Mercurial > repos > dereeper > sniplay
changeset 2:feb40a9a8eae draft
Uploaded
| author | dereeper |
|---|---|
| date | Fri, 10 Jul 2015 10:38:11 -0400 |
| parents | 420b57c3c185 |
| children | 345f88a8f483 |
| files | MDSplot/MDSbasedOnIBSmatrix.pl MDSplot/MDSbasedOnIBSmatrix.pl.org MDSplot/mdsplot.sh MDSplot/mdsplot.xml MDSplot/test-data/analyse.ibs_matrix.txt MDSplot/test-data/analyse.log MDSplot/test-data/analyse.mds_plot.txt MDSplot/test-data/input.map MDSplot/test-data/input.ped PedToFasta/Ped2Fasta.pl PedToFasta/pedToFasta.xml PedToFasta/test-data/result.fa PedToFasta/test-data/sample.ped Rooting/Rooting.pl Rooting/Rootings_54.jar Rooting/rooting.xml Rooting/rooting.xml~ Rooting/test-data/newick Rooting/test-data/out_tree Rooting/test-data/out_tree.log SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh SNP_density/test-data/hapmap SNP_density/test-data/result.txt SNP_density/test-data/result_bysample.txt VCF2Hapmap/VCF2FastaAndHapmap.pl VCF2Hapmap/vcf2FastaAndHapmap.sh VCF2Hapmap/vcf2FastaAndHapmap.xml check_gwas_inputs/CheckGWASInputs.pl check_gwas_inputs/CheckGWASInputs.sh check_gwas_inputs/CheckGWASInputs.xml check_gwas_inputs/CheckGWASInputs.xml~ egglib/CalculateDiversityIndexes.pl egglib/CalculateDiversityIndexes.sh egglib/CalculateDiversityIndexes.xml egglib/egglib-2.1.5/bin/eggstats egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp egglib/egglib-2.1.5/include/egglib-cpp/BaseDiversity.hpp egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp egglib/egglib-2.1.5/include/egglib-cpp/Consensus.hpp egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp egglib/egglib-2.1.5/include/egglib-cpp/Convert.hpp egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp egglib/egglib-2.1.5/include/egglib-cpp/Edge.hpp egglib/egglib-2.1.5/include/egglib-cpp/EggException.hpp egglib/egglib-2.1.5/include/egglib-cpp/FStatistics.hpp egglib/egglib-2.1.5/include/egglib-cpp/Fasta.hpp egglib/egglib-2.1.5/include/egglib-cpp/HFStatistics.hpp egglib/egglib-2.1.5/include/egglib-cpp/HaplotypeDiversity.hpp egglib/egglib-2.1.5/include/egglib-cpp/LinkageDisequilibrium.hpp egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp egglib/egglib-2.1.5/include/egglib-cpp/Ms.hpp egglib/egglib-2.1.5/include/egglib-cpp/Mutation.hpp egglib/egglib-2.1.5/include/egglib-cpp/Mutator.hpp egglib/egglib-2.1.5/include/egglib-cpp/NucleotideDiversity.hpp egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp egglib/egglib-2.1.5/include/egglib-cpp/Random.hpp egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp egglib/egglib-2.1.5/include/egglib-cpp/config.h egglib/egglib-2.1.5/lib/libegglib-cpp.a hapmap2mlmm/HapmapToMLMMFiles.pl hapmap2mlmm/HapmapToMLMMFiles.sh hapmap2mlmm/HapmapToMLMMFiles.xml hapmap2mlmm/transpose.awk ped2bed/ped2bed.sh ped2bed/ped2bed.xml tool_dependencies.xml |
| diffstat | 73 files changed, 377 insertions(+), 15942 deletions(-) [+] |
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--- a/MDSplot/MDSbasedOnIBSmatrix.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $PLINK_EXE= "plink"; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --in <input> - -o, --out <output> -~; -$usage .= "\n"; - -my ($in,$out); - - -GetOptions( - "in=s" => \$in, - "out=s" => \$out -); - -die $usage - if ( !$in || !$out); - - -my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1"; -system($plink_command); - -my $awk_cmd = "awk \{\'print \$1\'\} $in.ped"; -my $inds = `$awk_cmd`; -my @individuals = split("\n",$inds); - -my %populations; -if (-e "$in.individual_info.txt") -{ - open(my $I,"$in.individual_info.txt"); - while(<$I>) - { - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my ($ind,$pop) = split(/;/,$line); - $populations{$ind} = $pop; - } - close($I); -} - -open(my $OUT,">$out.mds_plot.txt"); -my $go = 0; -open(my $O,"$out.mds"); -while(<$O>) -{ - if ($go) - { - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - if ($line =~/^ /) - { - my $ind = $i[1]; - my $pop = "Pop1"; - if ($populations{$ind}) - { - $pop = $populations{$ind}; - } - print $OUT "$pop $ind ".$i[4]." ".$i[5]."\n"; - } - if ($line =~/^\w/) - { - my $ind = $i[0]; - my $pop = "Pop1"; - if ($populations{$ind}) - { - $pop = $populations{$ind}; - } - print $OUT "$pop $ind ".$i[3]." ".$i[4]."\n"; - } - - } - if (/C1/){$go = 1;} -} -close($O); -close($OUT); - - -my $j = 0; -open(my $IBS,">$out.ibs_matrix.txt"); -print $IBS "Individuals " . join("\t",@individuals)."\n"; -open(my $O2,"$out.mibs"); -while(<$O2>) -{ - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - print $IBS $individuals[$j]. " ". join("\t",@i)."\n"; - $j++; -} -close($O2); -close($IBS); - - - - - -
--- a/MDSplot/MDSbasedOnIBSmatrix.pl.org Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink"; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --in <input> - -o, --out <output> -~; -$usage .= "\n"; - -my ($in,$out); - - -GetOptions( - "in=s" => \$in, - "out=s" => \$out -); - -die $usage - if ( !$in || !$out); - - -my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1"; -system($plink_command); - -my $awk_cmd = "awk \{\'print \$1\'\} $in.ped"; -my $inds = `$awk_cmd`; -my @individuals = split("\n",$inds); - - -open(my $OUT,">$out.mds_plot.txt"); -my $go = 0; -open(my $O,"$out.mds"); -while(<$O>) -{ - if ($go) - { - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - my $ind = $i[1]; - print $OUT "$ind ".$i[4]." ".$i[5]."\n"; - } - if (/C1/){$go = 1;} -} -close($O); -close($OUT); - - -my $j = 0; -open(my $IBS,">$out.ibs_matrix.txt"); -print $IBS "Individuals " . join("\t",@individuals)."\n"; -open(my $O2,"$out.mibs"); -while(<$O2>) -{ - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - print $IBS $individuals[$j]. " ". join("\t",@i)."\n"; - $j++; -} -close($O2); -close($IBS); - - - - - -
--- a/MDSplot/mdsplot.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) -ped=$1 -map=$2 -fileout_label=$3 -fileout_matrix=$4 -fileout_plot=$5 -fileout_log=$6 - -rsync -a $ped input.ped -rsync -a $map input.map - -perl $tool_path/MDSbasedOnIBSmatrix.pl --in input --out $fileout_label - -rm -f input.ped input.map - -cp $fileout_label.ibs_matrix.txt $fileout_matrix -cp $fileout_label.mds_plot.txt $fileout_plot -cp input.plink.log $fileout_log - - -rm -f $fileout_label.ibs_matrix.txt $fileout_label.mds_plot.txt input.plink.log
--- a/MDSplot/mdsplot.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,232 +0,0 @@ -<tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> IBS matrix / multi-dimensional scaling</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - <requirement type="package" version="1.07">plink</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="bash"> - mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> - <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> - <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" /> - <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" /> - <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - - <test> - <param name="fileped" value="input.ped" /> - <param name="filemap" value="input.map" /> - <output name="fileout_matrix" file="output.ibs_matrix.txt" /> - <output name="fileout_plot" file="output.mds_plot.txt" /> - <output name="fileout_log" file="output.log" /> - </test> - - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - - -.. class:: infomark - -**Authors** plink_ - -.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ - - | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. - - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - -.. class:: infomark - -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - ---------------------------------------------------- - - - -======== -MDS plot -======== - ------------ -Description ------------ - - Compute an IBS matrix and a multi-dimensional scaling. - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== =============== -Name output file(s) format -=============== ========================== =============== -VCFtools Filter PED and MAP file tabular and MAP -=============== ========================== =============== - - - ----------- -Input file ----------- - -PED file - -MAP file - 4 columns tabular file: chromosome, snp id, genetic distance, bp position - - ----------- -Parameters ----------- - -Output name - Output base name for the ouput files - - ------------- -Output files ------------- - -Output_name.ibs_matrix.txt - Tabular file with IBS matrix - -Output_name.mds_plot.txt - File to construct mds plot - -Output_name.log - Log file - ------------- -Dependencies ------------- -plink - version 1.07 - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -PED file ------------ - -:: - - IRAT112 1 0 0 1 1 1 1 4 4 ... - IAC25 1 0 0 1 1 1 1 4 4 ... - CIRAD409 1 0 0 1 1 3 3 1 1 ... - - -MAP file ------------ - -:: - - Chr1 Chr1:4299 0 4299 - Chr1 Chr1:26710 0 26710 - Chr1 Chr1:56184 0 56184 - Chr1 Chr1:93272 0 93272 - - - -Parameters -========== - -Output name -> densities - - -Output files -============ - -densities.ibs_matrix.txt ------------------------- - -:: - - Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ... - IRAT112 1 0.93691 0.937407 0.734724 0.943368 ... - IAC25 0.93691 1 0.958768 0.723299 0.965723 ... - - -densities.mds_plot.txt ----------------------- - -:: - - IRAT112 -0.0969382 0.0376036 - IAC25 -0.0918126 0.0501177 - - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> - -</tool>
--- a/MDSplot/test-data/analyse.ibs_matrix.txt Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE CUIABANA BICOBRANCO CAAWA/FORTUNA6 CANELADEFERRO CIRAD358 COLOMBIA1 CIRAD409 BAGANANASALAO BAKUNGH FOHISOMOTRA KAKANI2 GUARANI DOURADOAGULHA IRAT13 DAWASANRED GRAZI IRAT144 IAC47 MOROBEREKAN IRAT362 GIZA171 IDSA77 IRAT216 IRAT177 CHAPHUMA CIRAD392 ARROZCEBADA INDANE DINORADO 63-104 IR63380-16 CANAROXA CICIHBETON IR68704-145-1-1-B HAWMOM IRAT364 IRAT212 KHAODAM 62667 IRAT234 NIPPONBARE_D JUMULA2 CUBA65 BABER CIRAD488 BENGALYVAKARINA ESPERANZA BULUPANDAK ARIAS GOMPA2 CT13582-15-5-M IRAT335 M202 IR65907-188-1-B IR71525-19-1-1 CNA-7_BO_1_1_33-13-6-1 IRAT257 IRAT109 KANIRANGA IR66421-096-2-1-1 GOGO GEMJYAJYANAM DANGREY BINULAWAN CAIAPO IGUAPECATETO IRAT170 IRAT380 ARAGUAIA GOGOLEMPAK JAOHAW CHALOYOE GANIGI GUNDILKUNING IRAT2 IRAT366 IRAT104 DAVAO HD1-4 CURINCA DAM CIRAD403 JUMALI JIMBRUKJOLOWORO GOGOLEMPUK CIRAD394 IR63372-08 IR60080-46A -IRAT112 1 0.93691 0.937407 0.734724 0.943368 0.819672 0.903626 0.850969 0.842524 0.802285 0.717834 0.836562 0.804272 0.832588 0.81073 0.614009 0.946846 0.943368 0.944362 0.688525 0.807253 0.712866 0.929955 0.782414 0.902136 0.692499 0.817188 0.796821 0.943865 0.697963 0.790859 0.787879 0.704918 0.833582 0.917039 0.769001 0.938897 0.682563 0.814704 0.707402 0.859911 0.787879 0.709389 0.945355 0.883259 0.703924 0.697963 0.843517 0.725286 0.725782 0.84302 0.876304 0.69995 0.74466 0.651267 0.836066 0.958271 0.651764 0.755092 0.859911 0.861898 0.905614 0.892201 0.739692 0.828117 0.80924 0.650273 0.644312 0.860407 0.853949 0.922504 0.944858 0.81073 0.908097 0.756085 0.674118 0.744163 0.785892 0.698957 0.944858 0.80775 0.857427 0.838053 0.931446 0.831098 0.721311 0.798808 0.592151 0.739692 0.757079 0.767014 0.781918 0.899155 -IAC25 0.93691 1 0.958768 0.723299 0.965723 0.825137 0.93691 0.836562 0.850969 0.772976 0.713363 0.807253 0.791853 0.819175 0.814208 0.602583 0.934426 0.966716 0.904123 0.676105 0.817685 0.706408 0.948336 0.811724 0.892697 0.693989 0.819672 0.784401 0.902633 0.677596 0.806259 0.812221 0.717337 0.813214 0.876801 0.757576 0.923497 0.706905 0.806259 0.69995 0.833582 0.777447 0.693989 0.904123 0.896672 0.703428 0.694486 0.813214 0.728763 0.747144 0.82464 0.864878 0.710383 0.758073 0.643815 0.834575 0.925981 0.674118 0.745653 0.839543 0.845504 0.900149 0.851962 0.764034 0.817685 0.814704 0.655738 0.644809 0.819175 0.834575 0.90313 0.90462 0.838053 0.928465 0.751615 0.666667 0.733731 0.800298 0.707402 0.902633 0.805266 0.846995 0.822653 0.955787 0.809737 0.700944 0.788376 0.591654 0.750124 0.751615 0.790363 0.769498 0.879781 -IAC165 0.937407 0.958768 1 0.722802 0.929459 0.839543 0.932439 0.862891 0.85544 0.786388 0.739692 0.817685 0.790363 0.817685 0.822653 0.596125 0.968703 0.929459 0.920517 0.677596 0.832091 0.704918 0.9846 0.822156 0.92002 0.688525 0.834078 0.794834 0.921013 0.685047 0.805763 0.823646 0.717834 0.826627 0.895181 0.769995 0.945852 0.688525 0.825633 0.694486 0.846001 0.77993 0.697466 0.920517 0.90611 0.694983 0.689021 0.809737 0.723299 0.745653 0.810233 0.87233 0.692002 0.76155 0.636364 0.849975 0.91853 0.66766 0.755092 0.866865 0.855936 0.916542 0.868356 0.746647 0.822156 0.813214 0.651267 0.632389 0.82464 0.844014 0.927471 0.921013 0.832588 0.963736 0.774963 0.661202 0.743169 0.796821 0.702931 0.921013 0.800795 0.864382 0.80924 0.98609 0.821162 0.709389 0.797814 0.588177 0.735718 0.774963 0.783905 0.780924 0.901143 -KARASUKARASURANKASU 0.734724 0.723299 0.722802 1 0.73075 0.748137 0.745653 0.766518 0.747144 0.796324 0.673125 0.738202 0.774466 0.753105 0.780924 0.630899 0.731247 0.73075 0.769498 0.802782 0.769498 0.677099 0.73224 0.749627 0.754098 0.817685 0.715847 0.721311 0.769001 0.837059 0.777943 0.775956 0.827124 0.740189 0.778937 0.707402 0.743169 0.675609 0.704421 0.80775 0.780427 0.748137 0.879285 0.770492 0.759066 0.828117 0.731744 0.743169 0.761053 0.669151 0.764531 0.71237 0.693989 0.737705 0.668157 0.735718 0.723795 0.781918 0.728266 0.764531 0.750621 0.741679 0.731247 0.689021 0.768505 0.751615 0.760556 0.754595 0.731247 0.806259 0.736711 0.769995 0.758073 0.699454 0.709389 0.858917 0.825633 0.753105 0.701937 0.769001 0.733234 0.769001 0.735718 0.731744 0.710879 0.874317 0.725286 0.598112 0.688028 0.710383 0.761053 0.735221 0.753105 -DOURADOPRECOCE 0.943368 0.965723 0.929459 0.73075 1 0.808743 0.9384 0.816195 0.837556 0.773472 0.71386 0.799801 0.789369 0.81073 0.813711 0.604074 0.911078 0.998013 0.89071 0.686538 0.841033 0.689021 0.942871 0.811227 0.874317 0.688525 0.79533 0.773969 0.88922 0.684054 0.795827 0.823646 0.724789 0.802782 0.862394 0.74615 0.898162 0.702434 0.792846 0.707402 0.832091 0.76304 0.700447 0.89071 0.895181 0.69697 0.698957 0.816692 0.721311 0.733731 0.841033 0.864382 0.705912 0.764531 0.634377 0.825137 0.929459 0.671634 0.733234 0.82613 0.834078 0.880775 0.838549 0.754595 0.806259 0.816195 0.664183 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0.859911 0.71535 0.764531 0.897665 0.720318 0.863885 0.888723 0.777447 0.880775 0.743666 0.787382 0.723795 0.785892 0.762543 0.726776 0.861401 0.853949 0.720318 0.707402 0.818182 0.729757 0.679583 0.81073 0.782414 0.762047 0.831595 0.702434 0.80775 0.831595 0.692002 0.718828 0.811724 0.802782 0.864382 0.808246 0.752111 0.825633 0.799801 0.693492 0.675609 0.867859 0.818679 0.862394 0.860904 0.768505 0.828117 0.770492 0.702434 0.74466 0.868852 0.765027 0.860904 0.841033 0.831098 0.832588 0.846498 0.72926 0.740686 0.735718 0.617486 0.707402 0.771485 0.750621 0.74764 0.845007 -CIRAD358 0.802285 0.772976 0.786388 0.796324 0.773472 0.799801 0.773472 0.793343 0.829608 1 0.644312 0.738202 0.783408 0.79384 0.851465 0.644809 0.794834 0.773472 0.816195 0.738202 0.866865 0.690015 0.795827 0.827124 0.77993 0.736215 0.717834 0.703428 0.815698 0.770492 0.752111 0.861401 0.737705 0.774963 0.795827 0.71237 0.805763 0.71535 0.723299 0.720318 0.848982 0.769001 0.774963 0.817188 0.783905 0.750621 0.680079 0.794834 0.706408 0.647293 0.786388 0.733234 0.732737 0.788376 0.682067 0.723795 0.787382 0.689518 0.704421 0.827124 0.752608 0.816195 0.76304 0.76155 0.743666 0.759563 0.702931 0.688028 0.820666 0.817188 0.802285 0.816692 0.711376 0.762047 0.800795 0.762543 0.77993 0.846498 0.741679 0.815698 0.895181 0.842524 0.791356 0.797317 0.703924 0.783905 0.706408 0.598112 0.739692 0.801788 0.693492 0.697466 0.808743 -COLOMBIA1 0.717834 0.713363 0.739692 0.673125 0.71386 0.652757 0.717834 0.733731 0.697466 0.644312 1 0.837556 0.678092 0.658718 0.68157 0.597119 0.742176 0.714853 0.729757 0.663686 0.674118 0.682067 0.737208 0.659215 0.774963 0.66766 0.863885 0.87531 0.730253 0.665176 0.728266 0.66468 0.650273 0.68455 0.723299 0.822653 0.740189 0.570293 0.822653 0.628912 0.672131 0.716344 0.658718 0.73075 0.73224 0.667163 0.599603 0.674615 0.659712 0.689021 0.661202 0.781918 0.567809 0.629409 0.609538 0.79533 0.714853 0.637854 0.836562 0.692996 0.782414 0.71386 0.736215 0.608544 0.777447 0.701937 0.634377 0.629409 0.686538 0.707899 0.701937 0.730253 0.694486 0.751118 0.635867 0.624441 0.692499 0.661699 0.578738 0.72926 0.622951 0.679583 0.660209 0.738698 0.864878 0.666667 0.87531 0.594138 0.60159 0.63686 0.725286 0.868356 0.738202 -CIRAD409 0.836562 0.807253 0.817685 0.738202 0.799801 0.726776 0.789866 0.828614 0.769498 0.738202 0.837556 1 0.767014 0.749627 0.746647 0.619473 0.834078 0.800795 0.887233 0.701937 0.735221 0.678589 0.815201 0.719324 0.87382 0.692002 0.93691 0.958271 0.88773 0.69846 0.742673 0.745653 0.707402 0.762543 0.859911 0.881769 0.847988 0.609538 0.871833 0.69697 0.790859 0.756582 0.722802 0.888227 0.783408 0.707402 0.685544 0.774466 0.701937 0.688525 0.738202 0.810233 0.620964 0.695479 0.651764 0.881272 0.809737 0.670144 0.916542 0.814704 0.843517 0.80775 0.850969 0.669647 0.820666 0.734228 0.654744 0.666667 0.774466 0.814704 0.794834 0.88773 0.740686 0.829111 0.698957 0.688525 0.718828 0.711873 0.630899 0.88773 0.69995 0.794337 0.753105 0.816692 0.921013 0.711873 0.959265 0.598609 0.655738 0.69995 0.755589 0.944362 0.861898 -BAGANANASALAO 0.804272 0.791853 0.790363 0.774466 0.789369 0.741182 0.824143 0.851962 0.85842 0.783408 0.678092 0.767014 1 0.918033 0.783905 0.620964 0.813711 0.790363 0.819175 0.743169 0.810233 0.673125 0.800795 0.772479 0.794834 0.731247 0.74764 0.73224 0.817685 0.760556 0.745156 0.817685 0.763537 0.860407 0.844511 0.740189 0.835569 0.704421 0.749131 0.77695 0.770492 0.751118 0.771982 0.819175 0.791853 0.734724 0.695976 0.795827 0.739195 0.669151 0.82613 0.758073 0.722802 0.810233 0.658222 0.759563 0.791356 0.718331 0.718331 0.754595 0.767511 0.796324 0.770989 0.749627 0.842027 0.776453 0.710879 0.712866 0.848485 0.801292 0.811227 0.819672 0.726279 0.76304 0.750124 0.76155 0.77695 0.787879 0.728763 0.817685 0.769995 0.789866 0.782414 0.800298 0.728763 0.762047 0.736215 0.591157 0.728763 0.750124 0.71535 0.747144 0.787879 -BAKUNGH 0.832588 0.819175 0.817685 0.753105 0.81073 0.793343 0.843517 0.818679 0.859911 0.79384 0.658718 0.749627 0.918033 1 0.805266 0.626428 0.84004 0.811724 0.845504 0.723795 0.814704 0.700447 0.821162 0.80775 0.820169 0.728763 0.730253 0.714853 0.846001 0.745156 0.77844 0.821162 0.739195 0.879781 0.87382 0.756582 0.863885 0.742673 0.755589 0.738698 0.816692 0.777447 0.753602 0.846498 0.839046 0.734228 0.736215 0.797317 0.737705 0.696473 0.847491 0.781421 0.766021 0.82762 0.679583 0.787879 0.817685 0.710879 0.700944 0.806756 0.788872 0.82464 0.801292 0.79384 0.820666 0.805763 0.704421 0.697466 0.852956 0.825633 0.825633 0.846001 0.757576 0.791356 0.793343 0.741182 0.740686 0.806259 0.771982 0.846995 0.779434 0.836066 0.803775 0.821659 0.711376 0.752608 0.716841 0.621461 0.766021 0.79533 0.742673 0.729757 0.817188 -FOHISOMOTRA 0.81073 0.814208 0.822653 0.780924 0.813711 0.82315 0.835569 0.81073 0.832091 0.851465 0.68157 0.746647 0.783905 0.805266 1 0.640338 0.834078 0.814704 0.822653 0.728763 0.860407 0.733234 0.833085 0.902136 0.820169 0.743666 0.727273 0.715847 0.822156 0.780924 0.789369 0.853949 0.765027 0.802285 0.814208 0.69697 0.834078 0.720815 0.773472 0.758569 0.859414 0.785395 0.77546 0.823646 0.874814 0.749131 0.736215 0.827124 0.732737 0.706408 0.833582 0.752608 0.739195 0.797814 0.68455 0.775956 0.815698 0.68306 0.751615 0.861401 0.786885 0.878291 0.773472 0.805763 0.806756 0.84153 0.714357 0.685544 0.82315 0.795827 0.834575 0.82315 0.796324 0.796324 0.835072 0.758073 0.779434 0.860904 0.748137 0.822156 0.891704 0.862891 0.82762 0.836562 0.71535 0.783408 0.718828 0.613512 0.812717 0.835072 0.705912 0.717834 0.84004 -KAKANI2 0.614009 0.602583 0.596125 0.630899 0.604074 0.613512 0.613015 0.615002 0.655241 0.644809 0.597119 0.619473 0.620964 0.626428 0.640338 1 0.614506 0.604074 0.624938 0.610532 0.649776 0.640835 0.591654 0.608048 0.602583 0.702931 0.597119 0.597615 0.623448 0.627919 0.669151 0.629409 0.613015 0.633383 0.627422 0.623448 0.61848 0.610532 0.60457 0.630402 0.613015 0.654247 0.608544 0.624938 0.631396 0.68455 0.737208 0.645306 0.627422 0.642822 0.630899 0.619473 0.625931 0.627919 0.894188 0.63388 0.606061 0.655241 0.610532 0.604074 0.590164 0.610035 0.628415 0.618977 0.628912 0.644809 0.587183 0.602086 0.659215 0.640835 0.617983 0.624441 0.61848 0.611525 0.597615 0.61699 0.620467 0.657228 0.643815 0.623448 0.624441 0.61848 0.637854 0.593145 0.604074 0.617486 0.597615 0.845007 0.595132 0.597615 0.677099 0.605564 0.617486 -GUARANI 0.946846 0.934426 0.968703 0.731247 0.911078 0.828117 0.925981 0.886239 0.87382 0.794834 0.742176 0.834078 0.813711 0.84004 0.834078 0.614506 1 0.912072 0.943865 0.69697 0.815698 0.730253 0.961252 0.801788 0.944362 0.694983 0.814704 0.79533 0.944362 0.705415 0.785395 0.80924 0.71237 0.850969 0.916542 0.769498 0.963239 0.691008 0.847988 0.714853 0.845504 0.802285 0.717834 0.944858 0.882762 0.703428 0.708395 0.832091 0.742673 0.741182 0.817685 0.875807 0.710383 0.747144 0.656731 0.869349 0.927968 0.651267 0.754595 0.887233 0.878291 0.925981 0.893691 0.740189 0.845504 0.81073 0.671634 0.652757 0.847988 0.865375 0.928962 0.944362 0.812221 0.936413 0.788376 0.68157 0.746647 0.821162 0.719324 0.943368 0.808246 0.888723 0.830601 0.961749 0.805763 0.729757 0.798311 0.603577 0.716344 0.789369 0.764531 0.781421 0.924491 -DOURADOAGULHA 0.943368 0.966716 0.929459 0.73075 0.998013 0.809737 0.939394 0.817188 0.838549 0.773472 0.714853 0.800795 0.790363 0.811724 0.814704 0.604074 0.912072 1 0.89071 0.686538 0.842027 0.690015 0.942871 0.811227 0.87531 0.687531 0.79533 0.774963 0.890214 0.685047 0.796821 0.82464 0.725782 0.804769 0.863388 0.747144 0.899155 0.702434 0.79384 0.708395 0.832091 0.764034 0.701441 0.891704 0.895181 0.69697 0.69995 0.817685 0.721311 0.734724 0.841033 0.865375 0.705912 0.765524 0.63537 0.82613 0.929459 0.670641 0.734228 0.827124 0.835072 0.881769 0.839543 0.755589 0.807253 0.817188 0.665176 0.653254 0.822653 0.821162 0.882762 0.891207 0.82464 0.901143 0.755092 0.675112 0.736215 0.785892 0.701937 0.891207 0.804769 0.834575 0.820169 0.941381 0.80924 0.706408 0.777943 0.582216 0.74764 0.756085 0.778937 0.761053 0.868356 -IRAT13 0.944362 0.904123 0.920517 0.769498 0.89071 0.82762 0.882762 0.892697 0.860407 0.816195 0.729757 0.887233 0.819175 0.845504 0.822653 0.624938 0.943865 0.89071 1 0.716344 0.805266 0.762543 0.913065 0.794337 0.942871 0.713363 0.830104 0.848485 0.997516 0.729757 0.802782 0.820666 0.736711 0.857427 0.970691 0.821659 0.958768 0.683557 0.839543 0.728266 0.875807 0.840537 0.759066 0.999006 0.878291 0.723795 0.725782 0.857427 0.726279 0.750621 0.821162 0.866369 0.701937 0.768505 0.677099 0.877794 0.907601 0.690512 0.806756 0.909588 0.909588 0.917536 0.943865 0.751615 0.85693 0.815201 0.673125 0.670144 0.873323 0.906607 0.902633 0.999503 0.801788 0.890214 0.782911 0.723795 0.759066 0.791853 0.711873 0.997516 0.777943 0.905117 0.857923 0.914555 0.814208 0.754098 0.853453 0.621957 0.723795 0.782911 0.803775 0.834575 0.946846 -DAWASANRED 0.688525 0.676105 0.677596 0.802782 0.686538 0.731744 0.71237 0.697466 0.71386 0.738202 0.663686 0.701937 0.743169 0.723795 0.728763 0.610532 0.69697 0.686538 0.716344 1 0.697466 0.637854 0.687034 0.69846 0.704918 0.741679 0.695479 0.694983 0.717834 0.820666 0.745653 0.695976 0.767014 0.722802 0.734724 0.675112 0.707899 0.642325 0.706905 0.76155 0.721311 0.710879 0.813214 0.717337 0.693989 0.758073 0.68455 0.728763 0.723795 0.629906 0.719324 0.661202 0.660705 0.689518 0.647789 0.707402 0.68455 0.707899 0.707899 0.703428 0.714357 0.708395 0.688028 0.659712 0.76006 0.721311 0.898162 0.914059 0.703924 0.74615 0.68455 0.716841 0.707899 0.663189 0.726776 0.79384 0.789369 0.701937 0.66766 0.717834 0.673125 0.706905 0.709389 0.688525 0.68455 0.806259 0.69697 0.605564 0.61997 0.727769 0.700944 0.707899 0.702931 -GRAZI 0.807253 0.817685 0.832091 0.769498 0.841033 0.791853 0.866865 0.830104 0.883259 0.866865 0.674118 0.735221 0.810233 0.814704 0.860407 0.649776 0.815698 0.842027 0.805266 0.697466 1 0.653254 0.840537 0.842027 0.802782 0.725286 0.728763 0.714357 0.804769 0.728763 0.777943 0.957774 0.749627 0.801788 0.808743 0.750124 0.815698 0.757079 0.74615 0.706408 0.821162 0.72926 0.736215 0.806259 0.881272 0.729757 0.697963 0.786885 0.727273 0.670144 0.824143 0.761053 0.76155 0.857923 0.675112 0.762543 0.80924 0.701441 0.71535 0.813214 0.760556 0.820169 0.756085 0.797317 0.773472 0.831098 0.678092 0.659215 0.837556 0.768505 0.822156 0.805763 0.77695 0.806756 0.801788 0.709886 0.750124 0.864382 0.768505 0.804769 0.879285 0.82762 0.790363 0.84302 0.722802 0.755092 0.717337 0.608048 0.77546 0.801788 0.727273 0.728266 0.799801 -IRAT144 0.712866 0.706408 0.704918 0.677099 0.689021 0.716344 0.701937 0.703924 0.679583 0.690015 0.682067 0.678589 0.673125 0.700447 0.733234 0.640835 0.730253 0.690015 0.762543 0.637854 0.653254 1 0.700447 0.754595 0.736215 0.660705 0.628415 0.648783 0.761053 0.66617 0.745156 0.657725 0.625435 0.704421 0.753105 0.647789 0.74615 0.608048 0.672628 0.661699 0.741679 0.898162 0.672628 0.762543 0.710383 0.656234 0.642325 0.714357 0.631893 0.867859 0.746647 0.733234 0.627422 0.655241 0.644312 0.700944 0.703924 0.624938 0.668654 0.757576 0.720815 0.776453 0.81073 0.728763 0.720815 0.712866 0.646299 0.645306 0.719324 0.763537 0.718828 0.76304 0.709389 0.678589 0.686538 0.682067 0.672628 0.68455 0.634377 0.761053 0.688525 0.782911 0.742673 0.702931 0.616493 0.656731 0.651764 0.668654 0.692002 0.685544 0.718331 0.642822 0.769001 -IAC47 0.929955 0.948336 0.9846 0.73224 0.942871 0.831098 0.941878 0.854446 0.846995 0.795827 0.737208 0.815201 0.800795 0.821162 0.833085 0.591654 0.961252 0.942871 0.913065 0.687034 0.840537 0.700447 1 0.831595 0.915549 0.689021 0.823646 0.79235 0.914555 0.691505 0.800298 0.837059 0.725286 0.824143 0.885743 0.765524 0.93542 0.691008 0.82315 0.703924 0.844511 0.773472 0.705912 0.914059 0.898659 0.695479 0.695479 0.803279 0.717834 0.741182 0.820666 0.868852 0.694486 0.771982 0.629906 0.847491 0.911078 0.668157 0.749627 0.859414 0.854446 0.90611 0.859911 0.749131 0.816692 0.80775 0.659712 0.638847 0.821162 0.835569 0.917039 0.913562 0.827124 0.950323 0.786388 0.670641 0.751615 0.793343 0.705415 0.913562 0.811227 0.857923 0.805763 0.989568 0.814704 0.71386 0.79533 0.582712 0.730253 0.787382 0.781421 0.77844 0.898659 -MOROBEREKAN 0.782414 0.811724 0.822156 0.749627 0.811227 0.829608 0.831098 0.765524 0.778937 0.827124 0.659215 0.719324 0.772479 0.80775 0.902136 0.608048 0.801788 0.811227 0.794337 0.69846 0.842027 0.754595 0.831595 1 0.789866 0.717337 0.715847 0.700447 0.792846 0.743666 0.767014 0.830601 0.768505 0.784898 0.785892 0.689518 0.803775 0.747144 0.743169 0.759066 0.898659 0.795827 0.745156 0.794337 0.857427 0.719821 0.714853 0.769995 0.725286 0.724789 0.862891 0.759066 0.751615 0.785395 0.64928 0.762543 0.790363 0.706408 0.724292 0.857923 0.751615 0.871833 0.751118 0.858917 0.772479 0.817188 0.698957 0.689021 0.787879 0.788376 0.803279 0.794834 0.772976 0.795827 0.852459 0.763537 0.756085 0.812717 0.758569 0.792846 0.881272 0.888227 0.807253 0.835072 0.703924 0.738202 0.704421 0.604074 0.850969 0.852459 0.717337 0.702434 0.818679 -IRAT362 0.902136 0.892697 0.92002 0.754098 0.874317 0.782414 0.885246 0.881272 0.852956 0.77993 0.774963 0.87382 0.794834 0.820169 0.820169 0.602583 0.944362 0.87531 0.942871 0.704918 0.802782 0.736215 0.915549 0.789866 1 0.710879 0.846498 0.848982 0.941381 0.706408 0.80924 0.813214 0.714357 0.836066 0.915549 0.82315 0.940387 0.676105 0.876801 0.711873 0.828614 0.80924 0.738698 0.942871 0.864878 0.728266 0.722305 0.814208 0.736711 0.759066 0.802782 0.87084 0.695479 0.744163 0.659712 0.917039 0.885246 0.684054 0.808246 0.887233 0.925981 0.905117 0.888723 0.727273 0.868356 0.803775 0.68157 0.660705 0.827124 0.863388 0.881272 0.943368 0.833085 0.88773 0.776453 0.702434 0.738698 0.794337 0.704421 0.941381 0.771485 0.886736 0.812717 0.919026 0.817685 0.731744 0.851962 0.602583 0.703428 0.776453 0.811227 0.835072 0.934426 -GIZA171 0.692499 0.693989 0.688525 0.817685 0.688525 0.697963 0.701441 0.713363 0.712866 0.736215 0.66766 0.692002 0.731247 0.728763 0.743666 0.702931 0.694983 0.687531 0.713363 0.741679 0.725286 0.660705 0.689021 0.717337 0.710879 1 0.696473 0.684054 0.712866 0.757079 0.798311 0.714853 0.735221 0.714853 0.723795 0.675112 0.716841 0.677099 0.682067 0.716841 0.720318 0.738698 0.74466 0.713363 0.724789 0.947839 0.795827 0.708892 0.822156 0.659712 0.737208 0.676105 0.693492 0.679583 0.735221 0.691505 0.688525 0.857923 0.692002 0.723299 0.723299 0.702434 0.677099 0.679583 0.759066 0.742176 0.745156 0.738202 0.686041 0.724292 0.705415 0.712866 0.735718 0.668157 0.692996 0.755092 0.764531 0.717834 0.694486 0.711873 0.690015 0.732737 0.693492 0.691505 0.686538 0.783408 0.687034 0.638351 0.672628 0.693989 0.834078 0.700944 0.704918 -IDSA77 0.817188 0.819672 0.834078 0.715847 0.79533 0.705415 0.783408 0.783408 0.741182 0.717834 0.863885 0.93691 0.74764 0.730253 0.727273 0.597119 0.814704 0.79533 0.830104 0.695479 0.728763 0.628415 0.823646 0.715847 0.846498 0.696473 1 0.960755 0.830601 0.684054 0.762047 0.71535 0.708892 0.731247 0.804769 0.887233 0.832588 0.612022 0.853453 0.682563 0.777447 0.703428 0.689518 0.830104 0.775956 0.710879 0.659215 0.747144 0.696473 0.677099 0.725782 0.786885 0.608544 0.673125 0.629409 0.85693 0.79235 0.670641 0.92002 0.756582 0.829111 0.788376 0.794834 0.660209 0.812221 0.731744 0.64928 0.660209 0.74615 0.76155 0.788376 0.830601 0.742176 0.84153 0.669647 0.655241 0.716344 0.693492 0.620467 0.830601 0.680576 0.736215 0.725782 0.832091 0.962245 0.697466 0.961749 0.583209 0.654247 0.669647 0.755092 0.945852 0.801788 -IRAT216 0.796821 0.784401 0.794834 0.721311 0.773969 0.709886 0.764034 0.795827 0.733731 0.703428 0.87531 0.958271 0.73224 0.714853 0.715847 0.597615 0.79533 0.774963 0.848485 0.694983 0.714357 0.648783 0.79235 0.700447 0.848982 0.684054 0.960755 1 0.848982 0.686538 0.749627 0.725782 0.707402 0.728763 0.821162 0.919523 0.813214 0.60457 0.860904 0.685047 0.76304 0.726776 0.706905 0.849478 0.758569 0.69846 0.668654 0.74764 0.694983 0.695479 0.704421 0.784401 0.602086 0.682563 0.625931 0.870343 0.772976 0.676105 0.949329 0.781918 0.863388 0.771982 0.815201 0.659712 0.823646 0.735221 0.648783 0.659712 0.741679 0.777943 0.759066 0.848982 0.746647 0.807253 0.672131 0.673621 0.704918 0.689021 0.613015 0.848982 0.667163 0.760556 0.727273 0.794834 0.944858 0.69697 0.995032 0.586687 0.640835 0.673125 0.759563 0.981123 0.82613 -IRAT177 0.943865 0.902633 0.921013 0.769001 0.88922 0.828117 0.882265 0.892201 0.859911 0.815698 0.730253 0.88773 0.817685 0.846001 0.822156 0.623448 0.944362 0.890214 0.997516 0.717834 0.804769 0.761053 0.914555 0.792846 0.941381 0.712866 0.830601 0.848982 1 0.72926 0.802285 0.820169 0.736215 0.85693 0.970194 0.821162 0.957278 0.682067 0.839046 0.727769 0.87531 0.84004 0.758569 0.99851 0.877794 0.723299 0.726279 0.857923 0.727769 0.750124 0.820666 0.865872 0.700447 0.768008 0.676602 0.877298 0.90611 0.688028 0.807253 0.909091 0.910084 0.917039 0.944362 0.750124 0.856433 0.814704 0.673621 0.670641 0.872827 0.90611 0.902136 0.998013 0.801292 0.89071 0.781421 0.723299 0.759563 0.791356 0.710383 0.998013 0.777447 0.90462 0.856433 0.915052 0.814704 0.754595 0.851962 0.622454 0.722305 0.782414 0.803279 0.835072 0.946349 -CHAPHUMA 0.697963 0.677596 0.685047 0.837059 0.684054 0.819672 0.719821 0.727769 0.71535 0.770492 0.665176 0.69846 0.760556 0.745156 0.780924 0.627919 0.705415 0.685047 0.729757 0.820666 0.728763 0.66617 0.691505 0.743666 0.706408 0.757079 0.684054 0.686538 0.72926 1 0.747144 0.724292 0.854943 0.718331 0.739195 0.655738 0.719324 0.637854 0.683557 0.880278 0.771485 0.735221 0.919026 0.73075 0.739195 0.756582 0.689021 0.748137 0.719324 0.638351 0.719821 0.679583 0.661202 0.708892 0.668157 0.692996 0.689021 0.733234 0.708395 0.742673 0.703924 0.721808 0.696473 0.701937 0.787382 0.749627 0.777447 0.788376 0.737208 0.793343 0.690015 0.730253 0.697466 0.662692 0.71535 0.912568 0.831595 0.748137 0.669151 0.72926 0.728266 0.744163 0.731744 0.692996 0.674118 0.914059 0.690512 0.611028 0.694983 0.71535 0.692499 0.700447 0.722305 -CIRAD392 0.790859 0.806259 0.805763 0.777943 0.795827 0.781421 0.809737 0.755092 0.764531 0.752111 0.728266 0.742673 0.745156 0.77844 0.789369 0.669151 0.785395 0.796821 0.802782 0.745653 0.777943 0.745156 0.800298 0.767014 0.80924 0.798311 0.762047 0.749627 0.802285 0.747144 1 0.763537 0.718331 0.785395 0.813214 0.777447 0.806259 0.684054 0.743666 0.710879 0.783905 0.827124 0.733731 0.803775 0.830104 0.802782 0.759066 0.772479 0.729757 0.814704 0.785892 0.781421 0.687531 0.747144 0.728266 0.787879 0.795827 0.756582 0.769498 0.782911 0.81073 0.809737 0.763537 0.737208 0.806756 0.829608 0.728266 0.713363 0.765524 0.784898 0.792846 0.803279 0.920517 0.783408 0.716841 0.704421 0.758569 0.727769 0.691505 0.803279 0.723795 0.781421 0.770989 0.803775 0.749131 0.743666 0.752608 0.655241 0.726279 0.717834 0.865872 0.763537 0.799305 -ARROZCEBADA 0.787879 0.812221 0.823646 0.775956 0.823646 0.789369 0.856433 0.838549 0.897665 0.861401 0.66468 0.745653 0.817685 0.821162 0.853949 0.629409 0.80924 0.82464 0.820666 0.695976 0.957774 0.657725 0.837059 0.830601 0.813214 0.714853 0.71535 0.725782 0.820169 0.724292 0.763537 1 0.742176 0.815201 0.841033 0.764531 0.80924 0.74466 0.738698 0.698957 0.81073 0.738698 0.750621 0.821659 0.861898 0.717337 0.704421 0.765524 0.714853 0.679583 0.798808 0.742673 0.748137 0.87531 0.658718 0.773969 0.788872 0.731744 0.723795 0.828614 0.770989 0.814704 0.769498 0.785892 0.773969 0.804769 0.672628 0.652757 0.820169 0.777943 0.811724 0.821162 0.787382 0.799305 0.794337 0.726279 0.748634 0.855936 0.758073 0.820169 0.87382 0.84302 0.77695 0.836562 0.706408 0.74764 0.728763 0.593641 0.74615 0.79533 0.736711 0.741679 0.812221 -INDANE 0.704918 0.717337 0.717834 0.827124 0.724789 0.800795 0.742673 0.73075 0.720318 0.737705 0.650273 0.707402 0.763537 0.739195 0.765027 0.613015 0.71237 0.725782 0.736711 0.767014 0.749627 0.625435 0.725286 0.768505 0.714357 0.735221 0.708892 0.707402 0.736215 0.854943 0.718331 0.742176 1 0.743169 0.736215 0.668654 0.726279 0.66468 0.682563 0.842524 0.76155 0.702434 0.849478 0.737705 0.761053 0.736711 0.678092 0.758073 0.720318 0.665176 0.728763 0.690512 0.66617 0.735718 0.642325 0.702931 0.69697 0.752111 0.701441 0.729757 0.705912 0.715847 0.697466 0.736711 0.77844 0.763537 0.697963 0.712866 0.738202 0.758569 0.69995 0.737208 0.700447 0.694486 0.730253 0.832091 0.796821 0.753105 0.679086 0.736215 0.71535 0.740189 0.751615 0.725782 0.69995 0.842524 0.710383 0.580229 0.727769 0.730253 0.685544 0.710383 0.714357 -DINORADO 0.833582 0.813214 0.826627 0.740189 0.802782 0.770492 0.838549 0.816692 0.863885 0.774963 0.68455 0.762543 0.860407 0.879781 0.802285 0.633383 0.850969 0.804769 0.857427 0.722802 0.801788 0.704421 0.824143 0.784898 0.836066 0.714853 0.731247 0.728763 0.85693 0.718331 0.785395 0.815201 0.743169 1 0.882762 0.753602 0.869846 0.712866 0.774466 0.723795 0.799801 0.784401 0.729757 0.85842 0.827124 0.725286 0.722305 0.825137 0.715847 0.69846 0.836562 0.797317 0.73224 0.831595 0.696473 0.794834 0.822653 0.721808 0.715847 0.802782 0.811724 0.837556 0.812221 0.74615 0.821659 0.802782 0.683557 0.687531 0.863885 0.814704 0.85842 0.857923 0.774466 0.799305 0.753602 0.69846 0.742673 0.788376 0.739195 0.857923 0.762543 0.815201 0.861401 0.82464 0.719324 0.719821 0.732737 0.63537 0.724292 0.754595 0.76155 0.74466 0.837059 -63-104 0.917039 0.876801 0.895181 0.778937 0.862394 0.82613 0.886239 0.884252 0.888723 0.795827 0.723299 0.859911 0.844511 0.87382 0.814208 0.627422 0.916542 0.863388 0.970691 0.734724 0.808743 0.753105 0.885743 0.785892 0.915549 0.723795 0.804769 0.821162 0.970194 0.739195 0.813214 0.841033 0.736215 0.882762 1 0.833085 0.932439 0.692996 0.812221 0.737705 0.856433 0.832091 0.768505 0.970691 0.882762 0.734228 0.742176 0.841033 0.737705 0.742176 0.831595 0.84004 0.711376 0.795827 0.68157 0.852459 0.879285 0.715847 0.808246 0.882265 0.883259 0.892201 0.917536 0.743169 0.866369 0.821659 0.689518 0.687531 0.866865 0.879285 0.886239 0.971187 0.811227 0.863885 0.77546 0.733234 0.767511 0.783408 0.721311 0.971187 0.769498 0.876801 0.850472 0.88922 0.796821 0.763537 0.825137 0.626428 0.71535 0.77546 0.813214 0.836066 0.919523 -IR63380-16 0.769001 0.757576 0.769995 0.707402 0.74615 0.708892 0.769001 0.785892 0.777447 0.71237 0.822653 0.881769 0.740189 0.756582 0.69697 0.623448 0.769498 0.747144 0.821659 0.675112 0.750124 0.647789 0.765524 0.689518 0.82315 0.675112 0.887233 0.919523 0.821162 0.655738 0.777447 0.764531 0.668654 0.753602 0.833085 1 0.788376 0.664183 0.804272 0.654247 0.736215 0.726776 0.676105 0.821659 0.764531 0.687531 0.695479 0.718828 0.677099 0.694486 0.713363 0.756582 0.661699 0.735221 0.672628 0.844511 0.737208 0.655241 0.900646 0.753105 0.839543 0.747144 0.785395 0.68455 0.792846 0.742176 0.629906 0.63686 0.787382 0.752111 0.757079 0.822156 0.774466 0.779434 0.685047 0.643815 0.678092 0.706905 0.672628 0.821162 0.687034 0.732737 0.728266 0.768008 0.878291 0.667163 0.920517 0.616493 0.653751 0.685047 0.787382 0.93542 0.797317 -CANAROXA 0.938897 0.923497 0.945852 0.743169 0.898162 0.819175 0.901143 0.88922 0.880775 0.805763 0.740189 0.847988 0.835569 0.863885 0.834078 0.61848 0.963239 0.899155 0.958768 0.707899 0.815698 0.74615 0.93542 0.803775 0.940387 0.716841 0.832588 0.813214 0.957278 0.719324 0.806259 0.80924 0.726279 0.869846 0.932439 0.788376 1 0.692996 0.846995 0.717834 0.864382 0.82315 0.728763 0.958768 0.88773 0.725286 0.721311 0.850969 0.731744 0.738202 0.836562 0.878788 0.71237 0.769995 0.674615 0.867362 0.918033 0.674118 0.770492 0.891207 0.895181 0.923 0.906607 0.76304 0.864382 0.826627 0.685544 0.671634 0.861898 0.874317 0.932936 0.959265 0.790363 0.917536 0.790363 0.695479 0.76155 0.808246 0.720318 0.958271 0.785395 0.889717 0.852459 0.93691 0.798808 0.742673 0.816195 0.619473 0.740189 0.790363 0.784401 0.798311 0.925484 -CICIHBETON 0.682563 0.706905 0.688525 0.675609 0.702434 0.700944 0.721311 0.68455 0.743666 0.71535 0.570293 0.609538 0.704421 0.742673 0.720815 0.610532 0.691008 0.702434 0.683557 0.642325 0.757079 0.608048 0.691008 0.747144 0.676105 0.677099 0.612022 0.60457 0.682067 0.637854 0.684054 0.74466 0.66468 0.712866 0.692996 0.664183 0.692996 1 0.620467 0.645306 0.703428 0.686041 0.638351 0.683557 0.724789 0.673621 0.651764 0.661202 0.697963 0.613015 0.745156 0.630402 0.961749 0.707402 0.655738 0.651764 0.687531 0.633383 0.616493 0.718331 0.661699 0.704421 0.646299 0.772976 0.66766 0.73224 0.640835 0.631893 0.708892 0.669647 0.690512 0.68306 0.698957 0.667163 0.746647 0.648783 0.646299 0.754595 0.926975 0.682067 0.728763 0.754595 0.694486 0.691505 0.600099 0.634377 0.607551 0.58768 0.724292 0.748634 0.674118 0.619473 0.702931 -IR68704-145-1-1-B 0.814704 0.806259 0.825633 0.704421 0.792846 0.715847 0.801788 0.817685 0.787382 0.723299 0.822653 0.871833 0.749131 0.755589 0.773472 0.60457 0.847988 0.79384 0.839543 0.706905 0.74615 0.672628 0.82315 0.743169 0.876801 0.682067 0.853453 0.860904 0.839046 0.683557 0.743666 0.738698 0.682563 0.774466 0.812221 0.804272 0.846995 0.620467 1 0.684054 0.767014 0.73075 0.692002 0.840537 0.790363 0.69846 0.670641 0.777447 0.733731 0.690512 0.751118 0.82315 0.637854 0.693492 0.644809 0.877298 0.801788 0.637357 0.818182 0.800795 0.859414 0.828614 0.818182 0.669647 0.825633 0.74615 0.673621 0.675609 0.763537 0.781918 0.792846 0.84004 0.754595 0.837059 0.705912 0.657725 0.724789 0.737705 0.649776 0.839046 0.714853 0.793343 0.748137 0.825633 0.828614 0.691008 0.861898 0.631396 0.656731 0.706905 0.73075 0.846001 0.846001 -HAWMOM 0.707402 0.69995 0.694486 0.80775 0.707402 0.804272 0.730253 0.725286 0.723795 0.720318 0.628912 0.69697 0.77695 0.738698 0.758569 0.630402 0.714853 0.708395 0.728266 0.76155 0.706408 0.661699 0.703924 0.759066 0.711873 0.716841 0.682563 0.685047 0.727769 0.880278 0.710879 0.698957 0.842524 0.723795 0.737705 0.654247 0.717834 0.645306 0.684054 1 0.740189 0.735718 0.88773 0.72926 0.724789 0.720318 0.71535 0.749627 0.749627 0.689518 0.768008 0.689021 0.66766 0.677596 0.652757 0.695479 0.702434 0.684054 0.702931 0.711376 0.705415 0.720318 0.687034 0.71535 0.806756 0.745156 0.76304 0.76304 0.737705 0.757079 0.701441 0.728763 0.705912 0.671138 0.729757 0.90611 0.797317 0.742673 0.671634 0.727769 0.711873 0.754595 0.749131 0.704421 0.686538 0.842027 0.689021 0.582712 0.687531 0.729757 0.680079 0.698957 0.725782 -IRAT364 0.859911 0.833582 0.846001 0.780427 0.832091 0.829608 0.824143 0.802285 0.785892 0.848982 0.672131 0.790859 0.770492 0.816692 0.859414 0.613015 0.845504 0.832091 0.875807 0.721311 0.821162 0.741679 0.844511 0.898659 0.828614 0.720318 0.777447 0.76304 0.87531 0.771485 0.783905 0.81073 0.76155 0.799801 0.856433 0.736215 0.864382 0.703428 0.767014 0.740189 1 0.783905 0.761053 0.876801 0.842524 0.728763 0.718828 0.821659 0.727273 0.69697 0.828117 0.803775 0.720815 0.767511 0.661202 0.785395 0.847988 0.693492 0.778937 0.906607 0.803279 0.891704 0.832588 0.790363 0.770492 0.794337 0.678092 0.681073 0.814704 0.82315 0.853949 0.876304 0.766021 0.821659 0.794834 0.746647 0.762047 0.797814 0.732737 0.87531 0.851465 0.87531 0.844014 0.846995 0.768505 0.767014 0.766021 0.613015 0.811227 0.795827 0.723299 0.757079 0.861401 -IRAT212 0.787879 0.777447 0.77993 0.748137 0.76304 0.791356 0.773969 0.775956 0.762543 0.769001 0.716344 0.756582 0.751118 0.777447 0.785395 0.654247 0.802285 0.764034 0.840537 0.710879 0.72926 0.898162 0.773472 0.795827 0.80924 0.738698 0.703428 0.726776 0.84004 0.735221 0.827124 0.738698 0.702434 0.784401 0.832091 0.726776 0.82315 0.686041 0.73075 0.735718 0.783905 1 0.740686 0.840537 0.791356 0.735221 0.71237 0.784401 0.714853 0.834575 0.82762 0.765524 0.704421 0.717337 0.710383 0.778937 0.796821 0.708892 0.719821 0.823646 0.798808 0.81073 0.811227 0.769995 0.796821 0.788872 0.71237 0.711376 0.786388 0.837556 0.778937 0.841033 0.789369 0.756582 0.766518 0.750124 0.74764 0.759563 0.711376 0.84004 0.73075 0.864878 0.79384 0.775956 0.689518 0.729757 0.728763 0.642325 0.726279 0.765524 0.794337 0.721808 0.84302 -KHAODAM 0.709389 0.693989 0.697466 0.879285 0.700447 0.818182 0.73224 0.753105 0.726776 0.774963 0.658718 0.722802 0.771982 0.753602 0.77546 0.608544 0.717834 0.701441 0.759066 0.813214 0.736215 0.672628 0.705912 0.745156 0.738698 0.74466 0.689518 0.706905 0.758569 0.919026 0.733731 0.750621 0.849478 0.729757 0.768505 0.676105 0.728763 0.638351 0.692002 0.88773 0.761053 0.740686 1 0.76006 0.752608 0.757079 0.688525 0.741679 0.718828 0.655738 0.743169 0.692002 0.660705 0.719324 0.645802 0.720318 0.69846 0.728763 0.718828 0.750124 0.731247 0.726279 0.717834 0.702434 0.796821 0.76006 0.77695 0.771982 0.752608 0.811724 0.702434 0.759563 0.71386 0.672131 0.725782 0.943865 0.849975 0.763537 0.668654 0.758569 0.718828 0.760556 0.737208 0.706408 0.68157 0.917536 0.710879 0.595628 0.688525 0.725782 0.706905 0.720815 0.742673 -62667 0.945355 0.904123 0.920517 0.770492 0.89071 0.828614 0.883756 0.892697 0.861401 0.817188 0.73075 0.888227 0.819175 0.846498 0.823646 0.624938 0.944858 0.891704 0.999006 0.717337 0.806259 0.762543 0.914059 0.794337 0.942871 0.713363 0.830104 0.849478 0.99851 0.73075 0.803775 0.821659 0.737705 0.85842 0.970691 0.821659 0.958768 0.683557 0.840537 0.72926 0.876801 0.840537 0.76006 1 0.879285 0.724789 0.726776 0.85842 0.727273 0.751615 0.822156 0.867362 0.701937 0.769498 0.678092 0.878788 0.907601 0.689518 0.80775 0.910581 0.910581 0.91853 0.944858 0.751615 0.857923 0.816195 0.674118 0.671138 0.874317 0.907601 0.902633 0.999503 0.802782 0.891207 0.782911 0.724789 0.76006 0.792846 0.711873 0.99851 0.778937 0.90611 0.857923 0.915549 0.814208 0.755092 0.853453 0.621957 0.723795 0.783905 0.804769 0.835569 0.947839 -IRAT234 0.883259 0.896672 0.90611 0.759066 0.895181 0.853949 0.902136 0.850472 0.853949 0.783905 0.73224 0.783408 0.791853 0.839046 0.874814 0.631396 0.882762 0.895181 0.878291 0.693989 0.881272 0.710383 0.898659 0.857427 0.864878 0.724789 0.775956 0.758569 0.877794 0.739195 0.830104 0.861898 0.761053 0.827124 0.882762 0.764531 0.88773 0.724789 0.790363 0.724789 0.842524 0.791356 0.752608 0.879285 1 0.730253 0.708395 0.810233 0.728763 0.737208 0.836562 0.828117 0.728266 0.803775 0.663686 0.819672 0.877298 0.698957 0.748634 0.857427 0.821659 0.884252 0.828117 0.795827 0.845504 0.879285 0.672628 0.651764 0.847988 0.811724 0.865375 0.878788 0.830104 0.883756 0.815201 0.718331 0.770492 0.827124 0.740189 0.878788 0.810233 0.863885 0.832588 0.90313 0.773969 0.764531 0.76155 0.61848 0.800795 0.815201 0.793343 0.773472 0.865872 -NIPPONBARE_D 0.703924 0.703428 0.694983 0.828117 0.69697 0.705415 0.707899 0.719821 0.720318 0.750621 0.667163 0.707402 0.734724 0.734228 0.749131 0.68455 0.703428 0.69697 0.723795 0.758073 0.729757 0.656234 0.695479 0.719821 0.728266 0.947839 0.710879 0.69846 0.723299 0.756582 0.802782 0.717337 0.736711 0.725286 0.734228 0.687531 0.725286 0.673621 0.69846 0.720318 0.728763 0.735221 0.757079 0.724789 0.730253 1 0.800298 0.717337 0.828614 0.670144 0.739692 0.689518 0.691008 0.681073 0.73075 0.709886 0.69995 0.826627 0.704421 0.728763 0.742673 0.71386 0.686538 0.682067 0.772479 0.74764 0.758569 0.752608 0.695479 0.722802 0.711873 0.724292 0.751118 0.672628 0.696473 0.764531 0.777943 0.724292 0.698957 0.723299 0.69846 0.737208 0.703924 0.698957 0.69995 0.800795 0.702434 0.631893 0.680079 0.697466 0.838549 0.71237 0.711376 -JUMULA2 0.697963 0.694486 0.689021 0.731744 0.698957 0.708395 0.718828 0.694983 0.707402 0.680079 0.599603 0.685544 0.695976 0.736215 0.736215 0.737208 0.708395 0.69995 0.725782 0.68455 0.697963 0.642325 0.695479 0.714853 0.722305 0.795827 0.659215 0.668654 0.726279 0.689021 0.759066 0.704421 0.678092 0.722305 0.742176 0.695479 0.721311 0.651764 0.670641 0.71535 0.718828 0.71237 0.688525 0.726776 0.708395 0.800298 1 0.705415 0.751118 0.692996 0.731744 0.677596 0.675112 0.681073 0.786388 0.714853 0.69697 0.739195 0.686538 0.729757 0.718828 0.700944 0.689518 0.675112 0.708892 0.741679 0.693989 0.688028 0.68157 0.708892 0.712866 0.726279 0.751118 0.683557 0.688525 0.700944 0.697466 0.703428 0.689021 0.726279 0.685544 0.740189 0.69995 0.69697 0.659215 0.702434 0.670641 0.657725 0.663189 0.689518 0.783905 0.683557 0.719324 -CUBA65 0.843517 0.813214 0.809737 0.743169 0.816692 0.801292 0.811724 0.813711 0.818182 0.794834 0.674615 0.774466 0.795827 0.797317 0.827124 0.645306 0.832091 0.817685 0.857427 0.728763 0.786885 0.714357 0.803279 0.769995 0.814208 0.708892 0.747144 0.74764 0.857923 0.748137 0.772479 0.765524 0.758073 0.825137 0.841033 0.718828 0.850969 0.661202 0.777447 0.749627 0.821659 0.784401 0.741679 0.85842 0.810233 0.717337 0.705415 1 0.71386 0.708395 0.80775 0.781421 0.680576 0.775956 0.683557 0.769001 0.829608 0.68306 0.748634 0.813711 0.818679 0.844511 0.808246 0.725286 0.791853 0.816692 0.689518 0.685544 0.839046 0.826627 0.816692 0.857923 0.763537 0.782414 0.728763 0.728266 0.735718 0.791356 0.682563 0.85693 0.765524 0.82613 0.891207 0.803775 0.745156 0.752608 0.751615 0.619473 0.748137 0.729757 0.729757 0.742673 0.835072 -BABER 0.725286 0.728763 0.723299 0.761053 0.721311 0.724789 0.736215 0.741182 0.729757 0.706408 0.659712 0.701937 0.739195 0.737705 0.732737 0.627422 0.742673 0.721311 0.726279 0.723795 0.727273 0.631893 0.717834 0.725286 0.736711 0.822156 0.696473 0.694983 0.727769 0.719324 0.729757 0.714853 0.720318 0.715847 0.737705 0.677099 0.731744 0.697963 0.733731 0.749627 0.727273 0.714853 0.718828 0.727273 0.728763 0.828614 0.751118 0.71386 1 0.689518 0.74615 0.694983 0.719324 0.661699 0.644809 0.703428 0.736215 0.733731 0.692996 0.74615 0.761053 0.701441 0.691008 0.692499 0.783905 0.751118 0.741182 0.736215 0.682067 0.69846 0.727273 0.726776 0.755589 0.704918 0.729757 0.737208 0.737705 0.745653 0.713363 0.725782 0.708892 0.762543 0.691505 0.720318 0.708395 0.749627 0.695976 0.602583 0.658718 0.73075 0.722802 0.707899 0.725782 -CIRAD488 