 111: 147-164. The returned parameter is + * the minimal number of recombination events, given by the + * number of non-overlapping pairs of segregating sites violating + * the rule of the four gamete. Only sites with two alleles are + * considered. Note that homoplasy (multiple mutations) mimicks + * recombination. The result of this function is not stored + * in this instance, and re-computed at each call. + * + * \param data the same CharMatrix instance as passed to the load + * method. The instance must not have been modified. + * + */ + unsigned int Rmin(CharMatrix& data) const; + + + + protected: + + // adds a pair of polymorphic sites + // assume position2>position1, + // sites are polymorphic with exactly 2 alleles + void add(CharMatrix& data, unsigned int position1, unsigned int position2); + + // Constructor help + void init(); + + // Destructor helper + void clear(); + + // Resizes arrays + void reset(); + + // Small helper + inline double min(double a, double b) { return (a>b)?a:b;} + + // Small helper + inline double max(double a, double b) { return (a>b)?b:a;} + + // Small helper + inline void check(unsigned int pos) { if (pos>=_n) throw EggRuntimeError("tried to access an invalid index"); } + + /* Performs correlation + * + * This function works independently from the rest of the class. + * + * \param n length of data arrays. + * \param x first data vector. + * \param y second data vector. + * \param r variable to receive the correlation coefficient. + * \param a variable to receive the regression slope. + */ + static void _correl(unsigned int n, const int* x, const double* y, double& r, double& a); + + // Distance between pairs + int* _d; + + // D (classical) measure of LD + double *_D; + + // D' + double *_Dp; + + // r, correlation coefficient + double *_r; + + // square r + double *_r2; + + // Data array (not managed by the instance) + unsigned int *_site1; + + // Data array (not managed by the instance) + unsigned int *_site2; + + // Number of pairs + unsigned int _n; + + private: + + /// Copy constructor not available + LinkageDisequilibrium(const LinkageDisequilibrium&) { } + + /// Assignment operator not available + LinkageDisequilibrium& operator=(const LinkageDisequilibrium&) { + return *this; + } + + + class Interval { + public: + Interval(unsigned int, unsigned int); + unsigned int a() const; + unsigned int b() const; + bool good() const; + void set_false(); + private: + unsigned int _a; + unsigned int _b; + unsigned int _good; + }; + + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,120 @@ +/* + Copyright 2008-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_MICROSATELLITEDIVERSITY_HPP +#define EGGLIB_MICROSATELLITEDIVERSITY_HPP + +#include "DataMatrix.hpp" +#include <cstdlib> + +namespace egglib { + + /** \brief Analyzes microsatellite data + * + * \ingroup polymorphism + * + * Use the load() method to analyze data. All sites will be analyzed + * and accessors allow to access the value of a given statistics for + * a given site. There is no out-of-bound checking implemented in + * accessors. + * + */ + class MicrosatelliteDiversity { + + public: + + /** \brief Creates an object + * + */ + MicrosatelliteDiversity(); + + + /** \brief Destroys an object + * + */ + virtual ~MicrosatelliteDiversity(); + + + /** \brief Performs the analysis + * + * \param dataMatrix the object to analyze. + * + * \param missingData the integer identifying missing data. + * + * \param noMissingData if true, no allele will be + * excluded (including the one identified by the argument + * missingData). + * + */ + void load(const DataMatrix& dataMatrix, + int missingData=999, bool noMissingData=false); + + + /// Number of sites (or markers) + unsigned int numberOfSites() const; + + /// Heterozygosity + double He(unsigned int siteIndex) const; + + /// Number of alleles + unsigned int numberOfAlleles(unsigned int siteIndex) const; + + /// Variance of allele size + double sizeVariance(unsigned int siteIndex) const; + + /// IAM-based estimator of theta + double thetaAssumingIAM(unsigned int siteIndex) const; + + /// SMM-based estimator of theta, calculated from He + double thetaAssumingSMMfromHe(unsigned int siteIndex) const; + + /// SMM-based estimator of theta, calculated from VarSize + double thetaAssumingSMMfromSizeVariance(unsigned int siteIndex) const; + + + protected: + + unsigned int v_numberOfSites; + double *v_He; + unsigned int *v_numberOfAlleles; + double *v_sizeVariance; + double *v_thetaAssumingIAM; + double *v_thetaAssumingSMMfromHe; + double *v_thetaAssumingSMMfromSizeVariance; + + void init(); + void clear(); + + + private: + + + /// No copy allowed + MicrosatelliteDiversity(const MicrosatelliteDiversity& source) { + } + + /// No copy allowed + MicrosatelliteDiversity& operator=(const MicrosatelliteDiversity& source) { + return *this; + } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Ms.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,199 @@ +/* + Copyright 2008,2009,2011 Stéphane De Mita and Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_GMS_HPP +#define EGGLIB_GMS_HPP + +#include "DataMatrix.hpp" +#include <string> +#include <istream> + +namespace egglib { + + /** \brief ms-like sequence format parser + * + * The class provides parsing (input) and formatting (output) + * operations in ms format, that is the format used by Richard + * Hudson's program ms for outputting genotypes and by the + * associated program samplestat for reading them. Both types of + * operations are available through static methods using either + * a string or a stream (which can be a stream to or from a file + * or a string). In either case, types from the STL are used. + * Although ms deals only with data coded with 0 and 1, the class Ms + * offers the possibility of both importing and exporting data coded + * with by integer. All methods have an option named "separated". If + * this option is true, the parser or formatter introduces a slight + * modification of the format: genotypes individual data are + * separated by a white space ("1 0 1 1" instead of "1011", allowing + * genotype values larger than 9: "1 0 11 1"). + * + * \ingroup core + * + */ + class Ms { + + public: + + /** \brief Imports a sequence alignment + * + * Creates a istringstream from the string and calls the + * overloaded method. + * + * \param str the string to parse. + * \param ns the expected number of sequences. + * \param separated true if a white space separator is placed + * between genotype at each site. + * + * \return A sequence alignment as a data matrix. + */ + static DataMatrix get(std::string, unsigned int ns, bool separated=false); + + + /** \brief Imports a sequence alignment + * + * Attemps to generate a DataMatrix object from the stream. + * Reads only one simulation and throws a SeqlibFormatError + * exception in case of format error. + * + * Allows any number of white lines before the //, but no other + * data. Supports \r at the end of lines (before the \n). + * Accepted symbols are all integers (0-9). + * + * \param stream the stream to parse. + * \param ns the expected number of sequences. + * \param separated true if a white space separator is placed + * between genotype at each site. + * + * \return A sequence alignment as a data matrix. + */ + static DataMatrix get(std::istream& stream, unsigned int ns, bool separated=false); + + + /** \brief Exports a sequence alignment + * + * Internally creates a stringstream, calls the overloaded method + * and returns the outcome. + * + * \param dataMatrix the alignment object to write. + * \param separated true if a white space separator must be placed + * between the genotype at each site. + * + */ + static std::string format(DataMatrix& dataMatrix, bool separated=false); + + + /** \brief Exports a sequence alignment + * + * Writes the formatted string to the stream 'on the fly'. The + * formatted string is guaranteed to starts with a // line and + * ends with an empty line. The client is expected to take care + * of writing any header and add an additional white line between + * simulations if needed. The method throws a SeqlibRuntimeError + * if the stream is not writable. The data matrix should contain + * only data within range 0-9 if separated is false (default) and + * any positive (>=0) integer if separated is true. Note that + * output generated with separated=true is never compatible with + * the original ms format, and that output generated with + * separator=false is compatible with the original ms format only + * if all alleles are 0 or 1 (which is not checked by this + * formatted). + * + * \param stream the stream (file or string stream) where to + * write the output. + * \param dataMatrix the alignment object to write. + * \param separated true if a white space separator must be placed + * between the genotype at each site. + * + */ + static void format(std::ostream& stream, DataMatrix& dataMatrix, bool separated=false); + + + /** \brief Returns the last tMRCA read by any Ms instance + * + * If a tMRCA value was present in the last simulation read by + * any Ms instance, it will be returned by this method. A value + * of -1. is returned if no simulation was read, or if the last + * simulation didn't contain a tMRCA value or if the last + * simulation provoked an exception before reaching the tMRCA + * line. + * + */ + static double tMRCA(); + + + /** \brief Returns the last "prob" read by any Ms instance + * + * "prob" is returned by ms when a fixed number of segregating + * sites is used in conjunction with a theta value. If a "prob" + * value was present in the last simulation read by any Ms + * instance, it will be returned by this method. A value of -1 + * is returned if no simulation was read, or if the last + * simulation didn't contain a "prob" value or if the last + * simulation provoked an exception before reaching the "prob" + * line. + * + */ + static double prob(); + + + /** \brief Returns the tree string found in the last simulation read by any Ms instance + * + * If one or more trees were present in the last simulation read + * by any Ms instance, they will be returned as a unique string + * by this method. An empty string is returned if no simulation + * was read, or if the last simulation, or if the last simulation + * didn't contain any tree value or if the last simulation + * provoked an exception before reaching the tree line. + * + * Note: the trees are returned as a single line. + * + */ + static std::string trees(); + + + private: + // Line parser (the last \n is extracted and discarded - no error upon EOF) + std::string next_line(std::istream& stream); + + /// tMRCA (-1 if not found in ms output) + static double _tMRCA; + + /// probability (-1 if not found in ms output) + static double _prob; + + /// tree string (maybe contain several trees) (empty string if not found in ms output) + static std::string _trees; + + + /// No instantiation allowed + Ms() { } + + /// A fortiori no destruction allowed + ~Ms() { } + + /// No copy allowed + Ms(const Ms&) { } + + /// No copy allowed + Ms& operator=(const Ms&) { return *this; } + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Mutation.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,63 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_MUTATION_HPP +#define EGGLIB_MUTATION_HPP + +#include <vector> +#include "Edge.hpp" + +namespace egglib { + + /** \brief Very simple container of some information relative to a mutation + * + * \ingroup coalesce + * + */ + class Mutation { + + public: + + /// Default constructor + Mutation(); + + /// Age + //double age; + + /// Mutation index (for finding in Edge) + unsigned int actualSiteIndex; + + /// Position + double position; + + /// Segment index + unsigned int segmentIndex; + + /// Pointer to edge + //const Edge* edge; + + private: + + void init(); + + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Mutator.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,397 @@ +/* + Copyright 2009, 2010, 2012 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_MUTATOR_HPP +#define EGGLIB_MUTATOR_HPP + + +#include "DataMatrix.hpp" +#include "Random.hpp" +#include "Arg.hpp" +#include "Mutation.hpp" + + +namespace egglib { + + + /** \brief Implements mutation models + * + * \ingroup coalesce + * + * Works with a previously built Ancestral Reconbination Graph. The + * user must sets options using the setter-based interface. After + * that he or she can call the method mute() that will generates + * a DataMatrix object. + * + * Genotype data are represented by integer numbers. Regardless of + * the mutation model, the ancestral state is always 0. The user can + * set the rate of mutation (or, alternatively, fix the number of + * mutations that occurred - which is the number of segregating sites + * only with an infinite site model). + * + * Other options fall into two separate groups: the positions of the + * mutated sites and the process of mutation (how new alleles are + * generated). + * + * Concerning allele generation, several mutation models are available + * (coded by single letters): + * - F: fixed number of alleles. Among other markers, this model is + * appropriate for simulating nucleotides. The user is able + * to choose the number of alleles (where 2 is the standard + * for an infinite site model and 4 for a finite site model). + * Mutator allows assigning independent weights between all + * different transition types and can draw randomly the + * ancestral states, providing a way to emulate evolution of + * nucleotides with multiple mutations at the same site and + * reversion. + * - I: infinite number of alleles. At a given site, each mutation + * raises a new allele. The value of the alleles is therefore + * irrelevant (it only denotes its order of appearance). This + * model does not permit homoplasy. + * - S: stepwise mutation model. In this model the value of the + * alleles are interpreted as a size (typically for simulating + * a microsatellite marker). Each mutation either increases + * or decreases the allele size by an increment of one. + * - T: two-phase mutation model. This model is a generalization + * of the stepwise mutation model (S). For a mutation, the + * increment (either increase or decrease) is 1 with the + * probability given by the parameter (1-TPMproba). With + * probability TPMproba, the increment is drawn from a + * geometric distribution of parameter given by the other + * parameter (TPMparam). + * + * By default, the program will assume an infinite site model (ISM). + * Each mutation will occur to a new position drawn from the interval + * [0,1]. It is possible to set any mutation model with an ISM + * (including microsatellite-like models I, S and T). Alternatively, + * the user can specify a finite number of sites available for + * mutation. For a microsatellite marker, the user will want to + * specify a single site. It is possible to set a finite number of + * sites for all mutation models. In all cases, the mutations will + * be forced to target these sites. It is possible to apply weights + * independently to all sites. The higher the weight value + * (comparatively to the other sites), the higher the probability + * that this site mutes. The weights needs not to be relative. In + * addition, the user can set the positions of the different sites. + * Nothings forces him or her to place them in order. Note that this + * does not affect the mutation process, but on the amount of + * recombination that will be allowed between sites. + * + */ + class Mutator { + + public: + + /** \brief Initializes with default values + * + * List of default values: + * - theta = 0 + * - fixedNumberOfMutations = 0 + * - model = F (fixed number of alleles) + * - fixed number of alleles = 2 + * - infinite site model + * - TPM parameters are both preset to 0.5 + * + */ + Mutator(); + + + /** \brief Destroys the object + * + */ + ~Mutator(); + + + /** \brief Copy constructor + * + */ + Mutator(const Mutator&); + + + /** \brief Assignement operator + * + */ + Mutator& operator=(const Mutator&); + + + /** \brief Restores default values of all parameters + * + */ + void reset(); + + + /** \brief Gets the fixed number of mutations + * + */ + unsigned int fixedNumberOfMutations() const; + + + /** \brief Sets the fixed number of mutations + * + * The value can be 0. It is not allowed to set both the + * fixed number of mutations and the mutation rate at + * non-zero value + * + */ + void fixedNumberOfMutations(unsigned int); + + + /** \brief Gets the mutation rate + * + */ + double mutationRate() const; + + + /** \brief Sets the mutation rate + * + * The value cannot be negative. The value can be 0. It is + * not allowed to set both the fixed number of mutations and + * the mutation rate at non-zero value + * + */ + void mutationRate(double); + + + /** \brief Gets the mutation model + * + * See the class documentation for the signification of the + * different one-letter codes. + * + */ + char mutationModel() const; + + + /** \brief Sets the mutation model + * + * The passed character must be one of F, I, S and T. See the + * class documentation for their signification. + * + */ + void mutationModel(char); + + + /** \brief Gets the fixed number of possible alleles + * + */ + unsigned int numberOfAlleles() const; + + + /** \brief Sets the fixed number of possible alleles + * + * The value must be larger than 1. This parameter is + * meaningful only for the fixed number allele model of + * mutation, and ignored otherwise. + * + */ + void numberOfAlleles(unsigned int); + + + /** \brief Sets a transition weight + * + * \param i row (previous allele index). + * \param j column (next allele index). + * \param value weight to apply. + * + * Indices i and j must be different. Weights can be any + * strictly positive value. + * + */ + void transitionWeight(unsigned int i, unsigned int j, double value); + + + /** \brief Gets a transition weight + * + * \param i row (previous allele index). + * \param j column (next allele index). + * + * Indices i and j must be different. + * + */ + double transitionWeight(unsigned int i, unsigned int j); + + + /** \brief Set to true to draw ancestral alleles randomly + * + * By default, the ancestral allele is always 0. If this + * variable is set to true, the ancestral allele will be + * randomly drawn from the defined number of alleles. This + * option is always ignored unless in combination with the + * Fixed Allele Number