0.725782 0.747144 0.745653 0.669151 0.733731 0.754098 0.745653 0.69697 0.679583 0.647293 0.689021 0.688525 0.669151 0.696473 0.706408 0.642822 0.741182 0.734724 0.750621 0.629906 0.670144 0.867859 0.741182 0.724789 0.759066 0.659712 0.677099 0.695479 0.750124 0.638351 0.814704 0.679583 0.665176 0.69846 0.742176 0.694486 0.738202 0.613015 0.690512 0.689518 0.69697 0.834575 0.655738 0.751615 0.737208 0.670144 0.692996 0.708395 0.689518 1 0.733731 0.757079 0.617486 0.672131 0.623448 0.732737 0.732737 0.646796 0.697466 0.727769 0.755589 0.725782 0.788872 0.725782 0.755589 0.751615 0.641331 0.631396 0.704421 0.709886 0.723795 0.751118 0.839543 0.723299 0.693492 0.661202 0.666667 0.696473 0.624441 0.751118 0.663686 0.768008 0.708892 0.741679 0.685047 0.646796 0.697466 0.637854 0.663189 0.693492 0.748137 0.690512 0.741182 -BENGALYVAKARINA 0.84302 0.82464 0.810233 0.764531 0.841033 0.767014 0.847988 0.77546 0.81073 0.786388 0.661202 0.738202 0.82613 0.847491 0.833582 0.630899 0.817685 0.841033 0.821162 0.719324 0.824143 0.746647 0.820666 0.862891 0.802782 0.737208 0.725782 0.704421 0.820666 0.719821 0.785892 0.798808 0.728763 0.836562 0.831595 0.713363 0.836562 0.745156 0.751118 0.768008 0.828117 0.82762 0.743169 0.822156 0.836562 0.739692 0.731744 0.80775 0.74615 0.733731 1 0.79384 0.764531 0.780427 0.68306 0.772479 0.853949 0.696473 0.704421 0.793343 0.785395 0.819175 0.780924 0.803279 0.800298 0.827124 0.714853 0.718828 0.815698 0.82315 0.82315 0.821659 0.788872 0.782911 0.794834 0.743666 0.76006 0.785892 0.763537 0.820666 0.789866 0.837556 0.805266 0.82315 0.721808 0.733234 0.708395 0.61699 0.791356 0.795827 0.752111 0.719324 0.80775 -ESPERANZA 0.876304 0.864878 0.87233 0.71237 0.864382 0.759563 0.843517 0.796821 0.782414 0.733234 0.781918 0.810233 0.758073 0.781421 0.752608 0.619473 0.875807 0.865375 0.866369 0.661202 0.761053 0.733234 0.868852 0.759066 0.87084 0.676105 0.786885 0.784401 0.865872 0.679583 0.781421 0.742673 0.690512 0.797317 0.84004 0.756582 0.878788 0.630402 0.82315 0.689021 0.803775 0.765524 0.692002 0.867362 0.828117 0.689518 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0.735718 0.658222 0.64928 0.728266 0.693989 0.708892 0.701441 0.703428 0.669647 0.775956 0.671138 0.661699 0.77695 0.958271 0.700447 0.74615 0.772976 0.712866 0.694983 0.596622 0.655738 0.605067 0.60308 0.737705 0.777943 0.676602 0.61699 0.721311 -ARIAS 0.74466 0.758073 0.76155 0.737705 0.764531 0.754098 0.783408 0.785395 0.831595 0.788376 0.629409 0.695479 0.810233 0.82762 0.797814 0.627919 0.747144 0.765524 0.768505 0.689518 0.857923 0.655241 0.771982 0.785395 0.744163 0.679583 0.673125 0.682563 0.768008 0.708892 0.747144 0.87531 0.735718 0.831595 0.795827 0.735221 0.769995 0.707402 0.693492 0.677596 0.767511 0.717337 0.719324 0.769498 0.803775 0.681073 0.681073 0.775956 0.661699 0.672131 0.780427 0.723299 0.720815 1 0.648286 0.717834 0.737705 0.716344 0.690512 0.766518 0.727769 0.768505 0.723299 0.769498 0.74466 0.782414 0.656234 0.65226 0.81073 0.745653 0.762543 0.769001 0.756085 0.736215 0.737208 0.688028 0.71237 0.781918 0.726776 0.768008 0.790859 0.773969 0.782414 0.772479 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0.80775 0.723795 0.79533 0.881272 0.759563 0.787879 0.775956 0.63388 0.869349 0.82613 0.877794 0.707402 0.762543 0.700944 0.847491 0.762543 0.917039 0.691505 0.85693 0.870343 0.877298 0.692996 0.787879 0.773969 0.702931 0.794834 0.852459 0.844511 0.867362 0.651764 0.877298 0.695479 0.785395 0.778937 0.720318 0.878788 0.819672 0.709886 0.714853 0.769001 0.703428 0.732737 0.772479 0.834575 0.671138 0.717834 0.686041 1 0.819175 0.671634 0.826627 0.84302 0.876801 0.855936 0.840537 0.69995 0.827124 0.777447 0.671138 0.671138 0.790859 0.831098 0.814208 0.878291 0.808743 0.87233 0.728266 0.687034 0.714357 0.755092 0.680079 0.878291 0.723299 0.840537 0.76155 0.848982 0.837059 0.704421 0.871336 0.630899 0.682067 0.72926 0.783905 0.85544 0.882265 -IRAT335 0.958271 0.925981 0.91853 0.723795 0.929459 0.800795 0.89071 0.842027 0.831595 0.787382 0.714853 0.809737 0.791356 0.817685 0.815698 0.606061 0.927968 0.929459 0.907601 0.68455 0.80924 0.703924 0.911078 0.790363 0.885246 0.688525 0.79235 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0.739195 0.68306 0.733731 0.646796 0.696473 0.650273 0.635867 0.716344 0.671634 0.671634 0.649776 1 0.679086 0.694486 0.677596 0.662692 0.654247 0.646796 0.717337 0.705415 0.691505 0.703428 0.650273 0.707402 0.653751 0.690015 0.706905 0.646299 0.643318 0.741182 0.716841 0.665176 0.635867 0.689021 0.645306 0.708892 0.66766 0.668654 0.660705 0.736711 0.680079 0.610532 0.647789 0.643318 0.79235 0.690015 0.680079 -IR65907-188-1-B 0.755092 0.745653 0.755092 0.728266 0.733234 0.71386 0.754098 0.769001 0.718828 0.704421 0.836562 0.916542 0.718331 0.700944 0.751615 0.610532 0.754595 0.734228 0.806756 0.707899 0.71535 0.668654 0.749627 0.724292 0.808246 0.692002 0.92002 0.949329 0.807253 0.708395 0.769498 0.723795 0.701441 0.715847 0.808246 0.900646 0.770492 0.616493 0.818182 0.702931 0.778937 0.719821 0.718828 0.80775 0.748634 0.704421 0.686538 0.748634 0.692996 0.697466 0.704421 0.740686 0.614009 0.690512 0.640835 0.826627 0.73224 0.679086 1 0.786885 0.817685 0.768008 0.771485 0.673621 0.809737 0.744163 0.66766 0.674615 0.727769 0.737208 0.744163 0.807253 0.768505 0.766518 0.673125 0.695479 0.705912 0.689021 0.623944 0.807253 0.690015 0.751615 0.73224 0.755092 0.912072 0.700944 0.948336 0.590661 0.671634 0.674118 0.745653 0.963239 0.806259 -IR71525-19-1-1 0.859911 0.839543 0.866865 0.764531 0.82613 0.834575 0.831098 0.847988 0.811724 0.827124 0.692996 0.814704 0.754595 0.806756 0.861401 0.604074 0.887233 0.827124 0.909588 0.703428 0.813214 0.757576 0.859414 0.857923 0.887233 0.723299 0.756582 0.781918 0.909091 0.742673 0.782911 0.828614 0.729757 0.802782 0.882265 0.753105 0.891207 0.718331 0.800795 0.711376 0.906607 0.823646 0.750124 0.910581 0.857427 0.728763 0.729757 0.813711 0.74615 0.727769 0.793343 0.81073 0.737705 0.766518 0.651267 0.84302 0.853949 0.694486 0.786885 1 0.84302 0.898659 0.867362 0.772479 0.788376 0.808246 0.679086 0.669151 0.802782 0.839046 0.851962 0.910084 0.795827 0.84153 0.812717 0.734724 0.741182 0.813711 0.739692 0.910084 0.825633 0.940884 0.818182 0.862891 0.740686 0.74615 0.782911 0.597119 0.77844 0.813711 0.735221 0.767014 0.942871 -CNA-7_BO_1_1_33-13-6-1 0.861898 0.845504 0.855936 0.750621 0.834078 0.76304 0.827124 0.84302 0.802782 0.752608 0.782414 0.843517 0.767511 0.788872 0.786885 0.590164 0.878291 0.835072 0.909588 0.714357 0.760556 0.720815 0.854446 0.751615 0.925981 0.723299 0.829111 0.863388 0.910084 0.703924 0.81073 0.770989 0.705912 0.811724 0.883259 0.839543 0.895181 0.661699 0.859414 0.705415 0.803279 0.798808 0.731247 0.910581 0.821659 0.742673 0.718828 0.818679 0.761053 0.755589 0.785395 0.843517 0.678092 0.727769 0.650273 0.876801 0.851962 0.677596 0.817685 0.84302 1 0.85693 0.85544 0.719821 0.87382 0.79235 0.693989 0.682067 0.804769 0.835072 0.852956 0.910084 0.821659 0.82464 0.750124 0.697963 0.736215 0.76304 0.689021 0.909091 0.736215 0.844511 0.796324 0.854943 0.814208 0.725286 0.865375 0.614009 0.689021 0.751118 0.813711 0.849478 0.891207 -IRAT257 0.905614 0.900149 0.916542 0.741679 0.880775 0.817685 0.885743 0.860904 0.864382 0.816195 0.71386 0.80775 0.796324 0.82464 0.878291 0.610035 0.925981 0.881769 0.917536 0.708395 0.820169 0.776453 0.90611 0.871833 0.905117 0.702434 0.788376 0.771982 0.917039 0.721808 0.809737 0.814704 0.715847 0.837556 0.892201 0.747144 0.923 0.704421 0.828614 0.720318 0.891704 0.81073 0.726279 0.91853 0.884252 0.71386 0.700944 0.844511 0.701441 0.725782 0.819175 0.829608 0.721808 0.768505 0.669151 0.855936 0.88773 0.662692 0.768008 0.898659 0.85693 1 0.864382 0.782414 0.832091 0.817188 0.686041 0.66617 0.848485 0.852956 0.902633 0.918033 0.813711 0.886239 0.781918 0.698957 0.756085 0.808743 0.73075 0.917039 0.85544 0.902136 0.865872 0.912568 0.767511 0.731247 0.774963 0.609041 0.774466 0.782911 0.766021 0.757079 0.923 -IRAT109 0.892201 0.851962 0.868356 0.731247 0.838549 0.780427 0.831595 0.843517 0.808246 0.76304 0.736215 0.850969 0.770989 0.801292 0.773472 0.628415 0.893691 0.839543 0.943865 0.688028 0.756085 0.81073 0.859911 0.751118 0.888723 0.677099 0.794834 0.815201 0.944362 0.696473 0.763537 0.769498 0.697466 0.812221 0.917536 0.785395 0.906607 0.646299 0.818182 0.687034 0.832588 0.811227 0.717834 0.944858 0.828117 0.686538 0.689518 0.808246 0.691008 0.788872 0.780924 0.868852 0.66468 0.723299 0.635867 0.840537 0.854446 0.654247 0.771485 0.867362 0.85544 0.864382 1 0.706408 0.804769 0.774963 0.638847 0.641828 0.827124 0.864382 0.851465 0.944362 0.76155 0.846001 0.732737 0.68157 0.719821 0.741679 0.675609 0.944362 0.724789 0.850969 0.808743 0.862394 0.778937 0.710879 0.814208 0.643318 0.682563 0.733731 0.764531 0.798311 0.903626 -KANIRANGA 0.739692 0.764034 0.746647 0.689021 0.754595 0.79384 0.776453 0.73075 0.752111 0.76155 0.608544 0.669647 0.749627 0.79384 0.805763 0.618977 0.740189 0.755589 0.751615 0.659712 0.797317 0.728763 0.749131 0.858917 0.727273 0.679583 0.660209 0.659712 0.750124 0.701937 0.737208 0.785892 0.736711 0.74615 0.743169 0.68455 0.76304 0.772976 0.669647 0.71535 0.790363 0.769995 0.702434 0.751615 0.795827 0.682067 0.675112 0.725286 0.692499 0.725782 0.803279 0.706408 0.787382 0.769498 0.654247 0.69995 0.743666 0.646796 0.673621 0.772479 0.719821 0.782414 0.706408 1 0.754595 0.800298 0.670144 0.667163 0.794834 0.729757 0.759563 0.752111 0.744163 0.723299 0.840537 0.718828 0.686538 0.825633 0.783408 0.750124 0.812717 0.809737 0.783408 0.751615 0.650273 0.700447 0.662692 0.614009 0.865872 0.840537 0.699454 0.660705 0.743169 -IR66421-096-2-1-1 0.828117 0.817685 0.822156 0.768505 0.806259 0.802782 0.832091 0.84302 0.825633 0.743666 0.777447 0.820666 0.842027 0.820666 0.806756 0.628912 0.845504 0.807253 0.85693 0.76006 0.773472 0.720815 0.816692 0.772479 0.868356 0.759066 0.812221 0.823646 0.856433 0.787382 0.806756 0.773969 0.77844 0.821659 0.866369 0.792846 0.864382 0.66766 0.825633 0.806756 0.770492 0.796821 0.796821 0.857923 0.845504 0.772479 0.708892 0.791853 0.783905 0.755589 0.800298 0.805763 0.686041 0.74466 0.663189 0.827124 0.808246 0.717337 0.809737 0.788376 0.87382 0.832091 0.804769 0.754595 1 0.815201 0.749627 0.741679 0.815698 0.799305 0.818182 0.857427 0.794834 0.789866 0.772976 0.779434 0.796821 0.788872 0.695976 0.856433 0.748137 0.822653 0.799305 0.820169 0.804272 0.800795 0.826627 0.61699 0.707899 0.772976 0.790859 0.837556 0.832588 -GOGO 0.80924 0.814704 0.813214 0.751615 0.816195 0.820666 0.839046 0.796324 0.799801 0.759563 0.701937 0.734228 0.776453 0.805763 0.84153 0.644809 0.81073 0.817188 0.815201 0.721311 0.831098 0.712866 0.80775 0.817188 0.803775 0.742176 0.731744 0.735221 0.814704 0.749627 0.829608 0.804769 0.763537 0.802782 0.821659 0.742176 0.826627 0.73224 0.74615 0.745156 0.794337 0.788872 0.76006 0.816195 0.879285 0.74764 0.741679 0.816692 0.751118 0.751615 0.827124 0.781918 0.735718 0.782414 0.678092 0.777447 0.817188 0.705415 0.744163 0.808246 0.79235 0.817188 0.774963 0.800298 0.815201 1 0.698957 0.682067 0.812717 0.797317 0.798311 0.815698 0.82464 0.791853 0.789866 0.724789 0.777943 0.826627 0.737705 0.814704 0.768008 0.821659 0.811227 0.810233 0.731744 0.76006 0.739195 0.631893 0.814208 0.789866 0.761053 0.750124 0.813711 -GEMJYAJYANAM 0.650273 0.655738 0.651267 0.760556 0.664183 0.711376 0.686041 0.669151 0.693492 0.702931 0.634377 0.654744 0.710879 0.704421 0.714357 0.587183 0.671634 0.665176 0.673125 0.898162 0.678092 0.646299 0.659712 0.698957 0.68157 0.745156 0.64928 0.648783 0.673621 0.777447 0.728266 0.672628 0.697963 0.683557 0.689518 0.629906 0.685544 0.640835 0.673621 0.76304 0.678092 0.71237 0.77695 0.674118 0.672628 0.758569 0.693989 0.689518 0.741182 0.641331 0.714853 0.628912 0.658222 0.656234 0.622454 0.671138 0.657228 0.691505 0.66766 0.679086 0.693989 0.686041 0.638847 0.670144 0.749627 0.698957 1 0.937407 0.649776 0.692002 0.659215 0.673621 0.695479 0.635867 0.731247 0.796324 0.768008 0.690512 0.662196 0.673621 0.657725 0.719324 0.678092 0.662196 0.639344 0.796821 0.651764 0.591157 0.616493 0.73224 0.690512 0.663686 0.674615 -DANGREY 0.644312 0.644809 0.632389 0.754595 0.653254 0.700447 0.670144 0.655241 0.675609 0.688028 0.629409 0.666667 0.712866 0.697466 0.685544 0.602086 0.652757 0.653254 0.670144 0.914059 0.659215 0.645306 0.638847 0.689021 0.660705 0.738202 0.660209 0.659712 0.670641 0.788376 0.713363 0.652757 0.712866 0.687531 0.687531 0.63686 0.671634 0.631893 0.675609 0.76304 0.681073 0.711376 0.771982 0.671138 0.651764 0.752608 0.688028 0.685544 0.736215 0.631396 0.718828 0.628912 0.64928 0.65226 0.636364 0.671138 0.647293 0.703428 0.674615 0.669151 0.682067 0.66617 0.641828 0.667163 0.741679 0.682067 0.937407 1 0.658718 0.689021 0.646299 0.670641 0.660705 0.626925 0.717337 0.794337 0.752111 0.671634 0.656234 0.670641 0.63388 0.701441 0.670144 0.641331 0.64928 0.784898 0.661699 0.607054 0.60457 0.718331 0.685544 0.672628 0.66468 -BINULAWAN 0.860407 0.819175 0.82464 0.731247 0.821659 0.802285 0.832588 0.835569 0.867859 0.820666 0.686538 0.774466 0.848485 0.852956 0.82315 0.659215 0.847988 0.822653 0.873323 0.703924 0.837556 0.719324 0.821162 0.787879 0.827124 0.686041 0.74615 0.741679 0.872827 0.737208 0.765524 0.820169 0.738202 0.863885 0.866865 0.787382 0.861898 0.708892 0.763537 0.737705 0.814704 0.786388 0.752608 0.874317 0.847988 0.695479 0.68157 0.839046 0.682067 0.704421 0.815698 0.794337 0.728266 0.81073 0.707402 0.790859 0.828614 0.650273 0.727769 0.802782 0.804769 0.848485 0.827124 0.794834 0.815698 0.812717 0.649776 0.658718 1 0.829608 0.857427 0.87382 0.750621 0.794337 0.780427 0.716344 0.736711 0.849975 0.736215 0.87382 0.817188 0.808246 0.87531 0.820666 0.74615 0.739692 0.74466 0.626428 0.774963 0.780427 0.738698 0.745653 0.842027 -CAIAPO 0.853949 0.834575 0.844014 0.806259 0.820169 0.806756 0.827124 0.825137 0.818679 0.817188 0.707899 0.814704 0.801292 0.825633 0.795827 0.640835 0.865375 0.821162 0.906607 0.74615 0.768505 0.763537 0.835569 0.788376 0.863388 0.724292 0.76155 0.777943 0.90611 0.793343 0.784898 0.777943 0.758569 0.814704 0.879285 0.752111 0.874317 0.669647 0.781918 0.757079 0.82315 0.837556 0.811724 0.907601 0.811724 0.722802 0.708892 0.826627 0.69846 0.709886 0.82315 0.828614 0.693989 0.745653 0.69995 0.831098 0.832091 0.707402 0.737208 0.839046 0.835072 0.852956 0.864382 0.729757 0.799305 0.797317 0.692002 0.689021 0.829608 1 0.830104 0.907104 0.751118 0.814704 0.742176 0.781421 0.782911 0.768008 0.69995 0.90611 0.739195 0.854446 0.801292 0.838053 0.742673 0.79384 0.781918 0.629906 0.726776 0.743169 0.789866 0.764034 0.871336 -IGUAPECATETO 0.922504 0.90313 0.927471 0.736711 0.882762 0.80775 0.879781 0.858917 0.862394 0.802285 0.701937 0.794834 0.811227 0.825633 0.834575 0.617983 0.928962 0.882762 0.902633 0.68455 0.822156 0.718828 0.917039 0.803279 0.881272 0.705415 0.788376 0.759066 0.902136 0.690015 0.792846 0.811724 0.69995 0.85842 0.886239 0.757079 0.932936 0.690512 0.792846 0.701441 0.853949 0.778937 0.702434 0.902633 0.865375 0.711873 0.712866 0.816692 0.727273 0.723795 0.82315 0.84153 0.708892 0.762543 0.66617 0.814208 0.906607 0.653751 0.744163 0.851962 0.852956 0.902633 0.851465 0.759563 0.818182 0.798311 0.659215 0.646299 0.857427 0.830104 1 0.90313 0.798808 0.899155 0.761053 0.670144 0.740189 0.808743 0.718828 0.901143 0.822653 0.836562 0.846995 0.915549 0.79235 0.713363 0.762047 0.609041 0.736711 0.761053 0.76304 0.753105 0.87233 -IRAT170 0.944858 0.90462 0.921013 0.769995 0.890214 0.828117 0.883259 0.893194 0.860904 0.816692 0.730253 0.88773 0.819672 0.846001 0.82315 0.624441 0.944362 0.891207 0.999503 0.716841 0.805763 0.76304 0.913562 0.794834 0.943368 0.712866 0.830601 0.848982 0.998013 0.730253 0.803279 0.821162 0.737208 0.857923 0.971187 0.822156 0.959265 0.68306 0.84004 0.728763 0.876304 0.841033 0.759563 0.999503 0.878788 0.724292 0.726279 0.857923 0.726776 0.751118 0.821659 0.866865 0.701441 0.769001 0.677596 0.878291 0.908097 0.690015 0.807253 0.910084 0.910084 0.918033 0.944362 0.752111 0.857427 0.815698 0.673621 0.670641 0.87382 0.907104 0.90313 1 0.802285 0.89071 0.783408 0.724292 0.759563 0.79235 0.711376 0.998013 0.77844 0.905614 0.85842 0.915052 0.814704 0.754595 0.853949 0.621461 0.724292 0.783408 0.804272 0.835072 0.947342 -IRAT380 0.81073 0.838053 0.832588 0.758073 0.82464 0.793343 0.850472 0.772976 0.768505 0.711376 0.694486 0.740686 0.726279 0.757576 0.796324 0.61848 0.812221 0.82464 0.801788 0.707899 0.77695 0.709389 0.827124 0.772976 0.833085 0.735718 0.742176 0.746647 0.801292 0.697466 0.920517 0.787382 0.700447 0.774466 0.811227 0.774466 0.790363 0.698957 0.754595 0.705912 0.766021 0.789369 0.71386 0.802782 0.830104 0.751118 0.751118 0.763537 0.755589 0.839543 0.788872 0.771485 0.703428 0.756085 0.663686 0.808743 0.825633 0.706905 0.768505 0.795827 0.821659 0.813711 0.76155 0.744163 0.794834 0.82464 0.695479 0.660705 0.750621 0.751118 0.798808 0.802285 1 0.80924 0.721808 0.682563 0.725782 0.752608 0.700447 0.801292 0.766518 0.804272 0.755092 0.830601 0.752111 0.704918 0.750621 0.595628 0.733234 0.722802 0.824143 0.760556 0.812221 -ARAGUAIA 0.908097 0.928465 0.963736 0.699454 0.901143 0.812221 0.902136 0.837556 0.828117 0.762047 0.751118 0.829111 0.76304 0.791356 0.796324 0.611525 0.936413 0.901143 0.890214 0.663189 0.806756 0.678589 0.950323 0.795827 0.88773 0.668157 0.84153 0.807253 0.89071 0.662692 0.783408 0.799305 0.694486 0.799305 0.863885 0.779434 0.917536 0.667163 0.837059 0.671138 0.821659 0.756582 0.672131 0.891207 0.883756 0.672628 0.683557 0.782414 0.704918 0.723299 0.782911 0.846001 0.669647 0.736215 0.651764 0.87233 0.892201 0.646299 0.766518 0.84153 0.82464 0.886239 0.846001 0.723299 0.789866 0.791853 0.635867 0.626925 0.794337 0.814704 0.899155 0.89071 0.80924 1 0.748634 0.635867 0.720815 0.771485 0.682563 0.89071 0.774466 0.839046 0.781918 0.952807 0.830601 0.684054 0.808246 0.60159 0.709389 0.749627 0.758569 0.79235 0.871833 -GOGOLEMPAK 0.756085 0.751615 0.774963 0.709389 0.755092 0.791356 0.782911 0.780924 0.770492 0.800795 0.635867 0.698957 0.750124 0.793343 0.835072 0.597615 0.788376 0.755092 0.782911 0.726776 0.801788 0.686538 0.786388 0.852459 0.776453 0.692996 0.669647 0.672131 0.781421 0.71535 0.716841 0.794337 0.730253 0.753602 0.77546 0.685047 0.790363 0.746647 0.705912 0.729757 0.794834 0.766518 0.725782 0.782911 0.815201 0.696473 0.688525 0.728763 0.729757 0.693492 0.794834 0.714853 0.775956 0.737208 0.645802 0.728266 0.762047 0.643318 0.673125 0.812717 0.750124 0.781918 0.732737 0.840537 0.772976 0.789866 0.731247 0.717337 0.780427 0.742176 0.761053 0.783408 0.721808 0.748634 1 0.734228 0.721808 0.838053 0.783905 0.782414 0.807253 0.852956 0.76006 0.786885 0.660705 0.728763 0.675112 0.577745 0.77993 0.998013 0.676105 0.674118 0.790363 -JAOHAW 0.674118 0.666667 0.661202 0.858917 0.674118 0.801788 0.69697 0.717834 0.702434 0.762543 0.624441 0.688525 0.76155 0.741182 0.758073 0.61699 0.68157 0.675112 0.723795 0.79384 0.709886 0.682067 0.670641 0.763537 0.702434 0.755092 0.655241 0.673621 0.723299 0.912568 0.704421 0.726279 0.832091 0.69846 0.733234 0.643815 0.695479 0.648783 0.657725 0.90611 0.746647 0.750124 0.943865 0.724789 0.718331 0.764531 0.700944 0.728266 0.737208 0.661202 0.743666 0.656731 0.671138 0.688028 0.648286 0.687034 0.663189 0.741182 0.695479 0.734724 0.697963 0.698957 0.68157 0.718828 0.779434 0.724789 0.796324 0.794337 0.716344 0.781421 0.670144 0.724292 0.682563 0.635867 0.734228 1 0.813711 0.748137 0.674118 0.723299 0.705415 0.777943 0.718828 0.671138 0.647293 0.898162 0.677596 0.595132 0.691008 0.734228 0.69846 0.687531 0.718331 -CHALOYOE 0.744163 0.733731 0.743169 0.825633 0.736215 0.773472 0.750124 0.768008 0.74466 0.77993 0.692499 0.718828 0.77695 0.740686 0.779434 0.620467 0.746647 0.736215 0.759066 0.789369 0.750124 0.672628 0.751615 0.756085 0.738698 0.764531 0.716344 0.704918 0.759563 0.831595 0.758569 0.748634 0.796821 0.742673 0.767511 0.678092 0.76155 0.646299 0.724789 0.797317 0.762047 0.74764 0.849975 0.76006 0.770492 0.777943 0.697466 0.735718 0.737705 0.666667 0.76006 0.716841 0.661699 0.71237 0.654744 0.714357 0.73224 0.716841 0.705912 0.741182 0.736215 0.756085 0.719821 0.686538 0.796821 0.777943 0.768008 0.752111 0.736711 0.782911 0.740189 0.759563 0.725782 0.720815 0.721808 0.813711 1 0.741679 0.673621 0.758569 0.735718 0.750621 0.727273 0.752111 0.704421 0.854943 0.707899 0.621461 0.679583 0.721808 0.723795 0.711873 0.743666 -GANIGI 0.785892 0.800298 0.796821 0.753105 0.783905 0.820169 0.805763 0.82464 0.868852 0.846498 0.661699 0.711873 0.787879 0.806259 0.860904 0.657228 0.821162 0.785892 0.791853 0.701937 0.864382 0.68455 0.793343 0.812717 0.794337 0.717834 0.693492 0.689021 0.791356 0.748137 0.727769 0.855936 0.753105 0.788376 0.783408 0.706905 0.808246 0.754595 0.737705 0.742673 0.797814 0.759563 0.763537 0.792846 0.827124 0.724292 0.703428 0.791356 0.745653 0.696473 0.785892 0.725782 0.77695 0.781918 0.695479 0.755092 0.789866 0.665176 0.689021 0.813711 0.76304 0.808743 0.741679 0.825633 0.788872 0.826627 0.690512 0.671634 0.849975 0.768008 0.808743 0.79235 0.752608 0.771485 0.838053 0.748137 0.741679 1 0.781918 0.791356 0.877794 0.838053 0.82464 0.795827 0.695479 0.764531 0.692002 0.610532 0.775956 0.838053 0.693989 0.691008 0.798311 -GUNDILKUNING 0.698957 0.707402 0.702931 0.701937 0.701937 0.71237 0.721808 0.717834 0.765027 0.741679 0.578738 0.630899 0.728763 0.771982 0.748137 0.643815 0.719324 0.701937 0.711873 0.66766 0.768505 0.634377 0.705415 0.758569 0.704421 0.694486 0.620467 0.613015 0.710383 0.669151 0.691505 0.758073 0.679086 0.739195 0.721311 0.672628 0.720318 0.926975 0.649776 0.671634 0.732737 0.711376 0.668654 0.711873 0.740189 0.698957 0.689021 0.682563 0.713363 0.624441 0.763537 0.651764 0.958271 0.726776 0.694983 0.680079 0.704918 0.635867 0.623944 0.739692 0.689021 0.73075 0.675609 0.783408 0.695976 0.737705 0.662196 0.656234 0.736215 0.69995 0.718828 0.711376 0.700447 0.682563 0.783905 0.674118 0.673621 0.781918 1 0.710383 0.74615 0.777943 0.719821 0.705912 0.609538 0.665673 0.615002 0.627919 0.727769 0.785892 0.680576 0.627919 0.722305 -IRAT2 0.944858 0.902633 0.921013 0.769001 0.890214 0.827124 0.882265 0.891207 0.860904 0.815698 0.72926 0.88773 0.817685 0.846995 0.822156 0.623448 0.943368 0.891207 0.997516 0.717834 0.804769 0.761053 0.913562 0.792846 0.941381 0.711873 0.830601 0.848982 0.998013 0.72926 0.803279 0.820169 0.736215 0.857923 0.971187 0.821162 0.958271 0.682067 0.839046 0.727769 0.87531 0.84004 0.758569 0.99851 0.878788 0.723299 0.726279 0.85693 0.725782 0.751118 0.820666 0.866865 0.700447 0.768008 0.676602 0.878291 0.90611 0.689021 0.807253 0.910084 0.909091 0.917039 0.944362 0.750124 0.856433 0.814704 0.673621 0.670641 0.87382 0.90611 0.901143 0.998013 0.801292 0.89071 0.782414 0.723299 0.758569 0.791356 0.710383 1 0.777447 0.90462 0.857427 0.916046 0.814704 0.753602 0.851962 0.623448 0.723299 0.783408 0.803279 0.835072 0.947342 -IRAT366 0.80775 0.805266 0.800795 0.733234 0.804769 0.800298 0.82464 0.796821 0.841033 0.895181 0.622951 0.69995 0.769995 0.779434 0.891704 0.624441 0.808246 0.804769 0.777943 0.673125 0.879285 0.688525 0.811227 0.881272 0.771485 0.690015 0.680576 0.667163 0.777447 0.728266 0.723795 0.87382 0.71535 0.762543 0.769498 0.687034 0.785395 0.728763 0.714853 0.711873 0.851465 0.73075 0.718828 0.778937 0.810233 0.69846 0.685544 0.765524 0.708892 0.663686 0.789866 0.719821 0.74615 0.790859 0.652757 0.723299 0.81073 0.645306 0.690015 0.825633 0.736215 0.85544 0.724789 0.812717 0.748137 0.768008 0.657725 0.63388 0.817188 0.739195 0.822653 0.77844 0.766518 0.774466 0.807253 0.705415 0.735718 0.877794 0.74615 0.777447 1 0.830104 0.803775 0.813711 0.691505 0.731744 0.669151 0.577745 0.796821 0.808246 0.655241 0.670144 0.79533 -IRAT104 0.857427 0.846995 0.864382 0.769001 0.833582 0.853949 0.845504 0.847491 0.831098 0.842524 0.679583 0.794337 0.789866 0.836066 0.862891 0.61848 0.888723 0.834575 0.905117 0.706905 0.82762 0.782911 0.857923 0.888227 0.886736 0.732737 0.736215 0.760556 0.90462 0.744163 0.781421 0.84302 0.740189 0.815201 0.876801 0.732737 0.889717 0.754595 0.793343 0.754595 0.87531 0.864878 0.760556 0.90611 0.863885 0.737208 0.740189 0.82613 0.762543 0.768008 0.837556 0.796324 0.772976 0.773969 0.661699 0.840537 0.853453 0.708892 0.751615 0.940884 0.844511 0.902136 0.850969 0.809737 0.822653 0.821659 0.719324 0.701441 0.808246 0.854446 0.836562 0.905614 0.804272 0.839046 0.852956 0.777943 0.750621 0.838053 0.777943 0.90462 0.830104 1 0.821659 0.859414 0.721311 0.753602 0.764531 0.60159 0.777943 0.853949 0.752608 0.746647 0.910581 -DAVAO 0.838053 0.822653 0.80924 0.735718 0.818182 0.809737 0.808246 0.799305 0.832588 0.791356 0.660209 0.753105 0.782414 0.803775 0.82762 0.637854 0.830601 0.820169 0.857923 0.709389 0.790363 0.742673 0.805763 0.807253 0.812717 0.693492 0.725782 0.727273 0.856433 0.731744 0.770989 0.77695 0.751615 0.861401 0.850472 0.728266 0.852459 0.694486 0.748137 0.749131 0.844014 0.79384 0.737208 0.857923 0.832588 0.703924 0.69995 0.891207 0.691505 0.708892 0.805266 0.768008 0.712866 0.782414 0.691008 0.76155 0.819175 0.66766 0.73224 0.818182 0.796324 0.865872 0.808743 0.783408 0.799305 0.811227 0.678092 0.670144 0.87531 0.801292 0.846995 0.85842 0.755092 0.781918 0.76006 0.718828 0.727273 0.82464 0.719821 0.857427 0.803775 0.821659 1 0.806259 0.721808 0.737208 0.730253 0.630899 0.763537 0.759066 0.728266 0.72926 0.837556 -HD1-4 0.931446 0.955787 0.98609 0.731744 0.941381 0.826627 0.942375 0.855936 0.846498 0.797317 0.738698 0.816692 0.800298 0.821659 0.836562 0.593145 0.961749 0.941381 0.914555 0.688525 0.84302 0.702931 0.989568 0.835072 0.919026 0.691505 0.832091 0.794834 0.915052 0.692996 0.803775 0.836562 0.725782 0.82464 0.88922 0.768008 0.93691 0.691505 0.825633 0.704421 0.846995 0.775956 0.706408 0.915549 0.90313 0.698957 0.69697 0.803775 0.720318 0.741679 0.82315 0.871336 0.694983 0.772479 0.633383 0.848982 0.912568 0.668654 0.755092 0.862891 0.854943 0.912568 0.862394 0.751615 0.820169 0.810233 0.662196 0.641331 0.820666 0.838053 0.915549 0.915052 0.830601 0.952807 0.786885 0.671138 0.752111 0.795827 0.705912 0.916046 0.813711 0.859414 0.806259 1 0.820169 0.716344 0.796821 0.58619 0.734724 0.787879 0.781918 0.77993 0.901143 -CURINCA 0.831098 0.809737 0.821162 0.710879 0.810233 0.720318 0.782414 0.769498 0.72926 0.703924 0.864878 0.921013 0.728763 0.711376 0.71535 0.604074 0.805763 0.80924 0.814208 0.68455 0.722802 0.616493 0.814704 0.703924 0.817685 0.686538 0.962245 0.944858 0.814704 0.674118 0.749131 0.706408 0.69995 0.719324 0.796821 0.878291 0.798808 0.600099 0.828614 0.686538 0.768505 0.689518 0.68157 0.814208 0.773969 0.69995 0.659215 0.745156 0.708395 0.685047 0.721808 0.798808 0.596622 0.669151 0.616493 0.837059 0.807253 0.660705 0.912072 0.740686 0.814208 0.767511 0.778937 0.650273 0.804272 0.731744 0.639344 0.64928 0.74615 0.742673 0.79235 0.814704 0.752111 0.830601 0.660705 0.647293 0.704421 0.695479 0.609538 0.814704 0.691505 0.721311 0.721808 0.820169 1 0.687531 0.946846 0.568306 0.651267 0.660705 0.745156 0.938897 0.785892 -DAM 0.721311 0.700944 0.709389 0.874317 0.705415 0.825137 0.743169 0.751118 0.740686 0.783905 0.666667 0.711873 0.762047 0.752608 0.783408 0.617486 0.729757 0.706408 0.754098 0.806259 0.755092 0.656731 0.71386 0.738202 0.731744 0.783408 0.697466 0.69697 0.754595 0.914059 0.743666 0.74764 0.842524 0.719821 0.763537 0.667163 0.742673 0.634377 0.691008 0.842027 0.767014 0.729757 0.917536 0.755092 0.764531 0.800795 0.702434 0.752608 0.749627 0.646796 0.733234 0.693989 0.655738 0.69846 0.656731 0.704421 0.709389 0.736711 0.700944 0.74615 0.725286 0.731247 0.710879 0.700447 0.800795 0.76006 0.796821 0.784898 0.739692 0.79384 0.713363 0.754595 0.704918 0.684054 0.728763 0.898162 0.854943 0.764531 0.665673 0.753602 0.731744 0.753602 0.737208 0.716344 0.687531 1 0.69995 0.60159 0.678589 0.728763 0.702931 0.709886 0.726776 -CIRAD403 0.798808 0.788376 0.797814 0.725286 0.77695 0.712866 0.768008 0.797814 0.735718 0.706408 0.87531 0.959265 0.736215 0.716841 0.718828 0.597615 0.798311 0.777943 0.853453 0.69697 0.717337 0.651764 0.79533 0.704421 0.851962 0.687034 0.961749 0.995032 0.851962 0.690512 0.752608 0.728763 0.710383 0.732737 0.825137 0.920517 0.816195 0.607551 0.861898 0.689021 0.766021 0.728763 0.710879 0.853453 0.76155 0.702434 0.670641 0.751615 0.695976 0.697466 0.708395 0.786388 0.605067 0.685544 0.627919 0.871336 0.77695 0.680079 0.948336 0.782911 0.865375 0.774963 0.814208 0.662692 0.826627 0.739195 0.651764 0.661699 0.74466 0.781918 0.762047 0.853949 0.750621 0.808246 0.675112 0.677596 0.707899 0.692002 0.615002 0.851962 0.669151 0.764531 0.730253 0.796821 0.946846 0.69995 1 0.584699 0.643815 0.675112 0.763537 0.981123 0.828117 -JUMALI 0.592151 0.591654 0.588177 0.598112 0.582216 0.605564 0.598112 0.591157 0.617486 0.598112 0.594138 0.598609 0.591157 0.621461 0.613512 0.845007 0.603577 0.582216 0.621957 0.605564 0.608048 0.668654 0.582712 0.604074 0.602583 0.638351 0.583209 0.586687 0.622454 0.611028 0.655241 0.593641 0.580229 0.63537 0.626428 0.616493 0.619473 0.58768 0.631396 0.582712 0.613015 0.642325 0.595628 0.621957 0.61848 0.631893 0.657725 0.619473 0.602583 0.637854 0.61699 0.610532 0.60308 0.580229 0.81073 0.630899 0.582216 0.610532 0.590661 0.597119 0.614009 0.609041 0.643318 0.614009 0.61699 0.631893 0.591157 0.607054 0.626428 0.629906 0.609041 0.621461 0.595628 0.60159 0.577745 0.595132 0.621461 0.610532 0.627919 0.623448 0.577745 0.60159 0.630899 0.58619 0.568306 0.60159 0.584699 1 0.600099 0.577745 0.645306 0.592648 0.603577 -JIMBRUKJOLOWORO 0.739692 0.750124 0.735718 0.688028 0.74764 0.771982 0.74764 0.715847 0.707402 0.739692 0.60159 0.655738 0.728763 0.766021 0.812717 0.595132 0.716344 0.74764 0.723795 0.61997 0.77546 0.692002 0.730253 0.850969 0.703428 0.672628 0.654247 0.640835 0.722305 0.694983 0.726279 0.74615 0.727769 0.724292 0.71535 0.653751 0.740189 0.724292 0.656731 0.687531 0.811227 0.726279 0.688525 0.723795 0.800795 0.680079 0.663189 0.748137 0.658718 0.663189 0.791356 0.721311 0.737705 0.759563 0.631396 0.682067 0.741679 0.647789 0.671634 0.77844 0.689021 0.774466 0.682563 0.865872 0.707899 0.814208 0.616493 0.60457 0.774963 0.726776 0.736711 0.724292 0.733234 0.709389 0.77993 0.691008 0.679583 0.775956 0.727769 0.723299 0.796821 0.777943 0.763537 0.734724 0.651267 0.678589 0.643815 0.600099 1 0.77993 0.680576 0.641828 0.739195 -GOGOLEMPUK 0.757079 0.751615 0.774963 0.710383 0.756085 0.791356 0.783905 0.780924 0.771485 0.801788 0.63686 0.69995 0.750124 0.79533 0.835072 0.597615 0.789369 0.756085 0.782911 0.727769 0.801788 0.685544 0.787382 0.852459 0.776453 0.693989 0.669647 0.673125 0.782414 0.71535 0.717834 0.79533 0.730253 0.754595 0.77546 0.685047 0.790363 0.748634 0.706905 0.729757 0.795827 0.765524 0.725782 0.783905 0.815201 0.697466 0.689518 0.729757 0.73075 0.693492 0.795827 0.715847 0.777943 0.738202 0.645802 0.72926 0.762047 0.643318 0.674118 0.813711 0.751118 0.782911 0.733731 0.840537 0.772976 0.789866 0.73224 0.718331 0.780427 0.743169 0.761053 0.783408 0.722802 0.749627 0.998013 0.734228 0.721808 0.838053 0.785892 0.783408 0.808246 0.853949 0.759066 0.787879 0.660705 0.728763 0.675112 0.577745 0.77993 1 0.677099 0.675112 0.791356 -CIRAD394 0.767014 0.790363 0.783905 0.761053 0.778937 0.725782 0.783905 0.742176 0.750621 0.693492 0.725286 0.755589 0.71535 0.742673 0.705912 0.677099 0.764531 0.778937 0.803775 0.700944 0.727273 0.718331 0.781421 0.717337 0.811227 0.834078 0.755092 0.759563 0.803279 0.692499 0.865872 0.736711 0.685544 0.76155 0.813214 0.787382 0.784401 0.674118 0.73075 0.680079 0.723299 0.794337 0.706905 0.804769 0.793343 0.838549 0.783905 0.729757 0.722802 0.748137 0.752111 0.770492 0.676602 0.714357 0.733234 0.783905 0.742176 0.79235 0.745653 0.735221 0.813711 0.766021 0.764531 0.699454 0.790859 0.761053 0.690512 0.685544 0.738698 0.789866 0.76304 0.804272 0.824143 0.758569 0.676105 0.69846 0.723795 0.693989 0.680576 0.803279 0.655241 0.752608 0.728266 0.781918 0.745156 0.702931 0.763537 0.645306 0.680576 0.677099 1 0.773472 0.781421 -IR63372-08 0.781918 0.769498 0.780924 0.735221 0.76006 0.712866 0.778937 0.796821 0.74764 0.697466 0.868356 0.944362 0.747144 0.729757 0.717834 0.605564 0.781421 0.761053 0.834575 0.707899 0.728266 0.642822 0.77844 0.702434 0.835072 0.700944 0.945852 0.981123 0.835072 0.700447 0.763537 0.741679 0.710383 0.74466 0.836066 0.93542 0.798311 0.619473 0.846001 0.698957 0.757079 0.721808 0.720815 0.835569 0.773472 0.71237 0.683557 0.742673 0.707899 0.690512 0.719324 0.769498 0.61699 0.697466 0.634873 0.85544 0.759066 0.690015 0.963239 0.767014 0.849478 0.757079 0.798311 0.660705 0.837556 0.750124 0.663686 0.672628 0.745653 0.764034 0.753105 0.835072 0.760556 0.79235 0.674118 0.687531 0.711873 0.691008 0.627919 0.835072 0.670144 0.746647 0.72926 0.77993 0.938897 0.709886 0.981123 0.592648 0.641828 0.675112 0.773472 1 0.812221 -IR60080-46A 0.899155 0.879781 0.901143 0.753105 0.867362 0.807253 0.869349 0.878291 0.845007 0.808743 0.738202 0.861898 0.787879 0.817188 0.84004 0.617486 0.924491 0.868356 0.946846 0.702931 0.799801 0.769001 0.898659 0.818679 0.934426 0.704918 0.801788 0.82613 0.946349 0.722305 0.799305 0.812221 0.714357 0.837059 0.919523 0.797317 0.925484 0.702931 0.846001 0.725782 0.861401 0.84302 0.742673 0.947839 0.865872 0.711376 0.719324 0.835072 0.725782 0.741182 0.80775 0.858917 0.721311 0.762047 0.672628 0.882265 0.880278 0.680079 0.806259 0.942871 0.891207 0.923 0.903626 0.743169 0.832588 0.813711 0.674615 0.66468 0.842027 0.871336 0.87233 0.947342 0.812221 0.871833 0.790363 0.718331 0.743666 0.798311 0.722305 0.947342 0.79533 0.910581 0.837556 0.901143 0.785892 0.726776 0.828117 0.603577 0.739195 0.791356 0.781421 0.812221 1
--- a/MDSplot/test-data/analyse.log Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ - -@----------------------------------------------------------@ -| PLINK! | v1.07 | 10/Aug/2009 | -|----------------------------------------------------------| -| (C) 2009 Shaun Purcell, GNU General Public License, v2 | -|----------------------------------------------------------| -| For documentation, citation & bug-report instructions: | -| http://pngu.mgh.harvard.edu/purcell/plink/ | -@----------------------------------------------------------@ - -Skipping web check... [ --noweb ] -Writing this text to log file [ analyse.log ] -Analysis started: Tue Jan 20 09:30:56 2015 - -Options in effect: - --file input - --noweb - --cluster - --matrix - --mds-plot 2 - --out analyse - -2013 (of 2013) markers to be included from [ input.map ] -93 individuals read from [ input.ped ] -93 individuals with nonmissing phenotypes -Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) -Missing phenotype value is also -9 -0 cases, 93 controls and 0 missing -93 males, 0 females, and 0 of unspecified sex -Before frequency and genotyping pruning, there are 2013 SNPs -Converting data to SNP-major format -93 founders and 0 non-founders found -Total genotyping rate in remaining individuals is 1 -0 SNPs failed missingness test ( GENO > 1 ) -0 SNPs failed frequency test ( MAF < 0 ) -Converting data to Individual-major format -After frequency and genotyping pruning, there are 2013 SNPs -After filtering, 0 cases, 93 controls and 0 missing -After filtering, 93 males, 0 females, and 0 of unspecified sex - - **Warning** this analysis typically requires whole-genome level data - to give accurate results - -Clustering individuals based on genome-wide IBS -Merge distance p-value constraint = 0 -IBS(g) calculation: 0 of 4278 IBS(g) calculation: 100 of 4278 IBS(g) calculation: 200 of 4278 IBS(g) calculation: 300 of 4278 IBS(g) calculation: 400 of 4278 IBS(g) calculation: 500 of 4278 IBS(g) calculation: 600 of 4278 IBS(g) calculation: 700 of 4278 IBS(g) calculation: 800 of 4278 IBS(g) calculation: 900 of 4278 IBS(g) calculation: 1000 of 4278 IBS(g) calculation: 1100 of 4278 IBS(g) calculation: 1200 of 4278 IBS(g) calculation: 1300 of 4278 IBS(g) calculation: 1400 of 4278 IBS(g) calculation: 1500 of 4278 IBS(g) calculation: 1600 of 4278 IBS(g) calculation: 1700 of 4278 IBS(g) calculation: 1800 of 4278 IBS(g) calculation: 1900 of 4278 IBS(g) calculation: 2000 of 4278 IBS(g) calculation: 2100 of 4278 IBS(g) calculation: 2200 of 4278 IBS(g) calculation: 2300 of 4278 IBS(g) calculation: 2400 of 4278 IBS(g) calculation: 2500 of 4278 IBS(g) calculation: 2600 of 4278 IBS(g) calculation: 2700 of 4278 IBS(g) calculation: 2800 of 4278 IBS(g) calculation: 2900 of 4278 IBS(g) calculation: 3000 of 4278 IBS(g) calculation: 3100 of 4278 IBS(g) calculation: 3200 of 4278 IBS(g) calculation: 3300 of 4278 IBS(g) calculation: 3400 of 4278 IBS(g) calculation: 3500 of 4278 IBS(g) calculation: 3600 of 4278 IBS(g) calculation: 3700 of 4278 IBS(g) calculation: 3800 of 4278 IBS(g) calculation: 3900 of 4278 IBS(g) calculation: 4000 of 4278 IBS(g) calculation: 4100 of 4278 IBS(g) calculation: 4200 of 4278 Writing IBS similarity matrix to [ analyse.mibs ] -Of these, 4278 are pairable based on constraints -Writing cluster progress to [ analyse.cluster0 ] -Writing cluster solution (1) [ analyse.cluster1 ] -Writing cluster solution (2) [ analyse.cluster2 ] -Writing cluster solution (3) [ analyse.cluster3 ] -Writing MDS solution to [ analyse.mds ] -MDS plot of individuals (not clusters) - -Analysis finished: Tue Jan 20 09:30:57 2015 -
--- a/MDSplot/test-data/analyse.mds_plot.txt Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -IRAT112 -0.0969382 0.0376036 -IAC25 -0.0918126 0.0501177 -IAC165 -0.104815 0.0453876 -KARASUKARASURANKASU 0.107782 -0.0683546 -DOURADOPRECOCE -0.0831697 0.0516412 -CUIABANA 0.0327877 0.0497752 -BICOBRANCO -0.0554177 0.0501857 -CAAWA/FORTUNA6 -0.052355 0.0170584 -CANELADEFERRO -0.0142283 0.0598394 -CIRAD358 0.0497841 0.0645487 -COLOMBIA1 -0.110347 -0.172742 -CIRAD409 -0.113614 -0.105898 -BAGANANASALAO 0.0247582 0.0186246 -BAKUNGH 0.0199022 0.0613692 -FOHISOMOTRA 0.0344309 0.0697592 -KAKANI2 0.147713 -0.0780455 -GUARANI -0.0892761 0.0387007 -DOURADOAGULHA -0.0831373 0.0514523 -IRAT13 -0.0757215 0.00312413 -DAWASANRED 0.131309 -0.102364 -GRAZI 0.0177091 0.0870472 -IRAT144 0.0146443 0.0067734 -IAC47 -0.0968934 0.0477667 -MOROBEREKAN 0.0395544 0.0952695 -IRAT362 -0.0921075 -0.00860852 -GIZA171 0.14498 -0.0932001 -IDSA77 -0.122827 -0.120219 -IRAT216 -0.120205 -0.136803 -IRAT177 -0.0762395 0.00230332 -CHAPHUMA 0.149543 -0.0680637 -CIRAD392 0.0187265 -0.047646 -ARROZCEBADA 0.0110416 0.0787137 -INDANE 0.108691 -0.0338065 -DINORADO -0.00819237 0.0386578 -63-104 -0.053974 -0.00204494 -IR63380-16 -0.0968028 -0.0931822 -CANAROXA -0.0756689 0.0253328 -CICIHBETON 0.108857 0.142633 -IR68704-145-1-1-B -0.103292 -0.071382 -HAWMOM 0.129651 -0.0473323 -IRAT364 -0.0118523 0.0472973 -IRAT212 0.0231616 -0.00146178 -KHAODAM 0.123936 -0.0654516 -62667 -0.0752552 0.00278556 -IRAT234 -0.0346607 0.0551203 -NIPPONBARE_D 0.133199 -0.0963396 -JUMULA2 0.104558 -0.0524994 -CUBA65 -0.0124835 0.013679 -BABER 0.090299 -0.0460696 -CIRAD488 -0.0201481 -0.0262103 -BENGALYVAKARINA 0.028631 0.0637662 -ESPERANZA -0.108888 -0.00812147 -BULUPANDAK 0.119762 0.143912 -ARIAS 0.0327948 0.0827878 -GOMPA2 0.133341 -0.0543414 -CT13582-15-5-M -0.0922561 -0.0543988 -IRAT335 -0.0886849 0.0522465 -M202 0.13463 -0.106462 -IR65907-188-1-B -0.0755893 -0.136821 -IR71525-19-1-1 -0.0353444 0.0478985 -CNA-7_BO_1_1_33-13-6-1 -0.0823478 -0.0435581 -IRAT257 -0.0606191 0.0564989 -IRAT109 -0.1006 -0.00959445 -KANIRANGA 0.0705459 0.129888 -IR66421-096-2-1-1 -0.00859728 -0.0570793 -GOGO 0.0232414 0.0351889 -GEMJYAJYANAM 0.170032 -0.0857315 -DANGREY 0.175792 -0.113683 -BINULAWAN -0.0208225 0.0611919 -CAIAPO -0.0149329 -0.0122987 -IGUAPECATETO -0.0740464 0.0552386 -IRAT170 -0.0756928 0.00297643 -IRAT380 -0.0210318 -0.00092536 -ARAGUAIA -0.123443 0.0273298 -GOGOLEMPAK 0.0598291 0.107462 -JAOHAW 0.17563 -0.0587865 -CHALOYOE 0.0904761 -0.0565325 -GANIGI 0.0526286 0.0960475 -GUNDILKUNING 0.116788 0.130234 -IRAT2 -0.0762849 0.00262428 -IRAT366 0.0273652 0.13551 -IRAT104 -0.00310702 0.0636479 -DAVAO -0.00538403 0.0564886 -HD1-4 -0.0960109 0.0459137 -CURINCA -0.128876 -0.121141 -DAM 0.129029 -0.0660183 -CIRAD403 -0.117849 -0.134651 -JUMALI 0.123992 -0.0843623 -JIMBRUKJOLOWORO 0.0549906 0.135017 -GOGOLEMPUK 0.0597267 0.10733 -CIRAD394 0.0040454 -0.0885135 -IR63372-08 -0.0951857 -0.140804 -IR60080-46A -0.0732581 0.0197832
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4837250 -Chr1 Chr1:4896826 0 4896826 -Chr1 Chr1:4988652 0 4988652 -Chr1 Chr1:4988653 0 4988653 -Chr1 Chr1:4988803 0 4988803 -Chr1 Chr1:4996172 0 4996172 -Chr1 Chr1:5004867 0 5004867 -Chr1 Chr1:5009237 0 5009237 -Chr1 Chr1:5009291 0 5009291 -Chr1 Chr1:5017806 0 5017806 -Chr1 Chr1:5027851 0 5027851 -Chr1 Chr1:5031814 0 5031814 -Chr1 Chr1:5031896 0 5031896 -Chr1 Chr1:5034463 0 5034463 -Chr1 Chr1:5051124 0 5051124 -Chr1 Chr1:5054027 0 5054027 -Chr1 Chr1:5087896 0 5087896 -Chr1 Chr1:5104630 0 5104630 -Chr1 Chr1:5131438 0 5131438 -Chr1 Chr1:5138666 0 5138666 -Chr1 Chr1:5138715 0 5138715 -Chr1 Chr1:5140272 0 5140272 -Chr1 Chr1:5152259 0 5152259 -Chr1 Chr1:5163525 0 5163525 -Chr1 Chr1:5244943 0 5244943 -Chr1 Chr1:5366002 0 5366002 -Chr1 Chr1:5548352 0 5548352 -Chr1 Chr1:5708805 0 5708805 -Chr1 Chr1:5720415 0 5720415 -Chr1 Chr1:5730222 0 5730222 -Chr1 Chr1:5744328 0 5744328 -Chr1 Chr1:5762097 0 5762097 -Chr1 Chr1:5763894 0 5763894 -Chr1 Chr1:5768517 0 5768517 -Chr1 Chr1:5768520 0 5768520 -Chr1 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-Chr1 Chr1:11222885 0 11222885 -Chr1 Chr1:11226698 0 11226698 -Chr1 Chr1:11232299 0 11232299 -Chr1 Chr1:11276184 0 11276184 -Chr1 Chr1:11350714 0 11350714 -Chr1 Chr1:11412878 0 11412878 -Chr1 Chr1:11418571 0 11418571 -Chr1 Chr1:11420766 0 11420766 -Chr1 Chr1:11420873 0 11420873 -Chr1 Chr1:11451409 0 11451409 -Chr1 Chr1:11519588 0 11519588 -Chr1 Chr1:11584178 0 11584178 -Chr1 Chr1:11585278 0 11585278 -Chr1 Chr1:11591192 0 11591192 -Chr1 Chr1:11596361 0 11596361 -Chr1 Chr1:11611147 0 11611147 -Chr1 Chr1:11611190 0 11611190 -Chr1 Chr1:11611212 0 11611212 -Chr1 Chr1:11631478 0 11631478 -Chr1 Chr1:11665440 0 11665440 -Chr1 Chr1:11670766 0 11670766 -Chr1 Chr1:11747889 0 11747889 -Chr1 Chr1:11777126 0 11777126 -Chr1 Chr1:11777129 0 11777129 -Chr1 Chr1:11814704 0 11814704 -Chr1 Chr1:11814773 0 11814773 -Chr1 Chr1:11858180 0 11858180 -Chr1 Chr1:11866889 0 11866889 -Chr1 Chr1:11911566 0 11911566 -Chr1 Chr1:11965076 0 11965076 -Chr1 Chr1:11984098 0 11984098 -Chr1 Chr1:12109820 0 12109820 -Chr1 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Chr1:18570089 0 18570089 -Chr1 Chr1:18571302 0 18571302 -Chr1 Chr1:18577494 0 18577494 -Chr1 Chr1:18579783 0 18579783 -Chr1 Chr1:18582085 0 18582085 -Chr1 Chr1:18596271 0 18596271 -Chr1 Chr1:18625873 0 18625873 -Chr1 Chr1:18633427 0 18633427 -Chr1 Chr1:18641673 0 18641673 -Chr1 Chr1:18663992 0 18663992 -Chr1 Chr1:18664031 0 18664031 -Chr1 Chr1:18665430 0 18665430 -Chr1 Chr1:18665444 0 18665444 -Chr1 Chr1:18708384 0 18708384 -Chr1 Chr1:18710810 0 18710810 -Chr1 Chr1:18725534 0 18725534 -Chr1 Chr1:18725537 0 18725537 -Chr1 Chr1:18780192 0 18780192 -Chr1 Chr1:18780231 0 18780231 -Chr1 Chr1:18828386 0 18828386 -Chr1 Chr1:18908050 0 18908050 -Chr1 Chr1:18927999 0 18927999 -Chr1 Chr1:18984881 0 18984881 -Chr1 Chr1:18988396 0 18988396 -Chr1 Chr1:19012605 0 19012605 -Chr1 Chr1:19031487 0 19031487 -Chr1 Chr1:19058808 0 19058808 -Chr1 Chr1:19080444 0 19080444 -Chr1 Chr1:19286858 0 19286858 -Chr1 Chr1:19286869 0 19286869 -Chr1 Chr1:19333051 0 19333051 -Chr1 Chr1:19355961 0 19355961 -Chr1 Chr1:19457517 0 19457517 -Chr1 Chr1:19463824 0 19463824 -Chr1 Chr1:19546252 0 19546252 -Chr1 Chr1:19548751 0 19548751 -Chr1 Chr1:19600679 0 19600679 -Chr1 Chr1:19616107 0 19616107 -Chr1 Chr1:19682153 0 19682153 -Chr1 Chr1:19682333 0 19682333 -Chr1 Chr1:19683507 0 19683507 -Chr1 Chr1:19692522 0 19692522 -Chr1 Chr1:19844645 0 19844645 -Chr1 Chr1:19875492 0 19875492 -Chr1 Chr1:19884303 0 19884303 -Chr1 Chr1:19890812 0 19890812 -Chr1 Chr1:19918575 0 19918575 -Chr1 Chr1:19960915 0 19960915 -Chr1 Chr1:20043559 0 20043559 -Chr1 Chr1:20043762 0 20043762 -Chr1 Chr1:20200430 0 20200430 -Chr1 Chr1:20244907 0 20244907 -Chr1 Chr1:20283003 0 20283003 -Chr1 Chr1:20297936 0 20297936 -Chr1 Chr1:20307459 0 20307459 -Chr1 Chr1:20414880 0 20414880 -Chr1 Chr1:20418207 0 20418207 -Chr1 Chr1:20453895 0 20453895 -Chr1 Chr1:20457891 0 20457891 -Chr1 Chr1:20480254 0 20480254 -Chr1 Chr1:20484206 0 20484206 -Chr1 Chr1:20502469 0 20502469 -Chr1 Chr1:20502498 0 20502498 -Chr1 Chr1:20527190 0 20527190 -Chr1 Chr1:20536861 0 20536861 -Chr1 Chr1:20583778 0 20583778 -Chr1 Chr1:20603211 0 20603211 -Chr1 Chr1:20628363 0 20628363 -Chr1 Chr1:20749512 0 20749512 -Chr1 Chr1:20808148 0 20808148 -Chr1 Chr1:20808185 0 20808185 -Chr1 Chr1:20808188 0 20808188 -Chr1 Chr1:20941827 0 20941827 -Chr1 Chr1:20985001 0 20985001 -Chr1 Chr1:21014787 0 21014787 -Chr1 Chr1:21044771 0 21044771 -Chr1 Chr1:21082093 0 21082093 -Chr1 Chr1:21126090 0 21126090 -Chr1 Chr1:21160401 0 21160401 -Chr1 Chr1:21160870 0 21160870 -Chr1 Chr1:21201262 0 21201262 -Chr1 Chr1:21201330 0 21201330 -Chr1 Chr1:21203185 0 21203185 -Chr1 Chr1:21237101 0 21237101 -Chr1 Chr1:21238922 0 21238922 -Chr1 Chr1:21240239 0 21240239 -Chr1 Chr1:21241093 0 21241093 -Chr1 Chr1:21275917 0 21275917 -Chr1 Chr1:21357238 0 21357238 -Chr1 Chr1:21385607 0 21385607 -Chr1 Chr1:21415113 0 21415113 -Chr1 Chr1:21440962 0 21440962 -Chr1 Chr1:21503565 0 21503565 -Chr1 Chr1:21562231 0 21562231 -Chr1 Chr1:21603665 0 21603665 -Chr1 Chr1:21672420 0 21672420 -Chr1 Chr1:21684647 0 21684647 -Chr1 Chr1:21687037 0 21687037 -Chr1 Chr1:21692496 0 21692496 -Chr1 Chr1:21700123 0 21700123 -Chr1 Chr1:21712360 0 21712360 -Chr1 Chr1:21750711 0 21750711 -Chr1 Chr1:21750725 0 21750725 -Chr1 Chr1:21788731 0 21788731 -Chr1 Chr1:21788887 0 21788887 -Chr1 Chr1:21793111 0 21793111 -Chr1 Chr1:21793114 0 21793114 -Chr1 Chr1:21811411 0 21811411 -Chr1 Chr1:22221087 0 22221087 -Chr1 Chr1:22362000 0 22362000 -Chr1 Chr1:22365064 0 22365064 -Chr1 Chr1:22366394 0 22366394 -Chr1 Chr1:22420228 0 22420228 -Chr1 Chr1:22434088 0 22434088 -Chr1 Chr1:22436948 0 22436948 -Chr1 Chr1:22438238 0 22438238 -Chr1 Chr1:22441431 0 22441431 -Chr1 Chr1:22446965 0 22446965 -Chr1 Chr1:22452793 0 22452793 -Chr1 Chr1:22452814 0 22452814 -Chr1 Chr1:22456223 0 22456223 -Chr1 Chr1:22456541 0 22456541 -Chr1 Chr1:22464901 0 22464901 -Chr1 Chr1:22464938 0 22464938 -Chr1 Chr1:22465695 0 22465695 -Chr1 Chr1:22467542 0 22467542 -Chr1 Chr1:22468575 0 22468575 -Chr1 Chr1:22486715 0 22486715 -Chr1 Chr1:22486765 0 22486765 -Chr1 Chr1:22507492 0 22507492 -Chr1 Chr1:22527085 0 22527085 -Chr1 Chr1:22557545 0 22557545 -Chr1 Chr1:22560937 0 22560937 -Chr1 Chr1:22591601 0 22591601 -Chr1 Chr1:22594675 0 22594675 -Chr1 Chr1:22617285 0 22617285 -Chr1 Chr1:22636521 0 22636521 -Chr1 Chr1:22672543 0 22672543 -Chr1 Chr1:22672589 0 22672589 -Chr1 Chr1:22674616 0 22674616 -Chr1 Chr1:22726998 0 22726998 -Chr1 Chr1:22739593 0 22739593 -Chr1 Chr1:22739596 0 22739596 -Chr1 Chr1:22739995 0 22739995 -Chr1 Chr1:22740010 0 22740010 -Chr1 Chr1:22780246 0 22780246 -Chr1 Chr1:22822065 0 22822065 -Chr1 Chr1:22828980 0 22828980 -Chr1 Chr1:22837071 0 22837071 -Chr1 Chr1:22837075 0 22837075 -Chr1 Chr1:22974966 0 22974966 -Chr1 Chr1:22974971 0 22974971 -Chr1 Chr1:22974974 0 22974974 -Chr1 Chr1:22975037 0 22975037 -Chr1 Chr1:22991392 0 22991392 -Chr1 Chr1:22991925 0 22991925 -Chr1 Chr1:23006900 0 23006900 -Chr1 Chr1:23006936 0 23006936 -Chr1 Chr1:23079278 0 23079278 -Chr1 Chr1:23083004 0 23083004 -Chr1 Chr1:23096859 0 23096859 -Chr1 Chr1:23103054 0 23103054 -Chr1 Chr1:23147512 0 23147512 -Chr1 Chr1:23151111 0 23151111 -Chr1 Chr1:23152355 0 23152355 -Chr1 Chr1:23168512 0 23168512 -Chr1 Chr1:23171855 0 23171855 -Chr1 Chr1:23183180 0 23183180 -Chr1 Chr1:23203034 0 23203034 -Chr1 Chr1:23216787 0 23216787 -Chr1 Chr1:23235085 0 23235085 -Chr1 Chr1:23248184 0 23248184 -Chr1 Chr1:23297650 0 23297650 -Chr1 Chr1:23324317 0 23324317 -Chr1 Chr1:23332211 0 23332211 -Chr1 Chr1:23338972 0 23338972 -Chr1 Chr1:23349168 0 23349168 -Chr1 Chr1:23351414 0 23351414 -Chr1 Chr1:23353553 0 23353553 -Chr1 Chr1:23366101 0 23366101 -Chr1 Chr1:23378783 0 23378783 -Chr1 Chr1:23392716 0 23392716 -Chr1 Chr1:23395515 0 23395515 -Chr1 Chr1:23395522 0 23395522 -Chr1 Chr1:23403909 0 23403909 -Chr1 Chr1:23404803 0 23404803 -Chr1 Chr1:23404854 0 23404854 -Chr1 Chr1:23426983 0 23426983 -Chr1 Chr1:23426986 0 23426986 -Chr1 Chr1:23431931 0 23431931 -Chr1 Chr1:23448547 0 23448547 -Chr1 Chr1:23530885 0 23530885 -Chr1 Chr1:23531955 0 23531955 -Chr1 Chr1:23543040 0 23543040 -Chr1 Chr1:23556083 0 23556083 -Chr1 Chr1:23575160 0 23575160 -Chr1 Chr1:23610833 0 23610833 -Chr1 Chr1:23610842 0 23610842 -Chr1 Chr1:23620798 0 23620798 -Chr1 Chr1:23624047 0 23624047 -Chr1 Chr1:23634488 0 23634488 -Chr1 Chr1:23648137 0 23648137 -Chr1 Chr1:23651986 0 23651986 -Chr1 Chr1:23721841 0 23721841 -Chr1 Chr1:23721844 0 23721844 -Chr1 Chr1:23731885 0 23731885 -Chr1 Chr1:23756111 0 23756111 -Chr1 Chr1:23762143 0 23762143 -Chr1 Chr1:23782998 0 23782998 -Chr1 Chr1:23785932 0 23785932 -Chr1 Chr1:23836611 0 23836611 -Chr1 Chr1:23857915 0 23857915 -Chr1 Chr1:23863742 0 23863742 -Chr1 Chr1:23882305 0 23882305 -Chr1 Chr1:23896573 0 23896573 -Chr1 Chr1:23897070 0 23897070 -Chr1 Chr1:23913125 0 23913125 -Chr1 Chr1:23922001 0 23922001 -Chr1 Chr1:23935969 0 23935969 -Chr1 Chr1:23939765 0 23939765 -Chr1 Chr1:23972022 0 23972022 -Chr1 Chr1:23986664 0 23986664 -Chr1 Chr1:24004564 0 24004564 -Chr1 Chr1:24034453 0 24034453 -Chr1 Chr1:24037402 0 24037402 -Chr1 Chr1:24049164 0 24049164 -Chr1 Chr1:24092946 0 24092946 -Chr1 Chr1:24093753 0 24093753 -Chr1 Chr1:24116624 0 24116624 -Chr1 Chr1:24116678 0 24116678 -Chr1 Chr1:24124359 0 24124359 -Chr1 Chr1:24129826 0 24129826 -Chr1 Chr1:24147784 0 24147784 -Chr1 Chr1:24234620 0 24234620 -Chr1 Chr1:24234629 0 24234629 -Chr1 Chr1:24234677 0 24234677 -Chr1 Chr1:24239996 0 24239996 -Chr1 Chr1:24240019 0 24240019 -Chr1 Chr1:24310319 0 24310319 -Chr1 Chr1:24336951 0 24336951 -Chr1 Chr1:24381824 0 24381824 -Chr1 Chr1:24462566 0 24462566 -Chr1 Chr1:24482154 0 24482154 -Chr1 Chr1:24489729 0 24489729 -Chr1 Chr1:24502190 0 24502190 -Chr1 Chr1:24510021 0 24510021 -Chr1 Chr1:24533617 0 24533617 -Chr1 Chr1:24560384 0 24560384 -Chr1 Chr1:24560461 0 24560461 -Chr1 Chr1:24563014 0 24563014 -Chr1 Chr1:24567170 0 24567170 -Chr1 Chr1:24593376 0 24593376 -Chr1 Chr1:24617946 0 24617946 -Chr1 Chr1:24640251 0 24640251 -Chr1 Chr1:24657015 0 24657015 -Chr1 Chr1:24657701 0 24657701 -Chr1 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Chr1:25012595 0 25012595 -Chr1 Chr1:25016468 0 25016468 -Chr1 Chr1:25067075 0 25067075 -Chr1 Chr1:25077288 0 25077288 -Chr1 Chr1:25091984 0 25091984 -Chr1 Chr1:25115923 0 25115923 -Chr1 Chr1:25136014 0 25136014 -Chr1 Chr1:25155677 0 25155677 -Chr1 Chr1:25160990 0 25160990 -Chr1 Chr1:25160993 0 25160993 -Chr1 Chr1:25230277 0 25230277 -Chr1 Chr1:25259414 0 25259414 -Chr1 Chr1:25262919 0 25262919 -Chr1 Chr1:25262924 0 25262924 -Chr1 Chr1:25266878 0 25266878 -Chr1 Chr1:25266881 0 25266881 -Chr1 Chr1:25266922 0 25266922 -Chr1 Chr1:25281106 0 25281106 -Chr1 Chr1:25281928 0 25281928 -Chr1 Chr1:25294455 0 25294455 -Chr1 Chr1:25298123 0 25298123 -Chr1 Chr1:25362835 0 25362835 -Chr1 Chr1:25371899 0 25371899 -Chr1 Chr1:25372636 0 25372636 -Chr1 Chr1:25414435 0 25414435 -Chr1 Chr1:25414438 0 25414438 -Chr1 Chr1:25498933 0 25498933 -Chr1 Chr1:25508055 0 25508055 -Chr1 Chr1:25593002 0 25593002 -Chr1 Chr1:25596880 0 25596880 -Chr1 Chr1:25642202 0 25642202 -Chr1 Chr1:25642232 0 25642232 -Chr1 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Chr1:27587166 0 27587166 -Chr1 Chr1:27596768 0 27596768 -Chr1 Chr1:27610155 0 27610155 -Chr1 Chr1:27666969 0 27666969 -Chr1 Chr1:27718132 0 27718132 -Chr1 Chr1:27735730 0 27735730 -Chr1 Chr1:27736608 0 27736608 -Chr1 Chr1:27737357 0 27737357 -Chr1 Chr1:27737916 0 27737916 -Chr1 Chr1:27759181 0 27759181 -Chr1 Chr1:27771876 0 27771876 -Chr1 Chr1:27868280 0 27868280 -Chr1 Chr1:27868311 0 27868311 -Chr1 Chr1:27873027 0 27873027 -Chr1 Chr1:27907035 0 27907035 -Chr1 Chr1:27941462 0 27941462 -Chr1 Chr1:27941465 0 27941465 -Chr1 Chr1:27949168 0 27949168 -Chr1 Chr1:27997299 0 27997299 -Chr1 Chr1:28028497 0 28028497 -Chr1 Chr1:28028544 0 28028544 -Chr1 Chr1:28051371 0 28051371 -Chr1 Chr1:28058059 0 28058059 -Chr1 Chr1:28099212 0 28099212 -Chr1 Chr1:28100175 0 28100175 -Chr1 Chr1:28113816 0 28113816 -Chr1 Chr1:28116035 0 28116035 -Chr1 Chr1:28121245 0 28121245 -Chr1 Chr1:28121248 0 28121248 -Chr1 Chr1:28121386 0 28121386 -Chr1 Chr1:28145665 0 28145665 -Chr1 Chr1:28152031 0 28152031 -Chr1 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Chr1:28624282 0 28624282 -Chr1 Chr1:28624318 0 28624318 -Chr1 Chr1:28629177 0 28629177 -Chr1 Chr1:28657314 0 28657314 -Chr1 Chr1:28657913 0 28657913 -Chr1 Chr1:28661347 0 28661347 -Chr1 Chr1:28661378 0 28661378 -Chr1 Chr1:28661381 0 28661381 -Chr1 Chr1:28662072 0 28662072 -Chr1 Chr1:28662082 0 28662082 -Chr1 Chr1:28669462 0 28669462 -Chr1 Chr1:28671486 0 28671486 -Chr1 Chr1:28671984 0 28671984 -Chr1 Chr1:28707366 0 28707366 -Chr1 Chr1:28707974 0 28707974 -Chr1 Chr1:28709069 0 28709069 -Chr1 Chr1:28709128 0 28709128 -Chr1 Chr1:28709131 0 28709131 -Chr1 Chr1:28739760 0 28739760 -Chr1 Chr1:28752523 0 28752523 -Chr1 Chr1:28776300 0 28776300 -Chr1 Chr1:28790241 0 28790241 -Chr1 Chr1:28797680 0 28797680 -Chr1 Chr1:28810134 0 28810134 -Chr1 Chr1:28818609 0 28818609 -Chr1 Chr1:28818659 0 28818659 -Chr1 Chr1:28839003 0 28839003 -Chr1 Chr1:28893652 0 28893652 -Chr1 Chr1:28911097 0 28911097 -Chr1 Chr1:28912479 0 28912479 -Chr1 Chr1:28920030 0 28920030 -Chr1 Chr1:28920035 0 28920035 -Chr1 Chr1:28937099 0 28937099 -Chr1 Chr1:28937110 0 28937110 -Chr1 Chr1:28950372 0 28950372 -Chr1 Chr1:28953029 0 28953029 -Chr1 Chr1:28975242 0 28975242 -Chr1 Chr1:28976173 0 28976173 -Chr1 Chr1:28976215 0 28976215 -Chr1 Chr1:28980467 0 28980467 -Chr1 Chr1:28985758 0 28985758 -Chr1 Chr1:28985794 0 28985794 -Chr1 Chr1:28992324 0 28992324 -Chr1 Chr1:28993573 0 28993573 -Chr1 Chr1:29062709 0 29062709 -Chr1 Chr1:29062777 0 29062777 -Chr1 Chr1:29069259 0 29069259 -Chr1 Chr1:29104165 0 29104165 -Chr1 Chr1:29110315 0 29110315 -Chr1 Chr1:29116135 0 29116135 -Chr1 Chr1:29143205 0 29143205 -Chr1 Chr1:29184329 0 29184329 -Chr1 Chr1:29221871 0 29221871 -Chr1 Chr1:29221916 0 29221916 -Chr1 Chr1:29240567 0 29240567 -Chr1 Chr1:29275468 0 29275468 -Chr1 Chr1:29290850 0 29290850 -Chr1 Chr1:29291614 0 29291614 -Chr1 Chr1:29294897 0 29294897 -Chr1 Chr1:29323260 0 29323260 -Chr1 Chr1:29338674 0 29338674 -Chr1 Chr1:29342748 0 29342748 -Chr1 Chr1:29368312 0 29368312 -Chr1 Chr1:29368316 0 29368316 -Chr1 Chr1:29381840 0 29381840 -Chr1 Chr1:29388895 0 29388895 -Chr1 Chr1:29426085 0 29426085 -Chr1 Chr1:29442134 0 29442134 -Chr1 Chr1:29442212 0 29442212 -Chr1 Chr1:29444106 0 29444106 -Chr1 Chr1:29445837 0 29445837 -Chr1 Chr1:29459338 0 29459338 -Chr1 Chr1:29462209 0 29462209 -Chr1 Chr1:29464821 0 29464821 -Chr1 Chr1:29520268 0 29520268 -Chr1 Chr1:29529194 0 29529194 -Chr1 Chr1:29529520 0 29529520 -Chr1 Chr1:29529573 0 29529573 -Chr1 Chr1:29540540 0 29540540 -Chr1 Chr1:29556065 0 29556065 -Chr1 Chr1:29556067 0 29556067 -Chr1 Chr1:29556722 0 29556722 -Chr1 Chr1:29556725 0 29556725 -Chr1 Chr1:29569341 0 29569341 -Chr1 Chr1:29615657 0 29615657 -Chr1 Chr1:29665399 0 29665399 -Chr1 Chr1:29676504 0 29676504 -Chr1 Chr1:29707926 0 29707926 -Chr1 Chr1:29732730 0 29732730 -Chr1 Chr1:29734245 0 29734245 -Chr1 Chr1:29736117 0 29736117 -Chr1 Chr1:29741984 0 29741984 -Chr1 Chr1:29741987 0 29741987 -Chr1 Chr1:29755512 0 29755512 -Chr1 Chr1:29758534 0 29758534 -Chr1 Chr1:29770060 0 29770060 -Chr1 Chr1:29770066 0 29770066 -Chr1 Chr1:29780222 0 29780222 -Chr1 Chr1:29805304 0 29805304 -Chr1 Chr1:29805469 0 29805469 -Chr1 Chr1:29810581 0 29810581 -Chr1 Chr1:29871968 0 29871968 -Chr1 Chr1:29894876 0 29894876 -Chr1 Chr1:29912009 0 29912009 -Chr1 Chr1:29934876 0 29934876 -Chr1 Chr1:29934926 0 29934926 -Chr1 Chr1:29956787 0 29956787 -Chr1 Chr1:29976618 0 29976618 -Chr1 Chr1:29976945 0 29976945 -Chr1 Chr1:29977025 0 29977025 -Chr1 Chr1:29981185 0 29981185 -Chr1 Chr1:29981189 0 29981189 -Chr1 Chr1:29988911 0 29988911 -Chr1 Chr1:29989242 0 29989242 -Chr1 Chr1:29993665 0 29993665 -Chr1 Chr1:29994545 0 29994545 -Chr1 Chr1:29994671 0 29994671 -Chr1 Chr1:30033870 0 30033870 -Chr1 Chr1:30037897 0 30037897 -Chr1 Chr1:30048246 0 30048246 -Chr1 Chr1:30048276 0 30048276 -Chr1 Chr1:30096375 0 30096375 -Chr1 Chr1:30157657 0 30157657 -Chr1 Chr1:30167454 0 30167454 -Chr1 Chr1:30183413 0 30183413 -Chr1 Chr1:30197987 0 30197987 -Chr1 Chr1:30244448 0 30244448 -Chr1 Chr1:30244449 0 30244449 -Chr1 Chr1:30265177 0 30265177 -Chr1 Chr1:30500836 0 30500836 -Chr1 Chr1:30557638 0 30557638 -Chr1 Chr1:30617594 0 30617594 -Chr1 Chr1:30632340 0 30632340 -Chr1 Chr1:30645778 0 30645778 -Chr1 Chr1:30666725 0 30666725 -Chr1 Chr1:30679434 0 30679434 -Chr1 Chr1:30715119 0 30715119 -Chr1 Chr1:30862865 0 30862865 -Chr1 Chr1:30875285 0 30875285 -Chr1 Chr1:30988314 0 30988314 -Chr1 Chr1:31252146 0 31252146 -Chr1 Chr1:31252678 0 31252678 -Chr1 Chr1:31252704 0 31252704 -Chr1 Chr1:31305056 0 31305056 -Chr1 Chr1:31353236 0 31353236 -Chr1 Chr1:31396730 0 31396730 -Chr1 Chr1:31421361 0 31421361 -Chr1 Chr1:31431656 0 31431656 -Chr1 Chr1:31453373 0 31453373 -Chr1 Chr1:31485589 0 31485589 -Chr1 Chr1:31509969 0 31509969 -Chr1 Chr1:31509971 0 31509971 -Chr1 Chr1:31510049 0 31510049 -Chr1 Chr1:31524422 0 31524422 -Chr1 Chr1:31557933 0 31557933 -Chr1 Chr1:31557936 0 31557936 -Chr1 Chr1:31557986 0 31557986 -Chr1 Chr1:31559810 0 31559810 -Chr1 Chr1:31559895 0 31559895 -Chr1 Chr1:31566399 0 31566399 -Chr1 Chr1:31569296 0 31569296 -Chr1 Chr1:31571201 0 31571201 -Chr1 Chr1:31571975 0 31571975 -Chr1 Chr1:31571987 0 31571987 -Chr1 Chr1:31577334 0 31577334 -Chr1 Chr1:31602416 0 31602416 -Chr1 Chr1:31608861 0 31608861 -Chr1 Chr1:31630945 0 31630945 -Chr1 Chr1:31656589 0 31656589 -Chr1 Chr1:31677735 0 31677735 -Chr1 Chr1:31684486 0 31684486 -Chr1 Chr1:31695659 0 31695659 -Chr1 Chr1:31779847 0 31779847 -Chr1 Chr1:31779850 0 31779850 -Chr1 Chr1:31779865 0 31779865 -Chr1 Chr1:31811093 0 31811093 -Chr1 Chr1:31811659 0 31811659 -Chr1 Chr1:31826446 0 31826446 -Chr1 Chr1:31850290 0 31850290 -Chr1 Chr1:31857928 0 31857928 -Chr1 Chr1:31857929 0 31857929 -Chr1 Chr1:31862466 0 31862466 -Chr1 Chr1:31862528 0 31862528 -Chr1 Chr1:31867111 0 31867111 -Chr1 Chr1:31876051 0 31876051 -Chr1 Chr1:31889377 0 31889377 -Chr1 Chr1:31889485 0 31889485 -Chr1 Chr1:31907055 0 31907055 -Chr1 Chr1:31927140 0 31927140 -Chr1 Chr1:31995350 0 31995350 -Chr1 Chr1:32015975 0 32015975 -Chr1 Chr1:32020723 0 32020723 -Chr1 Chr1:32043018 0 32043018 -Chr1 Chr1:32077755 0 32077755 -Chr1 Chr1:32084837 0 32084837 -Chr1 Chr1:32099526 0 32099526 -Chr1 Chr1:32109172 0 32109172 -Chr1 Chr1:32111760 0 32111760 -Chr1 Chr1:32112621 0 32112621 -Chr1 Chr1:32112622 0 32112622 -Chr1 Chr1:32119131 0 32119131 -Chr1 Chr1:32133860 0 32133860 -Chr1 Chr1:32139702 0 32139702 -Chr1 Chr1:32139722 0 32139722 -Chr1 Chr1:32153707 0 32153707 -Chr1 Chr1:32165197 0 32165197 -Chr1 Chr1:32217903 0 32217903 -Chr1 Chr1:32331774 0 32331774 -Chr1 Chr1:32360773 0 32360773 -Chr1 Chr1:32449071 0 32449071 -Chr1 Chr1:32499753 0 32499753 -Chr1 Chr1:32510853 0 32510853 -Chr1 Chr1:32527882 0 32527882 -Chr1 Chr1:32527981 0 32527981 -Chr1 Chr1:32587107 0 32587107 -Chr1 Chr1:32598032 0 32598032 -Chr1 Chr1:32610324 0 32610324 -Chr1 Chr1:32632614 0 32632614 -Chr1 Chr1:32654599 0 32654599 -Chr1 Chr1:32734148 0 32734148 -Chr1 Chr1:32735557 0 32735557 -Chr1 Chr1:32738743 0 32738743 -Chr1 Chr1:32741911 0 32741911 -Chr1 Chr1:32999294 0 32999294 -Chr1 Chr1:33076887 0 33076887 -Chr1 Chr1:33081781 0 33081781 -Chr1 Chr1:33091343 0 33091343 -Chr1 Chr1:33091346 0 33091346 -Chr1 Chr1:33093016 0 33093016 -Chr1 Chr1:33099125 0 33099125 -Chr1 Chr1:33101161 0 33101161 -Chr1 Chr1:33284722 0 33284722 -Chr1 Chr1:33293797 0 33293797 -Chr1 Chr1:33327786 0 33327786 -Chr1 Chr1:33327839 0 33327839 -Chr1 Chr1:33336223 0 33336223 -Chr1 Chr1:33336318 0 33336318 -Chr1 Chr1:33364796 0 33364796 -Chr1 Chr1:33496512 0 33496512 -Chr1 Chr1:33783168 0 33783168 -Chr1 Chr1:33783179 0 33783179 -Chr1 Chr1:33783182 0 33783182 -Chr1 Chr1:33871635 0 33871635 -Chr1 Chr1:33920570 0 33920570 -Chr1 Chr1:33921227 0 33921227 -Chr1 Chr1:33930751 0 33930751 -Chr1 Chr1:33973542 0 33973542 -Chr1 Chr1:33974278 0 33974278 -Chr1 Chr1:33974856 0 33974856 -Chr1 Chr1:34039707 0 34039707 -Chr1 Chr1:34109518 0 34109518 -Chr1 Chr1:34167104 0 34167104 -Chr1 Chr1:34187435 0 34187435 -Chr1 Chr1:34203919 0 34203919 -Chr1 Chr1:34225494 0 34225494 -Chr1 Chr1:34226293 0 34226293 -Chr1 Chr1:34237359 0 34237359 -Chr1 Chr1:34290046 0 34290046 -Chr1 Chr1:34290097 0 34290097 -Chr1 Chr1:34307022 0 34307022 -Chr1 Chr1:34307825 0 34307825 -Chr1 Chr1:34327301 0 34327301 -Chr1 Chr1:34335058 0 34335058 -Chr1 Chr1:34422874 0 34422874 -Chr1 Chr1:34429355 0 34429355 -Chr1 Chr1:34435745 0 34435745 -Chr1 Chr1:34446335 0 34446335 -Chr1 Chr1:34461102 0 34461102 -Chr1 Chr1:34511690 0 34511690 -Chr1 Chr1:34512803 0 34512803 -Chr1 Chr1:34514240 0 34514240 -Chr1 Chr1:34546434 0 34546434 -Chr1 Chr1:34546490 0 34546490 -Chr1 Chr1:34550321 0 34550321 -Chr1 Chr1:34551808 0 34551808 -Chr1 Chr1:34568945 0 34568945 -Chr1 Chr1:34571150 0 34571150 -Chr1 Chr1:34588553 0 34588553 -Chr1 Chr1:34600584 0 34600584 -Chr1 Chr1:34680506 0 34680506 -Chr1 Chr1:34707422 0 34707422 -Chr1 Chr1:34712326 0 34712326 -Chr1 Chr1:34729316 0 34729316 -Chr1 Chr1:34731317 0 34731317 -Chr1 Chr1:34739250 0 34739250 -Chr1 Chr1:34745122 0 34745122 -Chr1 Chr1:34745238 0 34745238 -Chr1 Chr1:34762181 0 34762181 -Chr1 Chr1:34762285 0 34762285 -Chr1 Chr1:34815236 0 34815236 -Chr1 Chr1:34815295 0 34815295 -Chr1 Chr1:34819411 0 34819411 -Chr1 Chr1:34846870 0 34846870 -Chr1 Chr1:34890450 0 34890450 -Chr1 Chr1:34896321 0 34896321 -Chr1 Chr1:34939106 0 34939106 -Chr1 Chr1:34965744 0 34965744 -Chr1 Chr1:34983193 0 34983193 -Chr1 Chr1:35001790 0 35001790 -Chr1 Chr1:35007259 0 35007259 -Chr1 Chr1:35008760 0 35008760 -Chr1 Chr1:35061621 0 35061621 -Chr1 Chr1:35086602 0 35086602 -Chr1 Chr1:35094231 0 35094231 -Chr1 Chr1:35108977 0 35108977 -Chr1 Chr1:35128150 0 35128150 -Chr1 Chr1:35144020 0 35144020 -Chr1 Chr1:35149305 0 35149305 -Chr1 Chr1:35180600 0 35180600 -Chr1 Chr1:35193967 0 35193967 -Chr1 Chr1:35200915 0 35200915 -Chr1 Chr1:35307114 0 35307114 -Chr1 Chr1:35347362 0 35347362 -Chr1 Chr1:35400756 0 35400756 -Chr1 Chr1:35596032 0 35596032 -Chr1 Chr1:35608865 0 35608865 -Chr1 Chr1:35638872 0 35638872 -Chr1 Chr1:35638984 0 35638984 -Chr1 Chr1:35742358 0 35742358 -Chr1 Chr1:35747789 0 35747789 -Chr1 Chr1:35958247 0 35958247 -Chr1 Chr1:35963677 0 35963677 -Chr1 Chr1:35967289 0 35967289 -Chr1 Chr1:36013936 0 36013936 -Chr1 Chr1:36029152 0 36029152 -Chr1 Chr1:36131798 0 36131798 -Chr1 Chr1:36132244 0 36132244 -Chr1 Chr1:36132263 0 36132263 -Chr1 Chr1:36135270 0 36135270 -Chr1 Chr1:36143155 0 36143155 -Chr1 Chr1:36231871 0 36231871 -Chr1 Chr1:36300575 0 36300575 -Chr1 Chr1:36370973 0 36370973 -Chr1 Chr1:36621359 0 36621359 -Chr1 Chr1:36696208 0 36696208 -Chr1 Chr1:36718312 0 36718312 -Chr1 Chr1:36718341 0 36718341 -Chr1 Chr1:36720865 0 36720865 -Chr1 Chr1:36740809 0 36740809 -Chr1 Chr1:36882749 0 36882749 -Chr1 Chr1:36882752 0 36882752 -Chr1 Chr1:36956337 0 36956337 -Chr1 Chr1:37046646 0 37046646 -Chr1 Chr1:37064309 0 37064309 -Chr1 Chr1:37137468 0 37137468 -Chr1 Chr1:37146622 0 37146622 -Chr1 Chr1:37189534 0 37189534 -Chr1 Chr1:37233741 0 37233741 -Chr1 Chr1:37583011 0 37583011 -Chr1 Chr1:37677255 0 37677255 -Chr1 Chr1:37712681 0 37712681 -Chr1 Chr1:37719614 0 37719614 -Chr1 Chr1:37723312 0 37723312 -Chr1 Chr1:37733048 0 37733048 -Chr1 Chr1:37764798 0 37764798 -Chr1 Chr1:37879500 0 37879500 -Chr1 Chr1:37975727 0 37975727 -Chr1 Chr1:38176391 0 38176391 -Chr1 Chr1:38233881 0 38233881 -Chr1 Chr1:38434703 0 38434703 -Chr1 Chr1:38434765 0 38434765 -Chr1 Chr1:38501100 0 38501100 -Chr1 Chr1:38515009 0 38515009 -Chr1 Chr1:38515041 0 38515041 -Chr1 Chr1:38515044 0 38515044 -Chr1 Chr1:38560569 0 38560569 -Chr1 Chr1:38654332 0 38654332 -Chr1 Chr1:38804627 0 38804627 -Chr1 Chr1:38808462 0 38808462 -Chr1 Chr1:38808537 0 38808537 -Chr1 Chr1:38836845 0 38836845 -Chr1 Chr1:38836848 0 38836848 -Chr1 Chr1:38853248 0 38853248 -Chr1 Chr1:38897705 0 38897705 -Chr1 Chr1:38904917 0 38904917 -Chr1 Chr1:38946119 0 38946119 -Chr1 Chr1:38960837 0 38960837 -Chr1 Chr1:38968039 0 38968039 -Chr1 Chr1:38970709 0 38970709 -Chr1 Chr1:38970729 0 38970729 -Chr1 Chr1:38996984 0 38996984 -Chr1 Chr1:39006552 0 39006552 -Chr1 Chr1:39021617 0 39021617 -Chr1 Chr1:39021775 0 39021775 -Chr1 Chr1:39021790 0 39021790 -Chr1 Chr1:39022928 0 39022928 -Chr1 Chr1:39029042 0 39029042 -Chr1 Chr1:39041227 0 39041227 -Chr1 Chr1:39069588 0 39069588 -Chr1 Chr1:39073687 0 39073687 -Chr1 Chr1:39073738 0 39073738 -Chr1 Chr1:39097844 0 39097844 -Chr1 Chr1:39101078 0 39101078 -Chr1 Chr1:39102140 0 39102140 -Chr1 Chr1:39102194 0 39102194 -Chr1 Chr1:39102232 0 39102232 -Chr1 Chr1:39102838 0 39102838 -Chr1 Chr1:39102892 0 39102892 -Chr1 Chr1:39108593 0 39108593 -Chr1 Chr1:39128415 0 39128415 -Chr1 Chr1:39133282 0 39133282 -Chr1 Chr1:39133285 0 39133285 -Chr1 Chr1:39134928 0 39134928 -Chr1 Chr1:39137464 0 39137464 -Chr1 Chr1:39140488 0 39140488 -Chr1 Chr1:39140501 0 39140501 -Chr1 Chr1:39140562 0 39140562 -Chr1 Chr1:39143929 0 39143929 -Chr1 Chr1:39143942 0 39143942 -Chr1 Chr1:39163136 0 39163136 -Chr1 Chr1:39168222 0 39168222 -Chr1 Chr1:39168248 0 39168248 -Chr1 Chr1:39176048 0 39176048 -Chr1 Chr1:39176083 0 39176083 -Chr1 Chr1:39176096 0 39176096 -Chr1 Chr1:39191305 0 39191305 -Chr1 Chr1:39200362 0 39200362 -Chr1 Chr1:39209686 0 39209686 -Chr1 Chr1:39245265 0 39245265 -Chr1 Chr1:39254110 0 39254110 -Chr1 Chr1:39256552 0 39256552 -Chr1 Chr1:39257845 0 39257845 -Chr1 Chr1:39260372 0 39260372 -Chr1 Chr1:39276276 0 39276276 -Chr1 Chr1:39282424 0 39282424 -Chr1 Chr1:39292491 0 39292491 -Chr1 Chr1:39300391 0 39300391 -Chr1 Chr1:39305750 0 39305750 -Chr1 Chr1:39305832 0 39305832 -Chr1 Chr1:39305833 0 39305833 -Chr1 Chr1:39416338 0 39416338 -Chr1 Chr1:39422113 0 39422113 -Chr1 Chr1:39422116 0 39422116 -Chr1 Chr1:39447228 0 39447228 -Chr1 Chr1:39448870 0 39448870 -Chr1 Chr1:39449861 0 39449861 -Chr1 Chr1:39466839 0 39466839 -Chr1 Chr1:39468037 0 39468037 -Chr1 Chr1:39470931 0 39470931 -Chr1 Chr1:39470949 0 39470949 -Chr1 Chr1:39472460 0 39472460 -Chr1 Chr1:39491532 0 39491532 -Chr1 Chr1:39506634 0 39506634 -Chr1 Chr1:39506654 0 39506654 -Chr1 Chr1:39511185 0 39511185 -Chr1 Chr1:39537504 0 39537504 -Chr1 Chr1:39553116 0 39553116 -Chr1 Chr1:39553118 0 39553118 -Chr1 Chr1:39554204 0 39554204 -Chr1 Chr1:39562746 0 39562746 -Chr1 Chr1:39562839 0 39562839 -Chr1 Chr1:39563425 0 39563425 -Chr1 Chr1:39563606 0 39563606 -Chr1 Chr1:39589518 0 39589518 -Chr1 Chr1:39605046 0 39605046 -Chr1 Chr1:39614442 0 39614442 -Chr1 Chr1:39614444 0 39614444 -Chr1 Chr1:39656022 0 39656022 -Chr1 Chr1:39663360 0 39663360 -Chr1 Chr1:39673624 0 39673624 -Chr1 Chr1:39681600 0 39681600 -Chr1 Chr1:39681665 0 39681665 -Chr1 Chr1:39700372 0 39700372 -Chr1 Chr1:39734217 0 39734217 -Chr1 Chr1:39734228 0 39734228 -Chr1 Chr1:39740660 0 39740660 -Chr1 Chr1:39780551 0 39780551 -Chr1 Chr1:39783176 0 39783176 -Chr1 Chr1:39791872 0 39791872 -Chr1 Chr1:39791875 0 39791875 -Chr1 Chr1:39818103 0 39818103 -Chr1 Chr1:39839114 0 39839114 -Chr1 Chr1:39839354 0 39839354 -Chr1 Chr1:39880825 0 39880825 -Chr1 Chr1:39912134 0 39912134 -Chr1 Chr1:39914173 0 39914173 -Chr1 Chr1:40019475 0 40019475 -Chr1 Chr1:40020184 0 40020184 -Chr1 Chr1:40047201 0 40047201 -Chr1 Chr1:40070589 0 40070589 -Chr1 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--- a/MDSplot/test-data/input.ped Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -IRAT112 1 0 0 1 1 1 1 4 4 2 2 1 1 4 4 2 2 1 1 1 1 4 4 4 4 1 1 1 1 4 4 1 1 1 1 1 1 4 4 4 4 3 3 4 4 2 2 1 1 3 3 1 1 1 1 4 4 1 1 1 1 2 2 1 1 4 4 1 1 1 1 4 4 2 2 4 4 1 1 1 1 4 4 3 3 1 1 1 1 1 1 1 1 4 4 2 2 1 1 4 4 4 4 4 4 4 4 1 1 4 4 4 4 4 4 4 4 4 4 1 1 1 1 4 4 4 4 3 3 4 4 1 1 1 1 4 4 1 1 1 1 4 4 1 1 4 4 1 1 3 3 4 4 4 4 2 2 1 1 4 4 1 1 4 4 1 1 4 4 1 1 1 1 4 4 1 1 4 4 1 1 4 4 4 4 1 1 4 4 2 2 2 2 4 4 2 2 1 1 1 1 3 3 3 3 4 4 4 4 3 3 3 3 2 2 1 1 2 2 4 4 1 1 1 1 4 4 1 1 4 4 1 1 4 4 4 4 4 4 4 4 3 3 1 1 4 4 4 4 4 4 1 1 1 1 4 4 4 4 1 1 4 4 1 1 1 1 3 3 4 4 4 4 3 3 4 4 1 1 3 3 3 3 3 3 1 1 2 2 4 4 1 1 1 1 1 1 4 4 4 4 1 1 4 4 1 1 1 1 4 4 4 4 3 3 2 2 4 4 4 4 1 1 3 3 2 2 3 3 4 4 1 1 4 4 4 4 4 4 2 2 3 3 1 1 1 1 1 1 1 1 4 4 1 1 1 1 4 4 1 1 1 1 1 1 1 1 4 4 4 4 4 4 1 1 2 2 4 4 4 4 1 1 4 4 2 2 3 3 3 3 1 1 3 3 4 4 1 1 3 3 4 4 1 1 4 4 2 2 2 2 1 1 1 1 4 4 4 4 4 4 2 2 1 1 1 1 4 4 1 1 4 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1 4 4 1 1 1 1 1 1 4 4 4 4 1 1 4 4 4 4 1 1 1 1 2 2 3 3 3 3 4 4 4 4 4 4 1 1 1 1 1 1 4 4 2 2 1 1 4 4 2 2 2 2 4 4 4 4 1 1 2 2 4 4 3 3 4 4 4 4 4 4 1 1 3 3 4 4 2 2 1 1 4 4 3 3 1 1 4 4 2 2 1 1 4 4 3 3 1 1 1 1 4 4 2 2 4 4 4 4 4 4 1 1 4 4 3 3 4 4 4 4 1 1 4 4 4 4 1 1 4 4 4 4 4 4 2 2 1 1 1 1 1 1 3 3 4 4 1 1 1 1 4 4 1 1 4 4 3 3 1 1 1 1 4 4 3 3 1 1 4 4 2 2 4 4 1 1 2 2 1 1 1 1 4 4 4 4 4 4 1 1 1 1 1 1 2 2 4 4 3 3 1 1 2 2 1 1 1 1 1 1 4 4 4 4 4 4 1 1 4 4 1 1 3 3 1 1 2 2 3 3 2 2 3 3 1 1 1 1 1 1 1 1 1 1 4 4 3 3 4 4 2 2 1 1 1 1 4 4 4 4 4 4 2 2 4 4 4 4 4 4 4 4 2 2 1 1 3 3 4 4 4 4 4 4 1 1 1 1 3 3 1 1 3 3 1 1 1 1 4 4 1 1 4 4 1 1 1 1 3 3 1 1 4 4 1 1 4 4 1 1 1 1 1 1 1 1 1 1 1 1 4 4 1 1 4 4 1 1 4 4 1 1 1 1 1 1 4 4 1 1 4 4 4 4 1 1 4 4 1 1 1 1 1 1 4 4 1 1 4 4 4 4 4 4 2 2 3 3 3 3 1 1 1 1 2 2 4 4 1 1 1 1 2 2 4 4 3 3 2 2 4 4 4 4 1 1 4 4 4 4 4 4 1 1 1 1 4 4
--- a/PedToFasta/Ped2Fasta.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ - -#!/usr/bin/perl - -use strict; -use Getopt::Long; - -my $usage = qq~Usage:$0 <args> [<opts>] - -where <args> are: - - -i, --in <PED input> - -o, --out <Fasta output> -~; -$usage .= "\n"; - -my ($input,$out); - - - -GetOptions( - "in=s" => \$input, - "out=s" => \$out, -); - - -die $usage - if ( !$input || !$out); - - -my %IUPAC = -( - '00'=> "?", - 'AA'=> "A", - 'CC'=> "C", - 'GG'=> "G", - 'TT'=> "T", - 'AG'=> "R", - 'GA'=> "R", - 'CT'=> "Y", - 'TC'=> "Y", - 'TG'=> "K", - 'GT'=> "K", - 'CG'=> "S", - 'GC'=> "S", - 'AT'=> "W", - 'TA'=> "W", - 'AC'=> "M", - 'CA'=> "M", -); - -open(my $O,">$out"); -open(my $P,$input) or die "File does not exist"; -while(<$P>) -{ - my $line = $_; - $line =~s/\r//g; - $line =~s/\n//g; - my @infos = split("\t",$_); - my $ind = $infos[0]; - print $O ">$ind\n"; - for (my $i = 6; $i <= $#infos; $i= $i+2) - { - my $code = $infos[$i].$infos[$i+1]; - my $letter = $IUPAC{$code}; - print $O $letter; - } - print $O "\n"; -} -close($P); -close($O);
--- a/PedToFasta/pedToFasta.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,171 +0,0 @@ -<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Convert PED file to Fasta File </description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="perl"> - Ped2Fasta.pl --in $filein --out $fileout - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="txt" optional="false" label="PED input" /> - <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> - <param name="filein" value="sample.ped" /> - <output name="fileout" file="result.fa" /> - </test> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr - ---------------------------------------------------- - -========= -Ped2Fasta -========= - ------------ -Description ------------ - - Convert PED file to Fasta File - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -VCFtools Filter VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Readseq Fasta alignment fasta -=========== ========================== ======= - - ----------- -Input file ----------- - -PED file - PED file usually from VCF tools - ----------- -Parameters ----------- - -Output file name - Prefix for the output fasta file - ------------- -Output files ------------- - -Fasta file - PED file conversion - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -PED file ---------- - -:: - - CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A - -Parameters -========== - -Output name -> pedFile - -Output files -============ - -pedFile.fa ----------- - -:: - - YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY - - - </help> - - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- a/PedToFasta/test-data/result.fa Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan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
--- a/PedToFasta/test-data/sample.ped Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A C G C T T C A C T G A G A G T G A C C T A G T G C G A G T G T C A G C T G A T C G T G A G T G A G C T G T G C G C T A G A T C T G C T C G A A G C T G A A G G A A T T C A T A T C T C T A T A G G A C T A G G C A G A T G C C G G A C A T C A G A G T G G C A T A C G C G T A T G A G A C T C T A T C A C T T G T C A T G A C G T C G A T A A G C T C A T A C T C T T C A C G T C T T G C T A T A G C T A G C T A G C T T C T G G T C T T A A G C A A C A T T G C T C T C G C T T C T A A G T C C G T G A G A T G A G C A G A G G A C T T C T A C T T C T C T G T C T C G T T C A G A C T G G T G A C T C T A G T G T C T G T G A T T A T G G A C T T A A G C A T C G A C G A T C T T A T C T C T A G A A G A G A G A G T C G A G C A G G T G A A T T G A T A G G T T G C T T C T C G T A C G T C T T C T C G C T A C G C G C T A G G A T G G A A C C G G T A C T G A G G A G T A G A T G A G A A G G A T C A T A G G T T G C T T A A G T G G A T C T A A T T A G T A C G A G A A G C T A G C T T C T A A T A G T C T C A G T G G T T A T C T C A G G A T A T C T C A G T G C T C G A G G A C T A T A G T C A T G C A T T C C T A T A T G T T C T C G T T C A T T C G A C A A G C T A G T C C T A G A G A T C T C T T C G C G A C T A G G A T G A G G A C T A C C A G C C G G A A G C T C T C T C G A G A C A T G A G A A G A G G C A T G A C T T C C A C T T C A G T C A T C T G A G A G C C G C T C T A C T C A G T G G T A G T G C T T A G T A G G A C T T C G A T C A G C A A C A T T C T A G A T C G C G C T A C T T C T C A G T C A T A T T A A T T A G A T C G A A G T C G A C T A T A T A C A C C T A G T C T C T C A G C G C T C T G A G A G A G A G A C T T C C T A G C T T C A G A G G T G T C A C T C A G A G A G A A G C G T C T G T C G A A G G A T C T A T C A G G A T C T A A G C T G C C T C T G A T C G A G A C T G C A G A C A C G T G A G T T C T C T C C A C A G A A T C T T G T A T C A C A G T C G A C G A T A G T C A G T C A C C T C A A C G A A G T C G C G A C T G A G A A G G C A G A G G C A G A G A C G T G A G T C T C T T C G A A G C T A C C T C T A G C T G A G A G T C T G A G A G A G A G A C T T C G A C T T C A T C T T C G C G A G A A C G T G A C T C T T C C G T C G A A G T C T C A T G A C A T C G C G A C T C T C T C A C A G A G A C T C T G A T A T G A C A T T A A T C T A G G A T A C T T C T C C G T A G A G A T C A G T C G A C T A G A G G A T C G A T C A G C T G A T C C T C T T C G A A G G A A T C A T C T G C A A T A G G A C T C T C T C T G A C A T C C G G C A G G A G A T A C T G A T A A G G A A G A T T C A G A T T C A G T G A T C T C T C A G T G A C T G A C A C T G A C T C A G A G A C T A G T C T C C T C T C T G A A C A G A G A T C T C T G A G C C T T C C G T C A G T C C T T C C T G C A T G T C T A C A G C T T C C T C T C T T C C T G A G A G T A T C T T C C A C T G A C T C A T A C T C T T C C G C T T C A C T A C T A C A T C G T C T A A T T A T C G A C T C T T C C G T C G A C T A C C A G A G A G A T C T G T C A G A T G A T C C T G A A G A G T G C T C T T C T G G A C T C T G A C T C T C A T C G A C A G A C T T C T C G T A T C T T A T A T C C T T G C T G A T C A T T A A G T C G A A C G C G C C T T C C T C T C T T G T C A G T C A G A G C T C T A G C T T C G A C T G A G T G A C T C T G T C T C T C T T A C T A G T C G A G A C T T C C T G A A C C T C T A G G A G A C T A T A G A G G T A G C T C T C T C T A G A G G A C T G A C T C T G T C T T C G A G A G A G A T A C T G T T A G A G A G A C A T C A T G A T C A G G A C G A T C G G C C T C T C T C T G A T C C T C T T C C T C G A G T C T C C A G A A G C T C G G A A T A C T C A G C T C T C T G A G A C T A G C T T A C T T C C T A C A T A T G A G A C T A C G A T C C T C T G A G A A C C T G A G A G C T G G A A G C T C T G C G A T C G T G A G A G A A C A G T A T C T C C A T A C T C T A C G A T A C T C T T A T A T C T C T C G T C G T C T G T C C T C T T C C T C T T C T A C T T C C G A G T A C G C T C T C T T C G A G A T C G C A G A C T C C T T C G A G A T C C G A T C T C T T C C T A T G A C T C T C G A G T C T C T G A G G A C T C T C T A C A T C T C T C T G A T A T A C T T G T C C A C T G A G A A G C A C T T C C G G A T G T C A C A C T C C T G A G A A G A T A G T C G A A G G A A C C T G T C T A G T G G A C T A G T C G A C G C T T C A G C T C G G A C A T C A T A T T A A T T A A T C T T G C T G A C G T C T C T A G T A C G A T A A T C T T A G C A C A C G C C A A G T G T C A G G C A T A T A C G T A T C T T C T C T A G T A G A G G T A G A T G A A T T C T A T A T A T C G C T C A G C G T C T C T C C T T C A G A G T A A C A C G A T A C T A G T C T C A T T C T G A G C A A T A G T C G A T C T C G A A G A T A T G A C T A C T C T C T C G A T C T C C T C A A G C T T C C T A G G A T C A G T A A G T C G A T C A T T A G T A T A C G A T A G A T C C T A G A G A G T C T A G C C T T A G A G C A G T C A T T C C G A G T C T G G A A G C T A G G A T G A G T C G A T C A T G C A T T A C T G A T A A G G A A G T G T C T G C T G A T C C T A T C T G T G T A G C T C T T C G A A G C T T C C T T C T C A G T G G A T C T G T C C A T C T C G A A T T C G T G A T A C A C T G A G A T G C T A G A G G A T C G A T C A G A T T C G C C T G A T C T G T C C A C G C T T C A G A T A G A C T A T G G C G A G C T C C T A G T A G C G A G A A G A G T C C G A C G C G A G A A T T G G A A G A G C T C T T C G A A G C T T A A T T C T C A G G A C T C A T C C A G A A G C T A T T A A G T C C T T C A G A C A G G T T G T C T G A T C A T C C T A G A C T C C T G T C A A T C A T C A G A T G A G T C T G A G C A G C A G T C G C T A G G C C T T C A G A T A C C A C G G C T G G A T C A C C T T G T C A G A T G A G A A G A G A G C T C T C G A G T G C T G A T C C T C T T C G A C T A G A G G T G A T C C T C T T A T C T C T A C T T C T A A G C T A G G T A C G A G T G A A G C T G A T C T A A T C A A C A G G A A G C T C T C T C T A T G C T A G C G A C A T A T A C T G A A T C T G C C T T C T A G A C T C T G A A G C T G A A G C T C T A G G A G A T A T C G C G C G A T C A G C T T C G C G A G A T G T A C T C G C A T C C G C G T G T C T C A G C A G A G A A G C T A T C A G A C T G A G T A G A G G A G A T G C T C T A T C G T C G A T C C T T C T C G A A G A C G A G A C T A T G A A G A G G A T C G C T C A G C T T C G A G A T A C G G A A C G C G A T C G C G A T A T C A G G C A G T C G A T G G T T A T C G A C T T C A T A G A T A G A G C T A C G T G A G T A G T G T G G A G T C T A C C A G T C T A G A C A G G A A G T C A G A G T C T C A G A C T A T A A G G A G A T C T C A T T A T C A G T G G A C T T C C T G A C T T C T C C T C T A G T C C T T A A G G A C T T C A C C T C G G C A T A G A G T G T C A G A G C T C T A G G A G T T C G C A C T A C A A T G A C T G A A C G A A G T C A G A C C T G A G A T A A G T A A G G T A G T C G C T G C T G C G C G A T C G C G A C T T C A C G A A G G A A G T A G T C T A G G C A G G A G T G T C T A G G A A C A C C T G A C A A G A T G A A G G A T G G A A T G A G A C T T C T G A T C T G A G T A G G A G A A C G T A G A G G C C T C T A T C G A G G T A G A G G A A C T C A T A T A T A T T G A G C T G A A G T C T C A C A T C A T C A G A G C T A G G A C A C T C T G C A T T C A C C A T C G A T C G C T G T A T A A G T C T A T C G A T A C T A T A T T C A G G A C T G A G C C G A C C T G T C A C G C T G A C G G A A G C T T C C T T C A C G T T A A T C A T G G C A G C A A G C T G A C G A G C T C A A G A G G A C T A T G A C T C A T G T C G A C T G C A T T A A C C G G T C T C T G C A T T C A G C T G A A G G A A C T C C T T A G C A G A T A T T C C T G A T C C A G C C G C T T C C T A G T C T C T A T C T C A C G A C T C G A C T A G A C T G A C T C T A G T G G A G A G A A G A C A G T C G A G A T A C T G C C T C T T A T C T C C A A T C T G A T C C T G A A T G A C T T C C T C G G A G A T C A G A G A G A C C A C A A G G C C T G T G A T A T A T G A G C T C T G A G A T G C T A G T C T A G A G A A G C T A T G A A G A G C T C A C T T C T C T A C T A T C T C T T A A G G A G A C T G A T C G A C G G A A T A C A G A G A G A T T C T C T C G T A T C T G A G A T C C G G A T G C A G A A G A G G A G C T G T C C A A T G T G A T C C A T G T G A G G C C A T G C T T C A G G A G A A G G T A G T C A G G T C T A G T C A C T C T C T C C T A G G A G A A C T G T G A C G A T A T C T C G T A T T C C A T A T C C G A T T A A G T C G A G T C T G T T A A T A G T G C T A G G A C T A C C T G A A T G A T C T A A T G A T C T A C A A G A G G A G A G A G A A G T G G A G C C T C A G T C T A G G A T G G A G T A T G A T C T C A T G T G C G C T C C T T A C T C A C G C T C G T C A G T A G A G A A G C A A G T A C A A G T A C G T A T C G C A G T C C T C T T A T A G A A G C T G A C G T A A T G C T G C G G A T C T C C T T C C T T C C A T C G A C T C G G A T A C G A T C T T C T C C A T C T A C T G A A G T C A T A G T C C T T C T A G C T C G A T C T C G A G T T A G A T C C T G A T C G A T A G T T C A C C G T C G A G A G A G T G A G A T A T C C T A T G T G C T G C G C T A C C G G A G A C T C T C T T C C T C T C T T C A G C T A G T A G C T A C A T C T A G A T G C T C A G A T A T C G A T G T C G A A G C A A C C T C T G A A C T C C A A T T C T G A T C T T C A G A T A G A G G A T C G A C T C T G A C T C T C T G A C T G C T C C T A T A T C T C T C T A G C T G A G A A G G C G A A G C T A G C A C T A C G T C T T G T C A G T C C G C T G T T C T A G A A T G A A G T C G C C T G A A T G T A G C T C T T A G A C T T C T C C T G T T C C A T A C T C A A T G A C T A C T A G C A G G T A G A T C T A G C A G A T C C T G A C T G T G A G C A G A G G A T A A G C A G A A G G T C T G A T C A G C T A G T C A G G A T C A G G T C T C T G A G A T C G A A G A C C G T G G A G T G A A T G T A G T A A C C T C A T C T G G A T A A G C G G A C T T C C T T G A G T A T C A G G A G A G T G A T C G A G A C T T A T A G T C T C T C T G A A C G A C T A G A G A C A G A T G C C T C G T C A T A T A G C T C A A T C T T G G A G T C G T C A G A C T C T A T G G C G T C G A G T A T C C T T C G A A G A G G C A G T C A G C T T G G A T C A T A T A T G A A C A T C T T C G C C T A G G A T C G T C T T C T C C G A T T C G T G A C A C T A G G T G A G A G A C T C T T A G C T G C T C G G T C T C T A C T C T C T C T C G T G A T G T C C T T C G C G C A G A G A G T C G A C G T A T C A G T C A G G T C A G C C T A G A G T A C A A G G C T C T G G A T C G T G T A T C T C T C T C T A C T G A G C T T A C T T C G A C T A G G A A C G A G C C A C A C T G C A C T G C T C T C T G C G A T G T C G A C T C A C T C G A G G T C T G T C T T C C T G T G A T G T C A T T C T G T C C T T C A G C T A G G A T G C T A T G A A G G A C T C T G C A G C T G A T A T A A G G A A G T A T C A C A G T A G A A G G A A G G A C T C G G A T A G T T C A G A C T A C T C T T C A G T C A G T C G A A G A G A G G A C T A G G A A G C T C T T C C T A T T C C T A G G A C T T C T C G A C A G T T C T C T C T A A T C A A T A G A G A G A G C T A G C T A G A G A G A T A C T G G A A G T C T A G T T G A G T C A G T C C A C T C A T C T C A G C T T C T A A G C T A G G A T A G A A T A G A C T C C T G C G A T A G A C T A G T C C T G A C A G T G A C A A T C G G A A G G T A G G A C T T C G A C T A G G T A T T A A C C G C T G A G A A G A G C G T A G T C T G C A C T G T C T A A G C G C T G C T C C G G C C T G A T G G A A G T G C G C T C T T C A G A T A G T C A T C T C T G A C T G A G A A G C T T C T C A G T C G A T C A G A G C T G A A T A T T C T C G A T C A G G C C T G A A G T C G A A C A G G T T C G C C T T A C T C A A T C T G A C T T C G A T C T C T C C G A T T C C T G A A C G A T G G A T C G C C T A T C T A G A T T C A G C T G A C T G A C T T C C T C T G A G A A C C T G A C T T A C T C T T C T C G A C T G A G C A C G A T C T G G A C T G A T C T G C A C T C T T C C T T C A G C G T A C G A C A G A G C T G A G C A T T C C T T A A T T C C T T A C T G A C T G A A G T C C G G A G A T C T C A G C T T G C T A G C T A G T C T C T C A G G A G A C G C T T G A G C A C T A G C A T C A T T A G C A G T A T C C T C A T C T G T C A G A G C A C T A T A G G T T C G A C T G A G A C T C T G A G T G A T C T C T A C T C T A T C T G A A G G A G A G C A G T C C G C T C T G A C T C T G A A T C T G A A G T A T G G A G A C T G A T A G C C T G A G A T C C T G A T C T C G A C T G A G A G A T C A G T G A C C T T A T C C A G C G A C T G A C T C T T A C G T A T G G A T A C T C T A C G C A C G A A T A G A G T C G T C T C T T C A G T C A G T G A T T C C T G A A G G T T C A G G A A C A T A C T A C T A G G C T G G T G T G T T C A G G C T G T A A T A C T C C T G C C A C T A G A G A C T A A G T G A C T G G A T C T C A G G A T G C A A G G T G T C T C T T A G A T G A T T G C T C T A G G A G A G A A C C T G A T A A G G A A T T G G C A G T G G T T C A C G A T A T C G A C G A G G A G T C T G T C G A T G A G C G A A G G A T C G T C T A T T C A T T C T C A C T C G A T C C T G A G A C T C G G A G A A G C T G A T C T G A T A G A G C T T C G T A C T A T A G T C T C T T A A C G A C A C T A G G A A G C T C G C T C T G A T A C A T C C T A G T C G C C G C T C T C T G A C G G A A T A T G A C G G T A G C T A G A G C A G T C T A T A G A G C G G A A G C T C T G C G A C T A G T C T C A G T C G A C T A C C G C T A G A G C T C A G A T C A G C T T C G A C A A G A T T C A G C T C A T A G T T A G A T C T G C T G A G A G T G A G A G T G C C T C T A C A G G A C T C T C T C T C T T C C A C T G A G A G A G A G T T C T C G T A G G A A T T C T C A T A C A G T C C T G A G A A G C T T C T C G T G A T C C T A G T C T C A G C T A C T G G A A G C T A G C T T A T A C T G A A G A G G A C T G A C T T C C G A T A C C A T A C T T A C A T C A T C G T C T C G A T A T A T A T C G A A G A G G A C T T A C T G T G C T G G A T C G C G C C T C T T C A T G A G A G A A C A C A G C G T C T C T G C T A G G T C T C T C A C T T G A G T C C T T C T G G A C T G C C A T C T C T A T C G A G C A T G A A G T A A G C T G T A G C T A G T C T C T C A G T C A G G T C T T C T C A G C T T G C T C T C T C T G A G C C T G T T A C T A C T A G C A C G A A G C T A G C A T G G A A C A G T C G C G A C T C G A G C T C T T C G A C A T C T G A G G A G A A T A G C T C T G A G A G A A G T C T C A T T C T C A T A G G A T G A T G T T G A G T C A G A T A G A T C T C G C A C T G A G A G C C A G A A T T A A T C G C A A G C A C G G A G T C T T A A G G A C T T C C T A T C T A G T C C G C T A G A C T A A C A G G C A T A G C T T G T G A G A G T A C G G C C T T C T C C T T C G A T C T C T C C A C T C T T C T C A C A G C T G T T C T C A G T A C T T C C T A G C T C T C T C T C T C T G A A C C T C T C T G A G A G A C T T C C T T C A G A G C T T G T A G A C T G A A G G A C T A T A T T C T G A C G A G T C G C T T C T C T C T C G A C T T A G A G A A G A G T G G C T C C G T C C A G A
--- a/Rooting/Rooting.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; -use Cwd ; -use FindBin qw ( $Bin $Script ); - -my $CURRENT_DIR = $Bin; - -my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar"; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <newick input> - -o, --output <newick output> -~; -$usage .= "\n"; - -my ($input,$outfile); - - -GetOptions( - "input=s" => \$input, - "output=s" => \$outfile -); - - -die $usage - if ( !$input || !$outfile); - -my $treefile = $input; - - -# replace negative values by 0 -open(T,$treefile); -open(T2,">$treefile.2"); -while(<T>) -{ - my $line = $_; - $line =~s/\-\d+\.*\d*\,/0,/g; - $line =~s/\-\d+\.*\d*\)/0\)/g; - print T2 $line; -} -close(T); -close(T2); - -my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1"; -system($rooting_command); - -unlink("$treefile.all"); -unlink("$treefile.2"); -rename("$treefile.midpoint",$outfile); - - - - -
--- a/Rooting/rooting.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,193 +0,0 @@ -<tool id="sniplay_rooting" name="Rooting" version="1.0.2"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Midpoint rooting of newick tree </description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - <requirement type="package">Rootings_54.jar</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="perl"> - Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> - <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> - <data name="fileout" type="data" format="txt" label="${fileout_label}" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - - <test> - <param name="filein" value="newick" /> - <output name="fileout" file="out_tree" /> - <output name="fileout_log" file="out_tree.log" /> - </test> - - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - - -.. class:: infomark - -**Authors** Jean-François Dufayard, CIRAD, South Green platform - - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - -.. class:: infomark - -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - ---------------------------------------------------- - - - - -======= -Rooting -======= - ------------ -Description ------------ - - Compute a midpoint newick rooted tree. - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=========== ========================== ======= -Name output file(s) format -=========== ========================== ======= -fastme Newick tree Newick -=========== ========================== ======= - - - ----------- -Input file ----------- - -Newick file - - ----------- -Parameters ----------- - -Output name - Output base name for the ouput files - - ------------- -Output files ------------- - -Output_name - Resulting tree rooted in newick format - -Output_name.log - Log file - ------------- -Dependencies ------------- -Rooting - CIRAD tool. Contact jean-francois.dufayard@cirad.fr - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -Newick file ------------ - -:: - - (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... - - -Parameters -========== - -Output name -> out tree - - -Output files -============ - -out tree --------- - -:: - - (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> - -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Rooting/rooting.xml~ Fri Jul 10 10:38:11 2015 -0400 @@ -0,0 +1,193 @@ +<tool id="sniplay_rooting" name="Rooting" version="1.0.2"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description> Midpoint rooting of newick tree </description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</requirement> + <requirement type="package">Rootings_54.jar</requirement> + </requirements> + + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> + <version_command> +<!-- + tool_binary -v +--> + </version_command> + + <!-- [REQUIRED] The command to execute --> + <command interpreter="perl"> + Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log + </command> + + <!-- [REQUIRED] Input files and tool parameters --> + <inputs> + <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> + <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> + </inputs> + + <!-- [REQUIRED] Output files --> + <outputs> + <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> + <data name="fileout" type="data" format="txt" label="${fileout_label}" /> + </outputs> + + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + + <test> + <param name="filein" value="newick" /> + <output name="fileout" file="out_tree" /> + <output name="fileout_log" file="out_tree.log" /> + </test> + + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help> + + +.. class:: infomark + +**Authors** Jean-François Dufayard, CIRAD, South Green platform + + +.. class:: infomark + +**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. + +.. class:: infomark + +**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr + +.. class:: infomark + +**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +--------------------------------------------------- + + + + +======= +Rooting +======= + +----------- +Description +----------- + + Compute a midpoint newick rooted tree. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=========== ========================== ======= +Name output file(s) format +=========== ========================== ======= +fastme Newick tree Newick +=========== ========================== ======= + + + +---------- +Input file +---------- + +Newick file + + +---------- +Parameters +---------- + +Output name + Output base name for the ouput files + + +------------ +Output files +------------ + +Output_name + Resulting tree rooted in newick format + +Output_name.log + Log file + +------------ +Dependencies +------------ +Rooting + CIRAD tool. Contact jean-francois.dufayard@cirad.fr + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Newick file +----------- + +:: + + (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... + + +Parameters +========== + +Output name -> out tree + + +Output files +============ + +out tree +-------- + +:: + + (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> + +</tool>
--- a/Rooting/test-data/newick Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); -
--- a/Rooting/test-data/out_tree Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -(ref:0.575788,(((((((((((((((((((((((PALAWAN:0.032789,KENDINGA5H:0.028863):0.031721,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.004581,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004869,DINORADO:0.065206):0.004898,((LUDAN:0.05423,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):8.8E-5):0.006838,CAAWA/FORT:0.05563):0.011439,CANELADEFE:0.050931):0.002897,PACHOLINHA:0.042509):0.002988,TRESMESES:0.028972):0.001209,((OS4:0.021016,OS6:0.01567):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.006303,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.004673,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.14437):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.04316,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.01418,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.05797):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.00344,(((((KUROKA:0.096901,IRAT144:0.032372):0.04063,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.03418):0.01106,CAIAPO:0.07222):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.001457,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.01125,(((IAC47:0.007321,(IAC165:5.0E-4,VARYLAVA90:0.00165):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.007912,IRAT234:0.037316):0.005647,MANDRIRAVI:0.049833):0.002593,RT1031-69:0.04352):0.005079,((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.00474):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):8.58E-4,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.02711,GRAZI:0.022678):7.63E-4):0.00987,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:0.0,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):9.71E-4):0.009442):0.002985):0.008281,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.02162,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.05943,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.001416,((GANIGI:0.040448,PULULAPA:0.03984):0.020258,GOGO:0.060904):0.005609):0.018877,CUIABANA:0.066182):0.020665,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.03265):0.012575,VIETNAM1:0.049323):0.00311,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.01445):0.01097):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.00624,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.043699,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.015245,(((JUMALI:0.07765,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607):0.14713500000000007);