model. + * + */ + void randomAncestralAllele(bool flag); + + + /** \brief true if ancestral alleles must be drawn randomly + * + */ + bool randomAncestralAllele() const; + + + /** \brief Gets the TPM probability parameter + * + */ + double TPMproba() const; + + + /** \brief Sets the TPM probability parameter + * + * This parameter is considered only if the mutation model + * is T (two-phase mutation model). It gives the probability + * that a mutation step is not fixed to be 1. If TPMproba is + * 0, the mutation model is SMM. + * + * The value must be >=0. and <=1. + * + */ + void TPMproba(double value); + + + /** \brief Gets the TPM distribution parameter + * + */ + double TPMparam() const; + + + /** \brief Sets the TPM distribution parameter + * + * This parameter is considered only if the mutation model + * is T (two-phase mutation model). It gives the parameter + * of the geometric distribution which is used to generate + * the mutation step (if it is not one). + * + * The value must be >=0. and <=1. + * + */ + void TPMparam(double value); + + + /** \brief Gets the number of mutable sites + * + * A value a zero must be interpreted as the infinite site + * model. Note that after all calls all data from the tables + * sitePositions and siteWeights will be reset. + * + */ + unsigned int numberOfSites() const; + + + /** \brief Sets the number of mutable sites + * + * The value of zero is accepted and imposed the infinite + * site model. + * + */ + void numberOfSites(unsigned int); + + + /** \brief Gets the position of a given site + * + */ + double sitePosition(unsigned int siteIndex) const; + + + /** \brief Set the position of a given site + * + * The position must be >=0 and <=1 + * + */ + void sitePosition(unsigned int siteIndex, double position); + + + /** \brief Gets the mutation weight of a given site + * + */ + double siteWeight(unsigned int siteIndex) const; + + + /** \brief Set the site weight of a given site + * + * The weight must be strictly positive. + * + */ + void siteWeight(unsigned int siteIndex, double weight); + + + /** \brief Performs mutation + * + * \param arg Ancestral recombination graph instance. If the + * ARG is partially built or not a all, or improperly so, + * the behaviour of this method is not defined. + * + * \param random The address of a Random instance to be + * used for generating random numbers. + * + * \return A DataMatrix instance containing simulated data. + * + */ + DataMatrix mute(Arg* arg, Random* random); + + + /** \brief Gets the last number of mutations + * + * Returns the number of mutations of the last call of mute( ). + * By default, this method returns 0. + * + */ + unsigned int numberOfMutations() const; + + + private: + + void clear(); + void init(); + void copy(const Mutator&); + + //int nextAllele(int allele, Random* random); + int TPMstep(double inTPMproba, Random* random); + void apply_mutation(unsigned int matrixIndex, + unsigned int actualSite, DataMatrix& data, + const Edge* edge, int allele, + unsigned int segment, Random* random); + + + char _model; + double _mutationRate; + unsigned int _fixedNumberOfMutations; + unsigned int _numberOfAlleles; + double** _transitionWeights; + bool _randomAncestralAllele; + unsigned int _numberOfSites; + double* _sitePositions; + double* _siteWeights; + double _TPMproba; + double _TPMparam; + int maxAllele; + unsigned int _numberOfMutations; + std::vector<Mutation> _cache_mutations; + unsigned int _cache_mutations_reserved; + + }; + + + bool compare(Mutation mutation1, Mutation mutation2); // returns True if mutation1 is older + +} + + + + +#endif +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/NucleotideDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,377 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_NUCLEOTIDEDIVERSITY_HPP +#define EGGLIB_NUCLEOTIDEDIVERSITY_HPP + + +#include "BaseDiversity.hpp" +#include <string> +#include <vector> + + + +namespace egglib { + + + /** \brief Performs analyzes of population genetics + * + * \ingroup polymorphism + * + * This class computes several summary statistics based on + * nucleotide analysis. Note that it is possible to use the same + * object to analyze different data set. Calling the load() method + * erases all data preivously computed (if any). Calling the load() + * method is absolutely required to compute any statistics. Some + * statistics are not computed by default, but are if the + * corresponding accessor is used (only load() is required). + * + * Note that "unsecure" accessors don't perform out-of-bound checks. + * + * S is the number of varying sites (only in sites that were not + * rejected). + * + * eta is the minimum number of mutations, that is the sum of the + * number of alleles minus 1 for each varying site. eta = S if all + * sites have no variant or 2 alleles. eta is computed independently + * of the option multiple and IS NOT computed over lseff sites. + * + * Pi is the average number of pairwise differences between sequences + * (expressed here per site) or (as computed here) the mean per site + * (unbiased) heterozygosity. Pi is zero if no polymorphic sites. + * + * D is the Tajima's test of neutrality + * Ref. Tajima F.: Statistical method for testing the neutral + * mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595. + * It is arbitrary set to 0 if no polymorphic sites. + * + * tW: thetaW: estimator of theta based on polymorphic sites (ref. + * e.g. Watterson 1975 Theor. Pop. Biol.). + * Both D and thetaW are computed assuming that rounded nseff samples + * have been sampled. + * The variance of D is computed using rounded nseff instead of ns. + * + * H is the Fay and Wu's test of neutrality. + * Z is the standardized version and E a similar test. + * Ref. Fay J. C., Wu C.-I.: Hitchhiking under positive Darwinian + * selection. Genetics 2000, 155:1405-1413. and Zeng K., Fu Y. X., + * Shi S., Wu C.-I.: Statistical tests for detecting positive + * selection by utilizing high-frequency variants. Genetics 2006, + * 174:1431-9. Both are arbitrary set to 0 if no polymorphic or + * orientable sites. + * + * tH and tL: theta H: estimators of theta based on derived + * polymorphic sites (ref in Fay and Wu and Zeng al.). The variance + * of H/Z are computed assuming that rounded nseff samples have + * been sampled. + * + */ + class NucleotideDiversity : public BaseDiversity { + + public: + + /** \brief Builds an object + * + */ + NucleotideDiversity(); + + + /** \brief Destroys an object + * + */ + virtual ~NucleotideDiversity(); + + + /** \brief Identifies polymorphic sites and computes basis + * statistics + * + * \param data an alignment object (subclass of CharMatrix). + * The presence of outgroup or of different populations will + * be detected based on the populationLabel members of the + * passed object. The populationLabel 999 will be interpreted + * as outgroups. If several outgroups are passed, sites were + * the outgroups are not consistent will be treated as "non- + * orientable". + * + * \param allowMultipleMutations if true, sites with more + * than two alleles will not be ignored. The sum of the + * frequencies of all alleles not matching the outgroup will + * treated as the derived allele frequency (for orientable + * sites). + * + * \param minimumExploitableData sites where the non-missing + * data (as defined by characterMapping) are at a frequency + * larger than this value will be removed from the analysis. + * Use 1. to take only 'complete' sites into account and 0. + * to use all sites. (The outgroup is not considered in this + * computation.) + * + * \param ignoreFrequency removes sites that are polymorph + * because of an allele at absolute frequency smaller than or + * equal to this value. If ignoreFrequency=1, no sites are + * removed, if ignoreFrequency=0, singleton sites are + * ignored. Such sites are completely removed from the + * analysis (not counted in lseff). Note that if more than + * one mutation is allowed, the site is removed only if all + * the alleles but one are smaller than or equal to this + * value. For example, an alignment column AAAAAAGAAT is + * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is + * conserved (including the third allele T which is a + * singleton). + * + * \param characterMapping a string giving the list of + * characters that should be considered as valid data. If a + * space is present in the string, the characters left of the + * space will be treated as valid data and the characters + * right of the space will be treated as missing data, that + * is tolerated but ignored. All characters not in the string + * will cause an EggInvalidCharacterError to be raised. + * + * \param useZeroAsAncestral if true, all outgroups (if + * present) will be ignored and the character "0" will be + * considered as ancestral for all sites, whatever the + * character mapping. + * + */ + virtual void load( + CharMatrix& data, + bool allowMultipleMutations=false, + double minimumExploitableData=1., + unsigned int ignoreFrequency=0, + std::string characterMapping=dnaMapping, + bool useZeroAsAncestral=false + ); + + + // accessors for the "site analysis" section + + /// Number of polymorphic sites + unsigned int S() const; + + /// Number of polymorphic orientable sites + unsigned int So() const; + + /// Minimum number of mutations + unsigned int eta() const; + + /// Average of per-site number of sequences effectively used + double nseff() const; + + /// Number of sites effectively used + unsigned int lseff() const; + + /// Average of number of sequences effectively used at orientable sites + double nseffo() const; + + /// Number of orientable sites + unsigned int lseffo() const; + + /// Number of detected populations + unsigned int npop() const; + + /// Label of the population with given index (unsecure) + unsigned int popLabel(unsigned int popIndex) const; // no check! + + + // accessors for the "diversity" section + + /// Nucleotide diversity + double Pi(); + + /// Watterson estimator of theta + double thetaW(); + + /// Average of Pi over populations + double average_Pi(); + + /// Pi of a given population (unsecure) + double pop_Pi(unsigned int popIndex); // no check! + + /// Tajima's D + double D(); + + // accessors for the "outgroup diversity" section + + /// Fay and Wu estimator of theta + double thetaH(); + + /// Zeng et al. estimator of theta + double thetaL(); + + /// Fay and Wu's H + double H(); + + /// Standardized H + double Z(); + + /// Zeng et al.'s E + double E(); + + // accessors for the "differentiation" section + + /// Number of sites with at least one fixed difference + unsigned int FixedDifferences(); + + /// Number of sites with at least one allele shared among at least two populations + unsigned int CommonAlleles(); + + /// Number of sites with at least one non-fixed allele shared among at least two populations + unsigned int SharedAlleles(); + + /// Number of sites with at least one allele specific to one population + unsigned int SpecificAlleles(); + + /// Number of sites with at least one derived allele specific to one population + unsigned int SpecificDerivedAlleles(); + + /// Number of polymorphisms in a given population (unsecure) + unsigned int Polymorphisms(unsigned int pop); + + /// Number of specific alleles for a given population (unsecure) + unsigned int SpecificAlleles(unsigned int pop); + + /// Number of specific derived allele for a given population (unsecure) + unsigned int SpecificDerivedAlleles(unsigned int pop); + + /// Number of fixed differences between a given pair of populations (unsecure; pop2 must be larger than pop1) + unsigned int FixedDifferences(unsigned int pop1, unsigned int pop2); + + /// Number of common alleles between a given pair of populations (unsecure; pop2 must be larger than pop1) + unsigned int CommonAlleles(unsigned int pop1, unsigned int pop2); + + /// Number of shared non-fixed alleles between a given pair of populations (unsecure; pop2 must be larger than pop1) + unsigned int SharedAlleles(unsigned int pop1, unsigned int pop2); + + + // accessor for the "triConfigurations" section + + /** \brief Number falling into one of the possible site configurations + * + * The statistics are limited to three populations. + * Assuming an unrooted A/G polymorphism (A and G can be + * substitued), the site configurations are: + * - 0: A&G A A specific 1 + * - 1: A&G A G specific 1 + fixed 2-3 + * - 2: A A&G A specific 2 + * - 3: A A&G G specific 2 + fixed 1-3 + * - 4: A A A&G specific 3 + * - 5: A G A&G specific 3 + fixed 1-2 + * - 6: A&G A&G A shared 1-2 + * - 7: A&G A A&G shared 1-3 + * - 8: A A&G A&G shared 2-3 + * - 9: A&G A&G A&G shared 1-2-3 + * - 10: A G G fixed 1 + * - 11: A G A fixed 2 + * - 12: A A G fixed 3 + * + * \param index must be an index from 0 to 12. + * + */ + unsigned int triConfiguration(unsigned int index); + + + /// Builds and returns the vector of positions of all polymorphic sites + std::vector<unsigned int> polymorphic_positions() const; + + + /** \brief Builds and returns the vector of positions of all singleton sites + * + * A site singleton when it is polymorphic according to + * parameter of the diversity analysis, when it has exactly two + * alleles and one of them is at absolute frequency 1 (one + * copy) disregarding the outgroup. + * + */ + std::vector<unsigned int> singleton_positions() const; + + + protected: + + /** \brief This class cannot be copied + * + */ + NucleotideDiversity(const NucleotideDiversity& source) { } + + + /** \brief This class cannot be copied + * + */ + NucleotideDiversity& operator=(const NucleotideDiversity& source) { return *this; } + + + void init(); // initializes values + void clear(); // free memory but doesn't initializes + + // diversity (without outgroup) + void diversity(); + + // diversity with outgroup + void outgroupDiversity(); + + // site patterns + void differentiation(); + + // triconfigurations + void triConfigurations(); + + + // holders for statistics, with booleans flagging groups of stats + + bool b_analysisSites; + + bool b_diversity; + + double v_Pi; // nucleotide diversity + double v_thetaW; // theta (Watterson estimator) + double v_average_Pi; // average diversity across populations + double *v_pop_Pi; // diversity per population + double v_D; // Tajima's D + + bool b_outgroupDiversity; + + double v_thetaH; // theta (Fay and Wu estimator) + double v_thetaL; // theta (Zeng estimator) + double v_H; // Fay and Wu's H + double v_Z; // normalized Fay and Wu's H + double v_E; // Zeng et al.'s E + + bool b_differentiation; + + unsigned int *v_pairwiseFixedDifferences; + unsigned int *v_pairwiseCommonAlleles; + unsigned int *v_pairwiseSharedAlleles; + unsigned int *v_popPolymorphic; + unsigned int *v_popSpecific; + unsigned int *v_popSpecificDerived; + unsigned int v_countFixedDifferences; + unsigned int v_countCommonAlleles; + unsigned int v_countSharedAlleles; + unsigned int v_countSpecificAlleles; + unsigned int v_countSpecificDerivedAlleles; + + + bool b_triConfigurations; + + unsigned int *v_triConfigurations; + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,279 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_PARAMSET_HPP +#define EGGLIB_PARAMSET_HPP + + +#include "DataMatrix.hpp" + + +namespace egglib { + + class Change; + class Controller; + + + /** \brief Set of parameters + * + * \ingroup coalesce + * + */ + class ParamSet { + + public: + + /** \brief Default constructor + * + * Initializes all parameters to reasonnable values (except + * that the sample size is null: 1 population, 0 samples, + * selfing rate of 0, recombination rate of 0, growth rate of + * 0, population size of 1 and no changes. + * + */ + ParamSet(); + + /** \brief Destructor + * + */ + ~ParamSet(); + + /** \brief Copy constructor + * + */ + ParamSet(const ParamSet&); + + /** \brief Assignment operator + * + */ + ParamSet& operator=(const ParamSet&); + + /** \brief Restores default value of all parameters + * + */ + void reset(); + + /** \brief Gets the number of populations + * + */ + unsigned int numberOfPopulations() const; + + /** \brief Gets a pairwise migration rate + * + * It is allowed to access a diagonal value. Diagonal + * values contain the sum of values of the corresponding + * line (diagonal cell excepted, of course). + * + */ + double pairwiseMigrationRate(unsigned int source, unsigned int dest) const; + + /** \brief Sets a pairwise migration rate + * + * It is not allowed to set a value on the diagonal (this + * would raise an exception). The method takes care of + * modifying the diagonal accordingly (still this is not + * relevant for the client); + * + */ + void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value); + + /** \brief Sets the migration rate for all matrix + * + */ + void migrationRate(double value); + + /** \brief Gets a population size + * + */ + double populationSize(unsigned int populationIndex) const; + + /** \brief Sets a population size + * + * The size must be strictly positive. + * + */ + void populationSize(unsigned int populationIndex, double value); + + /** \brief Gets a growth rate + * + */ + double growthRate(unsigned int populationIndex) const; + + /** \brief Sets a growth rate + * + */ + void growthRate(unsigned int populationIndex, double value); + + /** \brief Gets the recombination rate + * + */ + double recombinationRate() const; + + /** \brief Sets the recombination rate + * + */ + void recombinationRate(double value); + + /** \brief Gets the number of recombining segments + * + */ + unsigned int numberOfSegments() const; + + /** \brief Sets the number of recombining segments + * + */ + void numberOfSegments(unsigned int value); + + /** \brief Gets the selfing rate + * + */ + double selfingRate() const; + + /** \brief Sets the selfing rate + * + */ + void selfingRate(double value); + + /** \brief Adds a population to the model + * + * \param migr pairwise migration rate between other + * population and the new one. + * + * The parameters for the new population are equivalent to + * the default parameters. + * + */ + void addPopulation(double migr); + + /** \brief Adds a change + * + * The change can be of any type derived from Change. A + * const Change* must be passed, so ParamSet will neither + * modify or delete the object itself. All passed Change + * object must be kept available for use by ParamSet. + * + */ + void addChange(const Change* change); + + /** \brief Gets the date of the next change + * + * Returns -1 if no change is planned. + * + */ + double nextChangeDate() const; + + /** \brief Applies the next change event + * + * \param controller the Change event might need to have + * access to simulation controller (to trigger coalescent + * events, for example). + * + */ + void nextChangeDo(Controller* controller); + + /** \brief Gets the number of single sample from a population + * + */ + unsigned int singles(unsigned int populationIndex) const; + + /** \brief Sets the number of single sample from a population + * + */ + void singles(unsigned int populationIndex, unsigned int value); + + /** \brief Gets the number of double sample from a population + * + */ + unsigned int doubles(unsigned int populationIndex) const; + + /** \brief Sets the number of double sample from a population + * + */ + void doubles(unsigned int populationIndex, unsigned int value); + + /** \brief Computes the total number of samples + * + */ + unsigned int numberOfSamples() const; + + /** \brief Gives the date of the last size change + * + * \param populationIndex the index of the population. + * \return The date where the last change occurred, or 0. if + * no change occurred during the simulation. + * + */ + double dateOfLastChange(unsigned int populationIndex) const; + + + /** \brief Sets the date of the last size change + * + * \param populationIndex the index of the population. + * \param date the date where the last change occurred, or 0. + * if no change occurred during the simulation. + * + */ + void dateOfLastChange(unsigned int populationIndex, double date) const; + + + /** \brief Set groups labels + * + * Sets the group labels of the DataMatrix, according to the + * current state of population structure, and assuming that + * the DataMatrix was generated by the class Arg. + * + * \param dataMatrix the DataMatrix object to modify. The + * number of sequences must match the total number of samples + * defined by the ParamSet object this method is called on. + * + * \param labelIndividuals by default, labels the different + * samples depending on the population they come from (0 + * being the label of the first population). If this flag is + * set to true, then the samples are labelled depending on + * the individual they come from, regardless of populations. + * In that case there can be only one or two genes for a + * given group label. + * + */ + void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false); + + private: + + void clear(); + void init(); + void copy(const ParamSet&); + + double _selfingRate; + double _recombinationRate; + unsigned int _numberOfSegments; + unsigned int _numberOfPopulations; + unsigned int* _singles; + unsigned int* _doubles; + double* _growthRates; + double* _populationSize; + double* _dateOfLastChange; + double** migrationMatrix; + unsigned int _numberOfChanges; + unsigned int nextChangeIndex; + Change const** changes; + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,143 @@ +/* + Copyright 2009-2010 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_POPULATION_HPP +#define EGGLIB_POPULATION_HPP + + +#include "Edge.hpp" + +namespace egglib { + + class Random; + + /** \brief Handles a single population + * + * \ingroup coalesce + * + */ + class Population { + + public: + + /** \brief Default constructor + * + * Generates an empty population. + * + */ + Population(); + + /** \brief Copy constructor + * + */ + Population(const Population& source); + + /** \brief Assignment operator + * + */ + Population& operator=(const Population& source); + + /** \brief Destructor + * + * The object only cleans Edge objects currently stored in it. + * + */ + ~Population(); + + /** \brief Standard constructor + * + * The Edge instances will be handled by address and they + * MUST be passed using the method set(). + * + * \param numberOfSegments number of recombining segments. + * + * \param numberOfLineages the number of lineages contained + * in this population. + * + * \param firstIndex the absolute index (or ID) of the first + * lineage (the other will have consecutive incremented + * ID's). + * + */ + Population(unsigned int numberOfSegments, + unsigned int numberOfLineages, unsigned firstIndex); + + /** \brief Gets the number of lineages + * + */ + unsigned int numberOfLineages() const; + + /** \brief Gets the efficient number of lineages + * + * The number of lineages is multiplied by the number of + * covered segments of each lineages. + * + */ + unsigned int efficientNumberOfLineages() const; + + /** \brief Sets the Edge of a lineage + * + * \param index the index of the lineage within the + * population. + * \param edge the address of the Edge instance representing + * the lineage. + * + */ + void set(unsigned int index, Edge* edge); + + /** \brief Removes and returns a random lineage. + * + * \param random pointer to simulator's random generator + * instance. + * + */ + Edge* extractRandomly(Random* random); + + /** \brief Removes and returns a given lineage. + * + * \param index the relative index of the lineage. + * + */ + Edge* extractByIndex(unsigned int index); + + /** \brief Appends a lineage to the object + * + */ + void push(Edge* edge); + + /** \brief Gets coverage + * + */ + unsigned int coverage(unsigned int edgeIndex) const; + + + private: + + void copy(const Population& source); + void clear(); + Edge* pick(unsigned int index); + void init(); + unsigned int _numberOfLineages; + unsigned int _efficientNumberOfLineages; + Edge** lineages; + }; + +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Random.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,134 @@ +/* + Copyright 2008,2009,2012 Stéphane De Mita, Mathieu Siol + Adapted from MStrat, developed by Charles-Edouard Coste, + Thomas M. Bataillon, Mathieu Cotisson, Guy Decoux, Chistophe Rozale, + Daniel J. Schoen and Jacques L. David. + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_RANDOM_HPP +#define EGGLIB_RANDOM_HPP + +namespace egglib { + + /** \brief Pseudo-random number generator + * + * \ingroup core + * + * Random is a pseudo-random number generator, adapted from a part of MStrat, + * developed by Charles-Edouard Coste, Thomas M. Bataillon, Mathieu Cotisson, + * Guy Decoux, Chistophe Rozale, Daniel J. Schoen and Jacques L. David. + * + * It uses two different seeds. By default, they are initialized to available + * arbitrary values. However, a given sequence can be repeated by passing the + * same two seeds. + * + */ + class Random { + public: + /** \brief Initializes using default seeds + * + * Uses the current system time and the memory address of the object as an attempt to generate unique sequences. + */ + Random(); + + /** \brief Initializes using given seeds + * + * This constructor can be used to reproduce a given sequence. + */ + Random(double seed1, double seed2); + + /** \brief Draws a number from an exponential distribution + * + * \param expectation the distribution mean (also 1/lambda + * where lambda is the rate parameter). + * + */ + double erand(double expectation); + + /** \brief Draws an integer from a uniform distribution bound by 0 and max (max is not included) + * + * max is not included. + * + */ + unsigned int irand(unsigned int max); + + /** \brief Draws an integer from a Poisson distribution with parameter p + * + * The Poisson transformation algorithm was taken from (in French) + * http://www.u-picardie.fr/~cochard/IEM/demos/C107/C107_3.htm. + */ + unsigned int prand(double p); + + /** \brief Draws a number from a normal distribution of expectation 0 and variance 1 + * + * The algorithm used is the polar form of the Box-Muller + * algorithm. \todo use the Ziggurat algorithm for the + * nrand() method of Random. + * + */ + double nrand(); + + /** \brief Draws a number from a geometric law + * + * \param param the parameter of the law + * + */ + unsigned int grand(double); + + /** \brief Draws a number from a uniform distribution between 0 and 1 + * + */ + double uniform(); + + /** \brief Gets the current value of the first seed + * + */ + double seed1() const; + + /** \brief Gets the current value of the second seed + * + */ + double seed2() const; + + /** \brief Sets the current value of the first seed + * + */ + void seed1(double); + + /** \brief Sets the current value of the second seed + * + */ + void seed2(double); + + private: + // First seed + double _seed1; + + // Second seed + double _seed2; + + /* since the normal random generator draws two numbers at + * a time, one is cached and returned at any subsequent call + */ + bool b_ncached; + double v_ncached; + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,207 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of the EggLib library. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + + +#ifndef EGGLIB_SITEPOLYMORPHISM_HPP +#define EGGLIB_SITEPOLYMORPHISM_HPP + + + +namespace egglib { + + + /** \brief Implements diversity analysis at the site level + * + * \ingroup polymorphism + * + * Data are loaded along with a population index. It is necessary to + * set the number of populations prior to use. + * + * Outgroup sequence must be loaded separetedly. There can be any + * number of outgroups, but they must be all consistent otherwise the + * site will be considered as not orientable. + * + */ + class SitePolymorphism { + + public: + + /** \brief Builds an object + * + */ + SitePolymorphism(); + + + /** \brief Builds an object + * + * \param npop number of populations + * + */ + SitePolymorphism(unsigned int npop); + + + /** \brief Destroys an object + * + */ + virtual ~SitePolymorphism(); + + + /** \brief Copy constructor + * + */ + SitePolymorphism(const SitePolymorphism& source); + + + /** \brief Assignment operator + * + */ + SitePolymorphism& operator=(const SitePolymorphism& source); + + + /** \brief Sets the number of populations + * + * NOTE THAT all previous data is lost. + * + */ + void numberOfPopulations(unsigned int npop); + + + /** \brief Adds a character + * + * \param populationIndex the index of the population from + * which is sampled this character (do not use "population + * label"). + * + * \param character the character value (it is assumed it + * represents a valid character. + * + */ + void load(unsigned int populationIndex, char character); + + + /** \brief Loads outgroup state + * + * There can be any number of outgroup states. Only + * characters that are considered as valid (whatever the list + * is) should be loaded. + * + */ + void outgroup(char state); + + + /** \brief Number of different alleles + * + */ + unsigned int numberOfAlleles() const; + + + /** \brief Gets an allele (unsecure) + * + * Assumes that the index provided lies in the valid range + * + */ + char allele(unsigned int index) const; + + + /** \brief Gets a frequency (unsecure) + * + * The sum of of frequencies of the allele over populations + * is computed. Not out-of-bounds check is performed. + * + */ + unsigned int alleleFrequency(unsigned int alleleIndex) const; + + + /** \brief Gets the frequency of an allele in one pop (unsecure) + * + * The frequency of the allele in the given population is + * returned. Not out-of-bounds check is performed. + * + */ + unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const; + + + /** \brief Sums the frequency of derived allele(s) + * + * This method assumes that the site is orientable. It will + * use as outgroup the first outgroup character entered, + * assuming at least one was entered and that all (if more + * than one) were identical. + * + */ + unsigned int derivedAlleleFrequency() const; + + + /** \brief Number of sequences that were analyzed + * + */ + unsigned int ns() const; + + + /** \brief Gets the number of analyzed sequences for a population + * + * No out-of-bound check is performed + * + */ + unsigned int ns(unsigned int popIndex) const; + + + /** \brief Checks if the site can be oriented + * + * Returns true if at least one outgroup datum has been + * loaded, if all outgroup data are identical (regardless of + * their value) and if the outgroup allele is one of the + * allele in the sample. + * + */ + bool isOrientable() const; + + bool isPolymorphic(unsigned int popIndex) const; + bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const; + bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const; + bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const; + bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const; + + + + + protected: + + // helpers + void init(); + void clear(); + void copy(const SitePolymorphism& site); + + + // data + unsigned int m_numberOfPopulations; + unsigned int m_numberOfStates; + char * m_states; + unsigned int ** m_frequencies; + unsigned int m_numberOfOutgroups; + char * m_outgroups; + unsigned int m_ns; + unsigned int * m_pop_ns; + + bool m_cache_orientable; + + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,140 @@ +/* + Copyright 2008-2009 Stéphane De Mita, Mathieu Siol + + This file is part of EggLib. + + EggLib is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + EggLib is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with EggLib. If not, see <http://www.gnu.org/licenses/>. +*/ + +#ifndef EGGLIB_STADEN_HPP +#define EGGLIB_STADEN_HPP + +#include <string> +#include <istream> +#include "Align.hpp" + +namespace egglib { + + /** \brief Parser of Staden output format + * + * \ingroup core + * + * The parser is available as a static method. It takes either a + * stream or a string containing data formatted by the program GAP4 + * of the Staden package (command 'dump contig to file'). + * + */ + class Staden { + + public: + + + /** \brief Parses a string + * + * \param string a string containing an alignment formatted + * by the program GAP4 of the Staden package. + * + * \param deleteConsensus if true, the sequence named + * "CONSENSUS" is deleted from the file (if it is present). + * + * \return An Align instance containing the data found in + * the Staden while, after recoding the character following + * the standard codes. + * + * This method opens a stream to the string and calls the + * overloaded method. + * + * The character replacement rules assume Staden default + * convention, as follows: + * - "-" codes for an unknown base and is replaced by "N". + * - "*" codes for an alignment gap and is replaced by "-". + * - A white space represents missing data and is replaced + * by "?". + * + */ + static Align parse(const std::string& string, bool deleteConsensus=true); + + + /** \brief Parses an open stream + * + * \param stream the open containing an alignment formatted + * by the program GAP4 of the Staden package. + * + * \param deleteConsensus if true, the sequence named + * "CONSENSUS" is deleted from the file (if it is present). + * + * \return An Align instance containing the data found in + * the Staden while, after recoding the character following + * the standard codes. + * + * The character replacement rules assume Staden default + * convention, as follows: + * - "-" codes for an unknown base and is replaced by "N". + * - "*" codes for an alignment gap and is replaced by "-". + * - A white space represents missing data and is replaced + * by "?". + * + */ + static Align parse(std::istream& stream, bool deleteConsensus=true); + + + private: + + /// Not allowed to instantiate this class + Staden() { } + + /// Not allowed to instantiate this class + Staden(const Staden& source) { } + + /// Not allowed to instantiate this class + ~Staden() { } + + + /* Gets the start position of sequences + * + * The functions gives total number of characters before the start of sequences + * and reads through until the next backspace (ignores the first line). + */ + static void getShift(); + + // Translates according to the Staden format + static char transforme(char); + + // Imports one sequence + static bool readOneSequence(); + + // Imports and concatenates one sequence + static bool readAppendOneSequence(); + + // Replaces dots by the matching character from CONSENSUS + static void undot(bool delete_consensus=true); + + // The number of characters before the start of sequences + static int shift; + + // The dynamically filled container (will result in an aligment) + static Container container; + + // The current position + static int currpos; + + // The reading stream + static std::istream* stream; + + // Stores unique 8 characters discriminating readings + static std::vector<std::string> ID; + }; +} + +#endif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/egglib/egglib-2.1.5/include/egglib-cpp/config.h Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,80 @@ +/* config.h. Generated from config.h.in by configure. */ +/* config.h.in. Generated from configure.ac by autoheader. */ + +/* Define to 1 if you have the <inttypes.h> header file. */ +#define HAVE_INTTYPES_H 1 + +/* Define to 1 if you have the `bpp-core' library (-lbpp-core). */ +/* #undef HAVE_LIBBPP_CORE */ + +/* Define to 1 if you have the `bpp-seq' library (-lbpp-seq). */ +/* #undef HAVE_LIBBPP_SEQ */ + +/* Define to 1 if you have the <memory.h> header file. */ +#define HAVE_MEMORY_H 1 + +/* Define to 1 if you have the `sqrt' function. */ +/* #undef HAVE_SQRT */ + +/* Define to 1 if stdbool.h conforms to C99. */ +#define HAVE_STDBOOL_H 1 + +/* Define to 1 if you have the <stdint.h> header file. */ +#define HAVE_STDINT_H 1 + +/* Define to 1 if you have the <stdlib.h> header file. */ +#define HAVE_STDLIB_H 1 + +/* Define to 1 if you have the <strings.h> header file. */ +#define HAVE_STRINGS_H 1 + +/* Define to 1 if you have the <string.h> header file. */ +#define HAVE_STRING_H 1 + +/* Define to 1 if you have the <sys/stat.h> header file. */ +#define HAVE_SYS_STAT_H 1 + +/* Define to 1 if you have the <sys/types.h> header file. */ +#define HAVE_SYS_TYPES_H 1 + +/* Define to 1 if you have the <unistd.h> header file. */ +#define HAVE_UNISTD_H 1 + +/* Define to 1 if the system has the type `_Bool'. */ +#define HAVE__BOOL 1 + +/* Name of package */ +#define PACKAGE "egglib-cpp" + +/* Define to the address where bug reports for this package should be sent. */ +#define PACKAGE_BUGREPORT "demita@gmail.com" + +/* Define to the full name of this package. */ +#define PACKAGE_NAME "EggLib C++ library" + +/* Define to the full name and version of this package. */ +#define PACKAGE_STRING "EggLib C++ library 2.1.5" + +/* Define to the one symbol short name of this package. */ +#define PACKAGE_TARNAME "egglib-cpp" + +/* Define to the home page for this package. */ +#define PACKAGE_URL "" + +/* Define to the version of this package. */ +#define PACKAGE_VERSION "2.1.5" + +/* Define to 1 if you have the ANSI C header files. */ +#define STDC_HEADERS 1 + +/* Version number of package */ +#define VERSION "2.1.5" + +/* Define to `__inline__' or `__inline' if that's what the C compiler + calls it, or to nothing if 'inline' is not supported under any name. */ +#ifndef __cplusplus +/* #undef inline */ +#endif + +/* Define to `unsigned int' if <sys/types.h> does not define. */ +/* #undef size_t */