--- a/SNP_density/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,124 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <Hapmap input> - -o, --out <output in tabular format> - -s, --step <step (in bp)> -~; -$usage .= "\n"; - -my ($input,$out,$step); - -GetOptions( - "input=s" => \$input, - "out=s" => \$out, - "step=s" => \$step, -); - - -die $usage - if ( !$input || !$step || !$out ); - -my $max_chr_num = 100; - -my %counts; -my %counts_by_ind; -open(my $HAPMAP,$input); -my $headers= <$HAPMAP>; -$headers=~s/\n//g; -$headers=~s/\r//g; -my @ind_names = split(/\t/,$headers); -my @individual_names; -for (my $i = 12; $i <= $#ind_names; $i++) -{ - push(@individual_names,$ind_names[$i]); -} -my %maximums; -while(<$HAPMAP>) -{ - my $line = $_; - $line=~s/\n//g; - $line=~s/\r//g; - my @infos = split(/\t/,$line); - my $chrom = $infos[2]; - my $position = $infos[3]; - if ($position > $maximums{$chrom}){$maximums{$chrom}=$position;} - my $classe_position = int($position/$step); - $counts{$chrom}{$classe_position}++; - - my $ref_allele = $infos[11]; - for (my $i = 12; $i <= $#infos; $i++) - { - if (!$counts_by_ind{$chrom}{$classe_position}{$i}){$counts_by_ind{$chrom}{$classe_position}{$i} = 0;} - if ($infos[$i] ne $ref_allele) - { - $counts_by_ind{$chrom}{$classe_position}{$i}++; - } - } -} -close($HAPMAP); - -####################################################### -# global -####################################################### -open(my $OUT,">$out"); -print $OUT "Chromosome Position SNPs\n"; -my $chr_num = 0; -foreach my $chrom(sort keys(%counts)) -{ - $chr_num++; - my $ref_counts = $counts{$chrom}; - my %final_counts = %$ref_counts; - my $x = 0; - #foreach my $classe_position(sort {$a<=>$b} keys(%final_counts)) - for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) - { - my $nb = 0; - if ($counts{$chrom}{$classe_position}) - { - $nb = $counts{$chrom}{$classe_position}; - } - $x += $step; - print $OUT "$chrom $x $nb\n"; - } - if ($chr_num >= $max_chr_num){last;} -} -close($OUT); - -####################################################### -# For each individual -####################################################### -open(my $OUT2,">$out.by_sample"); -$chr_num = 0; -print $OUT2 "Chromosome ".join("\t",@individual_names) . "\n"; -foreach my $chrom(sort keys(%counts_by_ind)) -{ - $chr_num++; - my $ref_counts = $counts_by_ind{$chrom}; - my %final_counts = %$ref_counts; - for (my $classe_position = 0; $classe_position <= $maximums{$chrom}/$step;$classe_position++) - { - print $OUT2 "$chrom"; - my $num_ind = 12; - foreach my $indiv(@individual_names) - { - my $val = 0; - - if ($counts_by_ind{$chrom}{$classe_position}{$num_ind}) - { - $val = $counts_by_ind{$chrom}{$classe_position}{$num_ind}; - } - print $OUT2 " $val"; - $num_ind++; - } - print $OUT2 "\n"; - } - if ($chr_num >= $max_chr_num){last;} -} -close($OUT2);
--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,207 +0,0 @@ -<tool id="sniplay_density" name="SNP density" version="1.2.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Calculate SNP densities along chromosome from HapMap</description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="bash"> - calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> - <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> - <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> - <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> -<!-- - <test> - <param name="input" value="input_test.txt" /> - <output name="output" file="output_test.txt" /> - </test> ---> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - -.. class:: infomark - -**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr - ---------------------------------------------------- - - - -============= -SNP densities -============= - ------------ -Description ------------ - - Calculate SNP densities along chromosome from HapMap - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Hapmap file hapmap -=============== ====================== =========== - - ----------- -Input file ----------- - -Hapmap file - File with SNPs - - ----------- -Parameters ----------- - -Step - Step in bp for the window to calculate SNP density - -Output name - Output base name for the two ouput files - - ------------- -Output files ------------- - -Output_name - Tabular file with SNP density in each postion - -Output_name.by_sample - Tabular file with SNP density for each sample - - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -hapmap file ------------ - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 - chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT - chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA - chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC - chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG - chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG - chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT - -Parameters -========== - -Step -> 200000 - -Output name -> densities - - -Output files -============ - -densities ---------- - -:: - - Chromosome Position SNPs - chr1 200000 355 - chr1 400000 228 - chr1 600000 63 - chr1 800000 191 - - -densities.by_sample -------------------- - -:: - - Chromosome BA58 BA59 BD54 - chr1 220 197 225 - chr1 130 119 133 - chr1 43 43 40 - chr1 139 167 141 - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapmap.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) -hapmap=$1 -fileout=$2 -fileout_bysample=$3 -step=$4 - -perl $tool_path/CalculateSlidingWindowsSNPdensitiesFromHapmap.pl -i $hapmap -o $fileout -s $step - -cp $fileout.by_sample $fileout_bysample -rm $fileout.by_sample -
--- a/SNP_density/test-data/hapmap Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3584 +0,0 @@ -rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54 -chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT -chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA -chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC -chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG -chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG -chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT -chr1:1398 [T/G] chr1 1398 Cc01_g00010:369 exon SYNONYMOUS_CODING gcA/gcC A/A 16.7% 3 TT TT NN TG -chr1:1394 [G/C] chr1 1394 Cc01_g00010:373 exon NON_SYNONYMOUS_CODING Cgt/Ggt R/G 16.7% 3 GG GG NN GC -chr1:1379 [A/T] chr1 1379 Cc01_g00010:388 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 16.7% 3 AA AA NN AT -chr1:1352 [T/C] chr1 1352 Cc01_g00010:415 exon NON_SYNONYMOUS_CODING Act/Gct T/A 33.3% 3 TT CC NN CC -chr1:1252 [T/A] chr1 1252 Cc01_g00010:515 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA -chr1:17176 [T/G] chr1 17176 Cc01_g00030:504 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TT TG TT -chr1:18041 [A/G] chr1 18041 Cc01_g00030:661 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 AA AA GG AG -chr1:18442 [C/A] chr1 18442 Cc01_g00030:929 exon NON_SYNONYMOUS_CODING tCc/tAc S/Y 25.0% 4 CC CC CA CA -chr1:18478 [T/C] chr1 18478 Cc01_g00030:965 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 25.0% 4 TT TT TC TC -chr1:18554 [T/G] chr1 18554 Cc01_g00030:1041 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT TT TG TG -chr1:19062 [T/A] chr1 19062 Cc01_g00030:1151 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN TT AA -chr1:19078 [A/G] chr1 19078 Cc01_g00030:1167 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA -chr1:19138 [T/C] chr1 19138 Cc01_g00030:1227 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT CT TC -chr1:22125 [C/T] chr1 22125 Cc01_g00030:1773 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC CT CT -chr1:22212 [T/C] chr1 22212 Cc01_g00030:1860 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT -chr1:22342 [T/A] chr1 22342 Cc01_g00030:1990 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 4 TT TT TA TA -chr1:22404 [C/T] chr1 22404 Cc01_g00030:2052 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC CT CT -chr1:22478 [C/G] chr1 22478 Cc01_g00030:2126 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC GG CC CC -chr1:22613 [C/T] chr1 22613 Cc01_g00030:2261 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 CC TT CC CC -chr1:22657 [C/T] chr1 22657 Cc01_g00030:2305 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC -chr1:22758 [A/G] chr1 22758 Cc01_g00030:2406 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AA AG AG -chr1:22903 [C/A] chr1 22903 Cc01_g00030:2551 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CC CA CA -chr1:22965 [G/T] chr1 22965 Cc01_g00030:2613 exon NON_SYNONYMOUS_CODING atG/atT M/I 12.5% 4 GG GG TG GG -chr1:23037 [A/G] chr1 23037 Cc01_g00030:2685 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA AA AG AG -chr1:24151 [A/G] chr1 24151 Cc01_g00030:3063 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA AG AG -chr1:24436 [T/C] chr1 24436 Cc01_g00030:3240 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT TC TC -chr1:25763 [G/C] chr1 25763 Cc01_g00030:3610 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 25.0% 4 GG GG GC GC -chr1:26910 [T/G] chr1 26910 Cc01_g00030:3889 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 25.0% 4 TT TT TG TG -chr1:26996 [C/T] chr1 26996 Cc01_g00030:3975 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 CC CC CT CT -chr1:27095 [A/T] chr1 27095 Cc01_g00030:4074 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT -chr1:27755 [C/T] chr1 27755 Cc01_g00030:4734 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC CT CT -chr1:30493 [C/T] chr1 30493 Cc01_g00030:4992 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC -chr1:30505 [C/T] chr1 30505 Cc01_g00030:5004 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CC TT CT -chr1:30560 [A/G] chr1 30560 Cc01_g00030:5059 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AG AA -chr1:30592 [T/C] chr1 30592 Cc01_g00030:5091 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT -chr1:32950 [A/G] chr1 32950 Cc01_g00030:5337 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AA AG AG -chr1:32968 [A/C] chr1 32968 Cc01_g00030:5355 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 4 AA CC AA AA -chr1:33022 [A/T] chr1 33022 Cc01_g00030:5409 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TT AA AA -chr1:33025 [T/A] chr1 33025 Cc01_g00030:5412 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT AA TT TT -chr1:33167 [T/C] chr1 33167 Cc01_g00030:5554 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 25.0% 4 TT CC TT TT -chr1:33196 [C/T] chr1 33196 Cc01_g00030:5583 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 CC TT CC CC -chr1:33467 [T/C] chr1 33467 Cc01_g00030:5854 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TC TC -chr1:37303 [G/A] chr1 37303 Cc01_g00040:129 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 GG NN NN AA -chr1:37602 [C/G] chr1 37602 Cc01_g00040:428 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC GG GG CG -chr1:37607 [T/G] chr1 37607 Cc01_g00040:433 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 50.0% 3 TT GG NN TG -chr1:38519 [A/C] chr1 38519 Cc01_g00040:507 exon SYNONYMOUS_CODING gcA/gcC A/A 33.3% 3 AA NN CC CC -chr1:38606 [G/A] chr1 38606 Cc01_g00040:594 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 4 GG AA GA GA -chr1:38657 [C/T] chr1 38657 Cc01_g00040:645 exon SYNONYMOUS_CODING caC/caT H/H 37.5% 4 CC TT TT CT -chr1:38927 [G/A] chr1 38927 Cc01_g00040:915 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN NN AA -chr1:38942 [G/C] chr1 38942 Cc01_g00040:930 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG NN CC CC -chr1:38952 [C/T] chr1 38952 Cc01_g00040:940 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 CC NN TT CT -chr1:38956 [T/C] chr1 38956 Cc01_g00040:944 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 3 TT NN CC TC -chr1:39103 [C/T] chr1 39103 Cc01_g00040:1091 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT -chr1:39113 [C/T] chr1 39113 Cc01_g00040:1101 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TT CT -chr1:39164 [T/G] chr1 39164 Cc01_g00040:1152 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 TT TG TT TT -chr1:39389 [T/C] chr1 39389 Cc01_g00040:1377 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 2 TT NN NN TC -chr1:77092 [C/G] chr1 77092 Cc01_g00050:8 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 25.0% 4 CC GG GG GG -chr1:77069 [C/A] chr1 77069 Cc01_g00050:31 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 12.5% 4 CC CA CC CC -chr1:77040 [A/C] chr1 77040 Cc01_g00050:60 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 AA CC CC CC -chr1:77030 [T/C] chr1 77030 Cc01_g00050:70 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC CC CC -chr1:76998 [C/A] chr1 76998 Cc01_g00050:102 exon SYNONYMOUS_CODING ccG/ccT P/P 50.0% 4 CC AA CA CA -chr1:76995 [T/C] chr1 76995 Cc01_g00050:105 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC -chr1:83837 [G/A] chr1 83837 Cc01_g00060:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA -chr1:84858 [A/C] chr1 84858 Cc01_g00060:392 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 37.5% 4 AA CC AA AC -chr1:84868 [C/T] chr1 84868 Cc01_g00060:402 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 4 CC TT CC TT -chr1:84880 [G/A] chr1 84880 Cc01_g00060:414 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GG AA -chr1:84991 [C/G] chr1 84991 Cc01_g00060:525 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 CC CC CG CC -chr1:105491 [C/A] chr1 105491 Cc01_g00070:36 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA -chr1:100754 [G/C] chr1 100754 Cc01_g00070:660 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 GG GC GG GG -chr1:100458 [A/C] chr1 100458 Cc01_g00070:720 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 37.5% 4 AA CC AA AC -chr1:100367 [C/A] chr1 100367 Cc01_g00070:811 exon STOP_GAINED Gga/Tga G/1 12.5% 4 CC CC CA CC -chr1:99870 [T/C] chr1 99870 Cc01_g00070:1068 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC -chr1:99742 [C/G] chr1 99742 Cc01_g00070:1196 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CC CG -chr1:99729 [G/A] chr1 99729 Cc01_g00070:1209 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GG GA -chr1:99727 [G/C] chr1 99727 Cc01_g00070:1211 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC -chr1:99642 [C/T] chr1 99642 Cc01_g00070:1296 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT -chr1:99567 [T/G] chr1 99567 Cc01_g00070:1371 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 TT TT TT TG -chr1:99549 [T/C] chr1 99549 Cc01_g00070:1389 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT CC TT TT -chr1:99448 [T/G] chr1 99448 Cc01_g00070:1490 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG -chr1:99354 [T/C] chr1 99354 Cc01_g00070:1584 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC -chr1:99162 [T/C] chr1 99162 Cc01_g00070:1776 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC -chr1:98368 [C/G] chr1 98368 Cc01_g00070:2112 exon NON_SYNONYMOUS_CODING agG/agC R/S 50.0% 2 CC NN NN GG -chr1:97071 [A/C] chr1 97071 Cc01_g00070:2285 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 AA CC CC CC -chr1:96611 [C/T] chr1 96611 Cc01_g00070:2292 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CT CC CC -chr1:95183 [T/C] chr1 95183 Cc01_g00070:2748 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TT TC -chr1:95134 [T/C] chr1 95134 Cc01_g00070:2797 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC TT TC -chr1:95116 [G/A] chr1 95116 Cc01_g00070:2815 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA -chr1:94898 [G/A] chr1 94898 Cc01_g00070:2895 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA -chr1:94841 [A/T] chr1 94841 Cc01_g00070:2952 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT -chr1:94700 [C/T] chr1 94700 Cc01_g00070:2994 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT -chr1:94679 [A/G] chr1 94679 Cc01_g00070:3015 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AA AG -chr1:93879 [T/C] chr1 93879 Cc01_g00070:3411 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 TT CC TT TC -chr1:93873 [C/T] chr1 93873 Cc01_g00070:3417 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CC CT -chr1:92117 [A/T] chr1 92117 Cc01_g00070:3663 exon SYNONYMOUS_CODING ctT/ctA L/L 25.0% 4 AA TT AA AA -chr1:92011 [A/C] chr1 92011 Cc01_g00070:3769 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC -chr1:91347 [G/A] chr1 91347 Cc01_g00070:4194 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG -chr1:90731 [A/C] chr1 90731 Cc01_g00070:4545 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AC AC AC -chr1:90332 [T/A] chr1 90332 Cc01_g00070:4746 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TT TA -chr1:90303 [A/G] chr1 90303 Cc01_g00070:4775 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 25.0% 4 AA GG AA AA -chr1:90289 [C/T] chr1 90289 Cc01_g00070:4789 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 CC TT CC CT -chr1:90161 [A/G] chr1 90161 Cc01_g00070:4917 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA -chr1:90128 [G/A] chr1 90128 Cc01_g00070:4950 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA -chr1:89792 [G/A] chr1 89792 Cc01_g00070:5127 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA GG GA -chr1:89745 [A/G] chr1 89745 Cc01_g00070:5174 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 37.5% 4 AA GG AA AG -chr1:89720 [T/C] chr1 89720 Cc01_g00070:5199 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC CC CC -chr1:89493 [A/G] chr1 89493 Cc01_g00070:5304 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG -chr1:89423 [A/C] chr1 89423 Cc01_g00070:5374 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 AA AA AA AC -chr1:89418 [A/T] chr1 89418 Cc01_g00070:5379 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 AA AA AA TA -chr1:88516 [T/G] chr1 88516 Cc01_g00070:5910 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 TT TT TT TG -chr1:87964 [T/C] chr1 87964 Cc01_g00070:6237 exon SYNONYMOUS_CODING agA/agG R/R 37.5% 4 TT CC TT TC -chr1:112990 [T/C] chr1 112990 Cc01_g00080:4 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 50.0% 4 TT TT CC CC -chr1:112983 [A/G] chr1 112983 Cc01_g00080:11 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 4 AA AA GG GG -chr1:112926 [A/T] chr1 112926 Cc01_g00080:68 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 50.0% 4 AA AA TT TT -chr1:112910 [T/C] chr1 112910 Cc01_g00080:84 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC -chr1:112909 [A/C] chr1 112909 Cc01_g00080:85 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC -chr1:112875 [C/A] chr1 112875 Cc01_g00080:119 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 12.5% 4 CC CC CA CC -chr1:112874 [G/A] chr1 112874 Cc01_g00080:120 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG GG GA GA -chr1:112792 [A/G] chr1 112792 Cc01_g00080:202 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA AA GG GG -chr1:112070 [T/C] chr1 112070 Cc01_g00080:274 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 37.5% 4 TT TT TC CC -chr1:111976 [T/C] chr1 111976 Cc01_g00080:368 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TC TT -chr1:111966 [G/C] chr1 111966 Cc01_g00080:378 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG -chr1:111413 [T/C] chr1 111413 Cc01_g00080:741 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 TT CC TT TT -chr1:111011 [T/A] chr1 111011 Cc01_g00080:879 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TT TA TT -chr1:111002 [G/A] chr1 111002 Cc01_g00080:888 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 GG AA AA AA -chr1:110176 [A/G] chr1 110176 Cc01_g00080:1233 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AA AG AA -chr1:127984 [A/G] chr1 127984 Cc01_g00090:15 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG -chr1:128022 [T/A] chr1 128022 Cc01_g00090:53 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 TT AA AA AA -chr1:128047 [A/G] chr1 128047 Cc01_g00090:78 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG -chr1:128072 [A/T] chr1 128072 Cc01_g00090:103 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA TT TT TT -chr1:128252 [T/C] chr1 128252 Cc01_g00090:283 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT CC CC CC -chr1:133985 [C/T] chr1 133985 Cc01_g00100:165 exon SYNONYMOUS_CODING tgC/tgT C/C 25.0% 4 CC CC TT CC -chr1:133990 [T/G] chr1 133990 Cc01_g00100:170 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 12.5% 4 TT TT TT TG -chr1:134007 [G/T] chr1 134007 Cc01_g00100:187 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT TT GT -chr1:134174 [T/A] chr1 134174 Cc01_g00100:354 exon SYNONYMOUS_CODING gtT/gtA V/V 25.0% 4 TT TT TA TA -chr1:134262 [G/A] chr1 134262 Cc01_g00100:442 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GA GG -chr1:134333 [T/C] chr1 134333 Cc01_g00100:513 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TT TC TC -chr1:134393 [C/A] chr1 134393 Cc01_g00100:573 exon SYNONYMOUS_CODING acC/acA T/T 37.5% 4 CC AA CC AC -chr1:134403 [C/T] chr1 134403 Cc01_g00100:583 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC CC TC CC -chr1:134481 [C/A] chr1 134481 Cc01_g00100:661 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC -chr1:134514 [T/C] chr1 134514 Cc01_g00100:694 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT TC TC TC -chr1:134570 [T/C] chr1 134570 Cc01_g00100:750 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TT CC TC -chr1:134580 [C/T] chr1 134580 Cc01_g00100:760 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT -chr1:134592 [C/G] chr1 134592 Cc01_g00100:772 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC GG CC CC -chr1:134603 [G/T] chr1 134603 Cc01_g00100:783 exon SYNONYMOUS_CODING acG/acT T/T 25.0% 4 GG GG TT GG -chr1:134957 [T/G] chr1 134957 Cc01_g00100:1137 exon SYNONYMOUS_CODING ccT/ccG P/P 37.5% 4 TT GG TT TG -chr1:135249 [C/A] chr1 135249 Cc01_g00100:1429 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 12.5% 4 CC CC CC CA -chr1:135260 [G/A] chr1 135260 Cc01_g00100:1440 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GG AA GA -chr1:135922 [T/C] chr1 135922 Cc01_g00110:53 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 37.5% 4 TT CC TT TC -chr1:135925 [A/G] chr1 135925 Cc01_g00110:56 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AA AG -chr1:136539 [G/A] chr1 136539 Cc01_g00120:13 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AA GG -chr1:136654 [A/T] chr1 136654 Cc01_g00120:128 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 AA AA TT AA -chr1:136658 [A/G] chr1 136658 Cc01_g00120:132 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG -chr1:136898 [A/G] chr1 136898 Cc01_g00120:372 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG -chr1:136996 [A/G] chr1 136996 Cc01_g00120:470 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GG AG -chr1:137035 [T/C] chr1 137035 Cc01_g00120:509 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT -chr1:137064 [G/A] chr1 137064 Cc01_g00120:538 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG AA AA GA -chr1:137153 [A/G] chr1 137153 Cc01_g00120:627 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AA AG -chr1:137300 [C/T] chr1 137300 Cc01_g00120:774 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC TT CC -chr1:137483 [G/A] chr1 137483 Cc01_g00120:957 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GG GA -chr1:137525 [A/G] chr1 137525 Cc01_g00120:999 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA GG AA -chr1:137571 [A/G] chr1 137571 Cc01_g00120:1045 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG GG AG -chr1:137669 [C/T] chr1 137669 Cc01_g00120:1143 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT -chr1:137725 [T/C] chr1 137725 Cc01_g00120:1199 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 TT TT TT TC -chr1:137873 [T/C] chr1 137873 Cc01_g00120:1347 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC -chr1:137891 [C/T] chr1 137891 Cc01_g00120:1365 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC -chr1:138059 [T/C] chr1 138059 Cc01_g00120:1533 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC TT TT -chr1:138108 [C/T] chr1 138108 Cc01_g00120:1582 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT CC CT -chr1:138227 [C/T] chr1 138227 Cc01_g00120:1701 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 CC CC TT CC -chr1:138383 [C/T] chr1 138383 Cc01_g00120:1857 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT -chr1:138386 [T/C] chr1 138386 Cc01_g00120:1860 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC -chr1:138497 [G/A] chr1 138497 Cc01_g00120:1971 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG -chr1:144606 [G/C] chr1 144606 Cc01_g00130:45 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG CC GC -chr1:144576 [C/G] chr1 144576 Cc01_g00130:75 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 CC GG GG GG -chr1:144519 [A/G] chr1 144519 Cc01_g00130:132 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA AA GG AA -chr1:144434 [T/A] chr1 144434 Cc01_g00130:217 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 37.5% 4 TT AA TT TA -chr1:144286 [C/G] chr1 144286 Cc01_g00130:365 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 50.0% 4 CC GG GG CC -chr1:147816 [C/T] chr1 147816 Cc01_g00140:18 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC TT NN NN -chr1:147821 [G/T] chr1 147821 Cc01_g00140:23 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 33.3% 3 GG TT NN GG -chr1:147823 [G/A] chr1 147823 Cc01_g00140:25 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG -chr1:147861 [G/A] chr1 147861 Cc01_g00140:63 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 GG GG NN AA -chr1:147863 [G/C] chr1 147863 Cc01_g00140:65 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 33.3% 3 GG GG NN CC -chr1:147872 [C/T] chr1 147872 Cc01_g00140:74 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 33.3% 3 CC TT NN CC -chr1:147974 [G/T] chr1 147974 Cc01_g00140:176 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT TT TT -chr1:148011 [T/G] chr1 148011 Cc01_g00140:213 exon SYNONYMOUS_CODING tcT/tcG S/S 25.0% 4 TT GG TT TT -chr1:148050 [T/C] chr1 148050 Cc01_g00140:252 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT CC TT -chr1:148062 [G/A] chr1 148062 Cc01_g00140:264 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA -chr1:148150 [A/G] chr1 148150 Cc01_g00140:352 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 AA AG AA AA -chr1:148165 [C/G] chr1 148165 Cc01_g00140:367 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 CC CC GG CC -chr1:148179 [C/G] chr1 148179 Cc01_g00140:381 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC -chr1:148184 [A/G] chr1 148184 Cc01_g00140:386 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG -chr1:148230 [C/T] chr1 148230 Cc01_g00140:432 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC TT CC CC -chr1:148933 [G/T] chr1 148933 Cc01_g00140:447 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT -chr1:148935 [G/T] chr1 148935 Cc01_g00140:449 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT -chr1:148943 [G/A] chr1 148943 Cc01_g00140:457 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA AA AA -chr1:148945 [A/G] chr1 148945 Cc01_g00140:459 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA GG GG GG -chr1:149174 [A/G] chr1 149174 Cc01_g00140:492 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 4 AA AG GG AG -chr1:149185 [A/G] chr1 149185 Cc01_g00140:503 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AA GG AA -chr1:149253 [C/T] chr1 149253 Cc01_g00140:571 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 CC TT TT TT -chr1:149279 [G/A] chr1 149279 Cc01_g00140:597 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG GA AA GA -chr1:150025 [G/C] chr1 150025 Cc01_g00140:698 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 12.5% 4 GG GG GG GC -chr1:150045 [G/A] chr1 150045 Cc01_g00140:718 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG -chr1:150080 [A/T] chr1 150080 Cc01_g00140:753 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA -chr1:150083 [G/A] chr1 150083 Cc01_g00140:756 exon SYNONYMOUS_CODING gtG/gtA V/V 50.0% 4 GG AG AA AG -chr1:151272 [C/T] chr1 151272 Cc01_g00140:847 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT -chr1:151277 [G/C] chr1 151277 Cc01_g00140:852 exon SYNONYMOUS_CODING ccG/ccC P/P 50.0% 4 GG GC CC CG -chr1:152592 [T/C] chr1 152592 Cc01_g00140:903 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TT TC -chr1:157051 [C/T] chr1 157051 Cc01_g00140:960 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC TT TT TT -chr1:160171 [C/A] chr1 160171 Cc01_g00140:1088 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA AA AA -chr1:160217 [A/G] chr1 160217 Cc01_g00140:1134 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA AG AA AG -chr1:160786 [C/T] chr1 160786 Cc01_g00140:1194 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC TC -chr1:161276 [A/G] chr1 161276 Cc01_g00140:1312 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA -chr1:161769 [A/T] chr1 161769 Cc01_g00140:1461 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 4 AA AT TT AT -chr1:161789 [A/C] chr1 161789 Cc01_g00140:1481 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA CA AA AA -chr1:161808 [A/T] chr1 161808 Cc01_g00140:1500 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA TA AA AA -chr1:161819 [G/A] chr1 161819 Cc01_g00140:1511 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 12.5% 4 GG GA GG GG -chr1:161837 [T/C] chr1 161837 Cc01_g00140:1529 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT CT -chr1:162050 [C/T] chr1 162050 Cc01_g00140:1545 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC CT CC -chr1:162069 [C/A] chr1 162069 Cc01_g00140:1564 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 12.5% 4 CC CC CC AC -chr1:162112 [A/T] chr1 162112 Cc01_g00140:1607 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 12.5% 4 AA AT AA AA -chr1:162135 [A/C] chr1 162135 Cc01_g00140:1630 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA CA -chr1:162634 [C/G] chr1 162634 Cc01_g00140:1650 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 CC CC CC GC -chr1:163489 [A/T] chr1 163489 Cc01_g00140:1854 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AT AA AA -chr1:168498 [C/T] chr1 168498 Cc01_g00150:90 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC TT CC -chr1:168595 [G/A] chr1 168595 Cc01_g00150:187 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA -chr1:168747 [A/T] chr1 168747 Cc01_g00150:339 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA AA TT -chr1:174617 [C/G] chr1 174617 Cc01_g00160:6 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC CC GG CC -chr1:174616 [C/T] chr1 174616 Cc01_g00160:7 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC CC TT CC -chr1:174601 [G/C] chr1 174601 Cc01_g00160:22 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 GG GC GG GG -chr1:174600 [A/G] chr1 174600 Cc01_g00160:23 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AA AG AA -chr1:174590 [C/A] chr1 174590 Cc01_g00160:33 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC -chr1:174580 [C/T] chr1 174580 Cc01_g00160:43 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TC TC CT -chr1:174572 [C/T] chr1 174572 Cc01_g00160:51 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TC TC CT -chr1:174565 [T/C] chr1 174565 Cc01_g00160:58 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CT TC TC -chr1:174562 [A/G] chr1 174562 Cc01_g00160:61 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA GA AA AG -chr1:174533 [C/G] chr1 174533 Cc01_g00160:90 exon SYNONYMOUS_CODING ctG/ctC L/L 25.0% 4 CC GG GG GG -chr1:174501 [C/T] chr1 174501 Cc01_g00160:122 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 37.5% 4 CC TC TT CC -chr1:174490 [C/T] chr1 174490 Cc01_g00160:133 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 4 CC TC TT TC -chr1:174472 [C/T] chr1 174472 Cc01_g00160:151 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 CC TC CC CC -chr1:174446 [T/C] chr1 174446 Cc01_g00160:177 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC -chr1:174440 [G/A] chr1 174440 Cc01_g00160:183 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 GG AG AA GG -chr1:174419 [C/T] chr1 174419 Cc01_g00160:204 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TC CT CC -chr1:174413 [G/C] chr1 174413 Cc01_g00160:210 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG -chr1:174411 [C/T] chr1 174411 Cc01_g00160:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 CC TC CT CC -chr1:174403 [T/C] chr1 174403 Cc01_g00160:220 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT CT TT TT -chr1:174401 [G/A] chr1 174401 Cc01_g00160:222 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GA AG GG -chr1:174374 [G/A] chr1 174374 Cc01_g00160:249 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG GG AA GG -chr1:174353 [G/A] chr1 174353 Cc01_g00160:270 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG -chr1:174324 [G/A] chr1 174324 Cc01_g00160:299 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 37.5% 4 GG GA GA GA -chr1:174310 [C/T] chr1 174310 Cc01_g00160:313 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 CC CT TT CT -chr1:174297 [C/T] chr1 174297 Cc01_g00160:326 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC CT -chr1:174295 [G/A] chr1 174295 Cc01_g00160:328 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GA GG GA -chr1:174280 [G/T] chr1 174280 Cc01_g00160:343 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 GG GT GT GG -chr1:174257 [G/A] chr1 174257 Cc01_g00160:366 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG GA GG -chr1:174251 [C/T] chr1 174251 Cc01_g00160:372 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CC CT CC -chr1:174248 [G/A] chr1 174248 Cc01_g00160:375 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG -chr1:174242 [A/T] chr1 174242 Cc01_g00160:381 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT -chr1:174232 [C/T] chr1 174232 Cc01_g00160:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CT CC -chr1:174225 [G/C] chr1 174225 Cc01_g00160:398 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GC GG GG -chr1:174208 [C/G] chr1 174208 Cc01_g00160:415 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 CC CG CC CC -chr1:174205 [G/A] chr1 174205 Cc01_g00160:418 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG GA AG GG -chr1:174192 [G/A] chr1 174192 Cc01_g00160:431 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG GA GA GG -chr1:174190 [G/A] chr1 174190 Cc01_g00160:433 exon STOP_GAINED Cag/Tag Q/5 25.0% 4 GG GA AG GG -chr1:174185 [A/T] chr1 174185 Cc01_g00160:438 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AT TA AA -chr1:174174 [C/T] chr1 174174 Cc01_g00160:449 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT TC CC -chr1:174172 [T/C] chr1 174172 Cc01_g00160:451 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT -chr1:174068 [G/C] chr1 174068 Cc01_g00160:555 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 16.7% 3 GG GC NN GG -chr1:174026 [G/T] chr1 174026 Cc01_g00160:597 exon NON_SYNONYMOUS_CODING agC/agA S/R 33.3% 3 GG TT NN GG -chr1:173945 [C/G] chr1 173945 Cc01_g00160:678 exon SYNONYMOUS_CODING gcG/gcC A/A 12.5% 4 CC CG CC CC -chr1:173942 [C/T] chr1 173942 Cc01_g00160:681 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT TT CT -chr1:173921 [G/A] chr1 173921 Cc01_g00160:702 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG AA AA GA -chr1:173846 [G/A] chr1 173846 Cc01_g00160:777 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 3 GG AA NN GA -chr1:173642 [A/T] chr1 173642 Cc01_g00160:981 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA TT AA AA -chr1:173627 [A/G] chr1 173627 Cc01_g00160:996 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA GG AA AA -chr1:173596 [C/A] chr1 173596 Cc01_g00160:1027 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 CC CA CC CC -chr1:173585 [G/A] chr1 173585 Cc01_g00160:1038 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AG AA AA -chr1:173444 [G/T] chr1 173444 Cc01_g00160:1179 exon SYNONYMOUS_CODING atC/atA I/I 25.0% 2 GG NN NN GT -chr1:173410 [C/T] chr1 173410 Cc01_g00160:1213 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 16.7% 3 CC CC NN CT -chr1:173230 [T/C] chr1 173230 Cc01_g00160:1393 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 16.7% 3 TT TT NN TC -chr1:173180 [C/T] chr1 173180 Cc01_g00160:1443 exon SYNONYMOUS_CODING tcG/tcA S/S 33.3% 3 CC TT NN CC -chr1:173126 [A/G] chr1 173126 Cc01_g00160:1497 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA GG AA AA -chr1:172613 [G/C] chr1 172613 Cc01_g00160:2010 exon SYNONYMOUS_CODING ctC/ctG L/L 50.0% 3 GG CC NN GC -chr1:172589 [G/T] chr1 172589 Cc01_g00160:2034 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 16.7% 3 GG GG NN TG -chr1:172499 [A/G] chr1 172499 Cc01_g00160:2124 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA NN GG AG -chr1:172355 [T/C] chr1 172355 Cc01_g00160:2268 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TC NN TT -chr1:172314 [T/C] chr1 172314 Cc01_g00160:2309 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 TT TC NN TT -chr1:172303 [G/A] chr1 172303 Cc01_g00160:2320 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 GG AA NN GG -chr1:172265 [T/C] chr1 172265 Cc01_g00160:2358 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 TT TT NN TC -chr1:172206 [G/A] chr1 172206 Cc01_g00160:2417 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 GG GA NN GG -chr1:172178 [T/C] chr1 172178 Cc01_g00160:2445 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 2 TT NN NN TC -chr1:172150 [T/C] chr1 172150 Cc01_g00160:2473 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 2 TT NN NN TC -chr1:181949 [A/C] chr1 181949 Cc01_g00170:492 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 2 AA NN NN CC -chr1:182195 [C/A] chr1 182195 Cc01_g00170:738 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 2 CC NN NN AA -chr1:182231 [G/A] chr1 182231 Cc01_g00170:774 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA -chr1:182291 [A/G] chr1 182291 Cc01_g00170:834 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 3 AA NN AG GG -chr1:182424 [G/A] chr1 182424 Cc01_g00170:861 exon SYNONYMOUS_CODING gcG/gcA A/A 33.3% 3 GG NN AA AA -chr1:182456 [A/G] chr1 182456 Cc01_g00170:893 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA NN AA AG -chr1:182483 [A/G] chr1 182483 Cc01_g00170:920 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG -chr1:182874 [A/G] chr1 182874 Cc01_g00170:1113 exon SYNONYMOUS_CODING ccA/ccG P/P 33.3% 3 AA NN AA GG -chr1:183107 [T/C] chr1 183107 Cc01_g00170:1346 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT -chr1:188621 [G/A] chr1 188621 Cc01_g00180:12 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA -chr1:188690 [C/A] chr1 188690 Cc01_g00180:81 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC -chr1:189264 [A/G] chr1 189264 Cc01_g00180:254 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AA AG AG -chr1:189346 [C/G] chr1 189346 Cc01_g00180:336 exon SYNONYMOUS_CODING cgC/cgG R/R 25.0% 4 CC GG GG GG -chr1:189357 [G/A] chr1 189357 Cc01_g00180:347 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA -chr1:189499 [G/C] chr1 189499 Cc01_g00180:489 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 4 GG CC CC GG -chr1:189586 [C/T] chr1 189586 Cc01_g00180:576 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT TT CC -chr1:190066 [A/G] chr1 190066 Cc01_g00180:780 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA -chr1:190127 [T/G] chr1 190127 Cc01_g00180:841 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 TT GG GG GG -chr1:190494 [C/T] chr1 190494 Cc01_g00180:1023 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 CC TT TT TT -chr1:190503 [A/G] chr1 190503 Cc01_g00180:1032 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG -chr1:190584 [T/C] chr1 190584 Cc01_g00180:1113 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT -chr1:190662 [A/G] chr1 190662 Cc01_g00180:1191 exon SYNONYMOUS_STOP taA/taG 3/3 25.0% 4 AA AA GG AA -chr1:193899 [T/C] chr1 193899 Cc01_g00190:67 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 TT CC TT TT -chr1:193871 [T/C] chr1 193871 Cc01_g00190:95 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 TT TT CC TC -chr1:193809 [A/T] chr1 193809 Cc01_g00190:157 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA TA -chr1:193801 [G/C] chr1 193801 Cc01_g00190:165 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 GG GG GG CG -chr1:193793 [C/T] chr1 193793 Cc01_g00190:173 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC CT CC TC -chr1:193735 [C/T] chr1 193735 Cc01_g00190:231 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CT CT TC -chr1:193681 [G/C] chr1 193681 Cc01_g00190:240 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG GC GG GC -chr1:193649 [T/G] chr1 193649 Cc01_g00190:272 exon NON_SYNONYMOUS_CODING gAc/gCc D/A 12.5% 4 TT TT TT TG -chr1:193584 [G/A] chr1 193584 Cc01_g00190:337 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 25.0% 4 GG GG AA GG -chr1:193551 [T/A] chr1 193551 Cc01_g00190:370 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 TT AA TT TA -chr1:193129 [T/A] chr1 193129 Cc01_g00190:445 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 25.0% 4 TT TT AA TT -chr1:192625 [A/G] chr1 192625 Cc01_g00190:654 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AA GG AA -chr1:191959 [T/C] chr1 191959 Cc01_g00190:689 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT CC TT -chr1:191385 [T/A] chr1 191385 Cc01_g00190:915 exon SYNONYMOUS_CODING tcA/tcT S/S 25.0% 4 TT AA AA AA -chr1:191370 [A/G] chr1 191370 Cc01_g00190:930 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AA GG AA -chr1:191325 [C/T] chr1 191325 Cc01_g00190:975 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT -chr1:199253 [T/C] chr1 199253 Cc01_g00200:6 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT CC TT -chr1:199193 [G/A] chr1 199193 Cc01_g00200:66 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GG GA -chr1:199148 [T/A] chr1 199148 Cc01_g00200:111 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 12.5% 4 TT TT TT AT -chr1:199134 [G/A] chr1 199134 Cc01_g00200:125 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG AG -chr1:199093 [A/C] chr1 199093 Cc01_g00200:166 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 37.5% 4 AA CC AA CA -chr1:199078 [T/C] chr1 199078 Cc01_g00200:181 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CC TT TT -chr1:198900 [A/T] chr1 198900 Cc01_g00200:262 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 12.5% 4 AA AA AA AT -chr1:198850 [G/A] chr1 198850 Cc01_g00200:312 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG GA -chr1:198811 [A/G] chr1 198811 Cc01_g00200:351 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 AA GG AA AA -chr1:198805 [A/G] chr1 198805 Cc01_g00200:357 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA AA GG AA -chr1:198802 [C/G] chr1 198802 Cc01_g00200:360 exon SYNONYMOUS_CODING gtG/gtC V/V 25.0% 4 CC CC GG CC -chr1:197996 [A/G] chr1 197996 Cc01_g00200:615 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG -chr1:197551 [A/G] chr1 197551 Cc01_g00200:963 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG AA AA -chr1:197200 [C/T] chr1 197200 Cc01_g00200:1207 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 CC TT CT CT -chr1:197177 [C/T] chr1 197177 Cc01_g00200:1230 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC TT TT TT -chr1:196815 [C/T] chr1 196815 Cc01_g00200:1344 exon SYNONYMOUS_CODING acG/acA T/T 50.0% 4 CC CT TT CT -chr1:196570 [A/T] chr1 196570 Cc01_g00200:1485 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AA AT -chr1:196315 [G/A] chr1 196315 Cc01_g00200:1584 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG GG AA GG -chr1:196047 [G/C] chr1 196047 Cc01_g00200:1668 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 GG GG CC GG -chr1:195875 [A/G] chr1 195875 Cc01_g00200:1698 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GG AA AA -chr1:195821 [A/G] chr1 195821 Cc01_g00200:1752 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA -chr1:208818 [T/C] chr1 208818 Cc01_g00220:430 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TC TT TC -chr1:207744 [G/A] chr1 207744 Cc01_g00220:618 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG GA GG GA -chr1:207027 [T/C] chr1 207027 Cc01_g00220:756 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TC TT TT -chr1:206648 [A/G] chr1 206648 Cc01_g00220:891 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA -chr1:206440 [T/C] chr1 206440 Cc01_g00220:1099 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC -chr1:206402 [A/G] chr1 206402 Cc01_g00220:1137 exon SYNONYMOUS_CODING ccT/ccC P/P 50.0% 4 AA AA GG GG -chr1:216024 [C/T] chr1 216024 Cc01_g00230:429 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN -chr1:218860 [T/C] chr1 218860 Cc01_g00230:1338 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TT CC -chr1:218862 [G/A] chr1 218862 Cc01_g00230:1340 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 GG GG AA GG -chr1:219273 [C/T] chr1 219273 Cc01_g00230:1566 exon SYNONYMOUS_CODING tcC/tcT S/S 33.3% 3 CC NN TT TT -chr1:219413 [G/A] chr1 219413 Cc01_g00230:1605 exon SYNONYMOUS_CODING ccG/ccA P/P 50.0% 3 GG NN GA AA -chr1:219545 [T/C] chr1 219545 Cc01_g00230:1737 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC -chr1:220134 [A/G] chr1 220134 Cc01_g00230:2126 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA GG GG GG -chr1:220340 [A/G] chr1 220340 Cc01_g00230:2332 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG -chr1:221669 [G/T] chr1 221669 Cc01_g00240:79 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 GG TT TT GG -chr1:221674 [T/C] chr1 221674 Cc01_g00240:84 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT TC -chr1:221714 [G/T] chr1 221714 Cc01_g00240:124 exon NON_SYNONYMOUS_CODING Ggg/Tgg G/W 25.0% 4 GG TT GG GG -chr1:221718 [G/A] chr1 221718 Cc01_g00240:128 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GG AG -chr1:221746 [A/T] chr1 221746 Cc01_g00240:156 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 AA AT AA AA -chr1:221763 [A/T] chr1 221763 Cc01_g00240:173 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA -chr1:221788 [C/T] chr1 221788 Cc01_g00240:198 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 CC CT CC CC -chr1:221833 [T/C] chr1 221833 Cc01_g00240:243 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT CT TT TT -chr1:221852 [C/T] chr1 221852 Cc01_g00240:262 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 CC CC CC CT -chr1:221853 [G/A] chr1 221853 Cc01_g00240:263 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 GG GG GG AA -chr1:221866 [A/T] chr1 221866 Cc01_g00240:276 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT -chr1:222383 [T/C] chr1 222383 Cc01_g00240:354 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT -chr1:222633 [T/C] chr1 222633 Cc01_g00240:417 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT -chr1:222951 [T/C] chr1 222951 Cc01_g00240:534 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT -chr1:224386 [T/A] chr1 224386 Cc01_g00240:726 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT -chr1:224660 [A/T] chr1 224660 Cc01_g00240:825 exon SYNONYMOUS_CODING ggA/ggT G/G 37.5% 4 AA TT AA AT -chr1:224706 [G/C] chr1 224706 Cc01_g00240:871 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 GG GG GC GG -chr1:225032 [G/A] chr1 225032 Cc01_g00240:933 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG -chr1:225065 [C/T] chr1 225065 Cc01_g00240:966 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC TC CC CC -chr1:225194 [C/T] chr1 225194 Cc01_g00240:1008 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC TT CC CT -chr1:226501 [T/C] chr1 226501 Cc01_g00240:1072 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC CT -chr1:226539 [C/A] chr1 226539 Cc01_g00240:1110 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA -chr1:226575 [T/C] chr1 226575 Cc01_g00240:1146 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 TT TC TT TT -chr1:226694 [C/G] chr1 226694 Cc01_g00240:1181 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC -chr1:232340 [C/T] chr1 232340 Cc01_g00250:33 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CC TT CC -chr1:232292 [G/A] chr1 232292 Cc01_g00250:81 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA AA AA -chr1:229696 [A/G] chr1 229696 Cc01_g00250:380 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AA AG -chr1:228604 [A/G] chr1 228604 Cc01_g00250:468 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA -chr1:250535 [A/C] chr1 250535 Cc01_g00260:69 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC -chr1:250487 [T/A] chr1 250487 Cc01_g00260:117 exon SYNONYMOUS_CODING acA/acT T/T 12.5% 4 TT TA TT TT -chr1:250388 [G/A] chr1 250388 Cc01_g00260:216 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG AA GG GG -chr1:246857 [G/A] chr1 246857 Cc01_g00260:529 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG GA GG -chr1:246722 [T/C] chr1 246722 Cc01_g00260:584 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT CC TT TC -chr1:246700 [A/G] chr1 246700 Cc01_g00260:606 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA GA -chr1:246674 [G/C] chr1 246674 Cc01_g00260:632 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GG GG GC -chr1:244939 [T/C] chr1 244939 Cc01_g00260:648 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TC TC TT -chr1:244750 [T/C] chr1 244750 Cc01_g00260:726 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TT TC -chr1:254013 [C/T] chr1 254013 Cc01_g00270:80 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC -chr1:254369 [A/G] chr1 254369 Cc01_g00270:114 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AA AG AA -chr1:254414 [C/T] chr1 254414 Cc01_g00270:159 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC -chr1:254486 [C/T] chr1 254486 Cc01_g00270:231 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CT CC CC -chr1:256173 [C/T] chr1 256173 Cc01_g00270:426 exon SYNONYMOUS_CODING ggC/ggT G/G 50.0% 4 CC CT TT CT -chr1:256269 [T/A] chr1 256269 Cc01_g00270:522 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 TT TT TT TA -chr1:256296 [C/G] chr1 256296 Cc01_g00270:549 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CC CG CC -chr1:256351 [G/C] chr1 256351 Cc01_g00270:604 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG -chr1:269489 [G/A] chr1 269489 Cc01_g00280:101 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GG GA -chr1:269514 [T/C] chr1 269514 Cc01_g00280:126 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC CC CC -chr1:269516 [T/C] chr1 269516 Cc01_g00280:128 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT TT TC -chr1:269724 [T/C] chr1 269724 Cc01_g00280:336 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC CC CC -chr1:269781 [G/A] chr1 269781 Cc01_g00280:393 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA -chr1:269793 [T/C] chr1 269793 Cc01_g00280:405 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TT TC -chr1:269833 [G/T] chr1 269833 Cc01_g00280:445 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT -chr1:269843 [T/C] chr1 269843 Cc01_g00280:455 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 TT TT TT CT -chr1:269847 [C/T] chr1 269847 Cc01_g00280:459 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CC CC CT -chr1:269904 [T/C] chr1 269904 Cc01_g00280:516 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC -chr1:269928 [C/T] chr1 269928 Cc01_g00280:540 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT -chr1:270027 [G/T] chr1 270027 Cc01_g00280:639 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT -chr1:270312 [A/C] chr1 270312 Cc01_g00280:924 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 AA AA CC AA -chr1:270383 [G/C] chr1 270383 Cc01_g00280:995 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GG GC -chr1:270395 [G/T] chr1 270395 Cc01_g00280:1007 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GG GT GG -chr1:270483 [T/C] chr1 270483 Cc01_g00280:1095 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TT TT TC -chr1:276780 [A/C] chr1 276780 Cc01_g00290:10 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 AA CC CC CC -chr1:274650 [T/G] chr1 274650 Cc01_g00290:196 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT -chr1:274413 [T/A] chr1 274413 Cc01_g00290:433 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TA TT -chr1:274345 [A/G] chr1 274345 Cc01_g00290:501 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA -chr1:273652 [G/A] chr1 273652 Cc01_g00290:639 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA GG GA -chr1:273576 [C/T] chr1 273576 Cc01_g00290:715 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC CC TT CC -chr1:273394 [C/T] chr1 273394 Cc01_g00290:897 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC CC TT CT -chr1:273220 [G/A] chr1 273220 Cc01_g00290:1071 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GG GA GG -chr1:273180 [C/G] chr1 273180 Cc01_g00290:1111 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 37.5% 4 CC CC GG CG -chr1:273178 [G/A] chr1 273178 Cc01_g00290:1113 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GG AA GA -chr1:288461 [C/T] chr1 288461 Cc01_g00300:50 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC -chr1:288120 [G/A] chr1 288120 Cc01_g00300:228 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 GG GG GA GG -chr1:287468 [G/A] chr1 287468 Cc01_g00300:469 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG GG AA GG -chr1:287403 [A/G] chr1 287403 Cc01_g00300:534 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA GG GG GG -chr1:287370 [C/T] chr1 287370 Cc01_g00300:567 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT -chr1:286545 [A/G] chr1 286545 Cc01_g00300:774 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA AA GG AA -chr1:286507 [G/A] chr1 286507 Cc01_g00300:812 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 37.5% 4 GG AA GG GA -chr1:286482 [G/C] chr1 286482 Cc01_g00300:837 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GG GG CG -chr1:285910 [C/A] chr1 285910 Cc01_g00300:942 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 CC AA CC AA -chr1:285897 [A/G] chr1 285897 Cc01_g00300:955 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG -chr1:285722 [T/G] chr1 285722 Cc01_g00300:1031 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 25.0% 4 TT TT GG TT -chr1:283896 [T/C] chr1 283896 Cc01_g00300:1335 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TT TC -chr1:283878 [G/A] chr1 283878 Cc01_g00300:1353 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG AA AA AA -chr1:283455 [A/T] chr1 283455 Cc01_g00300:1569 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AT AA AA -chr1:283107 [T/C] chr1 283107 Cc01_g00300:1682 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TC TT TT -chr1:280180 [T/C] chr1 280180 Cc01_g00300:1872 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC CC CC -chr1:293608 [T/C] chr1 293608 Cc01_g00310:9 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC -chr1:293593 [G/A] chr1 293593 Cc01_g00310:24 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA GA GA -chr1:293581 [A/T] chr1 293581 Cc01_g00310:36 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA AT AT AT -chr1:293556 [G/A] chr1 293556 Cc01_g00310:61 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 GG GA GA GA -chr1:293548 [G/A] chr1 293548 Cc01_g00310:69 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 GG GG GA GG -chr1:293524 [A/G] chr1 293524 Cc01_g00310:93 exon SYNONYMOUS_CODING aaT/aaC N/N 37.5% 4 AA GG GG AG -chr1:290571 [T/C] chr1 290571 Cc01_g00310:310 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT -chr1:300689 [C/A] chr1 300689 Cc01_g00320:60 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 CC CC CC CA -chr1:300911 [G/T] chr1 300911 Cc01_g00320:111 exon SYNONYMOUS_CODING cgG/cgT R/R 25.0% 4 GG TT TT TT -chr1:301164 [A/C] chr1 301164 Cc01_g00320:219 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA -chr1:301180 [G/T] chr1 301180 Cc01_g00320:235 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG -chr1:304719 [T/A] chr1 304719 Cc01_g00320:558 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TT TA -chr1:304779 [A/C] chr1 304779 Cc01_g00320:618 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 AA AA AC AA -chr1:329247 [C/A] chr1 329247 Cc01_g00330:270 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC AA CC CC -chr1:329217 [G/A] chr1 329217 Cc01_g00330:300 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG AA GA GA -chr1:329108 [G/A] chr1 329108 Cc01_g00330:409 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GA GG GG -chr1:329088 [A/G] chr1 329088 Cc01_g00330:429 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA -chr1:328149 [A/G] chr1 328149 Cc01_g00330:456 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA GA AA -chr1:328065 [T/G] chr1 328065 Cc01_g00330:540 exon SYNONYMOUS_CODING tcA/tcC S/S 50.0% 4 TT GG TG TG -chr1:327708 [A/C] chr1 327708 Cc01_g00330:644 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 12.5% 4 AA AC AA AA -chr1:327632 [C/T] chr1 327632 Cc01_g00330:720 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC TT CC CT -chr1:327519 [A/C] chr1 327519 Cc01_g00330:760 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 25.0% 4 AA CC CC CC -chr1:327109 [T/C] chr1 327109 Cc01_g00330:833 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT TT TT TC -chr1:320096 [C/G] chr1 320096 Cc01_g00330:1285 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 37.5% 4 CC GG GG CG -chr1:319913 [T/C] chr1 319913 Cc01_g00330:1358 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC -chr1:319903 [G/C] chr1 319903 Cc01_g00330:1368 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 GG GG GC GG -chr1:319887 [G/T] chr1 319887 Cc01_g00330:1384 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 GG TT GG GT -chr1:319879 [C/A] chr1 319879 Cc01_g00330:1392 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA -chr1:319682 [T/A] chr1 319682 Cc01_g00330:1589 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 TT AA AA TA -chr1:319581 [C/T] chr1 319581 Cc01_g00330:1690 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 CC CC CT CC -chr1:319379 [A/G] chr1 319379 Cc01_g00330:1892 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG -chr1:319299 [A/C] chr1 319299 Cc01_g00330:1972 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 AA AA AC AA -chr1:319123 [G/A] chr1 319123 Cc01_g00330:2148 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG -chr1:319112 [G/C] chr1 319112 Cc01_g00330:2159 exon NON_SYNONYMOUS_CODING gCc/gGc A/G 12.5% 4 GG GG GC GG -chr1:319087 [C/A] chr1 319087 Cc01_g00330:2184 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CC CA -chr1:319073 [G/A] chr1 319073 Cc01_g00330:2198 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 GG GG GG GA -chr1:319033 [A/G] chr1 319033 Cc01_g00330:2238 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA -chr1:317552 [C/T] chr1 317552 Cc01_g00330:2468 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 CC CC CT CC -chr1:315675 [A/T] chr1 315675 Cc01_g00330:2530 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT AT -chr1:315443 [G/A] chr1 315443 Cc01_g00330:2691 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG -chr1:315404 [C/T] chr1 315404 Cc01_g00330:2730 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT TT CT -chr1:315126 [A/G] chr1 315126 Cc01_g00330:2787 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 AA GG GG GG -chr1:315087 [C/G] chr1 315087 Cc01_g00330:2826 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CC CG -chr1:312979 [T/C] chr1 312979 Cc01_g00330:3198 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT -chr1:312964 [C/T] chr1 312964 Cc01_g00330:3213 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 CC TT TT CT -chr1:312879 [G/A] chr1 312879 Cc01_g00330:3298 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 37.5% 4 GG AA AA GA -chr1:312680 [G/A] chr1 312680 Cc01_g00330:3393 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 GG AA AA GA -chr1:312672 [T/A] chr1 312672 Cc01_g00330:3401 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 37.5% 4 TT AA AA TA -chr1:312546 [A/G] chr1 312546 Cc01_g00330:3527 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA -chr1:312321 [G/C] chr1 312321 Cc01_g00330:3752 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 GG GG GG GC -chr1:312307 [C/G] chr1 312307 Cc01_g00330:3766 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 50.0% 4 CC GG CG GC -chr1:312213 [G/A] chr1 312213 Cc01_g00330:3860 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG GA -chr1:312086 [T/C] chr1 312086 Cc01_g00330:3987 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT CC TC TC -chr1:311898 [T/C] chr1 311898 Cc01_g00330:4175 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC -chr1:311859 [C/T] chr1 311859 Cc01_g00330:4214 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 4 CC TT CT CT -chr1:311729 [T/C] chr1 311729 Cc01_g00330:4344 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TC TT -chr1:311665 [C/T] chr1 311665 Cc01_g00330:4408 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 CC TT CC CT -chr1:311522 [T/C] chr1 311522 Cc01_g00330:4551 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT -chr1:311476 [T/G] chr1 311476 Cc01_g00330:4597 exon NON_SYNONYMOUS_CODING Act/Cct T/P 12.5% 4 TT TT GT TT -chr1:311457 [C/A] chr1 311457 Cc01_g00330:4616 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 37.5% 4 CC AA AA CA -chr1:311357 [G/C] chr1 311357 Cc01_g00330:4716 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC -chr1:311161 [A/G] chr1 311161 Cc01_g00330:4912 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 4 AA GG AG AG -chr1:311057 [G/A] chr1 311057 Cc01_g00330:5016 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GG GA GG -chr1:311024 [T/C] chr1 311024 Cc01_g00330:5049 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TC TT -chr1:310991 [A/G] chr1 310991 Cc01_g00330:5082 exon SYNONYMOUS_CODING ggT/ggC G/G 37.5% 4 AA GG AA AG -chr1:310760 [T/C] chr1 310760 Cc01_g00330:5229 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TC TT -chr1:331033 [C/T] chr1 331033 Cc01_g00340:332 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 33.3% 3 CC TT NN TT -chr1:339763 [C/T] chr1 339763 Cc01_g00350:9 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC CT CT -chr1:339901 [G/C] chr1 339901 Cc01_g00350:147 exon SYNONYMOUS_CODING acG/acC T/T 12.5% 4 GG GG GG GC -chr1:339988 [A/G] chr1 339988 Cc01_g00350:234 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA -chr1:346095 [A/G] chr1 346095 Cc01_g00350:384 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG -chr1:346128 [C/G] chr1 346128 Cc01_g00350:417 exon NON_SYNONYMOUS_CODING atC/atG I/M 25.0% 4 CC CC GG CC -chr1:346300 [T/C] chr1 346300 Cc01_g00350:489 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT -chr1:346330 [A/G] chr1 346330 Cc01_g00350:519 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA GG AA AA -chr1:346342 [T/C] chr1 346342 Cc01_g00350:531 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT CC TT TT -chr1:349895 [T/C] chr1 349895 Cc01_g00360:87 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT CC NN NN -chr1:350036 [C/G] chr1 350036 Cc01_g00360:228 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 2 CC CG NN NN -chr1:350043 [T/C] chr1 350043 Cc01_g00360:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 50.0% 2 TT CC NN NN -chr1:350373 [G/A] chr1 350373 Cc01_g00360:565 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 16.7% 3 GG GA NN GG -chr1:350416 [A/G] chr1 350416 Cc01_g00360:608 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 50.0% 2 AA GG NN NN -chr1:350429 [T/C] chr1 350429 Cc01_g00360:621 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT TT NN CC -chr1:350537 [A/T] chr1 350537 Cc01_g00360:729 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 AA AA AA TT -chr1:350672 [G/A] chr1 350672 Cc01_g00360:864 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 2 GG GA NN NN -chr1:350729 [C/T] chr1 350729 Cc01_g00360:921 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC -chr1:350738 [A/C] chr1 350738 Cc01_g00360:930 exon SYNONYMOUS_CODING ccA/ccC P/P 25.0% 4 AA AA CC AA -chr1:351014 [T/C] chr1 351014 Cc01_g00360:1206 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 2 TT CC NN NN -chr1:351188 [G/C] chr1 351188 Cc01_g00360:1380 exon SYNONYMOUS_CODING ccG/ccC P/P 33.3% 3 GG CC NN CC -chr1:351329 [A/T] chr1 351329 Cc01_g00360:1521 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 3 AA TT NN AT -chr1:392985 [A/G] chr1 392985 Cc01_g00370:84 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA -chr1:393004 [C/T] chr1 393004 Cc01_g00370:103 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT -chr1:393006 [G/C] chr1 393006 Cc01_g00370:105 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 GG GG CG GG -chr1:393015 [G/A] chr1 393015 Cc01_g00370:114 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 GG AA AA AG -chr1:393081 [C/A] chr1 393081 Cc01_g00370:180 exon SYNONYMOUS_CODING atC/atA I/I 50.0% 3 CC NN AA CA -chr1:393089 [T/A] chr1 393089 Cc01_g00370:188 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 TT TT TT TA -chr1:393111 [C/T] chr1 393111 Cc01_g00370:210 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TT TT CT -chr1:393120 [C/T] chr1 393120 Cc01_g00370:219 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC TT TT CT -chr1:393139 [G/A] chr1 393139 Cc01_g00370:238 exon NON_SYNONYMOUS_CODING Gct/Act A/T 50.0% 4 GG AA AA GG -chr1:393271 [G/A] chr1 393271 Cc01_g00370:370 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA NN GG -chr1:393315 [G/A] chr1 393315 Cc01_g00370:414 exon SYNONYMOUS_CODING ggG/ggA G/G 16.7% 3 GG GG NN GA -chr1:393339 [G/T] chr1 393339 Cc01_g00370:438 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 50.0% 3 GG TT NN GT -chr1:393342 [G/A] chr1 393342 Cc01_g00370:441 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 GG NN NN GA -chr1:397208 [G/C] chr1 397208 Cc01_g00380:63 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG CC CC GC -chr1:397217 [T/C] chr1 397217 Cc01_g00380:72 exon SYNONYMOUS_CODING acT/acC T/T 37.5% 4 TT CC CC TC -chr1:397228 [G/T] chr1 397228 Cc01_g00380:83 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG TT TT TT -chr1:397253 [T/C] chr1 397253 Cc01_g00380:108 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC TT TT -chr1:397269 [T/A] chr1 397269 Cc01_g00380:124 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 50.0% 4 TT AA AA TT -chr1:397270 [T/C] chr1 397270 Cc01_g00380:125 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 TT CC CC TT -chr1:397361 [G/T] chr1 397361 Cc01_g00380:216 exon SYNONYMOUS_CODING gtG/gtT V/V 50.0% 4 GG GG TT TT -chr1:397547 [C/A] chr1 397547 Cc01_g00380:402 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC AA AA AA -chr1:397566 [T/G] chr1 397566 Cc01_g00380:421 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 12.5% 4 TT TT TT TG -chr1:397576 [T/C] chr1 397576 Cc01_g00380:431 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT -chr1:398909 [G/C] chr1 398909 Cc01_g00380:456 exon SYNONYMOUS_CODING ggG/ggC G/G 12.5% 4 GG GG GC GG -chr1:398940 [A/G] chr1 398940 Cc01_g00380:487 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG GA AA -chr1:398942 [C/T] chr1 398942 Cc01_g00380:489 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC TT TC CC -chr1:398951 [C/T] chr1 398951 Cc01_g00380:498 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC TT TC CC -chr1:399320 [T/C] chr1 399320 Cc01_g00380:867 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT -chr1:399344 [C/T] chr1 399344 Cc01_g00380:891 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC -chr1:399368 [C/T] chr1 399368 Cc01_g00380:915 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT TT TT -chr1:399404 [A/T] chr1 399404 Cc01_g00380:951 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA -chr1:399453 [T/G] chr1 399453 Cc01_g00380:1000 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 25.0% 4 TT GG GG GG -chr1:399557 [C/T] chr1 399557 Cc01_g00380:1104 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC -chr1:399739 [C/G] chr1 399739 Cc01_g00380:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC -chr1:399765 [C/T] chr1 399765 Cc01_g00380:1312 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT -chr1:399795 [C/A] chr1 399795 Cc01_g00380:1342 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CC CC AC -chr1:399796 [A/G] chr1 399796 Cc01_g00380:1343 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 25.0% 4 AA AA AA GG -chr1:399801 [A/G] chr1 399801 Cc01_g00380:1348 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 4 AA GG AA GG -chr1:399809 [C/G] chr1 399809 Cc01_g00380:1356 exon SYNONYMOUS_CODING gtC/gtG V/V 37.5% 4 CC GG CC GC -chr1:420355 [T/C] chr1 420355 Cc01_g00390:538 exon SYNONYMOUS_CODING Tta/Cta L/L 50.0% 2 TT NN NN CC -chr1:421363 [C/T] chr1 421363 Cc01_g00390:1546 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 CC NN NN TT -chr1:421532 [A/C] chr1 421532 Cc01_g00390:1715 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 37.5% 4 AA CC CC AC -chr1:421534 [A/G] chr1 421534 Cc01_g00390:1717 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA AG AG AA -chr1:421540 [G/A] chr1 421540 Cc01_g00390:1723 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 GG AG AG GA -chr1:421556 [T/A] chr1 421556 Cc01_g00390:1739 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 TT TT TA TT -chr1:421570 [T/C] chr1 421570 Cc01_g00390:1753 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 TT TC TT TT -chr1:421572 [C/T] chr1 421572 Cc01_g00390:1755 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT -chr1:421577 [C/T] chr1 421577 Cc01_g00390:1760 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 CC CC CC CT -chr1:421612 [A/G] chr1 421612 Cc01_g00390:1795 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 AA AA AG AA -chr1:422090 [G/C] chr1 422090 Cc01_g00390:2123 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 33.3% 3 GG NN CC GG -chr1:422353 [G/A] chr1 422353 Cc01_g00390:2386 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN NN GA -chr1:422467 [C/G] chr1 422467 Cc01_g00390:2500 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 33.3% 3 CC NN CC GG -chr1:422483 [C/A] chr1 422483 Cc01_g00390:2516 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 CC NN AA CC -chr1:422740 [G/T] chr1 422740 Cc01_g00390:2686 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 25.0% 2 GG NN NN GT -chr1:422742 [T/G] chr1 422742 Cc01_g00390:2688 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 2 TT NN NN TG -chr1:422746 [A/T] chr1 422746 Cc01_g00390:2692 exon STOP_GAINED Aaa/Taa K/8 25.0% 2 AA NN NN AT -chr1:422747 [A/C] chr1 422747 Cc01_g00390:2693 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 25.0% 2 AA NN NN AC -chr1:422885 [A/C] chr1 422885 Cc01_g00390:2831 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 33.3% 3 AA CC NN AA -chr1:445244 [A/G] chr1 445244 Cc01_g00410:59 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG -chr1:445214 [A/T] chr1 445214 Cc01_g00410:89 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 37.5% 4 AA TT AT AA -chr1:445148 [T/G] chr1 445148 Cc01_g00410:155 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 16.7% 3 TT TG NN TT -chr1:445013 [T/C] chr1 445013 Cc01_g00410:185 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TC TT TT -chr1:444990 [C/T] chr1 444990 Cc01_g00410:208 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT -chr1:444968 [G/A] chr1 444968 Cc01_g00410:230 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 GG GG GA GG -chr1:444952 [A/G] chr1 444952 Cc01_g00410:246 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG -chr1:444930 [G/A] chr1 444930 Cc01_g00410:268 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA -chr1:444929 [T/C] chr1 444929 Cc01_g00410:269 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC -chr1:444921 [T/C] chr1 444921 Cc01_g00410:277 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT TC TT CT -chr1:444904 [G/A] chr1 444904 Cc01_g00410:294 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA -chr1:444879 [G/A] chr1 444879 Cc01_g00410:319 exon STOP_GAINED Cag/Tag Q/7 12.5% 4 GG GG GG GA -chr1:561287 [C/G] chr1 561287 Cc01_g00420:1568 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 2 CC NN NN GG -chr1:562257 [A/G] chr1 562257 Cc01_g00420:2449 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA GG NN AA -chr1:562260 [A/G] chr1 562260 Cc01_g00420:2452 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA GG NN AA -chr1:562358 [T/C] chr1 562358 Cc01_g00420:2550 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 2 TT NN NN TC -chr1:563082 [G/C] chr1 563082 Cc01_g00420:3274 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 33.3% 3 GG CC NN GG -chr1:563087 [A/G] chr1 563087 Cc01_g00420:3279 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA GG NN AA -chr1:563172 [C/T] chr1 563172 Cc01_g00420:3364 exon SYNONYMOUS_CODING Ctg/Ttg L/L 16.7% 3 CC CC NN CT -chr1:563178 [G/A] chr1 563178 Cc01_g00420:3370 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 16.7% 3 GG GG NN GA -chr1:563217 [A/G] chr1 563217 Cc01_g00420:3409 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 33.3% 3 AA NN GG AA -chr1:563316 [A/G] chr1 563316 Cc01_g00420:3439 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 AA NN AA GG -chr1:563359 [C/A] chr1 563359 Cc01_g00420:3482 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 50.0% 2 CC NN AA NN -chr1:563503 [T/C] chr1 563503 Cc01_g00420:3626 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT TT TC TC -chr1:563700 [T/A] chr1 563700 Cc01_g00420:3784 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 2 TT NN NN AA -chr1:563763 [G/A] chr1 563763 Cc01_g00420:3847 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG -chr1:563764 [A/T] chr1 563764 Cc01_g00420:3848 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 25.0% 4 AA TT AA AA -chr1:563780 [G/C] chr1 563780 Cc01_g00420:3864 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG GG GG CC -chr1:563788 [G/A] chr1 563788 Cc01_g00420:3872 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG AA GG GG -chr1:563836 [T/C] chr1 563836 Cc01_g00420:3920 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN -chr1:564119 [C/T] chr1 564119 Cc01_g00420:4122 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 2 CC NN TT NN -chr1:564245 [G/A] chr1 564245 Cc01_g00420:4248 exon SYNONYMOUS_CODING ggG/ggA G/G 50.0% 2 GG NN AA NN -chr1:564250 [A/C] chr1 564250 Cc01_g00420:4253 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 50.0% 2 AA NN CC NN -chr1:564302 [A/G] chr1 564302 Cc01_g00420:4305 exon SYNONYMOUS_CODING tcA/tcG S/S 50.0% 4 AA GG GG AA -chr1:564307 [C/T] chr1 564307 Cc01_g00420:4310 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 33.3% 3 CC NN TT CC -chr1:564313 [T/A] chr1 564313 Cc01_g00420:4316 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TT TT AA -chr1:564315 [G/T] chr1 564315 Cc01_g00420:4318 exon NON_SYNONYMOUS_CODING Gac/Tac D/Y 12.5% 4 GG GG GG GT -chr1:564335 [C/G] chr1 564335 Cc01_g00420:4338 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC -chr1:564360 [T/G] chr1 564360 Cc01_g00420:4363 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 33.3% 3 TT GG NN GG -chr1:564391 [G/T] chr1 564391 Cc01_g00420:4394 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 33.3% 3 GG GG NN TT -chr1:564393 [C/G] chr1 564393 Cc01_g00420:4396 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 16.7% 3 CC CG NN CC -chr1:564416 [T/C] chr1 564416 Cc01_g00420:4419 exon SYNONYMOUS_CODING tcT/tcC S/S 33.3% 3 TT CC NN CC -chr1:564424 [C/A] chr1 564424 Cc01_g00420:4427 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 2 CC CA NN NN -chr1:564550 [T/A] chr1 564550 Cc01_g00420:4553 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 TT AA AA NN -chr1:624837 [T/G] chr1 624837 Cc01_g00430:60 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG -chr1:624841 [C/G] chr1 624841 Cc01_g00430:64 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 2 CC NN NN GG -chr1:625917 [T/G] chr1 625917 Cc01_g00430:987 exon SYNONYMOUS_CODING ctT/ctG L/L 50.0% 2 TT NN NN GG -chr1:625940 [G/C] chr1 625940 Cc01_g00430:1010 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 50.0% 2 GG NN NN CC -chr1:626077 [A/C] chr1 626077 Cc01_g00430:1147 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 50.0% 2 AA CC NN NN -chr1:626259 [G/A] chr1 626259 Cc01_g00430:1329 exon SYNONYMOUS_CODING ctG/ctA L/L 25.0% 2 GG NN NN GA -chr1:626317 [G/C] chr1 626317 Cc01_g00430:1387 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG NN NN GC -chr1:626491 [A/G] chr1 626491 Cc01_g00430:1561 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG -chr1:626499 [A/T] chr1 626499 Cc01_g00430:1569 exon SYNONYMOUS_CODING ccA/ccT P/P 50.0% 2 AA NN NN TT -chr1:626536 [C/T] chr1 626536 Cc01_g00430:1606 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC NN TT NN -chr1:626555 [C/G] chr1 626555 Cc01_g00430:1625 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN -chr1:626820 [T/C] chr1 626820 Cc01_g00430:1857 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TT TC -chr1:626826 [A/T] chr1 626826 Cc01_g00430:1863 exon SYNONYMOUS_CODING ccA/ccT P/P 16.7% 3 AA NN AA AT -chr1:626895 [G/A] chr1 626895 Cc01_g00430:1932 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN AA NN -chr1:626907 [G/A] chr1 626907 Cc01_g00430:1944 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG -chr1:626917 [T/C] chr1 626917 Cc01_g00430:1954 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TC TT -chr1:626930 [G/C] chr1 626930 Cc01_g00430:1967 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 GG GG GG GC -chr1:626944 [G/A] chr1 626944 Cc01_g00430:1981 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG GA AG GG -chr1:626953 [G/A] chr1 626953 Cc01_g00430:1990 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA AA AG -chr1:626958 [A/C] chr1 626958 Cc01_g00430:1995 exon NON_SYNONYMOUS_CODING ttA/ttC L/F 12.5% 4 AA AA AC AA -chr1:626960 [T/G] chr1 626960 Cc01_g00430:1997 exon NON_SYNONYMOUS_CODING gTg/gGg V/G 25.0% 4 TT TG GT TT -chr1:626962 [A/G] chr1 626962 Cc01_g00430:1999 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 25.0% 4 AA GA AA AG -chr1:626990 [T/A] chr1 626990 Cc01_g00430:2027 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 12.5% 4 TT TT TT TA -chr1:626992 [G/A] chr1 626992 Cc01_g00430:2029 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 GG GA GG AG -chr1:627002 [G/A] chr1 627002 Cc01_g00430:2039 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG -chr1:627009 [C/T] chr1 627009 Cc01_g00430:2046 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CC TT CC -chr1:627032 [G/T] chr1 627032 Cc01_g00430:2069 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GT GG GT -chr1:627051 [A/G] chr1 627051 Cc01_g00430:2088 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA GG GG GG -chr1:627058 [G/C] chr1 627058 Cc01_g00430:2095 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG CC CC GC -chr1:627068 [C/T] chr1 627068 Cc01_g00430:2105 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC TT TT CT -chr1:627110 [C/T] chr1 627110 Cc01_g00430:2147 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CC CT -chr1:627131 [C/T] chr1 627131 Cc01_g00430:2168 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT -chr1:627366 [G/T] chr1 627366 Cc01_g00430:2307 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG TT NN NN -chr1:627379 [T/G] chr1 627379 Cc01_g00430:2320 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 2 TT GG NN NN -chr1:627697 [G/A] chr1 627697 Cc01_g00430:2548 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 2 GG NN AA NN -chr1:627713 [A/T] chr1 627713 Cc01_g00430:2564 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 50.0% 2 AA NN TT NN -chr1:627715 [G/C] chr1 627715 Cc01_g00430:2566 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN CC NN -chr1:627727 [T/C] chr1 627727 Cc01_g00430:2578 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 TT NN CC NN -chr1:627753 [T/G] chr1 627753 Cc01_g00430:2604 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 2 TT NN GG NN -chr1:627759 [C/A] chr1 627759 Cc01_g00430:2610 exon NON_SYNONYMOUS_CODING caC/caA H/Q 50.0% 2 CC NN AA NN -chr1:627760 [G/A] chr1 627760 Cc01_g00430:2611 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 2 GG NN GA NN -chr1:627858 [C/T] chr1 627858 Cc01_g00430:2709 exon SYNONYMOUS_CODING ccC/ccT P/P 50.0% 2 CC NN NN TT -chr1:694337 [T/C] chr1 694337 Cc01_g00440:1131 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT CC NN NN -chr1:694724 [A/C] chr1 694724 Cc01_g00440:1518 exon SYNONYMOUS_CODING gtA/gtC V/V 50.0% 2 AA NN NN CC -chr1:694734 [G/A] chr1 694734 Cc01_g00440:1528 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA -chr1:695273 [C/G] chr1 695273 Cc01_g00440:2067 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 2 CC NN NN CG -chr1:695280 [A/G] chr1 695280 Cc01_g00440:2074 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN NN GG -chr1:695301 [T/A] chr1 695301 Cc01_g00440:2095 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 25.0% 2 TT NN NN TA -chr1:695306 [A/G] chr1 695306 Cc01_g00440:2100 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 2 AA NN NN AG -chr1:695389 [A/C] chr1 695389 Cc01_g00440:2183 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AC AC -chr1:695751 [A/G] chr1 695751 Cc01_g00440:2506 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 50.0% 4 AA GG AA GG -chr1:696170 [A/G] chr1 696170 Cc01_g00440:2790 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG -chr1:696187 [A/T] chr1 696187 Cc01_g00440:2807 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 50.0% 2 AA NN NN TT -chr1:696190 [T/C] chr1 696190 Cc01_g00440:2810 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 TT NN NN CC -chr1:696193 [C/A] chr1 696193 Cc01_g00440:2813 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 50.0% 2 CC NN NN AA -chr1:696194 [A/G] chr1 696194 Cc01_g00440:2814 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 2 AA NN NN GG -chr1:696282 [A/T] chr1 696282 Cc01_g00440:2902 exon NON_SYNONYMOUS_CODING Act/Tct T/S 50.0% 2 AA NN NN TT -chr1:696283 [C/T] chr1 696283 Cc01_g00440:2903 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 CC NN NN TT -chr1:696299 [T/A] chr1 696299 Cc01_g00440:2919 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 2 TT NN NN TA -chr1:696368 [T/G] chr1 696368 Cc01_g00440:2988 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 2 TT NN NN GG -chr1:696565 [A/G] chr1 696565 Cc01_g00440:3131 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN GG AA -chr1:696569 [C/T] chr1 696569 Cc01_g00440:3135 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC NN TT CC -chr1:696578 [G/A] chr1 696578 Cc01_g00440:3144 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG NN AA GG -chr1:696580 [A/G] chr1 696580 Cc01_g00440:3146 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 33.3% 3 AA NN GG AA -chr1:696589 [A/T] chr1 696589 Cc01_g00440:3155 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA NN TT AA -chr1:696664 [C/A] chr1 696664 Cc01_g00440:3230 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC AA CC NN -chr1:698121 [T/A] chr1 698121 Cc01_g00450:9 exon STOP_GAINED taT/taA Y3* 25.0% 4 TT TA TT TA -chr1:698290 [C/A] chr1 698290 Cc01_g00450:59 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 12.5% 4 CC CC CC CA -chr1:698302 [A/G] chr1 698302 Cc01_g00450:71 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AG AG AA -chr1:698316 [G/T] chr1 698316 Cc01_g00450:85 exon STOP_GAINED Gga/Tga G/9 37.5% 4 GG TG TG TG -chr1:698328 [G/A] chr1 698328 Cc01_g00450:97 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AG GA GA -chr1:698331 [A/G] chr1 698331 Cc01_g00450:100 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 37.5% 4 AA GA AG AG -chr1:698332 [G/A] chr1 698332 Cc01_g00450:101 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 37.5% 4 GG GA AG AG -chr1:698333 [A/G] chr1 698333 Cc01_g00450:102 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG -chr1:698339 [A/G] chr1 698339 Cc01_g00450:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG GG GG -chr1:698350 [C/T] chr1 698350 Cc01_g00450:119 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 37.5% 4 CC TC CT CT -chr1:698355 [A/G] chr1 698355 Cc01_g00450:124 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG -chr1:698372 [C/G] chr1 698372 Cc01_g00450:141 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG -chr1:698398 [T/G] chr1 698398 Cc01_g00450:167 exon STOP_GAINED tTa/tGa L/6 33.3% 3 TT TT NN GG -chr1:698411 [T/C] chr1 698411 Cc01_g00450:180 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC TT TT -chr1:698426 [G/A] chr1 698426 Cc01_g00450:195 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG GA GG GA -chr1:698432 [G/A] chr1 698432 Cc01_g00450:201 exon STOP_GAINED tgG/tgA W/7 50.0% 4 GG AA GA GA -chr1:698434 [A/G] chr1 698434 Cc01_g00450:203 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 AA GG GG AG -chr1:714525 [A/G] chr1 714525 Cc01_g00470:91 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN GG NN -chr1:714606 [C/A] chr1 714606 Cc01_g00470:172 exon NON_SYNONYMOUS_CODING Cgt/Agt R/S 50.0% 4 CC AA CC AA -chr1:714611 [G/A] chr1 714611 Cc01_g00470:177 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG GG AA GG -chr1:714616 [T/A] chr1 714616 Cc01_g00470:182 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 33.3% 3 TT NN TT AA -chr1:714635 [G/A] chr1 714635 Cc01_g00470:201 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG NN AA AA -chr1:714636 [C/G] chr1 714636 Cc01_g00470:202 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 33.3% 3 CC NN GG GG -chr1:715733 [C/G] chr1 715733 Cc01_g00470:1198 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 50.0% 4 CC GG GG CC -chr1:715736 [T/G] chr1 715736 Cc01_g00470:1201 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 TT TT TT TG -chr1:715743 [C/A] chr1 715743 Cc01_g00470:1208 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 50.0% 4 CC AA AA CC -chr1:715749 [G/T] chr1 715749 Cc01_g00470:1214 exon NON_SYNONYMOUS_CODING cGc/cTc R/L 50.0% 4 GG TT TT GG -chr1:715750 [C/T] chr1 715750 Cc01_g00470:1215 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CC CC TC -chr1:715751 [G/A] chr1 715751 Cc01_g00470:1216 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA -chr1:715769 [G/A] chr1 715769 Cc01_g00470:1234 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 2 GG NN NN GA -chr1:715779 [A/G] chr1 715779 Cc01_g00470:1244 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA NN NN GG -chr1:715853 [G/C] chr1 715853 Cc01_g00470:1318 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 50.0% 2 GG NN NN CC -chr1:716060 [A/C] chr1 716060 Cc01_g00470:1525 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 50.0% 2 AA NN CC NN -chr1:716123 [G/A] chr1 716123 Cc01_g00470:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG NN AA NN -chr1:716482 [G/A] chr1 716482 Cc01_g00470:1836 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA GG -chr1:716498 [G/C] chr1 716498 Cc01_g00470:1852 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC -chr1:716510 [G/A] chr1 716510 Cc01_g00470:1864 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA -chr1:716535 [A/G] chr1 716535 Cc01_g00470:1889 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG AA AA -chr1:716594 [T/C] chr1 716594 Cc01_g00470:1948 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 37.5% 4 TT CC TC CC -chr1:716622 [A/G] chr1 716622 Cc01_g00470:1976 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 12.5% 4 AA AA AA AG -chr1:716696 [C/T] chr1 716696 Cc01_g00470:2050 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 33.3% 3 CC NN TT CC -chr1:716714 [G/C] chr1 716714 Cc01_g00470:2068 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 16.7% 3 GG NN GG GC -chr1:716724 [A/G] chr1 716724 Cc01_g00470:2078 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 3 AA NN GG AG -chr1:716729 [G/C] chr1 716729 Cc01_g00470:2083 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 33.3% 3 GG NN CC GG -chr1:716741 [G/A] chr1 716741 Cc01_g00470:2095 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 2 GG NN NN AA -chr1:716770 [C/T] chr1 716770 Cc01_g00470:2124 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 2 CC NN NN TT -chr1:716789 [C/A] chr1 716789 Cc01_g00470:2143 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 50.0% 2 CC NN NN AA -chr1:716793 [C/A] chr1 716793 Cc01_g00470:2147 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 2 CC NN NN CA -chr1:716863 [T/C] chr1 716863 Cc01_g00470:2217 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 TT NN CC TT -chr1:716867 [G/C] chr1 716867 Cc01_g00470:2221 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG NN CC GG -chr1:716879 [A/T] chr1 716879 Cc01_g00470:2233 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA NN AA AT -chr1:716880 [A/T] chr1 716880 Cc01_g00470:2234 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 33.3% 3 AA NN TT AA -chr1:717010 [T/C] chr1 717010 Cc01_g00470:2364 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC -chr1:717382 [A/G] chr1 717382 Cc01_g00470:2502 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA NN AA AG -chr1:717405 [A/G] chr1 717405 Cc01_g00470:2525 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AA AA AG -chr1:718555 [G/T] chr1 718555 Cc01_g00480:7 exon STOP_GAINED Gga/Tga G3* 50.0% 4 GG TT GT GT -chr1:718570 [A/G] chr1 718570 Cc01_g00480:22 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 25.0% 4 AA GG GG GG -chr1:718578 [A/G] chr1 718578 Cc01_g00480:30 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG GG GG -chr1:718579 [A/G] chr1 718579 Cc01_g00480:31 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG -chr1:718589 [T/C] chr1 718589 Cc01_g00480:41 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 TT TC CT CT -chr1:718602 [A/G] chr1 718602 Cc01_g00480:54 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA -chr1:718616 [A/G] chr1 718616 Cc01_g00480:68 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA GA AG AG -chr1:718623 [A/G] chr1 718623 Cc01_g00480:75 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GA AG AG -chr1:718626 [A/C] chr1 718626 Cc01_g00480:78 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 37.5% 4 AA AC CA CA -chr1:718632 [A/G] chr1 718632 Cc01_g00480:84 exon SYNONYMOUS_CODING ggA/ggG G/G 37.5% 4 AA GG GG GA -chr1:718633 [C/T] chr1 718633 Cc01_g00480:85 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT -chr1:718636 [G/A] chr1 718636 Cc01_g00480:88 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG AG GA GA -chr1:718676 [A/G] chr1 718676 Cc01_g00480:128 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA GA AA AA -chr1:719091 [T/A] chr1 719091 Cc01_g00480:135 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA AT TT -chr1:720709 [G/A] chr1 720709 Cc01_g00490:200 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 33.3% 3 GG NN AA AA -chr1:757845 [A/T] chr1 757845 Cc01_g00500:54 exon SYNONYMOUS_CODING acT/acA T/T 50.0% 3 AA TT AT NN -chr1:757827 [A/T] chr1 757827 Cc01_g00500:72 exon SYNONYMOUS_CODING acT/acA T/T 37.5% 4 AA TT AT TT -chr1:757176 [T/A] chr1 757176 Cc01_g00500:160 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 TT TT TT TA -chr1:757171 [A/C] chr1 757171 Cc01_g00500:165 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 AA AC AC CA -chr1:757169 [C/G] chr1 757169 Cc01_g00500:167 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC GC CC -chr1:757141 [T/C] chr1 757141 Cc01_g00500:195 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC -chr1:756891 [T/C] chr1 756891 Cc01_g00500:213 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT CT TT TT -chr1:756475 [G/A] chr1 756475 Cc01_g00500:399 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA -chr1:756448 [T/C] chr1 756448 Cc01_g00500:426 exon SYNONYMOUS_CODING tcA/tcG S/S 33.3% 3 TT NN TT CC -chr1:763230 [A/C] chr1 763230 Cc01_g00510:245 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 50.0% 2 AA NN NN CC -chr1:765710 [A/G] chr1 765710 Cc01_g00520:150 exon SYNONYMOUS_CODING acA/acG T/T 50.0% 3 AA NN AG GG -chr1:765774 [C/G] chr1 765774 Cc01_g00520:214 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 50.0% 2 CC NN NN GG -chr1:767708 [C/T] chr1 767708 Cc01_g00520:2019 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 3 CC TT NN CT -chr1:767754 [T/C] chr1 767754 Cc01_g00520:2065 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT -chr1:767773 [T/C] chr1 767773 Cc01_g00520:2084 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 TT TC TT TT -chr1:767784 [A/G] chr1 767784 Cc01_g00520:2095 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA GG AA AG -chr1:768089 [T/G] chr1 768089 Cc01_g00520:2142 exon NON_SYNONYMOUS_CODING agT/agG S/R 16.7% 3 TT NN TG TT -chr1:768095 [G/T] chr1 768095 Cc01_g00520:2148 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 16.7% 3 GG NN GT GG -chr1:768097 [G/T] chr1 768097 Cc01_g00520:2150 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 16.7% 3 GG NN GT GG -chr1:768140 [A/T] chr1 768140 Cc01_g00520:2193 exon SYNONYMOUS_CODING ctA/ctT L/L 50.0% 3 AA NN AT TT -chr1:768149 [G/T] chr1 768149 Cc01_g00520:2202 exon SYNONYMOUS_CODING gcG/gcT A/A 50.0% 3 GG NN GT TT -chr1:768210 [A/G] chr1 768210 Cc01_g00520:2263 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 3 AA NN AG GG -chr1:768322 [G/A] chr1 768322 Cc01_g00520:2375 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG NN GA GG -chr1:768476 [T/G] chr1 768476 Cc01_g00520:2529 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 25.0% 4 TT GG TT TT -chr1:768570 [G/A] chr1 768570 Cc01_g00520:2623 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 GG NN GA AA -chr1:768621 [A/C] chr1 768621 Cc01_g00520:2674 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 33.3% 3 AA NN CC AA -chr1:768623 [G/C] chr1 768623 Cc01_g00520:2676 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 50.0% 3 GG NN GC CC -chr1:768653 [C/T] chr1 768653 Cc01_g00520:2706 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC NN TT CC -chr1:768703 [C/T] chr1 768703 Cc01_g00520:2756 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 16.7% 3 CC NN CC CT -chr1:768709 [T/G] chr1 768709 Cc01_g00520:2762 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 16.7% 3 TT NN TT TG -chr1:768710 [T/G] chr1 768710 Cc01_g00520:2763 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 16.7% 3 TT NN TT TG -chr1:768718 [G/C] chr1 768718 Cc01_g00520:2771 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 33.3% 3 GG NN CC CC -chr1:768724 [C/T] chr1 768724 Cc01_g00520:2777 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 16.7% 3 CC NN CC CT -chr1:768748 [A/G] chr1 768748 Cc01_g00520:2801 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA NN AA GG -chr1:768806 [A/G] chr1 768806 Cc01_g00520:2859 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 3 AA NN AG GG -chr1:768948 [G/A] chr1 768948 Cc01_g00520:2917 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA AA GG -chr1:768971 [T/C] chr1 768971 Cc01_g00520:2940 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC NN TT -chr1:772576 [A/T] chr1 772576 Cc01_g00530:220 exon STOP_GAINED Aaa/Taa K/4 37.5% 4 AA TT TT AT -chr1:772604 [A/G] chr1 772604 Cc01_g00530:248 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 3 AA NN GG AG -chr1:787097 [G/A] chr1 787097 Cc01_g00550:1089 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 3 GG NN AA GA -chr1:787673 [T/G] chr1 787673 Cc01_g00550:1596 exon NON_SYNONYMOUS_CODING caT/caG H/Q 33.3% 3 TT GG NN GG -chr1:788087 [C/T] chr1 788087 Cc01_g00550:1680 exon SYNONYMOUS_CODING ctC/ctT L/L 16.7% 3 CC NN CC CT -chr1:788159 [G/A] chr1 788159 Cc01_g00550:1752 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GA GG GG -chr1:788273 [C/A] chr1 788273 Cc01_g00550:1866 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 25.0% 4 CC AA CC CC -chr1:788275 [C/T] chr1 788275 Cc01_g00550:1868 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC TT CT CT -chr1:788383 [C/G] chr1 788383 Cc01_g00550:1886 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC NN GG NN -chr1:788482 [C/T] chr1 788482 Cc01_g00550:1985 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC -chr1:788491 [G/A] chr1 788491 Cc01_g00550:1994 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 GG GG GA GG -chr1:788516 [A/G] chr1 788516 Cc01_g00550:2019 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG -chr1:788558 [A/G] chr1 788558 Cc01_g00550:2061 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 AA GG AA AA -chr1:788560 [T/C] chr1 788560 Cc01_g00550:2063 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 TT CC TT TT -chr1:788561 [C/G] chr1 788561 Cc01_g00550:2064 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG CC CC -chr1:788694 [G/A] chr1 788694 Cc01_g00550:2197 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 GG AA GG GA -chr1:788708 [G/A] chr1 788708 