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmap2mlmm/HapmapToMLMMFiles.pl Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,117 @@ +#!/usr/bin/perl + +use strict; +use Switch; +use Getopt::Long; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -h, --hapmap <Hapmap input file> + -m, --map <Map output file> + -g, --geno <Genotype output file> + -p, --path <Path for transpose executable> +~; +$usage .= "\n"; + +my ($hapmap,$map,$geno,$path); + + +GetOptions( + "geno=s" => \$geno, + "map=s" => \$map, + "hapmap=s" => \$hapmap, + "path=s" => \$path, +); + + +die $usage + if ( !$geno || !$map || !$hapmap || !$path); + +my $TRANSPOSE_EXE = "$path/transpose.awk"; + +my @snps; +my %chrom_pos; +my $num_line = 0; +open(my $O,">geno_transposed"); +open(my $H,$hapmap); +while(<$H>) +{ + $num_line++; + my $line = $_; + chomp($line); + $line =~s/\r//g; + $line =~s/\n//g; + my @infos = split(/\t/,$line); + if ($num_line == 1) + { + print $O "Ind_id"; + for (my $i = 11; $i <= $#infos; $i++) + { + my $individual = $infos[$i]; + print $O " " . $individual; + } + print $O "\n"; + } + elsif ($num_line > 1) + { + my $snp = $infos[0]; + my $variation = $infos[1]; + my %scores; + if ($variation =~/(\w)\/(\w)/) + { + my $allele1 = $1; + my $allele2 = $2; + $scores{$allele1} = 0; + $scores{$allele2} = 1; + } + my $chrom = $infos[2]; + my $pos = $infos[3]; + $chrom_pos{$snp}{"chrom"} = $chrom; + $chrom_pos{$snp}{"pos"} = $pos; + push(@snps,$snp); + print $O "$snp"; + for (my $i = 11; $i <= $#infos; $i++) + { + my $genotype = $infos[$i]; + my @alleles = split("",$genotype); + if ($genotype ne "NN") + { + my $score = $scores{$alleles[0]} + $scores{$alleles[1]}; + print $O " $score"; + } + else + { + print $O " NA"; + } + } + print $O "\n"; + } +} +close($H); +close($O); + +open(my $M,">$map"); +print $M "SNP Chr Pos\n"; +foreach my $snp(@snps) +{ + print $M "$snp " . $chrom_pos{$snp}{"chrom"} . " ". $chrom_pos{$snp}{"pos"} . "\n"; +} +close($M); + +system("$TRANSPOSE_EXE geno_transposed >geno_transposed2"); + +open(my $F,">$geno"); +open(my $G,"geno_transposed2"); +while(<$G>) +{ + my $line = $_; + $line =~s/ /\t/g; + print $F $line; +} +close($G); +close($F); + +unlink("geno_transposed"); +unlink("geno_transposed2"); + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmap2mlmm/HapmapToMLMMFiles.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,11 @@ +#!/bin/bash +hapmap=$1 +map=$2 +geno=$3 + +directory=`dirname $0` + +perl $directory/HapmapToMLMMFiles.pl -h $hapmap -g $geno -m $map -p $directory + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmap2mlmm/HapmapToMLMMFiles.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,158 @@ +<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> + <description>converts a hapmap file into MLMM input files</description> + <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot + </command> + <inputs> + <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> + </inputs> + <outputs> + <data format="txt" name="snp_info" label="SNP Info file"/> + <data format="txt" name="genot" label="Genotyping file for MLMM"/> + </outputs> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + + + +.. class:: infomark + +**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** South Green. + +--------------------------------------------------- + + +================= +HapmapToMLMMFiles +================= + +----------- +Description +----------- + + | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Fasta alignment fasta +=============== ====================== =========== + + +**Downstream tool** + +=========== ========================== ======= +Name input file(s) format +=========== ========================== ======= +MLMM +=========== ========================== ======= + + + +---------- +Input file +---------- + +Hapmap file + Allelic file in Hapmap format + + + +------------ +Output files +------------ + +SNP Info file + +Genotyping file for MLMM + + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA + + +Output files +============ + +SNP Info file +------------- + +:: + + SNP Chr Pos + SNP1 1 3102 + SNP2 1 4648 + SNP3 1 7601 + + +Genotyping file for MLMM +------------------------ + +:: + + Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14 + Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0 + Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hapmap2mlmm/transpose.awk Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,27 @@ +#!/usr/bin/gawk -f + +BEGIN { + max_x =0; + max_y =0; +} + +{ + max_y++; + for( i=1; i<=NF; i++ ) + { + if (i>max_x) max_x=i; + A[i,max_y] = $i; + } +} + +END { + for ( x=1; x<=max_x; x++ ) + { + for ( y=1; y<=max_y; y++ ) + { + if ( (x,y) in A ) printf "%s",A[x,y]; + if ( y!=max_y ) printf " "; + } + printf "\n"; + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ped2bed/ped2bed.sh Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,20 @@ +#!/bin/bash +ped=$1 +map=$2 +bed=$3 +fam=$4 +bim=$5 +logs=$6 + +directory=`dirname $0` +mkdir tmpdir$$ +cp -rf $ped tmpdir$$/input.ped +cp -rf $map tmpdir$$/input.map + +plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1 + +mv tmpdir$$/out.bed $bed +mv tmpdir$$/out.fam $fam +mv tmpdir$$/out.bim $bim + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ped2bed/ped2bed.xml Fri Jul 10 04:39:30 2015 -0400 @@ -0,0 +1,196 @@ +<tool id="ped2bed" name="plink: ped2bed" version="1.24"> + <description>Convert ped to bed</description> + <requirements> + <requirement type="package" version="1.07">plink</requirement> + </requirements> + <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs + </command> + <inputs> + <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/> + <param format="txt" name="map" type="data" label="Map file" help="Map file"/> + </inputs> + <outputs> + <data format="txt" name="bed" label="Bed file"/> + <data format="txt" name="fam" label="Fam file"/> + <data format="txt" name="bim" label="Bim file"/> + <data format="txt" name="logs" label="All Logs"/> + </outputs> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + +.. class:: infomark + +**Authors** plink_ + +.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ + + | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. + +.. class:: infomark + +**Galaxy integration** South Green. + +.. class:: infomark + +**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + + +--------------------------------------------------- + + + +======= +Ped2Bed +======= + +----------- +Description +----------- + + | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + | For further informations, please visite the plink website_. + +.. _website: http://pngu.mgh.harvard.edu/purcell/plink/ + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ========================== =========== +Name output file(s) format +=============== ========================== =========== +VCFtools filter PED and map files ped and map +=============== ========================== =========== + + +**Downstream tool** + +=========== ========================== ======= +Name input file(s) format +=========== ========================== ======= +Admixture Bed, fam and bim file txt +=========== ========================== ======= + + +---------- +Input file +---------- + +PED file + Allelic file in PED format + +MAP file + + + +------------ +Output files +------------ + +Bed file + +Fam file + +Bim file + +All logs + Log file + + +------------ +Dependencies +------------ +plink + version 1.07 + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +PED file +-------- + +:: + + AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T + BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T + +MAP file +-------- + +:: + + 0 Chr1:4299 0 4299 + 0 Chr1:26710 0 26710 + 0 Chr1:56184 0 56184 + 0 Chr1:93272 0 93272 + + +Output files +============ + +Bed file +-------- + +:: + + binary file + +Fam file +-------- + +:: + + AZUCENA AZUCENA 0 0 0 -9 + BULUPANDAK BULUPANDAK 0 0 0 -9 + +Bim file +-------- + +:: + + 0 Chr1:4299 0 4299 A G + 0 Chr8:18058 0 18058 C T + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- a/snpEff/SnpEff.pl Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Getopt::Long; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <input VCF> - -o, --output <output> - -g, --gff <GFF annotation> - -f, --fasta <Fasta of chromosomes> - -h, --html <HTML output> -~; -$usage .= "\n"; - -my ($input,$output,$gff,$fasta,$html); - - -GetOptions( - "input=s" => \$input, - "output=s" => \$output, - "gff=s" => \$gff, - "fasta=s" => \$fasta, - "html=s" => \$html -); - - -die $usage - if ( !$input || !$output || !$fasta || !$gff || !$html); - - -if (!-e $gff){ - die "Error: GFF input does not exist\n" -} -if (!-e $fasta){ - die "Error: Fasta input does not exist\n" -} - -#my $SNPEFF_PATH = "/usr/local/bioinfo/galaxy/galaxy_dist/tools/SNiPlay/SnpEff/snpEff"; -my $SNPEFF_PATH = $ENV{SNPEFF_JAR_PATH}; - - -my $session = $$; -mkdir($session); -mkdir("$session/data"); -mkdir("$session/data/genomes"); -mkdir("$session/data/myspecies"); - -system("cp -rf $fasta $session/data/genomes/myspecies.fa"); -system("cp -rf $gff $session/data/myspecies/genes.gff"); - -open(my $C,"$SNPEFF_PATH/snpEff.config"); -open(my $C2,">$session/snpEff.config"); -while(<$C>) -{ - if (/data_dir/) - { - print $C2 "data_dir = ./data\n"; - } - elsif (/^genomes/) - { - print $C2 "genomes : \\n"; - print $C2 "myspecies, myspecies \\n"; - } - else - { - print $C2 $_; - } -} -print $C2 "myspecies.genome : myspecies\n"; -close($C); -close($C2); - - -my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies"; -system($build_cmd); - -my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output"; -system($eff_cmd); - - -system("rm -rf $session");