Cc01_g00550:2211 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG -chr1:788716 [A/C] chr1 788716 Cc01_g00550:2219 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 AA AC AA AA -chr1:836275 [A/G] chr1 836275 Cc01_g00570:39 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 2 AA NN NN AG -chr1:836319 [C/T] chr1 836319 Cc01_g00570:83 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC -chr1:836362 [T/A] chr1 836362 Cc01_g00570:126 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TA TT TT -chr1:837674 [G/C] chr1 837674 Cc01_g00570:1378 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 50.0% 2 GG NN NN CC -chr1:837956 [A/G] chr1 837956 Cc01_g00570:1660 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 AA GG NN AA -chr1:837958 [T/A] chr1 837958 Cc01_g00570:1662 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 TT AA NN TT -chr1:837989 [A/G] chr1 837989 Cc01_g00570:1693 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN -chr1:838599 [A/T] chr1 838599 Cc01_g00570:2303 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 16.7% 3 AA AA NN AT -chr1:838628 [T/C] chr1 838628 Cc01_g00570:2332 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 33.3% 3 TT CC NN CC -chr1:838667 [T/A] chr1 838667 Cc01_g00570:2338 exon NON_SYNONYMOUS_CODING Tca/Aca S/T 25.0% 2 TT TA NN NN -chr1:838670 [A/G] chr1 838670 Cc01_g00570:2341 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 AA GA NN NN -chr1:838676 [A/G] chr1 838676 Cc01_g00570:2347 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 50.0% 2 AA GG NN NN -chr1:838683 [C/G] chr1 838683 Cc01_g00570:2354 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 50.0% 2 CC GG NN NN -chr1:838689 [C/T] chr1 838689 Cc01_g00570:2360 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 33.3% 3 CC TT CC NN -chr1:838705 [C/T] chr1 838705 Cc01_g00570:2376 exon SYNONYMOUS_CODING ctC/ctT L/L 33.3% 3 CC CC TT NN -chr1:838717 [T/A] chr1 838717 Cc01_g00570:2388 exon SYNONYMOUS_CODING tcT/tcA S/S 50.0% 2 TT AA NN NN -chr1:839122 [G/A] chr1 839122 Cc01_g00570:2689 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 50.0% 2 GG AA NN NN -chr1:839352 [G/A] chr1 839352 Cc01_g00570:2919 exon SYNONYMOUS_CODING agG/agA R/R 50.0% 2 GG NN NN AA -chr1:839601 [A/T] chr1 839601 Cc01_g00570:3168 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA NN NN TT -chr1:839786 [G/A] chr1 839786 Cc01_g00570:3353 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 GG NN NN AA -chr1:839932 [G/A] chr1 839932 Cc01_g00570:3499 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 2 GG NN NN GA -chr1:928733 [T/C] chr1 928733 Cc01_g00580:26 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 TT NN TT TC -chr1:928809 [A/G] chr1 928809 Cc01_g00580:102 exon SYNONYMOUS_CODING ccA/ccG P/P 50.0% 2 AA NN NN GG -chr1:928827 [A/G] chr1 928827 Cc01_g00580:120 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 2 AA NN NN AG -chr1:928836 [A/G] chr1 928836 Cc01_g00580:129 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 2 AA NN NN GA -chr1:928904 [A/G] chr1 928904 Cc01_g00580:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 2 AA NN NN GA -chr1:966451 [A/G] chr1 966451 Cc01_g00590:185 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 2 AA NN NN GG -chr1:966652 [A/G] chr1 966652 Cc01_g00590:386 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG -chr1:966654 [A/G] chr1 966654 Cc01_g00590:388 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 2 AA NN NN GG -chr1:966661 [A/C] chr1 966661 Cc01_g00590:395 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 50.0% 2 AA NN NN CC -chr1:966719 [A/G] chr1 966719 Cc01_g00590:453 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 2 AA NN NN GG -chr1:966803 [T/C] chr1 966803 Cc01_g00590:486 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 2 TT NN NN CC -chr1:966831 [G/C] chr1 966831 Cc01_g00590:514 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GG GG GC -chr1:966834 [A/G] chr1 966834 Cc01_g00590:517 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA GG GG GG -chr1:966846 [G/A] chr1 966846 Cc01_g00590:529 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 GG AA AA AG -chr1:966866 [C/T] chr1 966866 Cc01_g00590:549 exon SYNONYMOUS_CODING cgC/cgT R/R 50.0% 2 CC NN NN TT -chr1:967049 [G/T] chr1 967049 Cc01_g00590:732 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 50.0% 2 GG NN NN TT -chr1:967059 [G/A] chr1 967059 Cc01_g00590:742 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG NN NN AA -chr1:967062 [A/G] chr1 967062 Cc01_g00590:745 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA NN NN GG -chr1:967063 [A/T] chr1 967063 Cc01_g00590:746 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 50.0% 2 AA NN NN TT -chr1:967183 [C/G] chr1 967183 Cc01_g00590:866 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 33.3% 3 CC CC NN GG -chr1:967752 [G/T] chr1 967752 Cc01_g00590:1435 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 3 GG TT NN GT -chr1:967768 [C/G] chr1 967768 Cc01_g00590:1451 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 CC GG NN GG -chr1:967992 [G/A] chr1 967992 Cc01_g00590:1675 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG NN AA AA -chr1:986447 [C/A] chr1 986447 Cc01_g00610:57 exon SYNONYMOUS_CODING cgC/cgA R/R 12.5% 4 CC CC CC CA -chr1:986448 [G/A] chr1 986448 Cc01_g00610:58 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GA GG AG -chr1:986456 [A/G] chr1 986456 Cc01_g00610:66 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG -chr1:986518 [T/G] chr1 986518 Cc01_g00610:128 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 25.0% 4 TT TG TG TT -chr1:986525 [G/T] chr1 986525 Cc01_g00610:135 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GG TG -chr1:986546 [G/A] chr1 986546 Cc01_g00610:156 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 2 GG NN NN GA -chr1:986690 [G/A] chr1 986690 Cc01_g00610:300 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 GG GG GG GA -chr1:986709 [G/A] chr1 986709 Cc01_g00610:319 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GG GA -chr1:986710 [A/T] chr1 986710 Cc01_g00610:320 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 AA AA AA AT -chr1:986736 [C/G] chr1 986736 Cc01_g00610:346 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 CC CG CC GG -chr1:987100 [C/T] chr1 987100 Cc01_g00610:546 exon SYNONYMOUS_CODING tcC/tcT S/S 16.7% 3 CC NN CC CT -chr1:987154 [T/A] chr1 987154 Cc01_g00610:600 exon NON_SYNONYMOUS_CODING agT/agA S/R 50.0% 4 TT AA TA TA -chr1:987159 [A/T] chr1 987159 Cc01_g00610:605 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA TA -chr1:987178 [A/G] chr1 987178 Cc01_g00610:624 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 4 AA GG AG AG -chr1:987200 [G/A] chr1 987200 Cc01_g00610:646 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG -chr1:987232 [T/G] chr1 987232 Cc01_g00610:678 exon SYNONYMOUS_CODING tcT/tcG S/S 50.0% 4 TT GG TG TG -chr1:987567 [A/T] chr1 987567 Cc01_g00610:1013 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 25.0% 4 AA AA AA TT -chr1:987582 [A/C] chr1 987582 Cc01_g00610:1028 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 33.3% 3 AA NN AA CC -chr1:987606 [G/A] chr1 987606 Cc01_g00610:1052 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA -chr1:987613 [T/C] chr1 987613 Cc01_g00610:1059 exon SYNONYMOUS_CODING acT/acC T/T 33.3% 3 TT NN TT CC -chr1:987648 [T/C] chr1 987648 Cc01_g00610:1094 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 16.7% 3 TT NN TT TC -chr1:987704 [A/C] chr1 987704 Cc01_g00610:1150 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 16.7% 3 AA NN AA AC -chr1:987875 [C/G] chr1 987875 Cc01_g00610:1286 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 33.3% 3 CC NN GG GG -chr1:988107 [A/G] chr1 988107 Cc01_g00610:1518 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG -chr1:988121 [A/G] chr1 988121 Cc01_g00610:1532 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 12.5% 4 AA AA AA AG -chr1:988128 [T/A] chr1 988128 Cc01_g00610:1539 exon NON_SYNONYMOUS_CODING agT/agA S/R 12.5% 4 TT TT TA TT -chr1:988129 [C/T] chr1 988129 Cc01_g00610:1540 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC TC CC TC -chr1:988136 [C/G] chr1 988136 Cc01_g00610:1547 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 CC CC CC GC -chr1:988162 [G/C] chr1 988162 Cc01_g00610:1573 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GG GC GC -chr1:997411 [A/G] chr1 997411 Cc01_g00620:25 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA NN AG AG -chr1:997409 [G/A] chr1 997409 Cc01_g00620:27 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 GG NN AA AA -chr1:997392 [T/C] chr1 997392 Cc01_g00620:44 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 TT NN TT CT -chr1:997300 [C/G] chr1 997300 Cc01_g00620:60 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC -chr1:997296 [G/A] chr1 997296 Cc01_g00620:64 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG -chr1:997213 [G/A] chr1 997213 Cc01_g00620:147 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 4 GG AA AA AA -chr1:997200 [C/A] chr1 997200 Cc01_g00620:160 exon NON_SYNONYMOUS_CODING Gcg/Tcg A/S 50.0% 3 CC AA NN CA -chr1:997185 [T/G] chr1 997185 Cc01_g00620:175 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT NN NN GG -chr1:997169 [A/G] chr1 997169 Cc01_g00620:191 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 25.0% 2 AA NN NN AG -chr1:997094 [A/G] chr1 997094 Cc01_g00620:266 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 2 AA NN NN AG -chr1:997051 [G/C] chr1 997051 Cc01_g00620:309 exon SYNONYMOUS_CODING tcC/tcG S/S 50.0% 2 GG NN NN CC -chr1:995391 [A/G] chr1 995391 Cc01_g00620:348 exon SYNONYMOUS_CODING ctT/ctC L/L 16.7% 3 AA AG NN AA -chr1:995363 [T/C] chr1 995363 Cc01_g00620:376 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 2 TT TC NN NN -chr1:994056 [G/T] chr1 994056 Cc01_g00620:1180 exon SYNONYMOUS_CODING Cgg/Agg R/R 50.0% 2 GG NN NN TT -chr1:994012 [A/C] chr1 994012 Cc01_g00620:1224 exon SYNONYMOUS_CODING cgT/cgG R/R 50.0% 2 AA NN NN CC -chr1:1105670 [T/C] chr1 1105670 Cc01_g00630:393 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT -chr1:1105722 [A/G] chr1 1105722 Cc01_g00630:445 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG GG GG -chr1:1124006 [T/C] chr1 1124006 Cc01_g00640:198 exon SYNONYMOUS_CODING atT/atC I/I 33.3% 3 TT CC NN TT -chr1:1124349 [T/C] chr1 1124349 Cc01_g00640:426 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT TT CC TT -chr1:1125855 [G/A] chr1 1125855 Cc01_g00640:1414 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GA NN GG -chr1:1125920 [T/A] chr1 1125920 Cc01_g00640:1479 exon SYNONYMOUS_CODING acT/acA T/T 33.3% 3 TT AA NN TT -chr1:1125966 [A/T] chr1 1125966 Cc01_g00640:1525 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA TT NN AA -chr1:1126013 [A/G] chr1 1126013 Cc01_g00640:1572 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA GG NN NN -chr1:1151834 [G/C] chr1 1151834 Cc01_g00670:239 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 GG GC GG GG -chr1:1153859 [G/A] chr1 1153859 Cc01_g00670:410 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GG GA -chr1:1153862 [A/G] chr1 1153862 Cc01_g00670:413 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 AA GG AG GG -chr1:1153873 [A/C] chr1 1153873 Cc01_g00670:424 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 AA AA AA AC -chr1:1154467 [T/G] chr1 1154467 Cc01_g00670:486 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT TG TG -chr1:1154473 [T/C] chr1 1154473 Cc01_g00670:492 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TT TC -chr1:1154482 [T/G] chr1 1154482 Cc01_g00670:501 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 TT TT TG TG -chr1:1154490 [C/G] chr1 1154490 Cc01_g00670:509 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 25.0% 4 CC CC CG CG -chr1:1154495 [A/G] chr1 1154495 Cc01_g00670:514 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA -chr1:1154499 [T/C] chr1 1154499 Cc01_g00670:518 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT -chr1:1154515 [C/G] chr1 1154515 Cc01_g00670:534 exon SYNONYMOUS_CODING ggC/ggG G/G 12.5% 4 CC CG CC CC -chr1:1154527 [G/T] chr1 1154527 Cc01_g00670:546 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GT GG GG -chr1:1154549 [A/G] chr1 1154549 Cc01_g00670:568 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA GA AA -chr1:1154550 [A/T] chr1 1154550 Cc01_g00670:569 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 37.5% 4 AA AT TA AT -chr1:1154579 [A/G] chr1 1154579 Cc01_g00670:598 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA -chr1:1154582 [T/G] chr1 1154582 Cc01_g00670:601 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT -chr1:1154588 [A/C] chr1 1154588 Cc01_g00670:607 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA -chr1:1154849 [G/A] chr1 1154849 Cc01_g00670:711 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GA AA -chr1:1154858 [G/A] chr1 1154858 Cc01_g00670:720 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GA GG GG -chr1:1154868 [A/G] chr1 1154868 Cc01_g00670:730 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA -chr1:1154885 [G/A] chr1 1154885 Cc01_g00670:747 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG AG GG GG -chr1:1154894 [A/G] chr1 1154894 Cc01_g00670:756 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA GA AA AA -chr1:1154916 [T/A] chr1 1154916 Cc01_g00670:778 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT AT TT TT -chr1:1154924 [T/C] chr1 1154924 Cc01_g00670:786 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT CT TT TT -chr1:1154929 [C/G] chr1 1154929 Cc01_g00670:791 exon STOP_GAINED tCa/tGa S/4 12.5% 4 CC GC CC CC -chr1:1154930 [A/G] chr1 1154930 Cc01_g00670:792 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA -chr1:1154936 [G/C] chr1 1154936 Cc01_g00670:798 exon NON_SYNONYMOUS_CODING agG/agC R/S 12.5% 4 GG CG GG GG -chr1:1154941 [T/C] chr1 1154941 Cc01_g00670:803 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT CT TT TT -chr1:1154946 [G/A] chr1 1154946 Cc01_g00670:808 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG -chr1:1154952 [A/T] chr1 1154952 Cc01_g00670:814 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 25.0% 4 AA TT AA AA -chr1:1154976 [A/G] chr1 1154976 Cc01_g00670:838 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA GA AA AA -chr1:1154985 [C/G] chr1 1154985 Cc01_g00670:847 exon NON_SYNONYMOUS_CODING Ctg/Gtg L/V 12.5% 4 CC GC CC CC -chr1:1155000 [G/A] chr1 1155000 Cc01_g00670:862 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG -chr1:1155003 [C/A] chr1 1155003 Cc01_g00670:865 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 12.5% 4 CC AC CC CC -chr1:1155015 [T/A] chr1 1155015 Cc01_g00670:877 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 TT AT TT TT -chr1:1155017 [A/G] chr1 1155017 Cc01_g00670:879 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA GA AA AA -chr1:1155021 [C/T] chr1 1155021 Cc01_g00670:883 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 CC TC CC CC -chr1:1155927 [G/A] chr1 1155927 Cc01_g00670:906 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG -chr1:1155945 [C/G] chr1 1155945 Cc01_g00670:924 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 CC CC CC CG -chr1:1155970 [G/A] chr1 1155970 Cc01_g00670:949 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG AG GG GG -chr1:1155978 [G/A] chr1 1155978 Cc01_g00670:957 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG AG GG GG -chr1:1156036 [C/G] chr1 1156036 Cc01_g00670:1015 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC GC CC CC -chr1:1156056 [G/T] chr1 1156056 Cc01_g00670:1035 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 12.5% 4 GG GG GG GT -chr1:1156075 [C/T] chr1 1156075 Cc01_g00670:1054 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 12.5% 4 CC CT CC CC -chr1:1156086 [A/T] chr1 1156086 Cc01_g00670:1065 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 AA TA AA AA -chr1:1156095 [A/G] chr1 1156095 Cc01_g00670:1074 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG GG -chr1:1156099 [A/C] chr1 1156099 Cc01_g00670:1078 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 12.5% 4 AA CA AA AA -chr1:1156677 [C/T] chr1 1156677 Cc01_g00670:1089 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CT CC CC -chr1:1156701 [T/G] chr1 1156701 Cc01_g00670:1113 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT GT TT TT -chr1:1156712 [T/A] chr1 1156712 Cc01_g00670:1124 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 12.5% 4 TT AT TT TT -chr1:1156733 [T/C] chr1 1156733 Cc01_g00670:1145 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 TT CC TC CC -chr1:1156813 [G/A] chr1 1156813 Cc01_g00670:1225 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 12.5% 4 GG GA GG GG -chr1:1156819 [A/G] chr1 1156819 Cc01_g00670:1231 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 12.5% 4 AA AG AA AA -chr1:1156820 [G/A] chr1 1156820 Cc01_g00670:1232 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG -chr1:1156883 [T/C] chr1 1156883 Cc01_g00670:1295 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT -chr1:1156892 [A/G] chr1 1156892 Cc01_g00670:1304 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA -chr1:1156901 [T/A] chr1 1156901 Cc01_g00670:1313 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TA TT TT -chr1:1156908 [C/T] chr1 1156908 Cc01_g00670:1320 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT CT -chr1:1165679 [A/T] chr1 1165679 Cc01_g00680:45 exon STOP_GAINED tgT/tgA C/5 37.5% 4 AA TT AT TT -chr1:1165649 [C/T] chr1 1165649 Cc01_g00680:75 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 CC TT CT TT -chr1:1165641 [A/G] chr1 1165641 Cc01_g00680:83 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 AA AA AG AA -chr1:1165640 [G/A] chr1 1165640 Cc01_g00680:84 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG AA AA AA -chr1:1165637 [A/G] chr1 1165637 Cc01_g00680:87 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA GG GG GG -chr1:1165630 [G/T] chr1 1165630 Cc01_g00680:94 exon NON_SYNONYMOUS_CODING Ccc/Acc P/T 25.0% 4 GG TT TT TT -chr1:1166386 [C/A] chr1 1166386 Cc01_g00690:200 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 33.3% 3 CC NN CC AA -chr1:1166466 [A/C] chr1 1166466 Cc01_g00690:280 exon NON_SYNONYMOUS_CODING Act/Cct T/P 16.7% 3 AA NN AA AC -chr1:1166542 [T/G] chr1 1166542 Cc01_g00690:356 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 33.3% 3 TT NN TT GG -chr1:1166804 [C/A] chr1 1166804 Cc01_g00690:618 exon SYNONYMOUS_CODING gcC/gcA A/A 25.0% 4 CC CC CC AA -chr1:1167034 [G/C] chr1 1167034 Cc01_g00700:60 exon NON_SYNONYMOUS_CODING agG/agC R/S 33.3% 3 GG NN GG CC -chr1:1167354 [A/G] chr1 1167354 Cc01_g00700:380 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 33.3% 3 AA NN AA GG -chr1:1167571 [G/T] chr1 1167571 Cc01_g00700:597 exon NON_SYNONYMOUS_CODING agG/agT R/S 33.3% 3 GG NN GG TT -chr1:1179790 [G/A] chr1 1179790 Cc01_g00710:105 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GG AA GG -chr1:1179828 [C/G] chr1 1179828 Cc01_g00710:143 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG GG GG -chr1:1179917 [A/T] chr1 1179917 Cc01_g00710:232 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 AA TT TT TT -chr1:1179943 [C/T] chr1 1179943 Cc01_g00710:258 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT -chr1:1179952 [T/C] chr1 1179952 Cc01_g00710:267 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC -chr1:1179953 [G/A] chr1 1179953 Cc01_g00710:268 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA -chr1:1179985 [C/T] chr1 1179985 Cc01_g00710:300 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC TT TT TT -chr1:1180012 [A/G] chr1 1180012 Cc01_g00710:327 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG GG GG -chr1:1180056 [T/C] chr1 1180056 Cc01_g00710:371 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC CC CC -chr1:1180061 [T/C] chr1 1180061 Cc01_g00710:376 exon STOP_LOST Tag/Cag 1/Q 25.0% 4 TT CC CC CC -chr1:1180063 [G/C] chr1 1180063 Cc01_g00710:378 exon STOP_LOST taG/taC 1/Y 33.3% 3 GG NN CC CC -chr1:1212493 [G/C] chr1 1212493 Cc01_g00720:7 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 33.3% 3 GG CC NN GG -chr1:1212477 [T/C] chr1 1212477 Cc01_g00720:23 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT CC TT TT -chr1:1212194 [A/T] chr1 1212194 Cc01_g00720:160 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 AA TT AA AA -chr1:1212184 [C/G] chr1 1212184 Cc01_g00720:170 exon NON_SYNONYMOUS_CODING gGg/gCg G/A 12.5% 4 CC CG CC CC -chr1:1212161 [G/A] chr1 1212161 Cc01_g00720:193 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 25.0% 4 GG AA GG GG -chr1:1212152 [A/G] chr1 1212152 Cc01_g00720:202 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG AA AA -chr1:1212124 [C/A] chr1 1212124 Cc01_g00720:230 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC -chr1:1211997 [A/T] chr1 1211997 Cc01_g00720:357 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT AA AA -chr1:1211930 [T/C] chr1 1211930 Cc01_g00720:424 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 25.0% 4 TT CC TT TT -chr1:1211567 [A/G] chr1 1211567 Cc01_g00720:530 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG AA AA -chr1:1211520 [G/T] chr1 1211520 Cc01_g00720:577 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 GG TT GG GG -chr1:1211473 [C/A] chr1 1211473 Cc01_g00720:624 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC AA CC CC -chr1:1211425 [A/G] chr1 1211425 Cc01_g00720:672 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA -chr1:1211423 [A/C] chr1 1211423 Cc01_g00720:674 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 25.0% 4 AA CC AA AA -chr1:1211422 [G/C] chr1 1211422 Cc01_g00720:675 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG CC GG GG -chr1:1211398 [G/C] chr1 1211398 Cc01_g00720:699 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 GG CC GG GG -chr1:1211397 [G/T] chr1 1211397 Cc01_g00720:700 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 GG TT GG GG -chr1:1211383 [C/T] chr1 1211383 Cc01_g00720:714 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 CC TT CC CC -chr1:1211377 [C/T] chr1 1211377 Cc01_g00720:720 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 CC TT CT CC -chr1:1211364 [T/G] chr1 1211364 Cc01_g00720:733 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 25.0% 4 TT GG TT TT -chr1:1211349 [C/T] chr1 1211349 Cc01_g00720:748 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 CC TT CT CC -chr1:1210891 [T/A] chr1 1210891 Cc01_g00720:758 exon NON_SYNONYMOUS_CODING cAt/cTt H/L 25.0% 4 TT AA TT TT -chr1:1210874 [A/G] chr1 1210874 Cc01_g00720:775 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG AA AA -chr1:1210869 [A/G] chr1 1210869 Cc01_g00720:780 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA -chr1:1210831 [T/A] chr1 1210831 Cc01_g00720:818 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 12.5% 4 TT TA TT TT -chr1:1210823 [G/A] chr1 1210823 Cc01_g00720:826 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 25.0% 4 GG AA GG GG -chr1:1210781 [C/T] chr1 1210781 Cc01_g00720:868 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC -chr1:1210772 [A/T] chr1 1210772 Cc01_g00720:877 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 25.0% 4 AA TT TT TT -chr1:1210770 [A/C] chr1 1210770 Cc01_g00720:879 exon STOP_GAINED taT/taG Y/3 25.0% 4 AA CC AA AA -chr1:1210745 [T/C] chr1 1210745 Cc01_g00720:904 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT TT CC -chr1:1210744 [A/G] chr1 1210744 Cc01_g00720:905 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 AA GG AA AA -chr1:1210728 [T/C] chr1 1210728 Cc01_g00720:921 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 TT CC TT TT -chr1:1210710 [A/T] chr1 1210710 Cc01_g00720:939 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 AA TT AA AA -chr1:1210708 [A/G] chr1 1210708 Cc01_g00720:941 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA GG AA AA -chr1:1210663 [A/G] chr1 1210663 Cc01_g00720:986 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 AA GG AA AA -chr1:1210651 [T/A] chr1 1210651 Cc01_g00720:998 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT AA TT TT -chr1:1210640 [G/C] chr1 1210640 Cc01_g00720:1009 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG CC GG GG -chr1:1210632 [A/G] chr1 1210632 Cc01_g00720:1017 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA AA AG GG -chr1:1210613 [A/T] chr1 1210613 Cc01_g00720:1036 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 AA TT AA AA -chr1:1210611 [T/C] chr1 1210611 Cc01_g00720:1038 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 TT CC TT TT -chr1:1210566 [G/A] chr1 1210566 Cc01_g00720:1083 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG AA GG GG -chr1:1210546 [T/A] chr1 1210546 Cc01_g00720:1103 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 TT AA TT TT -chr1:1210538 [C/T] chr1 1210538 Cc01_g00720:1111 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT CC CC -chr1:1210516 [T/A] chr1 1210516 Cc01_g00720:1133 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT TT AA -chr1:1210512 [C/T] chr1 1210512 Cc01_g00720:1137 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC -chr1:1210505 [C/A] chr1 1210505 Cc01_g00720:1144 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 25.0% 4 CC AA CC CC -chr1:1242676 [A/G] chr1 1242676 Cc01_g00730:1 exon START_LOST Atg/Gtg M/V 25.0% 4 AA GG AA AA -chr1:1242683 [C/T] chr1 1242683 Cc01_g00730:8 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CT CC CC -chr1:1242684 [A/G] chr1 1242684 Cc01_g00730:9 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG AA -chr1:1242698 [C/T] chr1 1242698 Cc01_g00730:23 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 12.5% 4 CC CC CT CC -chr1:1242721 [C/G] chr1 1242721 Cc01_g00730:46 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC GG CC CG -chr1:1242729 [T/G] chr1 1242729 Cc01_g00730:54 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 37.5% 4 TT GG TT TG -chr1:1242731 [C/A] chr1 1242731 Cc01_g00730:56 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 12.5% 4 CC CA CC CC -chr1:1242744 [A/T] chr1 1242744 Cc01_g00730:69 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 50.0% 4 AA TT AT AT -chr1:1242762 [T/C] chr1 1242762 Cc01_g00730:87 exon SYNONYMOUS_CODING taT/taC Y/Y 50.0% 4 TT CC TC TC -chr1:1242783 [A/G] chr1 1242783 Cc01_g00730:108 exon NON_SYNONYMOUS_CODING atA/atG I/M 50.0% 4 AA GG AG AG -chr1:1242791 [G/C] chr1 1242791 Cc01_g00730:116 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 12.5% 4 GG GC GG GG -chr1:1242950 [G/T] chr1 1242950 Cc01_g00730:275 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG TT GG GG -chr1:1243019 [G/C] chr1 1243019 Cc01_g00730:344 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 25.0% 4 GG CC GG GG -chr1:1243020 [T/A] chr1 1243020 Cc01_g00730:345 exon SYNONYMOUS_CODING cgT/cgA R/R 25.0% 4 TT AA TT TT -chr1:1244895 [G/T] chr1 1244895 Cc01_g00730:369 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 GG TT GG GG -chr1:1244933 [T/A] chr1 1244933 Cc01_g00730:407 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT AA TT TT -chr1:1245002 [C/A] chr1 1245002 Cc01_g00730:476 exon NON_SYNONYMOUS_CODING cCt/cAt P/H 25.0% 4 CC CC CC AA -chr1:1245030 [G/A] chr1 1245030 Cc01_g00730:504 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG AA GG GG -chr1:1245060 [T/A] chr1 1245060 Cc01_g00730:534 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TA TT TT -chr1:1245492 [A/G] chr1 1245492 Cc01_g00730:553 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AA AG AG -chr1:1245530 [A/G] chr1 1245530 Cc01_g00730:591 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA AA AG AG -chr1:1245533 [T/C] chr1 1245533 Cc01_g00730:594 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT -chr1:1245549 [C/A] chr1 1245549 Cc01_g00730:610 exon NON_SYNONYMOUS_CODING Ctg/Atg L/M 25.0% 4 CC CC CA CA -chr1:1245553 [A/G] chr1 1245553 Cc01_g00730:614 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG -chr1:1245566 [G/C] chr1 1245566 Cc01_g00730:627 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC GG GG -chr1:1253676 [T/C] chr1 1253676 Cc01_g00740:865 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT TC TC -chr1:1256457 [G/T] chr1 1256457 Cc01_g00750:100 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 2 GG NN NN GT -chr1:1262785 [G/T] chr1 1262785 Cc01_g00760:45 exon SYNONYMOUS_CODING tcC/tcA S/S 50.0% 2 GG NN NN TT -chr1:1269842 [C/T] chr1 1269842 Cc01_g00770:45 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC CC NN CT -chr1:1269935 [C/G] chr1 1269935 Cc01_g00770:138 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GG GG CG -chr1:1269943 [G/A] chr1 1269943 Cc01_g00770:146 exon STOP_GAINED tGg/tAg W/9 37.5% 4 GG AA AA GA -chr1:1269976 [T/C] chr1 1269976 Cc01_g00770:179 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 TT TT TC TT -chr1:1270017 [T/C] chr1 1270017 Cc01_g00770:220 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT -chr1:1270071 [A/C] chr1 1270071 Cc01_g00770:274 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 12.5% 4 AA AA AA AC -chr1:1270072 [G/A] chr1 1270072 Cc01_g00770:275 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG -chr1:1270081 [T/C] chr1 1270081 Cc01_g00770:284 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TT CT -chr1:1270085 [T/C] chr1 1270085 Cc01_g00770:288 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TT TT CT -chr1:1270104 [A/T] chr1 1270104 Cc01_g00770:307 exon NON_SYNONYMOUS_CODING Agg/Tgg R/W 12.5% 4 AA AA AT AA -chr1:1276100 [G/T] chr1 1276100 Cc01_g00770:317 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG TT TT TT -chr1:1278052 [G/A] chr1 1278052 Cc01_g00780:52 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA -chr1:1278096 [A/T] chr1 1278096 Cc01_g00780:96 exon NON_SYNONYMOUS_CODING agA/agT R/S 50.0% 4 AA TT AT AT -chr1:1278097 [A/G] chr1 1278097 Cc01_g00780:97 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 4 AA GG AG AG -chr1:1278180 [T/C] chr1 1278180 Cc01_g00780:180 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 4 TT CC CC CC -chr1:1278211 [T/C] chr1 1278211 Cc01_g00780:211 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT CC TC TT -chr1:1279216 [A/G] chr1 1279216 Cc01_g00780:409 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 25.0% 4 AA AA AG AG -chr1:1287721 [T/C] chr1 1287721 Cc01_g00790:16 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 50.0% 3 TT TC NN CC -chr1:1287672 [C/T] chr1 1287672 Cc01_g00790:31 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC CC TT CC -chr1:1287643 [T/C] chr1 1287643 Cc01_g00790:60 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT -chr1:1287637 [C/T] chr1 1287637 Cc01_g00790:66 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT -chr1:1286824 [G/A] chr1 1286824 Cc01_g00790:136 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA -chr1:1286808 [T/C] chr1 1286808 Cc01_g00790:152 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TC TT TT -chr1:1285473 [T/C] chr1 1285473 Cc01_g00790:246 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC TC CC -chr1:1285472 [G/A] chr1 1285472 Cc01_g00790:247 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG -chr1:1284801 [T/C] chr1 1284801 Cc01_g00790:399 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TC TT -chr1:1287857 [C/A] chr1 1287857 Cc01_g00800:142 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 CC NN NN AA -chr1:1287818 [C/G] chr1 1287818 Cc01_g00800:181 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 50.0% 2 CC GG NN NN -chr1:1291612 [T/C] chr1 1291612 Cc01_g00810:61 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT -chr1:1291633 [A/T] chr1 1291633 Cc01_g00810:82 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 25.0% 4 AA AA AA TT -chr1:1291665 [T/C] chr1 1291665 Cc01_g00810:114 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TT CC -chr1:1291715 [A/G] chr1 1291715 Cc01_g00810:164 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GG AG AA -chr1:1291716 [C/T] chr1 1291716 Cc01_g00810:165 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 CC CC CC TT -chr1:1291740 [G/T] chr1 1291740 Cc01_g00810:189 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG GG GG TT -chr1:1292034 [T/A] chr1 1292034 Cc01_g00810:396 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT AA AA AA -chr1:1292248 [A/G] chr1 1292248 Cc01_g00810:510 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG -chr1:1293103 [C/T] chr1 1293103 Cc01_g00810:767 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC -chr1:1293122 [C/G] chr1 1293122 Cc01_g00810:786 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC CC GG -chr1:1293811 [T/C] chr1 1293811 Cc01_g00810:813 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 TT TT TT CC -chr1:1293815 [C/A] chr1 1293815 Cc01_g00810:817 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 CC AA AA CC -chr1:1293824 [C/T] chr1 1293824 Cc01_g00810:826 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC TT TT CC -chr1:1293825 [A/G] chr1 1293825 Cc01_g00810:827 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 4 AA GG GG AA -chr1:1293978 [A/T] chr1 1293978 Cc01_g00810:882 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AA AA TT -chr1:1294013 [G/A] chr1 1294013 Cc01_g00810:917 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 GG GG GG GA -chr1:1294044 [A/T] chr1 1294044 Cc01_g00810:948 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA AA AA TT -chr1:1294134 [C/T] chr1 1294134 Cc01_g00810:1038 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CC CC TT -chr1:1294702 [C/T] chr1 1294702 Cc01_g00810:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CT CC -chr1:1294781 [G/C] chr1 1294781 Cc01_g00810:1300 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG -chr1:1294832 [A/T] chr1 1294832 Cc01_g00810:1351 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 4 AA TT TT AA -chr1:1294843 [G/T] chr1 1294843 Cc01_g00810:1362 exon SYNONYMOUS_CODING ggG/ggT G/G 25.0% 4 GG TT TT TT -chr1:1294891 [T/G] chr1 1294891 Cc01_g00810:1410 exon NON_SYNONYMOUS_CODING atT/atG I/M 37.5% 4 TT GG TG GG -chr1:1294916 [G/T] chr1 1294916 Cc01_g00810:1435 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GT GG -chr1:1299931 [A/C] chr1 1299931 Cc01_g00820:42 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 AA AC AA AC -chr1:1299953 [G/A] chr1 1299953 Cc01_g00820:64 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA -chr1:1300252 [C/T] chr1 1300252 Cc01_g00820:219 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 CC CC TT CC -chr1:1300382 [C/T] chr1 1300382 Cc01_g00820:349 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 CC CC TT CC -chr1:1300390 [T/C] chr1 1300390 Cc01_g00820:357 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TT CC TT -chr1:1300457 [T/C] chr1 1300457 Cc01_g00820:424 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT -chr1:1300540 [T/C] chr1 1300540 Cc01_g00820:507 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TT CC TT -chr1:1300948 [C/T] chr1 1300948 Cc01_g00820:915 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 CC TT TT CT -chr1:1301593 [T/C] chr1 1301593 Cc01_g00820:1152 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT CC TT -chr1:1302393 [T/C] chr1 1302393 Cc01_g00820:1332 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT -chr1:1304941 [C/T] chr1 1304941 Cc01_g00820:2055 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT TT CC -chr1:1306040 [A/T] chr1 1306040 Cc01_g00820:2256 exon SYNONYMOUS_CODING ggA/ggT G/G 25.0% 4 AA AA TT AA -chr1:1306100 [A/G] chr1 1306100 Cc01_g00820:2316 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GG AA -chr1:1306364 [T/C] chr1 1306364 Cc01_g00820:2482 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 TT TT CC TT -chr1:1306387 [A/G] chr1 1306387 Cc01_g00820:2505 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA -chr1:1307153 [T/C] chr1 1307153 Cc01_g00820:2580 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TC TT TT -chr1:1307312 [T/C] chr1 1307312 Cc01_g00820:2652 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT TT CC TT -chr1:1307738 [A/T] chr1 1307738 Cc01_g00820:2802 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA TT AA -chr1:1308482 [A/T] chr1 1308482 Cc01_g00820:2964 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AT AA AA -chr1:1308494 [G/A] chr1 1308494 Cc01_g00820:2976 exon SYNONYMOUS_CODING agG/agA R/R 16.7% 3 GG GA NN GG -chr1:1308608 [C/A] chr1 1308608 Cc01_g00830:24 exon STOP_GAINED tgC/tgA C8* 16.7% 3 CC CA NN CC -chr1:1309677 [C/G] chr1 1309677 Cc01_g00830:163 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CG CG CC -chr1:1314539 [G/A] chr1 1314539 Cc01_g00840:25 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 3 GG AA NN GA -chr1:1314673 [G/A] chr1 1314673 Cc01_g00840:159 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA -chr1:1314823 [C/G] chr1 1314823 Cc01_g00840:309 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 CC GG GG GG -chr1:1314984 [G/A] chr1 1314984 Cc01_g00840:470 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 37.5% 4 GG GG AA GA -chr1:1315015 [G/C] chr1 1315015 Cc01_g00840:501 exon SYNONYMOUS_CODING gcG/gcC A/A 37.5% 4 GG GG CC GC -chr1:1315050 [A/G] chr1 1315050 Cc01_g00840:536 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 16.7% 3 AA AG NN AA -chr1:1315120 [C/A] chr1 1315120 Cc01_g00840:606 exon SYNONYMOUS_CODING acC/acA T/T 12.5% 4 CC CC CC CA -chr1:1315139 [T/A] chr1 1315139 Cc01_g00840:625 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 16.7% 3 TT TT NN TA -chr1:1315156 [T/G] chr1 1315156 Cc01_g00840:642 exon SYNONYMOUS_CODING tcT/tcG S/S 16.7% 3 TT TT NN TG -chr1:1315218 [T/C] chr1 1315218 Cc01_g00840:704 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 3 TT NN CC TC -chr1:1315234 [C/T] chr1 1315234 Cc01_g00840:720 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC CC NN TT -chr1:1315240 [C/T] chr1 1315240 Cc01_g00840:726 exon SYNONYMOUS_CODING caC/caT H/H 33.3% 3 CC CC NN TT -chr1:1315338 [A/T] chr1 1315338 Cc01_g00840:824 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 33.3% 3 AA TT NN AA -chr1:1324380 [G/A] chr1 1324380 Cc01_g00850:82 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AA AA AA -chr1:1324392 [A/G] chr1 1324392 Cc01_g00850:94 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 37.5% 4 AA GG GG AG -chr1:1324409 [G/C] chr1 1324409 Cc01_g00850:111 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 GG GG GG CG -chr1:1326674 [T/C] chr1 1326674 Cc01_g00850:270 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT CC CC TC -chr1:1326698 [A/G] chr1 1326698 Cc01_g00850:294 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA -chr1:1327530 [G/C] chr1 1327530 Cc01_g00850:418 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 25.0% 4 GG CC CC CC -chr1:1327531 [A/G] chr1 1327531 Cc01_g00850:419 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA GG GG AG -chr1:1327575 [C/G] chr1 1327575 Cc01_g00850:463 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CC GC -chr1:1327581 [G/A] chr1 1327581 Cc01_g00850:469 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG -chr1:1327613 [C/T] chr1 1327613 Cc01_g00850:501 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC TT TT TT -chr1:1327618 [C/T] chr1 1327618 Cc01_g00850:506 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC TT TT TT -chr1:1327624 [C/A] chr1 1327624 Cc01_g00850:512 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 37.5% 4 CC AA AA CA -chr1:1327630 [G/T] chr1 1327630 Cc01_g00850:518 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 GG TT TT TT -chr1:1327639 [T/G] chr1 1327639 Cc01_g00850:527 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 TT GG GG GG -chr1:1327826 [T/C] chr1 1327826 Cc01_g00850:714 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT CC CC CC -chr1:1327904 [C/T] chr1 1327904 Cc01_g00850:792 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC TT CT CC -chr1:1328126 [A/G] chr1 1328126 Cc01_g00850:859 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AA AG -chr1:1328127 [A/T] chr1 1328127 Cc01_g00850:860 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 AA AA AA AT -chr1:1332539 [C/A] chr1 1332539 Cc01_g00860:529 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 37.5% 4 CC CA CA CA -chr1:1332405 [T/C] chr1 1332405 Cc01_g00860:663 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TC TT TT -chr1:1332138 [T/C] chr1 1332138 Cc01_g00860:930 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC -chr1:1331004 [A/G] chr1 1331004 Cc01_g00860:1047 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 AA GG AA AA -chr1:1330827 [G/A] chr1 1330827 Cc01_g00860:1224 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GA GG GG -chr1:1330803 [T/A] chr1 1330803 Cc01_g00860:1248 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 TT TA TT TT -chr1:1330755 [A/G] chr1 1330755 Cc01_g00860:1296 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AG AA AA -chr1:1349945 [T/C] chr1 1349945 Cc01_g00870:84 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TC TT -chr1:1349954 [T/C] chr1 1349954 Cc01_g00870:93 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT -chr1:1350532 [C/T] chr1 1350532 Cc01_g00870:144 exon SYNONYMOUS_CODING ggC/ggT G/G 37.5% 4 CC CC TC TT -chr1:1350732 [C/T] chr1 1350732 Cc01_g00870:344 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 37.5% 4 CC CC CT TT -chr1:1400299 [A/G] chr1 1400299 Cc01_g00880:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GG GG GG -chr1:1400306 [C/T] chr1 1400306 Cc01_g00880:30 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CC CC TT -chr1:1400308 [A/G] chr1 1400308 Cc01_g00880:32 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG -chr1:1400337 [T/G] chr1 1400337 Cc01_g00880:61 exon NON_SYNONYMOUS_CODING Tgg/Ggg W/G 25.0% 4 TT GG GG GG -chr1:1400339 [G/A] chr1 1400339 Cc01_g00880:63 exon STOP_GAINED tgG/tgA W/1 25.0% 4 GG AA AA AA -chr1:1400381 [A/C] chr1 1400381 Cc01_g00880:105 exon SYNONYMOUS_CODING ccA/ccC P/P 33.3% 3 AA CC NN CC -chr1:1410529 [A/G] chr1 1410529 Cc01_g00890:10 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 AA NN NN GG -chr1:1410533 [C/T] chr1 1410533 Cc01_g00890:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 33.3% 3 CC CC NN TT -chr1:1410555 [T/C] chr1 1410555 Cc01_g00890:36 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT CC TT TT -chr1:1410556 [T/C] chr1 1410556 Cc01_g00890:37 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 50.0% 4 TT TT CC CC -chr1:1410561 [C/T] chr1 1410561 Cc01_g00890:42 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 CC CC TT TT -chr1:1410563 [A/G] chr1 1410563 Cc01_g00890:44 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA GG GG GG -chr1:1410566 [C/T] chr1 1410566 Cc01_g00890:47 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 4 CC CC TT TT -chr1:1410569 [A/C] chr1 1410569 Cc01_g00890:50 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 25.0% 4 AA CC CC CC -chr1:1410570 [G/A] chr1 1410570 Cc01_g00890:51 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 4 GG GG AA AA -chr1:1410580 [A/C] chr1 1410580 Cc01_g00890:61 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA -chr1:1410597 [C/G] chr1 1410597 Cc01_g00890:78 exon NON_SYNONYMOUS_CODING caC/caG H/Q 25.0% 4 CC GG GG GG -chr1:1427295 [C/G] chr1 1427295 Cc01_g00900:7 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 25.0% 4 CC CG CC CG -chr1:1427282 [G/A] chr1 1427282 Cc01_g00900:20 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG AA AA GA -chr1:1427281 [G/A] chr1 1427281 Cc01_g00900:21 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GA AG -chr1:1427279 [G/A] chr1 1427279 Cc01_g00900:23 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG -chr1:1427275 [A/T] chr1 1427275 Cc01_g00900:27 exon SYNONYMOUS_CODING ccT/ccA P/P 12.5% 4 AA AA AA TA -chr1:1427274 [A/G] chr1 1427274 Cc01_g00900:28 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 AA AA AA GA -chr1:1427261 [C/A] chr1 1427261 Cc01_g00900:41 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 CC CC CC AC -chr1:1427118 [T/C] chr1 1427118 Cc01_g00900:66 exon SYNONYMOUS_CODING ttA/ttG L/L 16.7% 3 TT NN TT CT -chr1:1427056 [T/C] chr1 1427056 Cc01_g00900:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TC TC TT -chr1:1427054 [C/T] chr1 1427054 Cc01_g00900:130 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC -chr1:1427045 [G/A] chr1 1427045 Cc01_g00900:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA GA AG -chr1:1427039 [G/T] chr1 1427039 Cc01_g00900:145 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 GG TG TG GT -chr1:1427035 [G/A] chr1 1427035 Cc01_g00900:149 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 GG GA AG AG -chr1:1427030 [A/T] chr1 1427030 Cc01_g00900:154 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT AT TA -chr1:1427016 [T/C] chr1 1427016 Cc01_g00900:168 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC CT TC -chr1:1427004 [G/A] chr1 1427004 Cc01_g00900:180 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GG GG GA -chr1:1427003 [C/T] chr1 1427003 Cc01_g00900:181 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 CC CC CT CT -chr1:1426994 [A/T] chr1 1426994 Cc01_g00900:190 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 25.0% 4 AA TA AA AT -chr1:1426981 [A/G] chr1 1426981 Cc01_g00900:203 exon NON_SYNONYMOUS_CODING cTc/cCc L/P 12.5% 4 AA AA AA AG -chr1:1426962 [T/C] chr1 1426962 Cc01_g00900:222 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CT CT TC -chr1:1426958 [C/T] chr1 1426958 Cc01_g00900:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TC CC CT -chr1:1426939 [A/T] chr1 1426939 Cc01_g00900:245 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA TA AA -chr1:1426936 [A/G] chr1 1426936 Cc01_g00900:248 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA AG AA GA -chr1:1426925 [A/G] chr1 1426925 Cc01_g00900:259 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 25.0% 4 AA AA AG GA -chr1:1426907 [T/A] chr1 1426907 Cc01_g00900:277 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 25.0% 4 TT TA AT TT -chr1:1426905 [G/A] chr1 1426905 Cc01_g00900:279 exon SYNONYMOUS_CODING atC/atT I/I 25.0% 4 GG AA AA AA -chr1:1433418 [A/G] chr1 1433418 Cc01_g00910:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA -chr1:1433394 [G/A] chr1 1433394 Cc01_g00910:126 exon SYNONYMOUS_CODING ctC/ctT L/L 50.0% 4 GG GA AA GA -chr1:1433392 [C/T] chr1 1433392 Cc01_g00910:128 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 CC CT CC CT -chr1:1433373 [C/G] chr1 1433373 Cc01_g00910:147 exon SYNONYMOUS_CODING ctG/ctC L/L 12.5% 4 CC CC CG CC -chr1:1432755 [C/T] chr1 1432755 Cc01_g00910:549 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 CC CC CT CC -chr1:1432742 [C/T] chr1 1432742 Cc01_g00910:562 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CT CC CC -chr1:1432732 [C/T] chr1 1432732 Cc01_g00910:572 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 CC TC CT CC -chr1:1432730 [T/C] chr1 1432730 Cc01_g00910:574 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CT TC TT -chr1:1432728 [T/G] chr1 1432728 Cc01_g00910:576 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GT TG TT -chr1:1432698 [A/G] chr1 1432698 Cc01_g00910:606 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA GA AA AA -chr1:1432697 [A/G] chr1 1432697 Cc01_g00910:607 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA GA AA AA -chr1:1432689 [G/C] chr1 1432689 Cc01_g00910:615 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GC GG GG -chr1:1432664 [C/A] chr1 1432664 Cc01_g00910:640 exon STOP_GAINED Gag/Tag E/4 12.5% 4 CC CA CC CC -chr1:1432663 [T/A] chr1 1432663 Cc01_g00910:641 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 TT TA TT TT -chr1:1432611 [A/G] chr1 1432611 Cc01_g00910:693 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA -chr1:1432605 [G/A] chr1 1432605 Cc01_g00910:699 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG GA AA GG -chr1:1432569 [C/T] chr1 1432569 Cc01_g00910:735 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 CC CC NN CT -chr1:1500031 [G/T] chr1 1500031 Cc01_g00920:49 exon NON_SYNONYMOUS_CODING Cca/Aca P/T 37.5% 4 GG GT GG TT -chr1:1500013 [A/T] chr1 1500013 Cc01_g00920:67 