--- a/snpEff/snpEff-pipe.sh Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#!/bin/bash -vcf=$1 -genome=$2 -gff=$3 -output=$4 -html=$5 -log=$6 - -directory=`dirname $0` - -/usr/bin/perl $directory/SnpEff.pl -i $vcf -f $genome -g $gff -o $output -h $html >>$log 2>&1 - - -
--- a/snpEff/snpEff.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -<tool id="snpEff" name="SnpEff" version="4.0"> - <description>predicts SNP effect from a genomic VCF file</description> - <requirements> - <requirement type="package" version="4.0">snpEff</requirement> - </requirements> - - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command> - <inputs> - <param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/> - <param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/> - <param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/> - - </inputs> - <outputs> - <data format="vcf" name="output" label="Annotated VCF" /> - <data format="html" name="statsFile" label="HTML statistics output"/> - <data format="txt" name="log" label="Log file"/> - </outputs> - - <help> - - - - - -.. class:: infomark - -**Program encapsulated in Galaxy by Southgreen** - -.. class:: infomark - -**SnpEff version 4.0** - ------ - -============== - Please cite: -============== - -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", **Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.**, Fly (Austin). 2012 Apr-Jun;6(2):80-92. - ------ - -=========== - Overview: -=========== - -Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). - ------ - -For further informations, please visite the SnpEff_ website. - - -.. _SnpEff: http://snpeff.sourceforge.net/ - </help> - -</tool> -
--- a/tassel/tassel.sh Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -#!/bin/bash - -analyseType=$1; -out1=$2; -out2=$3; -out3=$4; -log1=$5; -galaxyOutDir=$6; - - -mkdir $galaxyOutDir - -# Suppression des 6 premiers arguments de la liste des arguments $@ -shift; shift; shift; shift; shift; shift; - -if [[ $analyseType == glm ]] -then - run_pipeline.pl $* >> $log1 2>&1 - mv "$galaxyOutDir/TASSELGLM1.txt" $out1 - mv "$galaxyOutDir/TASSELGLM2.txt" $out2 -fi - -if [[ $analyseType == mlm ]] -then - run_pipeline.pl $* >> $log1 2>&1 - mv "$galaxyOutDir/TASSELMLM1.txt" $out1 - mv "$galaxyOutDir/TASSELMLM2.txt" $out2 - mv "$galaxyOutDir/TASSELMLM3.txt" $out3 -fi - -if [[ $analyseType == ld ]] -then - run_pipeline.pl $* >> $log1 2>&1 -fi - - -if [[ $analyseType == ck ]] -then - run_pipeline.pl $* >> $log1 2>&1 - mv "$galaxyOutDir/kinship.txt" $out1 -fi
--- a/tassel/tassel.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,153 +0,0 @@ -<tool id="Tassel" name="Tassel" version="5.0"> - <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description> - <requirements> - <requirement type="package" version="5.0">tassel</requirement> - </requirements> - <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ -#if $analysis_opts.fonction_selector == "mlm": - -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq - -fork2 -r $analysis_opts.trait - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait - #end if - -fork4 -k $analysis_opts.kinship - -combineA -input1 -input2 - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -input3 - #end if - -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -runfork3 - #end if - -runfork4 - -#else if $analysis_opts.fonction_selector == "glm": - -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq - -fork2 -r $analysis_opts.trait - #if $analysis_opts.add_file.additional_file_selector == "yes": - -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait - #end if - -combineA -input1 -input2 - #if $analysis_opts.add_file.additional_file_selector == "yes": - -input3 - #end if - -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2 - #if $analysis_opts.add_file.additional_file_selector == "yes": - -runfork3 - #end if -#else if $analysis_opts.fonction_selector == "ld": - -fork1 -h $hapmap - -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1 -#else if $analysis_opts.fonction_selector == "ck": - -fork1 -h $hapmap - -ck -export tmpdir$$/kinship -runfork1 -#end if - </command> - <inputs> - <param format="txt" name="hapmap" type="data" label="HapMap file"/> - <conditional name="analysis_opts"> - <param name="fonction_selector" type="select" label="Type of analysis"> - <option value="mlm" selected="True">MLM</option> - <option value="glm">GLM</option> - <option value="ld">Linkage Disequilibrium</option> - <option value="ck">Kinship</option> - </param> - <when value="glm"> - <param format="txt" name="trait" type="data" label="Trait file"/> - <conditional name="add_file"> - <param name="additional_file_selector" type="select" label="Add structure file"> - <option value="no" selected="True">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param format="txt" name="structure" type="data" label="Structure file"/> - </when> - </conditional> - </when> - <when value="mlm"> - <param format="txt" name="trait" type="data" label="Trait file"/> - <param format="txt" name="kinship" type="data" label="Kinship file"/> - <conditional name="add_structure_file"> - <param name="additional_file_selector" type="select" label="Add structure file"> - <option value="no" selected="True">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param format="txt" name="structure" type="data" label="Structure file"/> - </when> - </conditional> - <param name="mlmVarCompEst" type="select" label="Variance Component Estimation"> - <option value="P3D" selected="True">P3D</option> - <option value="EachMarker">EachMarker</option> - </param> - <param name="mlmCompressionLevel" type="select" label="Compression Level"> - <option value="Optimum" selected="True">Optimum</option> - <option value="Custom">Custom</option> - <option value="None">None</option> - </param> - </when> - <when value="ld"></when> - <when value="ck"></when> - </conditional> - <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/> - </inputs> - <outputs> - <data format="txt" name="output1" label="Tassel output"> - <change_format> - <when input="analysis_opts['fonction_selector']" value="ld" format="png"/> - </change_format> - </data> - - <data format="txt" name="output2" label="Allele effects"> - <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter> - </data> - - <data format="txt" name="output3" label="Compression file"> - <filter>analysis_opts['fonction_selector'] == "mlm"</filter> - </data> - - <data format="txt" name="log" label="Log file"/> - </outputs> - <help> - -.. class:: infomark - -**Program encapsulated in Galaxy by Southgreen** - -.. class:: infomark - -**Tassel** - ------ - -========== - Authors: -========== - -**Terry Casstevens** - ------ - -========== - Overview -========== - -Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. - ------ - -For further informations, please visite the website of TASSEL_. - - -.. _TASSEL: http://www.maizegenetics.net/tassel/ - - </help> -<!-- -<tests> - <test> - <param name="input" value="genotyping_file.inp" /> - <output name="output" file="phase_output" /> - </test> -</tests> ---> -</tool>
--- a/tassel/tool-data/tool_dependencies.xml Mon Mar 23 05:57:27 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="tassel" version="5.0"> - <repository changeset_revision="097d4c366e0d" name="package_tassel_5_0" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> -</tool_dependency> - -
--- a/tool_dependencies.xml Mon Mar 23 05:57:27 2015 -0400 +++ b/tool_dependencies.xml Fri Jul 10 04:39:30 2015 -0400 @@ -1,20 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="plink" version="1.07"> - <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> - <package name="admixture" version="1.23"> - <repository changeset_revision="61e04b2aa621" name="package_admixture_1_23" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> - <package name="tassel" version="5.0"> - <repository changeset_revision="097d4c366e0d" name="package_tassel_5_0" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> - <package name="vcftools" version="0.1.12b"> - <repository changeset_revision="a655cb1dfc58" name="package_vcftools_0_1_12b" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> - <package name="snpEff" version="4.0"> - <repository name="package_snpeff_4_0" owner="iuc" changeset_revision="6bc55957927b" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> - -