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA TA AT AA -chr1:1499982 [C/T] chr1 1499982 Cc01_g00920:98 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC NN TT NN -chr1:1499966 [C/T] chr1 1499966 Cc01_g00920:114 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 2 CC NN TT NN -chr1:1499954 [T/C] chr1 1499954 Cc01_g00920:126 exon SYNONYMOUS_CODING gcA/gcG A/A 33.3% 3 TT CC CC NN -chr1:1499939 [C/T] chr1 1499939 Cc01_g00920:141 exon SYNONYMOUS_CODING ctG/ctA L/L 33.3% 3 CC TT TT NN -chr1:1499937 [T/A] chr1 1499937 Cc01_g00920:143 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 33.3% 3 TT AA AA NN -chr1:1499906 [T/C] chr1 1499906 Cc01_g00920:174 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC CC TT -chr1:1499782 [C/G] chr1 1499782 Cc01_g00920:298 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 2 CC NN CG NN -chr1:1499780 [C/G] chr1 1499780 Cc01_g00920:300 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 2 CC NN CG NN -chr1:1499449 [G/A] chr1 1499449 Cc01_g00920:631 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 50.0% 2 GG NN AA NN -chr1:1500757 [A/G] chr1 1500757 Cc01_g00930:205 exon SYNONYMOUS_CODING Ttg/Ctg L/L 16.7% 3 AA NN AA AG -chr1:1500735 [C/G] chr1 1500735 Cc01_g00930:227 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 16.7% 3 CC NN CC CG -chr1:1500625 [A/G] chr1 1500625 Cc01_g00930:337 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 2 AA NN NN AG -chr1:1500270 [T/C] chr1 1500270 Cc01_g00930:605 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TC TT -chr1:1500265 [G/T] chr1 1500265 Cc01_g00930:610 exon NON_SYNONYMOUS_CODING Cgc/Agc R/S 12.5% 4 GG GG GT GG -chr1:1500257 [C/A] chr1 1500257 Cc01_g00930:618 exon SYNONYMOUS_CODING ctG/ctT L/L 12.5% 4 CC CC CC CA -chr1:1527537 [A/C] chr1 1527537 Cc01_g00940:47 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 12.5% 4 AA AC AA AA -chr1:1527535 [G/C] chr1 1527535 Cc01_g00940:49 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG CG GC GC -chr1:1527534 [C/A] chr1 1527534 Cc01_g00940:50 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 12.5% 4 CC CC CA CC -chr1:1527525 [G/C] chr1 1527525 Cc01_g00940:59 exon STOP_GAINED tCa/tGa S/0 37.5% 4 GG CG GC GC -chr1:1527523 [C/T] chr1 1527523 Cc01_g00940:61 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 25.0% 4 CC CT CC CT -chr1:1527516 [A/G] chr1 1527516 Cc01_g00940:68 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 25.0% 4 AA AG GA AA -chr1:1527513 [T/C] chr1 1527513 Cc01_g00940:71 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC CC CC -chr1:1527501 [T/C] chr1 1527501 Cc01_g00940:83 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 25.0% 4 TT TT CT TC -chr1:1527490 [C/A] chr1 1527490 Cc01_g00940:94 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 CC CC AC CC -chr1:1527489 [A/G] chr1 1527489 Cc01_g00940:95 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA -chr1:1527479 [A/T] chr1 1527479 Cc01_g00940:105 exon NON_SYNONYMOUS_CODING agT/agA S/R 37.5% 4 AA AT TT TT -chr1:1527475 [A/G] chr1 1527475 Cc01_g00940:109 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA AG GA AA -chr1:1527337 [T/C] chr1 1527337 Cc01_g00940:124 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC CT TC -chr1:1527336 [G/A] chr1 1527336 Cc01_g00940:125 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 12.5% 4 GG GA GG GG -chr1:1527333 [G/A] chr1 1527333 Cc01_g00940:128 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG -chr1:1527325 [C/T] chr1 1527325 Cc01_g00940:136 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 CC CT CC CC -chr1:1527324 [A/G] chr1 1527324 Cc01_g00940:137 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA -chr1:1527323 [C/T] chr1 1527323 Cc01_g00940:138 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC TC -chr1:1527310 [G/T] chr1 1527310 Cc01_g00940:151 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 GG GG GG TG -chr1:1527283 [G/A] chr1 1527283 Cc01_g00940:178 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA GA GA -chr1:1527277 [T/C] chr1 1527277 Cc01_g00940:184 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 TT TT TC TT -chr1:1527264 [C/A] chr1 1527264 Cc01_g00940:197 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 CC CA CC CC -chr1:1527261 [T/C] chr1 1527261 Cc01_g00940:200 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 TT CC CC CC -chr1:1527259 [G/A] chr1 1527259 Cc01_g00940:202 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 25.0% 4 GG AA AA AA -chr1:1527237 [G/A] chr1 1527237 Cc01_g00940:224 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 GG GG GA AG -chr1:1527236 [C/T] chr1 1527236 Cc01_g00940:225 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC -chr1:1531686 [A/G] chr1 1531686 Cc01_g00950:645 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA GG NN GG -chr1:1531682 [A/G] chr1 1531682 Cc01_g00950:649 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 AA GG NN GG -chr1:1531673 [C/T] chr1 1531673 Cc01_g00950:658 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 CC TT CC CT -chr1:1531659 [A/G] chr1 1531659 Cc01_g00950:672 exon SYNONYMOUS_CODING atT/atC I/I 12.5% 4 AA AA AA AG -chr1:1531644 [A/T] chr1 1531644 Cc01_g00950:687 exon SYNONYMOUS_CODING cgT/cgA R/R 50.0% 4 AA TT TT AA -chr1:1531643 [A/T] chr1 1531643 Cc01_g00950:688 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 37.5% 4 AA TT TT TA -chr1:1531641 [C/T] chr1 1531641 Cc01_g00950:690 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC -chr1:1531626 [C/G] chr1 1531626 Cc01_g00950:705 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 50.0% 4 CC GG GG CC -chr1:1531625 [A/G] chr1 1531625 Cc01_g00950:706 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 25.0% 4 AA AA GG AA -chr1:1531616 [T/C] chr1 1531616 Cc01_g00950:715 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT TT CC TT -chr1:1531606 [T/C] chr1 1531606 Cc01_g00950:725 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 33.3% 3 TT NN CC TT -chr1:1531575 [A/G] chr1 1531575 Cc01_g00950:756 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AG AG -chr1:1531524 [G/A] chr1 1531524 Cc01_g00950:807 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG -chr1:1531385 [A/C] chr1 1531385 Cc01_g00950:946 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 12.5% 4 AA AA AA AC -chr1:1531373 [T/G] chr1 1531373 Cc01_g00950:958 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TT TG TT -chr1:1531330 [C/T] chr1 1531330 Cc01_g00950:1001 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CC CT -chr1:1531324 [C/G] chr1 1531324 Cc01_g00950:1007 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG GG GC -chr1:1530921 [T/A] chr1 1530921 Cc01_g00950:1410 exon NON_SYNONYMOUS_CODING agA/agT R/S 33.3% 3 TT AA NN AA -chr1:1530898 [T/A] chr1 1530898 Cc01_g00950:1433 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 50.0% 3 TT AA NN TA -chr1:1530757 [C/T] chr1 1530757 Cc01_g00950:1574 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 50.0% 2 CC TT NN NN -chr1:1530731 [T/G] chr1 1530731 Cc01_g00950:1600 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 50.0% 2 TT GG NN NN -chr1:1530707 [G/A] chr1 1530707 Cc01_g00950:1624 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 2 GG AA NN NN -chr1:1530676 [G/C] chr1 1530676 Cc01_g00950:1655 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 3 GG GC NN CC -chr1:1530668 [T/C] chr1 1530668 Cc01_g00950:1663 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 TT CC TT TT -chr1:1530661 [T/G] chr1 1530661 Cc01_g00950:1670 exon NON_SYNONYMOUS_CODING aAa/aCa K/T 12.5% 4 TT TG TT TT -chr1:1530629 [T/G] chr1 1530629 Cc01_g00950:1702 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT TT TT GG -chr1:1530627 [T/C] chr1 1530627 Cc01_g00950:1704 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT CT TT TT -chr1:1530607 [C/T] chr1 1530607 Cc01_g00950:1724 exon STOP_GAINED tGg/tAg W/5 16.7% 3 CC TC CC NN -chr1:1530606 [C/A] chr1 1530606 Cc01_g00950:1725 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 16.7% 3 CC AC CC NN -chr1:1530597 [T/G] chr1 1530597 Cc01_g00950:1734 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 16.7% 3 TT GT TT NN -chr1:1530532 [T/C] chr1 1530532 Cc01_g00950:1799 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 33.3% 3 TT CC TT NN -chr1:1530520 [T/G] chr1 1530520 Cc01_g00950:1811 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 16.7% 3 TT TG TT NN -chr1:1530290 [T/C] chr1 1530290 Cc01_g00950:2041 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 33.3% 3 TT TT NN CC -chr1:1530289 [A/G] chr1 1530289 Cc01_g00950:2042 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 33.3% 3 AA AA NN GG -chr1:1530287 [C/A] chr1 1530287 Cc01_g00950:2044 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 33.3% 3 CC CC NN AA -chr1:1530286 [C/T] chr1 1530286 Cc01_g00950:2045 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC CC CC TT -chr1:1538660 [T/G] chr1 1538660 Cc01_g00960:57 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TG TT TT -chr1:1538676 [T/C] chr1 1538676 Cc01_g00960:73 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TC TT TT -chr1:1538690 [A/G] chr1 1538690 Cc01_g00960:87 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AG AA AA -chr1:1538747 [G/A] chr1 1538747 Cc01_g00960:144 exon SYNONYMOUS_CODING ctG/ctA L/L 12.5% 4 GG GA GG GG -chr1:1538777 [T/C] chr1 1538777 Cc01_g00960:174 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT -chr1:1538784 [G/T] chr1 1538784 Cc01_g00960:181 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GT GG GG -chr1:1538792 [T/G] chr1 1538792 Cc01_g00960:189 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT -chr1:1538814 [G/C] chr1 1538814 Cc01_g00960:211 exon NON_SYNONYMOUS_CODING Gcc/Ccc A/P 12.5% 4 GG GC GG GG -chr1:1538834 [T/C] chr1 1538834 Cc01_g00960:231 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT -chr1:1538885 [C/T] chr1 1538885 Cc01_g00960:282 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC -chr1:1539091 [G/A] chr1 1539091 Cc01_g00960:488 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA GG GG -chr1:1539183 [A/G] chr1 1539183 Cc01_g00960:580 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA -chr1:1539211 [C/G] chr1 1539211 Cc01_g00960:608 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CC CC CG -chr1:1539272 [G/T] chr1 1539272 Cc01_g00960:669 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 GG GT GG GG -chr1:1539343 [G/A] chr1 1539343 Cc01_g00960:740 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG -chr1:1539365 [A/G] chr1 1539365 Cc01_g00960:762 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AG AA AA -chr1:1539374 [T/G] chr1 1539374 Cc01_g00960:771 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT GT TT TT -chr1:1539408 [T/C] chr1 1539408 Cc01_g00960:805 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT CT TT TT -chr1:1539428 [C/T] chr1 1539428 Cc01_g00960:825 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CT CC CC -chr1:1539430 [G/T] chr1 1539430 Cc01_g00960:827 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GT GG GG -chr1:1539431 [G/T] chr1 1539431 Cc01_g00960:828 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 12.5% 4 GG GT GG GG -chr1:1539509 [A/T] chr1 1539509 Cc01_g00960:906 exon SYNONYMOUS_CODING ggA/ggT G/G 12.5% 4 AA AT AA AA -chr1:1539636 [T/G] chr1 1539636 Cc01_g00960:1033 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 TT TG TT TT -chr1:1539709 [C/G] chr1 1539709 Cc01_g00960:1106 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC -chr1:1539758 [C/T] chr1 1539758 Cc01_g00960:1155 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC -chr1:1539788 [A/G] chr1 1539788 Cc01_g00960:1185 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA GA AA AA -chr1:1539824 [A/G] chr1 1539824 Cc01_g00960:1221 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA -chr1:1540980 [G/A] chr1 1540980 Cc01_g00960:1273 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG AG GG GG -chr1:1540985 [T/A] chr1 1540985 Cc01_g00960:1278 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 TT TA TT TT -chr1:1541027 [G/A] chr1 1541027 Cc01_g00960:1320 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA GG GG -chr1:1541065 [A/G] chr1 1541065 Cc01_g00960:1358 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AG AA AA -chr1:1542189 [G/A] chr1 1542189 Cc01_g00960:1460 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 12.5% 4 GG GA GG GG -chr1:1542199 [C/A] chr1 1542199 Cc01_g00960:1470 exon SYNONYMOUS_CODING ggC/ggA G/G 37.5% 4 CC AA CA AA -chr1:1542239 [G/A] chr1 1542239 Cc01_g00960:1510 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 12.5% 4 GG GA GG GG -chr1:1542286 [T/C] chr1 1542286 Cc01_g00960:1557 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT -chr1:1542364 [A/G] chr1 1542364 Cc01_g00960:1635 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG -chr1:1542404 [T/G] chr1 1542404 Cc01_g00960:1675 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 12.5% 4 TT TG TT TT -chr1:1542434 [A/C] chr1 1542434 Cc01_g00960:1705 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 12.5% 4 AA CA AA AA -chr1:1546352 [C/G] chr1 1546352 Cc01_g00970:32 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 50.0% 4 CC GG CG CG -chr1:1546365 [A/G] chr1 1546365 Cc01_g00970:45 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA GG AG GG -chr1:1546409 [G/T] chr1 1546409 Cc01_g00970:89 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 50.0% 4 GG TT GT GT -chr1:1546414 [A/C] chr1 1546414 Cc01_g00970:94 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 4 AA CC AC AC -chr1:1546454 [G/C] chr1 1546454 Cc01_g00970:134 exon NON_SYNONYMOUS_CODING cGc/cCc R/P 50.0% 4 GG CC GC GC -chr1:1546477 [C/G] chr1 1546477 Cc01_g00970:157 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC GG CG GG -chr1:1546480 [A/G] chr1 1546480 Cc01_g00970:160 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 37.5% 4 AA GG AG GG -chr1:1546484 [T/G] chr1 1546484 Cc01_g00970:164 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 50.0% 4 TT GG TG TG -chr1:1546521 [C/G] chr1 1546521 Cc01_g00970:201 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG -chr1:1546531 [A/T] chr1 1546531 Cc01_g00970:211 exon NON_SYNONYMOUS_CODING Acg/Tcg T/S 25.0% 4 AA TT AA AA -chr1:1546532 [C/G] chr1 1546532 Cc01_g00970:212 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 CC CG CC CC -chr1:1546549 [C/G] chr1 1546549 Cc01_g00970:229 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC GG CC CC -chr1:1546652 [C/A] chr1 1546652 Cc01_g00970:257 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 CC AA CA CC -chr1:1546674 [G/A] chr1 1546674 Cc01_g00970:279 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA -chr1:1546728 [A/G] chr1 1546728 Cc01_g00970:333 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG AG GG -chr1:1547036 [C/T] chr1 1547036 Cc01_g00970:641 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 25.0% 4 CC CT CT CC -chr1:1547145 [G/A] chr1 1547145 Cc01_g00970:750 exon SYNONYMOUS_CODING cgG/cgA R/R 37.5% 4 GG AA GA AA -chr1:1547237 [A/G] chr1 1547237 Cc01_g00970:842 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AG GG -chr1:1547280 [A/G] chr1 1547280 Cc01_g00970:885 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA GG AG GG -chr1:1547353 [T/A] chr1 1547353 Cc01_g00970:958 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 37.5% 4 TT AA TA TT -chr1:1547421 [G/A] chr1 1547421 Cc01_g00970:1026 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG -chr1:1547527 [G/A] chr1 1547527 Cc01_g00970:1132 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 GG GA GG GG -chr1:1547536 [T/A] chr1 1547536 Cc01_g00970:1141 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 25.0% 4 TT TT TT AA -chr1:1547613 [T/C] chr1 1547613 Cc01_g00970:1218 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT -chr1:1547682 [G/A] chr1 1547682 Cc01_g00970:1287 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 GG GA GG GG -chr1:1547853 [C/G] chr1 1547853 Cc01_g00970:1458 exon SYNONYMOUS_CODING gcC/gcG A/A 12.5% 4 CC CG CC CC -chr1:1547901 [A/G] chr1 1547901 Cc01_g00970:1506 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA GG AG GG -chr1:1547985 [C/T] chr1 1547985 Cc01_g00970:1590 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CT CC CC -chr1:1548006 [G/A] chr1 1548006 Cc01_g00970:1611 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GG GG AA -chr1:1548171 [A/C] chr1 1548171 Cc01_g00970:1776 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 AA AA AA CC -chr1:1548194 [C/A] chr1 1548194 Cc01_g00970:1799 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 37.5% 4 CC AA CA AA -chr1:1548347 [G/A] chr1 1548347 Cc01_g00970:1952 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG -chr1:1548414 [G/A] chr1 1548414 Cc01_g00970:2019 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG -chr1:1548432 [T/C] chr1 1548432 Cc01_g00970:2037 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT CT TT TT -chr1:1548609 [A/G] chr1 1548609 Cc01_g00970:2214 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AA AG -chr1:1548632 [C/T] chr1 1548632 Cc01_g00970:2237 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 37.5% 4 CC TT CT TT -chr1:1548721 [A/C] chr1 1548721 Cc01_g00970:2326 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AC AA AC -chr1:1565335 [T/C] chr1 1565335 Cc01_g00980:2 exon START_LOST aTg/aCg M/T 12.5% 4 TT TC TT TT -chr1:1565363 [T/A] chr1 1565363 Cc01_g00980:30 exon SYNONYMOUS_CODING ggT/ggA G/G 12.5% 4 TT TA TT TT -chr1:1566976 [A/G] chr1 1566976 Cc01_g00980:324 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA -chr1:1567002 [G/A] chr1 1567002 Cc01_g00980:350 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GA GG GG -chr1:1567012 [C/T] chr1 1567012 Cc01_g00980:360 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC -chr1:1568715 [T/C] chr1 1568715 Cc01_g00980:465 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TT TC -chr1:1568812 [A/G] chr1 1568812 Cc01_g00980:562 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA -chr1:1568822 [T/C] chr1 1568822 Cc01_g00980:572 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TC TT TT -chr1:1569214 [G/A] chr1 1569214 Cc01_g00980:702 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 GG GA GG GG -chr1:1570049 [T/G] chr1 1570049 Cc01_g00980:976 exon NON_SYNONYMOUS_CODING Tcc/Gcc S/A 12.5% 4 TT TG TT TT -chr1:1570069 [G/C] chr1 1570069 Cc01_g00980:996 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 GG GC GG GG -chr1:1570255 [A/G] chr1 1570255 Cc01_g00980:1068 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA -chr1:1570279 [A/T] chr1 1570279 Cc01_g00980:1092 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT -chr1:1570408 [C/T] chr1 1570408 Cc01_g00980:1221 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT -chr1:1578648 [G/A] chr1 1578648 Cc01_g00990:84 exon SYNONYMOUS_CODING tcC/tcT S/S 25.0% 4 GG GG GG AA -chr1:1577422 [G/C] chr1 1577422 Cc01_g00990:216 exon SYNONYMOUS_CODING cgC/cgG R/R 12.5% 4 GG GC GG GG -chr1:1574681 [T/G] chr1 1574681 Cc01_g00990:474 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 TT TT TG TT -chr1:1589010 [G/A] chr1 1589010 Cc01_g01000:168 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GA GG -chr1:1588986 [T/A] chr1 1588986 Cc01_g01000:192 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 TT TA TT TT -chr1:1588914 [T/G] chr1 1588914 Cc01_g01000:264 exon SYNONYMOUS_CODING ctA/ctC L/L 25.0% 4 TT GG TT TT -chr1:1588838 [G/A] chr1 1588838 Cc01_g01000:340 exon STOP_GAINED Cga/Tga R/4 25.0% 4 GG AA GG GG -chr1:1588837 [C/A] chr1 1588837 Cc01_g01000:341 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 CC AA CC CC -chr1:1588277 [T/C] chr1 1588277 Cc01_g01000:901 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT CC TT TT -chr1:1588220 [G/A] chr1 1588220 Cc01_g01000:958 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 GG GG GA GG -chr1:1588137 [G/A] chr1 1588137 Cc01_g01000:1041 exon SYNONYMOUS_CODING caC/caT H/H 25.0% 4 GG AA GG GG -chr1:1588135 [A/G] chr1 1588135 Cc01_g01000:1043 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG -chr1:1587967 [G/A] chr1 1587967 Cc01_g01000:1211 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 25.0% 4 GG GG GA GA -chr1:1587921 [A/G] chr1 1587921 Cc01_g01000:1257 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AG AG -chr1:1587798 [C/T] chr1 1587798 Cc01_g01000:1380 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 CC TT CC CC -chr1:1587708 [C/T] chr1 1587708 Cc01_g01000:1470 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TT CC CC -chr1:1587646 [G/C] chr1 1587646 Cc01_g01000:1532 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 25.0% 4 GG GC GC GG -chr1:1587588 [T/A] chr1 1587588 Cc01_g01000:1590 exon SYNONYMOUS_CODING atA/atT I/I 25.0% 4 TT AA TT TT -chr1:1587577 [C/T] chr1 1587577 Cc01_g01000:1601 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC -chr1:1587576 [A/T] chr1 1587576 Cc01_g01000:1602 exon NON_SYNONYMOUS_CODING agT/agA S/R 25.0% 4 AA TT AA AA -chr1:1587527 [G/T] chr1 1587527 Cc01_g01000:1651 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 GG TT GG GG -chr1:1587435 [G/T] chr1 1587435 Cc01_g01000:1743 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 GG TT GG GG -chr1:1595916 [A/T] chr1 1595916 Cc01_g01010:153 exon SYNONYMOUS_CODING gtT/gtA V/V 37.5% 4 AA AT AT AT -chr1:1595665 [A/C] chr1 1595665 Cc01_g01010:278 exon NON_SYNONYMOUS_CODING gTt/gGt V/G 25.0% 4 AA AC AC AA -chr1:1594252 [G/A] chr1 1594252 Cc01_g01010:651 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 GG GA GA GA -chr1:1594186 [T/C] chr1 1594186 Cc01_g01010:717 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC -chr1:1593925 [G/A] chr1 1593925 Cc01_g01010:858 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 GG GA GA GA -chr1:1593817 [T/G] chr1 1593817 Cc01_g01010:966 exon SYNONYMOUS_CODING cgA/cgC R/R 37.5% 4 TT TG TG TG -chr1:1593814 [T/C] chr1 1593814 Cc01_g01010:969 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT -chr1:1593634 [C/T] chr1 1593634 Cc01_g01010:1056 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC -chr1:1593035 [T/A] chr1 1593035 Cc01_g01010:1221 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT -chr1:1593017 [G/A] chr1 1593017 Cc01_g01010:1239 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG AA GA AA -chr1:1592810 [A/G] chr1 1592810 Cc01_g01010:1341 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG -chr1:1591963 [T/C] chr1 1591963 Cc01_g01010:1515 exon SYNONYMOUS_CODING cgA/cgG R/R 37.5% 4 TT TC TC TC -chr1:1591951 [A/G] chr1 1591951 Cc01_g01010:1527 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA AG AG AG -chr1:1591930 [G/A] chr1 1591930 Cc01_g01010:1548 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 GG GG GA GA -chr1:1591377 [A/G] chr1 1591377 Cc01_g01010:1560 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AG AA -chr1:1590960 [G/A] chr1 1590960 Cc01_g01010:1788 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG GA GA GA -chr1:1590951 [A/G] chr1 1590951 Cc01_g01010:1797 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA -chr1:1605944 [G/T] chr1 1605944 Cc01_g01020:27 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 GG GT GG GG -chr1:1605987 [T/G] chr1 1605987 Cc01_g01020:70 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 TT TT TG TT -chr1:1606067 [C/G] chr1 1606067 Cc01_g01020:150 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 37.5% 4 CC GG CG GG -chr1:1606163 [A/C] chr1 1606163 Cc01_g01020:246 exon SYNONYMOUS_CODING acA/acC T/T 12.5% 4 AA AA AA AC -chr1:1609099 [T/C] chr1 1609099 Cc01_g01020:536 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TC TT TT -chr1:1609547 [G/C] chr1 1609547 Cc01_g01020:822 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 GG GC GG GG -chr1:1609736 [C/A] chr1 1609736 Cc01_g01020:912 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC CA CC CA -chr1:1609752 [G/C] chr1 1609752 Cc01_g01020:928 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 37.5% 4 GG CC GC CC -chr1:1609769 [A/C] chr1 1609769 Cc01_g01020:945 exon SYNONYMOUS_CODING ctA/ctC L/L 12.5% 4 AA AA AC AA -chr1:1610622 [A/G] chr1 1610622 Cc01_g01020:1431 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 AA AG AA AA -chr1:1610842 [A/G] chr1 1610842 Cc01_g01020:1560 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA -chr1:1612395 [C/A] chr1 1612395 Cc01_g01020:2229 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 CC CA CC CC -chr1:1613838 [C/T] chr1 1613838 Cc01_g01020:2532 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC TT CC TT -chr1:1613901 [C/T] chr1 1613901 Cc01_g01020:2595 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CC CT -chr1:1615545 [T/G] chr1 1615545 Cc01_g01030:18 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT TG TT TT -chr1:1615529 [T/C] chr1 1615529 Cc01_g01030:34 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT -chr1:1615508 [C/T] chr1 1615508 Cc01_g01030:55 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 37.5% 4 CC TT CT TT -chr1:1615506 [C/T] chr1 1615506 Cc01_g01030:57 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT -chr1:1615500 [T/G] chr1 1615500 Cc01_g01030:63 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 TT TT TT GT -chr1:1615496 [T/C] chr1 1615496 Cc01_g01030:67 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT CT -chr1:1615491 [C/T] chr1 1615491 Cc01_g01030:72 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 CC TT CT TT -chr1:1615477 [G/A] chr1 1615477 Cc01_g01030:86 exon NON_SYNONYMOUS_CODING cCt/cTt P/L 12.5% 4 GG GG GG AG -chr1:1615472 [T/G] chr1 1615472 Cc01_g01030:91 exon NON_SYNONYMOUS_CODING Atc/Ctc I/L 37.5% 4 TT GG TG GG -chr1:1615458 [C/T] chr1 1615458 Cc01_g01030:105 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC -chr1:1615440 [T/C] chr1 1615440 Cc01_g01030:123 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT CT -chr1:1615335 [C/T] chr1 1615335 Cc01_g01030:132 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT CT TT -chr1:1615256 [A/T] chr1 1615256 Cc01_g01030:211 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 AA AA AA AT -chr1:1620903 [A/T] chr1 1620903 Cc01_g01040:366 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AT AA AA -chr1:1619369 [G/A] chr1 1619369 Cc01_g01040:648 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA GA GA -chr1:1619341 [G/C] chr1 1619341 Cc01_g01040:676 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CC GC CC -chr1:1619334 [C/T] chr1 1619334 Cc01_g01040:683 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CT TT -chr1:1619270 [C/G] chr1 1619270 Cc01_g01040:747 exon SYNONYMOUS_CODING tcG/tcC S/S 37.5% 4 CC GG CG GG -chr1:1619124 [A/G] chr1 1619124 Cc01_g01040:893 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AG AA -chr1:1618988 [A/G] chr1 1618988 Cc01_g01040:1029 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG -chr1:1618984 [C/G] chr1 1618984 Cc01_g01040:1033 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CC CC CG -chr1:1618978 [C/G] chr1 1618978 Cc01_g01040:1039 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 CC CG CG CG -chr1:1618886 [A/G] chr1 1618886 Cc01_g01040:1131 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AA AA AG -chr1:1618879 [T/A] chr1 1618879 Cc01_g01040:1138 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 TT TT TT TA -chr1:1618858 [T/G] chr1 1618858 Cc01_g01040:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT GG TG GG -chr1:1618504 [G/A] chr1 1618504 Cc01_g01040:1396 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG GA -chr1:1618376 [T/G] chr1 1618376 Cc01_g01040:1524 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 TT TG TT TT -chr1:1618358 [G/C] chr1 1618358 Cc01_g01040:1542 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC GC -chr1:1618326 [C/T] chr1 1618326 Cc01_g01040:1574 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 12.5% 4 CC CC CT CC -chr1:1618307 [G/C] chr1 1618307 Cc01_g01040:1593 exon SYNONYMOUS_CODING ctC/ctG L/L 12.5% 4 GG GG GG CG -chr1:1618184 [A/G] chr1 1618184 Cc01_g01040:1716 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA -chr1:1618117 [G/C] chr1 1618117 Cc01_g01040:1783 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 37.5% 4 GG CG GG CC -chr1:1618040 [C/G] chr1 1618040 Cc01_g01040:1860 exon NON_SYNONYMOUS_CODING caG/caC Q/H 12.5% 4 CC CC CG CC -chr1:1618037 [G/A] chr1 1618037 Cc01_g01040:1863 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG GA GA GA -chr1:1618016 [T/C] chr1 1618016 Cc01_g01040:1884 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TC TT -chr1:1617998 [G/C] chr1 1617998 Cc01_g01040:1902 exon SYNONYMOUS_CODING ggC/ggG G/G 25.0% 4 GG GG GC CG -chr1:1617793 [C/T] chr1 1617793 Cc01_g01040:2107 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 37.5% 4 CC CT CT CT -chr1:1617773 [T/C] chr1 1617773 Cc01_g01040:2127 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC -chr1:1617769 [T/C] chr1 1617769 Cc01_g01040:2131 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 TT TT TT TC -chr1:1617757 [C/T] chr1 1617757 Cc01_g01040:2143 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT -chr1:1617670 [C/T] chr1 1617670 Cc01_g01040:2230 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 37.5% 4 CC CT CC TT -chr1:1617634 [C/T] chr1 1617634 Cc01_g01040:2266 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CC CT -chr1:1617479 [A/G] chr1 1617479 Cc01_g01040:2421 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG AA AA -chr1:1617238 [G/A] chr1 1617238 Cc01_g01040:2662 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GA GG GG -chr1:1617119 [A/T] chr1 1617119 Cc01_g01040:2725 exon NON_SYNONYMOUS_CODING Tgt/Agt C/S 25.0% 4 AA AT AT AA -chr1:1626903 [A/C] chr1 1626903 Cc01_g01050:132 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 AA CC AC CC -chr1:1626922 [C/G] chr1 1626922 Cc01_g01050:151 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 CC CG CG CC -chr1:1626973 [G/T] chr1 1626973 Cc01_g01050:202 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 GG GT GG TT -chr1:1627071 [T/C] chr1 1627071 Cc01_g01050:300 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TT CC -chr1:1627227 [T/C] chr1 1627227 Cc01_g01050:456 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TC TC TT -chr1:1628554 [A/G] chr1 1628554 Cc01_g01050:650 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 25.0% 4 AA AG AG AA -chr1:1628584 [A/G] chr1 1628584 Cc01_g01050:680 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 37.5% 4 AA GA AA GG -chr1:1628763 [G/A] chr1 1628763 Cc01_g01050:859 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GG GA -chr1:1628787 [G/C] chr1 1628787 Cc01_g01050:883 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 37.5% 4 GG GC GG CC -chr1:1628828 [A/G] chr1 1628828 Cc01_g01050:924 exon SYNONYMOUS_CODING gcA/gcG A/A 37.5% 4 AA AG AA GG -chr1:1628942 [A/G] chr1 1628942 Cc01_g01050:1038 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 AA GG AG GG -chr1:1630053 [T/C] chr1 1630053 Cc01_g01050:1464 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TC TT -chr1:1633739 [A/G] chr1 1633739 Cc01_g01060:12 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 AA AG AG AG -chr1:1633649 [T/C] chr1 1633649 Cc01_g01060:102 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC -chr1:1633602 [T/C] chr1 1633602 Cc01_g01060:149 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 12.5% 4 TT CT TT TT -chr1:1633503 [G/A] chr1 1633503 Cc01_g01060:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GA GG GG -chr1:1633430 [A/T] chr1 1633430 Cc01_g01060:321 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 AA AT AA AA -chr1:1633429 [G/T] chr1 1633429 Cc01_g01060:322 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GT GG GG -chr1:1633388 [A/T] chr1 1633388 Cc01_g01060:363 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 AA AA AT AA -chr1:1752682 [C/T] chr1 1752682 Cc01_g01120:21 exon SYNONYMOUS_CODING acG/acA T/T 33.3% 3 CC TT NN TT -chr1:1752654 [A/T] chr1 1752654 Cc01_g01120:49 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 37.5% 4 AA AT TT AA -chr1:1752632 [G/T] chr1 1752632 Cc01_g01120:71 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 37.5% 4 GG GT TT GG -chr1:1752577 [C/A] chr1 1752577 Cc01_g01120:126 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 CC CA CA CC -chr1:1752535 [T/C] chr1 1752535 Cc01_g01120:168 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 TT TT CC TT -chr1:1752526 [C/T] chr1 1752526 Cc01_g01120:177 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 CC CC TT CC -chr1:1750532 [T/G] chr1 1750532 Cc01_g01120:970 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 50.0% 2 TT NN NN GG -chr1:1750461 [C/T] chr1 1750461 Cc01_g01120:1041 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 CC TT CT TT -chr1:1750442 [C/T] chr1 1750442 Cc01_g01120:1060 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 37.5% 4 CC TT CT TT -chr1:1760523 [C/A] chr1 1760523 Cc01_g01130:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 12.5% 4 CC CC CA CC -chr1:1760522 [G/C] chr1 1760522 Cc01_g01130:136 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 GG GG GC GG -chr1:1760486 [A/C] chr1 1760486 Cc01_g01130:172 exon NON_SYNONYMOUS_CODING Tcg/Gcg S/A 12.5% 4 AA AA AA AC -chr1:1760383 [C/T] chr1 1760383 Cc01_g01130:275 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC -chr1:1760328 [T/A] chr1 1760328 Cc01_g01130:330 exon SYNONYMOUS_CODING atA/atT I/I 50.0% 4 TT AA TT AA -chr1:1760185 [T/A] chr1 1760185 Cc01_g01130:473 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 TT TA TA TT -chr1:1760173 [C/A] chr1 1760173 Cc01_g01130:485 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 CC CC CC CA -chr1:1760172 [T/G] chr1 1760172 Cc01_g01130:486 exon NON_SYNONYMOUS_CODING agA/agC R/S 12.5% 4 TT TT TT TG -chr1:1759408 [A/G] chr1 1759408 Cc01_g01130:603 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA -chr1:1759378 [G/A] chr1 1759378 Cc01_g01130:633 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GA GG -chr1:1759372 [A/G] chr1 1759372 Cc01_g01130:639 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 AA AG AG AA -chr1:1759371 [T/A] chr1 1759371 Cc01_g01130:640 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 25.0% 4 TT TA TA TT -chr1:1759364 [T/G] chr1 1759364 Cc01_g01130:647 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 TT TG TT TT -chr1:1759335 [G/A] chr1 1759335 Cc01_g01130:676 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG GA GA GG -chr1:1758971 [A/G] chr1 1758971 Cc01_g01130:1040 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 3 AA GG AG NN -chr1:1758937 [G/A] chr1 1758937 Cc01_g01130:1074 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 3 GG AA GA NN -chr1:1758885 [C/G] chr1 1758885 Cc01_g01130:1126 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 33.3% 3 CC GG CC NN -chr1:1758882 [C/T] chr1 1758882 Cc01_g01130:1129 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 3 CC TT CT NN -chr1:1758778 [G/A] chr1 1758778 Cc01_g01130:1233 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG GA GG GG -chr1:1758772 [A/G] chr1 1758772 Cc01_g01130:1239 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AG AA AA -chr1:1758762 [T/C] chr1 1758762 Cc01_g01130:1249 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 TT TC TT TT -chr1:1768762 [G/C] chr1 1768762 Cc01_g01140:100 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG GC GG GC -chr1:1768873 [T/C] chr1 1768873 Cc01_g01140:211 exon SYNONYMOUS_CODING Tta/Cta L/L 12.5% 4 TT TT TT TC -chr1:1768956 [T/A] chr1 1768956 Cc01_g01140:294 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 TT TT TT TA -chr1:1768961 [C/A] chr1 1768961 Cc01_g01140:299 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CC CA -chr1:1768967 [C/G] chr1 1768967 Cc01_g01140:305 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 50.0% 4 CC CG CG GG -chr1:1769000 [A/G] chr1 1769000 Cc01_g01140:338 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 AA AA AA AG -chr1:1769038 [T/C] chr1 1769038 Cc01_g01140:376 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TC TT TT -chr1:1769040 [T/G] chr1 1769040 Cc01_g01140:378 exon SYNONYMOUS_CODING tcT/tcG S/S 12.5% 4 TT TT TT TG -chr1:1769074 [T/C] chr1 1769074 Cc01_g01140:412 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TT TC -chr1:1769115 [T/C] chr1 1769115 Cc01_g01140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TT TT TC -chr1:1769145 [C/T] chr1 1769145 Cc01_g01140:483 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 CC CT CT TT -chr1:1769183 [C/T] chr1 1769183 Cc01_g01140:521 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 25.0% 4 CC CT CC CT -chr1:1769193 [A/T] chr1 1769193 Cc01_g01140:531 exon SYNONYMOUS_CODING atA/atT I/I 12.5% 4 AA AT AA AA -chr1:1769201 [C/T] chr1 1769201 Cc01_g01140:539 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 CC CT CC CT -chr1:1769253 [A/C] chr1 1769253 Cc01_g01140:591 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 AA AA AA AC -chr1:1769277 [T/A] chr1 1769277 Cc01_g01140:615 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 TT TA TT TA -chr1:1769279 [G/A] chr1 1769279 Cc01_g01140:617 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA -chr1:1769288 [A/C] chr1 1769288 Cc01_g01140:626 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AA CA -chr1:1769296 [A/G] chr1 1769296 Cc01_g01140:634 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 AA AG AA AG -chr1:1769367 [T/C] chr1 1769367 Cc01_g01140:705 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TT TC TC -chr1:1769374 [G/A] chr1 1769374 Cc01_g01140:712 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA -chr1:1769389 [C/T] chr1 1769389 Cc01_g01140:727 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT -chr1:1769398 [T/C] chr1 1769398 Cc01_g01140:736 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TT TC -chr1:1769433 [T/G] chr1 1769433 Cc01_g01140:771 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 TT TG TT TT -chr1:1769441 [C/T] chr1 1769441 Cc01_g01140:779 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 37.5% 4 CC CT CT CT -chr1:1769448 [A/T] chr1 1769448 Cc01_g01140:786 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 37.5% 4 AA AT AT AT -chr1:1769482 [A/T] chr1 1769482 Cc01_g01140:820 exon STOP_GAINED Aga/Tga R/4 12.5% 4 AA AA AA TA -chr1:1769483 [G/T] chr1 1769483 Cc01_g01140:821 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 12.5% 4 GG GG GG TG -chr1:1769501 [C/G] chr1 1769501 Cc01_g01140:839 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 CC CG CC CC -chr1:1769639 [A/G] chr1 1769639 Cc01_g01140:977 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 AA AA AA AG -chr1:1769671 [C/A] chr1 1769671 Cc01_g01140:1009 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 12.5% 4 CC CA CC CC -chr1:1769978 [A/G] chr1 1769978 Cc01_g01140:1256 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 4 AA AG AA AG -chr1:1769992 [A/G] chr1 1769992 Cc01_g01140:1270 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG -chr1:1770017 [G/T] chr1 1770017 Cc01_g01140:1295 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 37.5% 4 GG GT GT GT -chr1:1770029 [C/T] chr1 1770029 Cc01_g01140:1307 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 37.5% 4 CC CT CT CT -chr1:1770045 [C/T] chr1 1770045 Cc01_g01140:1323 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT -chr1:1770067 [C/T] chr1 1770067 Cc01_g01140:1345 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 CC CC CT CT -chr1:1770389 [C/G] chr1 1770389 Cc01_g01140:1667 exon STOP_GAINED tCa/tGa S/6 12.5% 4 CC CG CC CC -chr1:1770417 [A/C] chr1 1770417 Cc01_g01140:1695 exon SYNONYMOUS_CODING atA/atC I/I 12.5% 4 AA AC AA AA -chr1:1770420 [C/A] chr1 1770420 Cc01_g01140:1698 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CA CC CC -chr1:1770531 [A/G] chr1 1770531 Cc01_g01140:1809 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AG AA AA -chr1:1770535 [A/G] chr1 1770535 Cc01_g01140:1813 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA -chr1:1770536 [G/A] chr1 1770536 Cc01_g01140:1814 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA -chr1:1770538 [C/T] chr1 1770538 Cc01_g01140:1816 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CC CC CT -chr1:1770756 [G/A] chr1 1770756 Cc01_g01140:1972 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG GA GA AA -chr1:1770764 [A/G] chr1 1770764 Cc01_g01140:1980 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG -chr1:1770768 [A/T] chr1 1770768 Cc01_g01140:1984 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AA AT -chr1:1770781 [G/T] chr1 1770781 Cc01_g01140:1997 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 GG GG GG GT -chr1:1770792 [C/G] chr1 1770792 Cc01_g01140:2008 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 25.0% 4 CC CC GC GC -chr1:1770794 [T/C] chr1 1770794 Cc01_g01140:2010 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC -chr1:1770795 [G/A] chr1 1770795 Cc01_g01140:2011 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG -chr1:1770797 [A/T] chr1 1770797 Cc01_g01140:2013 exon SYNONYMOUS_CODING gtA/gtT V/V 12.5% 4 AA AT AA AA -chr1:1770804 [G/C] chr1 1770804 Cc01_g01140:2020 exon NON_SYNONYMOUS_CODING Gca/Cca A/P 12.5% 4 GG GC GG GG -chr1:1770806 [A/G] chr1 1770806 Cc01_g01140:2022 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AG AA AA -chr1:1770807 [A/T] chr1 1770807 Cc01_g01140:2023 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AT AA AA -chr1:1771162 [C/T] chr1 1771162 Cc01_g01140:2032 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC TT TC TT -chr1:1771185 [T/A] chr1 1771185 Cc01_g01140:2055 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 TT AA AT AA -chr1:1771201 [C/A] chr1 1771201 Cc01_g01140:2071 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 37.5% 4 CC AA AC AA -chr1:1775047 [T/C] chr1 1775047 Cc01_g01150:43 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 2 TT TC NN NN -chr1:1774997 [A/G] chr1 1774997 Cc01_g01150:93 exon SYNONYMOUS_CODING gtT/gtC V/V 33.3% 3 AA AG NN AG -chr1:1774994 [A/G] chr1 1774994 Cc01_g01150:96 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA AG GG GA -chr1:1774991 [C/T] chr1 1774991 Cc01_g01150:99 exon SYNONYMOUS_CODING gtG/gtA V/V 25.0% 4 CC TT TT TT -chr1:1774981 [A/G] chr1 1774981 Cc01_g01150:109 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 AA AG AG AG -chr1:1774977 [C/T] chr1 1774977 Cc01_g01150:113 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT -chr1:1774975 [C/T] chr1 1774975 Cc01_g01150:115 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 37.5% 4 CC TC TC TC -chr1:1774972 [T/G] chr1 1774972 Cc01_g01150:118 exon NON_SYNONYMOUS_CODING Act/Cct T/P 37.5% 4 TT TG TG TG -chr1:1774959 [A/G] chr1 1774959 Cc01_g01150:131 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 37.5% 4 AA GA GA GA -chr1:1774957 [A/C] chr1 1774957 Cc01_g01150:133 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 37.5% 4 AA CC CC AC -chr1:1774955 [C/A] chr1 1774955 Cc01_g01150:135 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 37.5% 4 CC AA AA CA -chr1:1774925 [A/C] chr1 1774925 Cc01_g01150:165 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 37.5% 4 AA AC AC AC -chr1:1774919 [A/G] chr1 1774919 Cc01_g01150:171 exon SYNONYMOUS_CODING ccT/ccC P/P 37.5% 4 AA AG AG AG -chr1:1774915 [C/G] chr1 1774915 Cc01_g01150:175 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC -chr1:1774911 [C/T] chr1 1774911 Cc01_g01150:179 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT TT CT -chr1:1774901 [C/A] chr1 1774901 Cc01_g01150:189 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 CC AA AA AA -chr1:1774894 [G/A] chr1 1774894 Cc01_g01150:196 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 37.5% 4 GG GA GA GA -chr1:1800628 [A/T] chr1 1800628 Cc01_g01180:18 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 37.5% 4 AA AT AA TT -chr1:1800604 [A/G] chr1 1800604 Cc01_g01180:42 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 4 AA GG AA GG -chr1:1800591 [A/C] chr1 1800591 Cc01_g01180:55 exon NON_SYNONYMOUS_CODING Ttg/Gtg L/V 12.5% 4 AA CA AA AA -chr1:1800153 [G/A] chr1 1800153 Cc01_g01180:237 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 GG GG GA GG -chr1:1800141 [C/A] chr1 1800141 Cc01_g01180:249 exon SYNONYMOUS_CODING tcG/tcT S/S 12.5% 4 CC CA CC CC -chr1:1800037 [A/T] chr1 1800037 Cc01_g01180:353 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 37.5% 4 AA TT AT TT -chr1:1799883 [A/G] chr1 1799883 Cc01_g01180:507 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 AA AG AA AA -chr1:1799858 [C/A] chr1 1799858 Cc01_g01180:532 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 CC AC CC CA -chr1:1799772 [C/T] chr1 1799772 Cc01_g01180:618 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT -chr1:1799746 [C/A] chr1 1799746 Cc01_g01180:644 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 25.0% 4 CC CA CC AC -chr1:1799703 [T/A] chr1 1799703 Cc01_g01180:687 exon SYNONYMOUS_CODING gcA/gcT A/A 37.5% 4 TT AT TA TA -chr1:1799683 [C/T] chr1 1799683 Cc01_g01180:707 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC -chr1:1799560 [G/A] chr1 1799560 Cc01_g01180:830 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GG GA -chr1:1799253 [G/A] chr1 1799253 Cc01_g01180:1137 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GG GA -chr1:1799138 [C/G] chr1 1799138 Cc01_g01180:1252 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 CC CC CC CG -chr1:1799114 [C/T] chr1 1799114 Cc01_g01180:1276 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT -chr1:1799096 [T/C] chr1 1799096 Cc01_g01180:1294 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TC TC TT -chr1:1798930 [C/T] chr1 1798930 Cc01_g01180:1460 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 37.5% 4 CC CT CT CT -chr1:1798825 [T/C] chr1 1798825 Cc01_g01180:1565 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 TT TT TT TC -chr1:1798812 [A/C] chr1 1798812 Cc01_g01180:1578 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 12.5% 4 AA AA AA AC -chr1:1798782 [T/C] chr1 1798782 Cc01_g01180:1608 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT TT TC -chr1:1798753 [T/A] chr1 1798753 Cc01_g01180:1637 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TT TA -chr1:1798733 [T/C] chr1 1798733 Cc01_g01180:1657 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT TC TC TC -chr1:1798724 [G/A] chr1 1798724 Cc01_g01180:1666 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG GA -chr1:1798690 [C/A] chr1 1798690 Cc01_g01180:1700 exon NON_SYNONYMOUS_CODING gGg/gTg G/V 12.5% 4 CC CC CC CA -chr1:1798665 [T/C] chr1 1798665 Cc01_g01180:1725 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT -chr1:1798471 [T/A] chr1 1798471 Cc01_g01180:1919 exon NON_SYNONYMOUS_CODING aAt/aTt N/I 12.5% 4 TT TT TT TA -chr1:1798453 [A/G] chr1 1798453 Cc01_g01180:1937 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 12.5% 4 AA AA AA AG -chr1:1798341 [G/A] chr1 1798341 Cc01_g01180:2049 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 GG AA GA AA -chr1:1798269 [T/C] chr1 1798269 Cc01_g01180:2121 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 TT TT TT TC -chr1:1798206 [A/G] chr1 1798206 Cc01_g01180:2184 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AA AG -chr1:1798185 [A/T] chr1 1798185 Cc01_g01180:2205 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 AA AA AA AT -chr1:1798172 [G/A] chr1 1798172 Cc01_g01180:2218 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA -chr1:1798019 [A/G] chr1 1798019 Cc01_g01180:2277 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG -chr1:1797997 [A/C] chr1 1797997 Cc01_g01180:2299 exon NON_SYNONYMOUS_CODING Tgc/Ggc C/G 12.5% 4 AA AA AC AA -chr1:1796639 [G/T] chr1 1796639 Cc01_g01180:2517 exon SYNONYMOUS_CODING ctC/ctA L/L 12.5% 4 GG GG GG GT -chr1:1796548 [C/T] chr1 1796548 Cc01_g01180:2608 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC CT -chr1:1796523 [G/C] chr1 1796523 Cc01_g01180:2633 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 12.5% 4 GG GG GG GC -chr1:1796504 [G/A] chr1 1796504 Cc01_g01180:2652 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG -chr1:1796501 [C/T] chr1 1796501 Cc01_g01180:2655 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CC CT -chr1:1796477 [A/G] chr1 1796477 Cc01_g01180:2679 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AA AA AG -chr1:1794530 [C/A] chr1 1794530 Cc01_g01180:2830 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 CC CC CC CA -chr1:1793183 [A/G] chr1 1793183 Cc01_g01180:2975 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA AA AA AG -chr1:1793145 [G/T] chr1 1793145 Cc01_g01180:3013 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT -chr1:1793065 [C/T] chr1 1793065 Cc01_g01180:3093 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC CT CC CC -chr1:1793054 [A/G] chr1 1793054 Cc01_g01180:3104 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 12.5% 4 AA AG AA AA -chr1:1793045 [G/T] chr1 1793045 Cc01_g01180:3113 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 12.5% 4 GG GT GG GG -chr1:1792939 [G/T] chr1 1792939 Cc01_g01180:3147 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 GG GT GG GG -chr1:1792909 [A/T] chr1 1792909 Cc01_g01180:3177 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA TA AA AA -chr1:1813729 [G/T] chr1 1813729 Cc01_g01190:306 exon SYNONYMOUS_CODING ccC/ccA P/P 16.7% 3 GG GT NN GG -chr1:1813726 [A/T] chr1 1813726 Cc01_g01190:309 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 AA AT NN AA -chr1:1813696 [T/G] chr1 1813696 Cc01_g01190:339 exon SYNONYMOUS_CODING atA/atC I/I 16.7% 3 TT TG NN TT -chr1:1818371 [T/C] chr1 1818371 Cc01_g01200:87 exon SYNONYMOUS_CODING gcA/gcG A/A 50.0% 4 TT TC CC TC -chr1:1818296 [A/T] chr1 1818296 Cc01_g01200:162 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA AA TT AA -chr1:1818188 [A/G] chr1 1818188 Cc01_g01200:270 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 AA AA AG AA -chr1:1818116 [A/C] chr1 1818116 Cc01_g01200:342 exon SYNONYMOUS_CODING ggT/ggG G/G 12.5% 4 AA AC AA AA -chr1:1818035 [A/G] chr1 1818035 Cc01_g01200:423 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA AG AG GG -chr1:1818018 [T/A] chr1 1818018 Cc01_g01200:440 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 50.0% 4 TT TA TA AA -chr1:1818013 [T/G] chr1 1818013 Cc01_g01200:445 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 25.0% 4 TT TT TG TG -chr1:1822497 [A/G] chr1 1822497 Cc01_g01210:153 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA AG AA AG -chr1:1822491 [C/G] chr1 1822491 Cc01_g01210:159 exon SYNONYMOUS_CODING ccG/ccC P/P 12.5% 4 CC CC CC CG -chr1:1822434 [C/T] chr1 1822434 Cc01_g01210:216 exon SYNONYMOUS_CODING caG/caA Q/Q 12.5% 4 CC CT CC CC -chr1:1822365 [A/G] chr1 1822365 Cc01_g01210:285 exon SYNONYMOUS_CODING ctT/ctC L/L 37.5% 4 AA GG AA AG -chr1:1822344 [G/C] chr1 1822344 Cc01_g01210:306 exon SYNONYMOUS_CODING ccC/ccG P/P 37.5% 4 GG CC GG GC -chr1:1822311 [G/C] chr1 1822311 Cc01_g01210:339 exon SYNONYMOUS_CODING gtC/gtG V/V 12.5% 4 GG GG GC GG -chr1:1822251 [G/A] chr1 1822251 Cc01_g01210:399 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG GA AG GA -chr1:1822215 [G/T] chr1 1822215 Cc01_g01210:435 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 12.5% 4 GG GG TG GG -chr1:1822206 [G/A] chr1 1822206 Cc01_g01210:444 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 GG AA AG AA -chr1:1871413 [G/T] chr1 1871413 Cc01_g01220:7 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 GG TT GT TT -chr1:1871774 [T/C] chr1 1871774 Cc01_g01220:65 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 12.5% 4 TT TT TT TC -chr1:1871782 [G/C] chr1 1871782 Cc01_g01220:73 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GG GC -chr1:1871785 [G/T] chr1 1871785 Cc01_g01220:76 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 25.0% 4 GG GT GG GT -chr1:1871959 [C/T] chr1 1871959 Cc01_g01220:118 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 CC CT CC CC -chr1:1871977 [G/C] chr1 1871977 Cc01_g01220:136 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 25.0% 4 GG GC GC GG -chr1:1871980 [T/G] chr1 1871980 Cc01_g01220:139 exon NON_SYNONYMOUS_CODING Ttt/Gtt F/V 12.5% 4 TT TG TT TT -chr1:1871994 [C/A] chr1 1871994 Cc01_g01220:153 exon NON_SYNONYMOUS_CODING ttC/ttA F/L 12.5% 4 CC AC CC CC -chr1:1872001 [T/C] chr1 1872001 Cc01_g01220:160 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 12.5% 4 TT CT TT TT -chr1:1872003 [C/T] chr1 1872003 Cc01_g01220:162 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC CT CT CT -chr1:1872004 [A/G] chr1 1872004 Cc01_g01220:163 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 AA AG AG AG -chr1:1872020 [G/A] chr1 1872020 Cc01_g01220:179 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG -chr1:1872035 [G/A] chr1 1872035 Cc01_g01220:194 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GA GG GA -chr1:1872037 [A/G] chr1 1872037 Cc01_g01220:196 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG -chr1:1872051 [A/G] chr1 1872051 Cc01_g01220:210 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA GG GA GG -chr1:1873065 [C/T] chr1 1873065 Cc01_g01220:247 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC CC CT -chr1:1873088 [T/C] chr1 1873088 Cc01_g01220:270 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TT TT TC -chr1:1874574 [C/T] chr1 1874574 Cc01_g01230:34 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CC CT -chr1:1874587 [T/G] chr1 1874587 Cc01_g01230:47 exon NON_SYNONYMOUS_CODING tTc/tGc F/C 12.5% 4 TT TT TG TT -chr1:1874774 [C/G] chr1 1874774 Cc01_g01230:135 exon STOP_GAINED taC/taG Y/5 12.5% 4 CC CC CG CC -chr1:1874797 [T/A] chr1 1874797 Cc01_g01230:158 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 25.0% 4 TT TT TA TA -chr1:1874808 [G/T] chr1 1874808 Cc01_g01230:169 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG GT -chr1:1874816 [G/T] chr1 1874816 Cc01_g01230:177 exon NON_SYNONYMOUS_CODING agG/agT R/S 12.5% 4 GG GT GG GG -chr1:1874818 [G/T] chr1 1874818 Cc01_g01230:179 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 25.0% 4 GG GG GT GT -chr1:1879776 [A/C] chr1 1879776 Cc01_g01240:27 exon NON_SYNONYMOUS_CODING tgT/tgG C/W 50.0% 4 AA AC AC CC -chr1:1879628 [G/C] chr1 1879628 Cc01_g01240:175 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 25.0% 4 GG GC GG GC -chr1:1879623 [T/C] chr1 1879623 Cc01_g01240:180 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT -chr1:1907384 [G/A] chr1 1907384 Cc01_g01250:29 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GA GG GA -chr1:1907400 [C/G] chr1 1907400 Cc01_g01250:45 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC GG GG GG -chr1:1907401 [A/G] chr1 1907401 Cc01_g01250:46 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 AA AG AG GA -chr1:1907418 [G/A] chr1 1907418 Cc01_g01250:63 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG GA GA AG -chr1:1907454 [A/C] chr1 1907454 Cc01_g01250:99 exon NON_SYNONYMOUS_CODING caA/caC Q/H 37.5% 4 AA AC AC CA -chr1:1907455 [A/G] chr1 1907455 Cc01_g01250:100 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AA AG AA -chr1:1907457 [C/G] chr1 1907457 Cc01_g01250:102 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 25.0% 4 CC GG GG GG -chr1:1907460 [T/A] chr1 1907460 Cc01_g01250:105 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 25.0% 4 TT TT AT TA -chr1:1907483 [A/C] chr1 1907483 Cc01_g01250:128 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 AA AA AA CA -chr1:1907485 [G/A] chr1 1907485 Cc01_g01250:130 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA -chr1:1907487 [C/T] chr1 1907487 Cc01_g01250:132 exon SYNONYMOUS_CODING gaC/gaT D/D 37.5% 4 CC CT CT TC -chr1:1907489 [T/G] chr1 1907489 Cc01_g01250:134 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 12.5% 4 TT TT TT GT -chr1:1907499 [G/A] chr1 1907499 Cc01_g01250:144 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 GG GG AG GA -chr1:1907514 [T/C] chr1 1907514 Cc01_g01250:159 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TC TC CT -chr1:1907532 [G/C] chr1 1907532 Cc01_g01250:177 exon SYNONYMOUS_CODING ggG/ggC G/G 25.0% 4 GG CC CC CC -chr1:1907552 [A/G] chr1 1907552 Cc01_g01250:197 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 37.5% 4 AA AG AG GA -chr1:1907554 [G/A] chr1 1907554 Cc01_g01250:199 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 25.0% 4 GG GG AG GA -chr1:1907571 [A/G] chr1 1907571 Cc01_g01250:216 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG GA -chr1:1907577 [G/A] chr1 1907577 Cc01_g01250:222 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 GG GG GA GG -chr1:1907584 [A/G] chr1 1907584 Cc01_g01250:229 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 37.5% 4 AA AG AG GA -chr1:1907613 [C/T] chr1 1907613 Cc01_g01250:258 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC CT CT TC -chr1:1907628 [G/A] chr1 1907628 Cc01_g01250:273 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA AG -chr1:1907636 [C/G] chr1 1907636 Cc01_g01250:281 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 37.5% 4 CC CG CG GC -chr1:1907643 [A/G] chr1 1907643 Cc01_g01250:288 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG GA -chr1:1907649 [G/T] chr1 1907649 Cc01_g01250:294 exon SYNONYMOUS_CODING ctG/ctT L/L 37.5% 4 GG GT GT TG -chr1:1907663 [A/T] chr1 1907663 Cc01_g01250:308 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA TA AA -chr1:1907745 [T/G] chr1 1907745 Cc01_g01250:390 exon SYNONYMOUS_CODING ggT/ggG G/G 25.0% 4 TT GG GG GG -chr1:1907751 [G/A] chr1 1907751 Cc01_g01250:396 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 GG GA GA GA -chr1:1907865 [G/A] chr1 1907865 Cc01_g01250:438 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA AA AA -chr1:1907867 [C/T] chr1 1907867 Cc01_g01250:440 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 50.0% 4 CC CT TT CT -chr1:1907913 [G/A] chr1 1907913 Cc01_g01250:486 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG AG GG GG -chr1:1907925 [C/T] chr1 1907925 Cc01_g01250:498 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 CC CT CT CT -chr1:1907951 [T/A] chr1 1907951 Cc01_g01250:524 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 37.5% 4 TT TA TA TA -chr1:1907955 [C/T] chr1 1907955 Cc01_g01250:528 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 CC CT CT CT -chr1:1907970 [G/A] chr1 1907970 Cc01_g01250:543 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG AG GG -chr1:1907971 [G/C] chr1 1907971 Cc01_g01250:544 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 GG GG CG GG -chr1:1907976 [A/G] chr1 1907976 Cc01_g01250:549 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 AA GA AA GA -chr1:1907998 [G/A] chr1 1907998 Cc01_g01250:571 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG AG GG -chr1:1908013 [C/G] chr1 1908013 Cc01_g01250:586 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CC GC -chr1:1908043 [T/C] chr1 1908043 Cc01_g01250:616 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC TC TC -chr1:1908051 [G/C] chr1 1908051 Cc01_g01250:624 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG CG GG CG -chr1:1908071 [A/T] chr1 1908071 Cc01_g01250:644 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 AA TT TT TT -chr1:1908072 [A/T] chr1 1908072 Cc01_g01250:645 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA AT AT AT -chr1:1908080 [G/C] chr1 1908080 Cc01_g01250:653 exon NON_SYNONYMOUS_CODING gGc/gCc G/A 37.5% 4 GG GC GC GC -chr1:1908088 [A/G] chr1 1908088 Cc01_g01250:661 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 37.5% 4 AA AG AG AG -chr1:1908103 [C/T] chr1 1908103 Cc01_g01250:676 exon SYNONYMOUS_CODING Cta/Tta L/L 37.5% 4 CC CT CT CT -chr1:1908119 [G/A] chr1 1908119 Cc01_g01250:692 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG GG GA GA -chr1:1908120 [G/T] chr1 1908120 Cc01_g01250:693 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG GT GT -chr1:1908140 [A/G] chr1 1908140 Cc01_g01250:713 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AA GA -chr1:1908345 [G/C] chr1 1908345 Cc01_g01250:738 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 25.0% 4 GG GC GG GC -chr1:1908360 [C/G] chr1 1908360 Cc01_g01250:753 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC CG GC -chr1:1908383 [A/T] chr1 1908383 Cc01_g01250:776 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 37.5% 4 AA TA AT TA -chr1:1908403 [C/G] chr1 1908403 Cc01_g01250:796 exon NON_SYNONYMOUS_CODING Ctc/Gtc L/V 12.5% 4 CC CC GC CC -chr1:1908407 [G/A] chr1 1908407 Cc01_g01250:800 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG -chr1:1908410 [G/A] chr1 1908410 Cc01_g01250:803 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG -chr1:1908447 [T/C] chr1 1908447 Cc01_g01250:840 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CT TC CT -chr1:1908449 [T/C] chr1 1908449 Cc01_g01250:842 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 TT TC TT TT -chr1:1908471 [C/G] chr1 1908471 Cc01_g01250:864 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 37.5% 4 CC GC CG GC -chr1:1908474 [C/T] chr1 1908474 Cc01_g01250:867 exon SYNONYMOUS_CODING tcC/tcT S/S 37.5% 4 CC TC CT TC -chr1:1908527 [T/C] chr1 1908527 Cc01_g01250:920 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT CC CC CC -chr1:1908549 [A/G] chr1 1908549 Cc01_g01250:942 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA -chr1:1908765 [G/A] chr1 1908765 Cc01_g01250:954 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG -chr1:1908789 [C/A] chr1 1908789 Cc01_g01250:978 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 CC CA CA CA -chr1:1908791 [A/C] chr1 1908791 Cc01_g01250:980 exon NON_SYNONYMOUS_CODING aAg/aCg K/T 12.5% 4 AA CA AA AA -chr1:1908792 [G/A] chr1 1908792 Cc01_g01250:981 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 GG AA AA AA -chr1:1908828 [C/T] chr1 1908828 Cc01_g01250:1017 exon SYNONYMOUS_CODING taC/taT Y/Y 37.5% 4 CC CT CT CT -chr1:1908831 [G/A] chr1 1908831 Cc01_g01250:1020 exon SYNONYMOUS_CODING gtG/gtA V/V 37.5% 4 GG GA GA GA -chr1:1908907 [A/G] chr1 1908907 Cc01_g01250:1096 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 AA GG GG GG -chr1:1908909 [A/G] chr1 1908909 Cc01_g01250:1098 exon NON_SYNONYMOUS_CODING atA/atG I/M 37.5% 4 AA AG AG AG -chr1:1908915 [T/C] chr1 1908915 Cc01_g01250:1104 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT TC TC TC -chr1:1908942 [G/A] chr1 1908942 Cc01_g01250:1131 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG AA AA AA -chr1:1908962 [G/A] chr1 1908962 Cc01_g01250:1151 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG AG -chr1:1908976 [A/G] chr1 1908976 Cc01_g01250:1165 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 12.5% 4 AA AA GA AA -chr1:1909020 [A/G] chr1 1909020 Cc01_g01250:1209 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA AA AG AA -chr1:1909071 [A/C] chr1 1909071 Cc01_g01250:1260 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA AC NN AC -chr1:1909091 [G/A] chr1 1909091 Cc01_g01250:1280 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 GG AG GA AG -chr1:1909122 [G/A] chr1 1909122 Cc01_g01250:1311 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG AA AA AA -chr1:1909165 [C/A] chr1 1909165 Cc01_g01250:1354 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CC CA CC -chr1:1909186 [G/A] chr1 1909186 Cc01_g01250:1375 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GG GA GG -chr1:1909203 [C/T] chr1 1909203 Cc01_g01250:1392 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC TC CC -chr1:1909210 [G/T] chr1 1909210 Cc01_g01250:1399 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GT GG GG -chr1:1909247 [G/C] chr1 1909247 Cc01_g01250:1436 exon NON_SYNONYMOUS_CODING tGt/tCt C/S 25.0% 4 GG CC CC CC -chr1:1909284 [G/A] chr1 1909284 Cc01_g01250:1473 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA GA GA -chr1:1909294 [C/G] chr1 1909294 Cc01_g01250:1483 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC GG GG GG -chr1:1909302 [T/C] chr1 1909302 Cc01_g01250:1491 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT CC CC CC -chr1:1909308 [C/T] chr1 1909308 Cc01_g01250:1497 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CC CC CT -chr1:1909332 [C/T] chr1 1909332 Cc01_g01250:1521 exon SYNONYMOUS_CODING tgC/tgT C/C 37.5% 4 CC TC TC TC -chr1:1909361 [G/A] chr1 1909361 Cc01_g01250:1550 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 GG GA GA GA -chr1:1909447 [G/A] chr1 1909447 Cc01_g01250:1636 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 37.5% 4 GG GA GA GA -chr1:1909475 [C/T] chr1 1909475 Cc01_g01250:1664 exon NON_SYNONYMOUS_CODING aCc/aTc T/I 25.0% 4 CC TT TT TT -chr1:1909487 [A/G] chr1 1909487 Cc01_g01250:1676 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA GA AA GA -chr1:1909530 [A/G] chr1 1909530 Cc01_g01250:1719 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AG AG AG -chr1:1909566 [A/G] chr1 1909566 Cc01_g01250:1755 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA GA AA AA -chr1:1909582 [C/T] chr1 1909582 Cc01_g01250:1771 exon STOP_GAINED Cga/Tga R/1 12.5% 4 CC CC CC CT -chr1:1909609 [G/A] chr1 1909609 Cc01_g01250:1798 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GG GG AG -chr1:1909635 [C/T] chr1 1909635 Cc01_g01250:1824 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 CC CT CT CT -chr1:1909662 [C/T] chr1 1909662 Cc01_g01250:1851 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC CT TT CT -chr1:1909686 [C/T] chr1 1909686 Cc01_g01250:1875 exon SYNONYMOUS_CODING ccC/ccT P/P 37.5% 4 CC CT CT CT -chr1:1909689 [A/T] chr1 1909689 Cc01_g01250:1878 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA TA AA -chr1:1909703 [A/G] chr1 1909703 Cc01_g01250:1892 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA -chr1:1909742 [G/T] chr1 1909742 Cc01_g01250:1931 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 37.5% 4 GG GT GT TG -chr1:1909746 [T/G] chr1 1909746 Cc01_g01250:1935 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 TT TG TG GT -chr1:1909748 [G/A] chr1 1909748 Cc01_g01250:1937 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 25.0% 4 GG AA AA AA -chr1:1909805 [G/A] chr1 1909805 Cc01_g01250:1994 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 37.5% 4 GG GA GA AG -chr1:1909856 [C/T] chr1 1909856 Cc01_g01250:2045 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 25.0% 4 CC TC CC CT -chr1:1909857 [A/T] chr1 1909857 Cc01_g01250:2046 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 AA TA AA AT -chr1:1909887 [G/A] chr1 1909887 Cc01_g01250:2076 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG AG GG GG -chr1:1909896 [A/G] chr1 1909896 Cc01_g01250:2085 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GG GG GG -chr1:1909917 [A/G] chr1 1909917 Cc01_g01250:2106 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG AG AG -chr1:1909941 [G/A] chr1 1909941 Cc01_g01250:2130 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GA GA -chr1:1909992 [C/G] chr1 1909992 Cc01_g01250:2181 exon NON_SYNONYMOUS_CODING agC/agG S/R 12.5% 4 CC GC CC CC -chr1:2012155 [G/A] chr1 2012155 Cc01_g01280:207 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 GG GA NN GG -chr1:2012138 [G/A] chr1 2012138 Cc01_g01280:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG AA AA AA -chr1:2012066 [A/G] chr1 2012066 Cc01_g01280:296 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 33.3% 3 AA GG GG NN -chr1:2011950 [C/G] chr1 2011950 Cc01_g01280:412 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG CC CC -chr1:2011879 [G/A] chr1 2011879 Cc01_g01280:483 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GA NN GG -chr1:2029017 [G/C] chr1 2029017 Cc01_g01300:239 exon NON_SYNONYMOUS_CODING gCg/gGg A/G 37.5% 4 GG CC CC GC -chr1:2028341 [A/G] chr1 2028341 Cc01_g01300:366 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG GG AG -chr1:2028339 [G/A] chr1 2028339 Cc01_g01300:368 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 GG AG GG GG -chr1:2028335 [A/C] chr1 2028335 Cc01_g01300:372 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 25.0% 4 AA CC CC CC -chr1:2028322 [C/T] chr1 2028322 Cc01_g01300:385 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC TC CC CC -chr1:2028306 [C/G] chr1 2028306 Cc01_g01300:401 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 CC CC CG CC -chr1:2028289 [T/C] chr1 2028289 Cc01_g01300:418 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 TT CC NN CC -chr1:2084455 [A/G] chr1 2084455 Cc01_g01330:36 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 AA AG AG GG -chr1:2084476 [G/C] chr1 2084476 Cc01_g01330:57 exon NON_SYNONYMOUS_CODING atG/atC M/I 37.5% 4 GG CG CC CC -chr1:2084479 [C/T] chr1 2084479 Cc01_g01330:60 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC TC CC CC -chr1:2084490 [C/A] chr1 2084490 Cc01_g01330:71 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC AC CC CC -chr1:2084532 [A/G] chr1 2084532 Cc01_g01330:113 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 50.0% 4 AA AG AG GG -chr1:2084551 [A/G] chr1 2084551 Cc01_g01330:132 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 AA GA AA AA -chr1:2084565 [C/G] chr1 2084565 Cc01_g01330:146 exon NON_SYNONYMOUS_CODING tCc/tGc S/C 50.0% 4 CC CG CG GG -chr1:2084606 [G/T] chr1 2084606 Cc01_g01330:187 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 50.0% 4 GG GT GT TT -chr1:2084666 [A/G] chr1 2084666 Cc01_g01330:247 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG AG GG -chr1:2084667 [C/T] chr1 2084667 Cc01_g01330:248 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 CC TT TT TT -chr1:2084687 [G/A] chr1 2084687 Cc01_g01330:268 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 50.0% 4 GG GA GA AA -chr1:2084690 [C/G] chr1 2084690 Cc01_g01330:271 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC -chr1:2084692 [A/G] chr1 2084692 Cc01_g01330:273 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA -chr1:2084718 [C/T] chr1 2084718 Cc01_g01330:299 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 33.3% 3 CC TT TT NN -chr1:2084791 [T/A] chr1 2084791 Cc01_g01330:372 exon SYNONYMOUS_CODING gcT/gcA A/A 12.5% 4 TT TT TA TT -chr1:2084820 [A/G] chr1 2084820 Cc01_g01330:401 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AA GA AG -chr1:2084834 [G/A] chr1 2084834 Cc01_g01330:415 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG AG -chr1:2084842 [G/C] chr1 2084842 Cc01_g01330:423 exon NON_SYNONYMOUS_CODING atG/atC M/I 25.0% 4 GG GG GC CG -chr1:2084851 [A/G] chr1 2084851 Cc01_g01330:432 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AA GA AG -chr1:2084863 [C/T] chr1 2084863 Cc01_g01330:444 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC CC TC CC -chr1:2084924 [A/T] chr1 2084924 Cc01_g01330:505 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 33.3% 3 AA AT AT NN -chr1:2085060 [T/C] chr1 2085060 Cc01_g01330:641 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 50.0% 2 TT NN CC NN -chr1:2085102 [A/C] chr1 2085102 Cc01_g01330:683 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 25.0% 4 AA AA CC AA -chr1:2085109 [T/G] chr1 2085109 Cc01_g01330:690 exon NON_SYNONYMOUS_CODING atT/atG I/M 25.0% 4 TT TT GG TT -chr1:2085145 [G/A] chr1 2085145 Cc01_g01330:726 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG GG AA GG -chr1:2085162 [C/G] chr1 2085162 Cc01_g01330:743 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 37.5% 4 CC CG GG CC -chr1:2085194 [G/A] chr1 2085194 Cc01_g01330:775 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GA GG GA -chr1:2085203 [C/A] chr1 2085203 Cc01_g01330:784 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 37.5% 4 CC CA CA CA -chr1:2085208 [A/G] chr1 2085208 Cc01_g01330:789 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG -chr1:2085218 [G/C] chr1 2085218 Cc01_g01330:799 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 37.5% 4 GG GC GG CC -chr1:2085227 [T/G] chr1 2085227 Cc01_g01330:808 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 37.5% 4 TT TG TT GG -chr1:2085271 [A/G] chr1 2085271 Cc01_g01330:852 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AG AA NN -chr1:2085356 [C/G] chr1 2085356 Cc01_g01330:937 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 16.7% 3 CC CC CG NN -chr1:2085358 [T/A] chr1 2085358 Cc01_g01330:939 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT TT TA NN -chr1:2086315 [G/T] chr1 2086315 Cc01_g01330:1073 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 25.0% 4 GG GG GT GT -chr1:2086354 [A/G] chr1 2086354 Cc01_g01330:1112 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA GG GA AA -chr1:2086380 [C/A] chr1 2086380 Cc01_g01330:1138 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 37.5% 4 CC CC CA AA -chr1:2086424 [A/G] chr1 2086424 Cc01_g01330:1182 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA AA AG GG -chr1:2086438 [C/T] chr1 2086438 Cc01_g01330:1196 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 CC TT TT TT -chr1:2086581 [G/T] chr1 2086581 Cc01_g01330:1261 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG -chr1:2086594 [T/C] chr1 2086594 Cc01_g01330:1274 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 25.0% 4 TT TT TC TC -chr1:2086608 [T/C] chr1 2086608 Cc01_g01330:1288 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 37.5% 4 TT TC TC TC -chr1:2086613 [T/C] chr1 2086613 Cc01_g01330:1293 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT TC TC TC -chr1:2086637 [C/A] chr1 2086637 Cc01_g01330:1317 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 CC CA CC AA -chr1:2086679 [G/A] chr1 2086679 Cc01_g01330:1359 exon SYNONYMOUS_CODING gaG/gaA E/E 12.5% 4 GG GG GG GA -chr1:2086682 [C/T] chr1 2086682 Cc01_g01330:1362 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CC CT CT -chr1:2086716 [G/A] chr1 2086716 Cc01_g01330:1396 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GG AA -chr1:2086756 [G/A] chr1 2086756 Cc01_g01330:1436 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GG GG GA -chr1:2086758 [C/G] chr1 2086758 Cc01_g01330:1438 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 25.0% 4 CC CC CG GC -chr1:2086789 [T/A] chr1 2086789 Cc01_g01330:1469 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 TT AA AA AA -chr1:2086811 [A/G] chr1 2086811 Cc01_g01330:1491 exon NON_SYNONYMOUS_CODING atA/atG I/M 25.0% 4 AA GG AA AA -chr1:2086840 [T/A] chr1 2086840 Cc01_g01330:1520 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT AA TT TT -chr1:2093852 [C/T] chr1 2093852 Cc01_g01340:4 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 CC CT NN CC -chr1:2093847 [C/A] chr1 2093847 Cc01_g01340:9 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 4 CC AC AA CA -chr1:2093810 [G/A] chr1 2093810 Cc01_g01340:46 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG AG GG GG -chr1:2093799 [A/G] chr1 2093799 Cc01_g01340:57 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GA GG AA -chr1:2093778 [A/G] chr1 2093778 Cc01_g01340:78 exon SYNONYMOUS_CODING gaT/gaC D/D 16.7% 3 AA AA NN GA -chr1:2093758 [G/A] chr1 2093758 Cc01_g01340:98 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 33.3% 3 GG GA NN GA -chr1:2093731 [C/A] chr1 2093731 Cc01_g01340:125 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 16.7% 3 CC CC NN CA -chr1:2093721 [C/G] chr1 2093721 Cc01_g01340:135 exon SYNONYMOUS_CODING tcG/tcC S/S 50.0% 4 CC CG GG CG -chr1:2093714 [A/C] chr1 2093714 Cc01_g01340:142 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 50.0% 4 AA AC CC AC -chr1:2093686 [A/G] chr1 2093686 Cc01_g01340:170 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 50.0% 4 AA AG GG AG -chr1:2093684 [T/C] chr1 2093684 Cc01_g01340:172 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 TT TC CC TC -chr1:2093683 [G/C] chr1 2093683 Cc01_g01340:173 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 12.5% 4 GG GC GG GG -chr1:2093672 [C/A] chr1 2093672 Cc01_g01340:184 exon STOP_GAINED Gag/Tag E/2 37.5% 4 CC CA CA CA -chr1:2093663 [G/A] chr1 2093663 Cc01_g01340:193 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 12.5% 4 GG GG GG AG -chr1:2093646 [A/G] chr1 2093646 Cc01_g01340:210 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 AA AG AG AA -chr1:2093644 [T/C] chr1 2093644 Cc01_g01340:212 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 37.5% 4 TT TC TC TC -chr1:2093642 [C/T] chr1 2093642 Cc01_g01340:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TC TC TC -chr1:2093636 [T/G] chr1 2093636 Cc01_g01340:220 exon NON_SYNONYMOUS_CODING Acc/Ccc T/P 25.0% 4 TT TG TG TT -chr1:2093635 [G/T] chr1 2093635 Cc01_g01340:221 exon NON_SYNONYMOUS_CODING aCc/aAc T/N 25.0% 4 GG GT GG GT -chr1:2093634 [G/A] chr1 2093634 Cc01_g01340:222 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG GA GG GG -chr1:2093633 [C/T] chr1 2093633 Cc01_g01340:223 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 CC CC CC CT -chr1:2093602 [A/T] chr1 2093602 Cc01_g01340:254 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 33.3% 3 AA AT NN AT -chr1:2093600 [C/G] chr1 2093600 Cc01_g01340:256 exon NON_SYNONYMOUS_CODING Gga/Cga G/R 16.7% 3 CC CG NN CC -chr1:2093588 [T/G] chr1 2093588 Cc01_g01340:268 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 16.7% 3 TT TG NN TT -chr1:2093575 [A/G] chr1 2093575 Cc01_g01340:281 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 50.0% 3 AA GG NN AG -chr1:2093569 [G/A] chr1 2093569 Cc01_g01340:287 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 16.7% 3 GG GG NN GA -chr1:2093565 [G/A] chr1 2093565 Cc01_g01340:291 exon SYNONYMOUS_CODING gaC/gaT D/D 16.7% 3 GG GG NN GA -chr1:2093525 [C/G] chr1 2093525 Cc01_g01340:331 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 50.0% 3 CC GG NN CG -chr1:2093515 [T/C] chr1 2093515 Cc01_g01340:341 exon SYNONYMOUS_STOP tAa/tGa 1/1 33.3% 3 TT CC NN TT -chr1:2095269 [G/A] chr1 2095269 Cc01_g01350:16 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 GG GA GG GG -chr1:2095295 [A/G] chr1 2095295 Cc01_g01350:42 exon SYNONYMOUS_CODING cgA/cgG R/R 12.5% 4 AA AG AA AA -chr1:2095321 [A/T] chr1 2095321 Cc01_g01350:68 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA AT AA AA -chr1:2095431 [C/A] chr1 2095431 Cc01_g01350:178 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 12.5% 4 CC CA CC CC -chr1:2095629 [C/T] chr1 2095629 Cc01_g01350:376 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 CC CC CT CT -chr1:2095745 [G/A] chr1 2095745 Cc01_g01350:492 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 GG GA AA GG -chr1:2095959 [C/G] chr1 2095959 Cc01_g01350:706 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 12.5% 4 CC CC CG CC -chr1:2095960 [A/G] chr1 2095960 Cc01_g01350:707 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG GA AA -chr1:2095964 [C/T] chr1 2095964 Cc01_g01350:711 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC TC CC -chr1:2095974 [C/T] chr1 2095974 Cc01_g01350:721 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC -chr1:2095975 [A/C] chr1 2095975 Cc01_g01350:722 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 AA AA CA AA -chr1:2095983 [A/C] chr1 2095983 Cc01_g01350:730 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 12.5% 4 AA AC AA AA -chr1:2096351 [T/A] chr1 2096351 Cc01_g01350:980 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT -chr1:2096710 [C/G] chr1 2096710 Cc01_g01350:1261 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CC CG CC -chr1:2100328 [A/C] chr1 2100328 Cc01_g01360:24 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 50.0% 3 AA NN AC CC -chr1:2100313 [T/A] chr1 2100313 Cc01_g01360:39 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA -chr1:2100304 [T/C] chr1 2100304 Cc01_g01360:48 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 TT CC CC TC -chr1:2100300 [C/T] chr1 2100300 Cc01_g01360:52 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 25.0% 4 CC TT TT TT -chr1:2100299 [G/A] chr1 2100299 Cc01_g01360:53 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG AA AA GA -chr1:2100295 [A/G] chr1 2100295 Cc01_g01360:57 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 AA GG GG AG -chr1:2100286 [A/G] chr1 2100286 Cc01_g01360:66 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG GG AA -chr1:2100277 [C/T] chr1 2100277 Cc01_g01360:75 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT TT TT -chr1:2100255 [C/T] chr1 2100255 Cc01_g01360:97 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC TT CT TT -chr1:2100252 [A/T] chr1 2100252 Cc01_g01360:100 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 37.5% 4 AA TT AT TT -chr1:2100249 [C/T] chr1 2100249 Cc01_g01360:103 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 CC TT CT TT -chr1:2100244 [A/T] chr1 2100244 Cc01_g01360:108 exon SYNONYMOUS_CODING ctT/ctA L/L 37.5% 4 AA TT AT TT -chr1:2100237 [T/C] chr1 2100237 Cc01_g01360:115 exon NON_SYNONYMOUS_CODING Acg/Gcg T/A 37.5% 4 TT CC TC CC -chr1:2100226 [G/A] chr1 2100226 Cc01_g01360:126 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 GG NN GG AA -chr1:2100223 [A/C] chr1 2100223 Cc01_g01360:129 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 50.0% 3 AA NN AC CC -chr1:2100218 [C/T] chr1 2100218 Cc01_g01360:134 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 2 CC NN CT NN -chr1:2100189 [T/C] chr1 2100189 Cc01_g01360:163 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 TT CC TT TC -chr1:2100184 [G/A] chr1 2100184 Cc01_g01360:168 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GA GG GA -chr1:2100164 [A/G] chr1 2100164 Cc01_g01360:188 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 3 AA GG NN AG -chr1:2100139 [A/G] chr1 2100139 Cc01_g01360:213 exon SYNONYMOUS_CODING agT/agC S/S 25.0% 2 AA NN NN AG -chr1:2105898 [A/G] chr1 2105898 Cc01_g01370:23 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 25.0% 4 AA AG AA AG -chr1:2105943 [C/G] chr1 2105943 Cc01_g01370:68 exon NON_SYNONYMOUS_CODING gCa/gGa A/G 12.5% 4 CC CC CG CC -chr1:2105974 [T/G] chr1 2105974 Cc01_g01370:99 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT TG TT TG -chr1:2105998 [T/C] chr1 2105998 Cc01_g01370:123 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT CT TT -chr1:2106006 [G/C] chr1 2106006 Cc01_g01370:131 exon NON_SYNONYMOUS_CODING aGc/aCc S/T 50.0% 4 GG CC GC GC -chr1:2106086 [G/A] chr1 2106086 Cc01_g01370:211 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG GA GG -chr1:2106188 [G/C] chr1 2106188 Cc01_g01370:313 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 25.0% 4 GG GC GG GC -chr1:2106190 [G/A] chr1 2106190 Cc01_g01370:315 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA -chr1:2106216 [C/G] chr1 2106216 Cc01_g01370:341 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC CG CC CG -chr1:2106220 [T/C] chr1 2106220 Cc01_g01370:345 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT TC TT TC -chr1:2106236 [T/C] chr1 2106236 Cc01_g01370:361 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT TC TT TC -chr1:2106264 [G/A] chr1 2106264 Cc01_g01370:389 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GG GA GG -chr1:2106271 [C/A] chr1 2106271 Cc01_g01370:396 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA -chr1:2106279 [G/A] chr1 2106279 Cc01_g01370:404 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 GG GG GA GA -chr1:2106291 [A/C] chr1 2106291 Cc01_g01370:416 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 37.5% 4 AA AC AC AC -chr1:2106302 [A/G] chr1 2106302 Cc01_g01370:427 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 50.0% 4 AA AG GG AG -chr1:2106324 [T/G] chr1 2106324 Cc01_g01370:449 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 37.5% 4 TT TG TG TG -chr1:2106332 [C/G] chr1 2106332 Cc01_g01370:457 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC -chr1:2106375 [A/G] chr1 2106375 Cc01_g01370:500 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 37.5% 4 AA AG AG AG -chr1:2106435 [A/T] chr1 2106435 Cc01_g01370:560 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 25.0% 4 AA AT AA AT -chr1:2106441 [T/G] chr1 2106441 Cc01_g01370:566 exon NON_SYNONYMOUS_CODING aTg/aGg M/R 25.0% 4 TT TG TT TG -chr1:2106443 [C/G] chr1 2106443 Cc01_g01370:568 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 12.5% 4 CC GC CC CC -chr1:2106602 [A/G] chr1 2106602 Cc01_g01370:633 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG AG AG -chr1:2106604 [T/G] chr1 2106604 Cc01_g01370:635 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 TT TG TG TG -chr1:2106695 [G/C] chr1 2106695 Cc01_g01370:726 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 GG CC GG GG -chr1:2106696 [A/G] chr1 2106696 Cc01_g01370:727 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 AA GG GG AA -chr1:2106708 [G/A] chr1 2106708 Cc01_g01370:739 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG -chr1:2106774 [A/G] chr1 2106774 Cc01_g01370:805 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AA AG -chr1:2106839 [T/C] chr1 2106839 Cc01_g01370:870 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 TT TC TT TC -chr1:2106857 [T/A] chr1 2106857 Cc01_g01370:888 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 50.0% 4 TT AA TA TA -chr1:2106878 [G/A] chr1 2106878 Cc01_g01370:909 exon SYNONYMOUS_CODING gaG/gaA E/E 37.5% 4 GG GA GA GA -chr1:2106908 [A/G] chr1 2106908 Cc01_g01370:939 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA GG AA AA -chr1:2107068 [C/A] chr1 2107068 Cc01_g01370:980 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC -chr1:2107109 [G/C] chr1 2107109 Cc01_g01370:1021 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GC GG -chr1:2107131 [A/C] chr1 2107131 Cc01_g01370:1043 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 25.0% 4 AA CA AA AC -chr1:2107150 [G/A] chr1 2107150 Cc01_g01370:1062 exon STOP_GAINED tgG/tgA W/4 12.5% 4 GG GA GG GG -chr1:2107161 [T/C] chr1 2107161 Cc01_g01370:1073 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 TT TT CT TT -chr1:2107171 [C/G] chr1 2107171 Cc01_g01370:1083 exon NON_SYNONYMOUS_CODING aaC/aaG N/K 12.5% 4 CC CC GC CC -chr1:2107215 [G/A] chr1 2107215 Cc01_g01370:1127 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 50.0% 4 GG AA GA GA -chr1:2107325 [A/C] chr1 2107325 Cc01_g01370:1159 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 AA AC AC AC -chr1:2107345 [A/G] chr1 2107345 Cc01_g01370:1179 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG AG AG -chr1:2107361 [T/A] chr1 2107361 Cc01_g01370:1195 exon NON_SYNONYMOUS_CODING Tct/Act S/T 37.5% 4 TT TA TA TA -chr1:2107390 [A/C] chr1 2107390 Cc01_g01370:1224 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA AC -chr1:2107405 [T/A] chr1 2107405 Cc01_g01370:1239 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA -chr1:2107431 [C/T] chr1 2107431 Cc01_g01370:1265 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 CC CT CT CT -chr1:2107467 [A/T] chr1 2107467 Cc01_g01370:1301 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 AA TA AA AA -chr1:2107472 [G/A] chr1 2107472 Cc01_g01370:1306 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 GG GG AG GG -chr1:2107516 [T/C] chr1 2107516 Cc01_g01370:1350 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 TT CC TC TC -chr1:2107607 [C/T] chr1 2107607 Cc01_g01370:1441 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT CT CT -chr1:2117223 [A/G] chr1 2117223 Cc01_g01380:117 exon SYNONYMOUS_CODING cgT/cgC R/R 33.3% 3 AA GG NN GG -chr1:2117210 [T/G] chr1 2117210 Cc01_g01380:130 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 33.3% 3 TT GG NN GG -chr1:2117175 [C/G] chr1 2117175 Cc01_g01380:165 exon SYNONYMOUS_CODING ctG/ctC L/L 50.0% 2 CC GG NN NN -chr1:2117171 [C/T] chr1 2117171 Cc01_g01380:169 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 CC TT NN NN -chr1:2116944 [A/G] chr1 2116944 Cc01_g01380:240 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 AA NN NN GG -chr1:2116934 [T/A] chr1 2116934 Cc01_g01380:250 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 TT NN NN AA -chr1:2116932 [C/G] chr1 2116932 Cc01_g01380:252 exon NON_SYNONYMOUS_CODING atG/atC M/I 50.0% 2 CC NN NN GG -chr1:2116917 [C/A] chr1 2116917 Cc01_g01380:267 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 CC NN NN AA -chr1:2116877 [T/A] chr1 2116877 Cc01_g01380:307 exon NON_SYNONYMOUS_CODING Ata/Tta I/L 50.0% 2 TT NN NN AA -chr1:2116873 [T/C] chr1 2116873 Cc01_g01380:311 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 TT NN NN CC -chr1:2116861 [A/G] chr1 2116861 Cc01_g01380:323 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 50.0% 2 AA NN NN GG -chr1:2169162 [C/G] chr1 2169162 Cc01_g01390:5 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 12.5% 4 CC CG CC CC -chr1:2169167 [C/G] chr1 2169167 Cc01_g01390:10 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 37.5% 4 CC CG CG CG -chr1:2169279 [A/G] chr1 2169279 Cc01_g01390:122 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 25.0% 4 AA GG GG GG -chr1:2169286 [A/T] chr1 2169286 Cc01_g01390:129 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA AA AT AA -chr1:2169346 [T/C] chr1 2169346 Cc01_g01390:189 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TC TC TT -chr1:2169353 [G/A] chr1 2169353 Cc01_g01390:196 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG -chr1:2169630 [T/A] chr1 2169630 Cc01_g01390:473 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT AA TA AA -chr1:2169828 [C/A] chr1 2169828 Cc01_g01390:671 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CA CA CC -chr1:2169829 [G/C] chr1 2169829 Cc01_g01390:672 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GC GG -chr1:2169862 [C/T] chr1 2169862 Cc01_g01390:705 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC -chr1:2169958 [T/C] chr1 2169958 Cc01_g01390:801 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT -chr1:2169967 [C/T] chr1 2169967 Cc01_g01390:810 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 CC CC CT CC -chr1:2170037 [G/C] chr1 2170037 Cc01_g01390:880 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 12.5% 4 GG GG GC GG -chr1:2170043 [G/A] chr1 2170043 Cc01_g01390:886 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GA GA GG -chr1:2170057 [C/T] chr1 2170057 Cc01_g01390:900 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC TC CC -chr1:2170129 [T/C] chr1 2170129 Cc01_g01390:972 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TT TC TT -chr1:2170192 [G/T] chr1 2170192 Cc01_g01390:1035 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GT GG GG -chr1:2170204 [T/C] chr1 2170204 Cc01_g01390:1047 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT -chr1:2170362 [A/T] chr1 2170362 Cc01_g01390:1080 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 AA AT AT AA -chr1:2170446 [T/C] chr1 2170446 Cc01_g01390:1164 exon SYNONYMOUS_CODING tgT/tgC C/C 37.5% 4 TT CC TC CC -chr1:2170635 [T/C] chr1 2170635 Cc01_g01390:1275 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 TT CC TT CC -chr1:2170650 [T/C] chr1 2170650 Cc01_g01390:1290 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT -chr1:2170761 [T/G] chr1 2170761 Cc01_g01390:1401 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 37.5% 4 TT GG TG GG -chr1:2170780 [C/T] chr1 2170780 Cc01_g01390:1420 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CT CC -chr1:2170800 [G/A] chr1 2170800 Cc01_g01390:1440 exon SYNONYMOUS_CODING tcG/tcA S/S 50.0% 4 GG AA GG AA -chr1:2170865 [C/A] chr1 2170865 Cc01_g01390:1505 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CA CC -chr1:2170868 [A/C] chr1 2170868 Cc01_g01390:1508 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 4 AA CC AA CC -chr1:2170873 [A/G] chr1 2170873 Cc01_g01390:1513 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 12.5% 4 AA AG AA AA -chr1:2170884 [C/T] chr1 2170884 Cc01_g01390:1524 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 4 CC TT CC TT -chr1:2174798 [C/T] chr1 2174798 Cc01_g01400:21 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC CT CT TT -chr1:2174809 [A/G] chr1 2174809 Cc01_g01400:32 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AG AG -chr1:2174843 [G/A] chr1 2174843 Cc01_g01400:66 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 GG GG GA GA -chr1:2174851 [G/A] chr1 2174851 Cc01_g01400:74 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 GG GG AG GG -chr1:2174873 [C/A] chr1 2174873 Cc01_g01400:96 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 25.0% 4 CC CC CA CA -chr1:2174883 [T/C] chr1 2174883 Cc01_g01400:106 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 TT TT TC TC -chr1:2174888 [T/C] chr1 2174888 Cc01_g01400:111 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TC TC -chr1:2174899 [T/C] chr1 2174899 Cc01_g01400:122 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 12.5% 4 TT TT TT CT -chr1:2174901 [C/T] chr1 2174901 Cc01_g01400:124 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 CC CC CT CT -chr1:2174903 [T/C] chr1 2174903 Cc01_g01400:126 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TT TC TC -chr1:2174906 [T/G] chr1 2174906 Cc01_g01400:129 exon SYNONYMOUS_CODING acT/acG T/T 25.0% 4 TT TT TG TG -chr1:2174908 [C/A] chr1 2174908 Cc01_g01400:131 exon NON_SYNONYMOUS_CODING aCa/aAa T/K 25.0% 4 CC CC CA CA -chr1:2174912 [T/G] chr1 2174912 Cc01_g01400:135 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 12.5% 4 TT TG TT TT -chr1:2174940 [C/A] chr1 2174940 Cc01_g01400:163 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CC CA CA -chr1:2174949 [T/G] chr1 2174949 Cc01_g01400:172 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 25.0% 4 TT TT TG TG -chr1:2174958 [G/A] chr1 2174958 Cc01_g01400:181 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 GG GG GA GA -chr1:2174961 [C/T] chr1 2174961 Cc01_g01400:184 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 37.5% 4 CC CC TT CT -chr1:2174991 [G/A] chr1 2174991 Cc01_g01400:214 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG GA GG GG -chr1:2174992 [A/G] chr1 2174992 Cc01_g01400:215 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA GA AA GA -chr1:2174997 [C/T] chr1 2174997 Cc01_g01400:220 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 50.0% 4 CC CT CT TT -chr1:2174999 [T/C] chr1 2174999 Cc01_g01400:222 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC TC -chr1:2175021 [G/C] chr1 2175021 Cc01_g01400:244 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 25.0% 4 GG GG GC GC -chr1:2175025 [C/G] chr1 2175025 Cc01_g01400:248 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 25.0% 4 CC CC CG CG -chr1:2175026 [T/C] chr1 2175026 Cc01_g01400:249 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 TT TT TC TC -chr1:2175072 [A/C] chr1 2175072 Cc01_g01400:295 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AC AA AA -chr1:2175151 [T/G] chr1 2175151 Cc01_g01400:374 exon NON_SYNONYMOUS_CODING cTt/cGt L/R 12.5% 4 TT TT TT TG -chr1:2175157 [C/A] chr1 2175157 Cc01_g01400:380 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 12.5% 4 CC CC CC AC -chr1:2175167 [C/T] chr1 2175167 Cc01_g01400:390 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC -chr1:2175183 [A/G] chr1 2175183 Cc01_g01400:406 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AG AA AA -chr1:2175248 [C/T] chr1 2175248 Cc01_g01400:471 exon SYNONYMOUS_CODING taC/taT Y/Y 33.3% 3 CC TT NN TT -chr1:2175317 [A/C] chr1 2175317 Cc01_g01400:540 exon SYNONYMOUS_CODING gtA/gtC V/V 12.5% 4 AA AA AA AC -chr1:2175371 [T/C] chr1 2175371 Cc01_g01400:594 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TT TC -chr1:2175512 [C/T] chr1 2175512 Cc01_g01400:735 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CC CT -chr1:2175561 [G/T] chr1 2175561 Cc01_g01400:784 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT GG GG -chr1:2175562 [C/G] chr1 2175562 Cc01_g01400:785 exon NON_SYNONYMOUS_CODING gCt/gGt A/G 25.0% 4 CC GG CC CC -chr1:2175613 [G/T] chr1 2175613 Cc01_g01400:836 exon NON_SYNONYMOUS_CODING cGt/cTt R/L 25.0% 4 GG GG GG TT -chr1:2175705 [T/A] chr1 2175705 Cc01_g01400:928 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 12.5% 4 TT TT TA TT -chr1:2175977 [G/A] chr1 2175977 Cc01_g01400:1088 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 GG GG GG GA -chr1:2176009 [G/A] chr1 2176009 Cc01_g01400:1120 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG -chr1:2176010 [A/C] chr1 2176010 Cc01_g01400:1121 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AC AA AA -chr1:2176046 [C/A] chr1 2176046 Cc01_g01400:1157 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 CC CA CC CC -chr1:2176075 [G/C] chr1 2176075 Cc01_g01400:1186 exon NON_SYNONYMOUS_CODING Gtg/Ctg V/L 12.5% 4 GG GG GC GG -chr1:2176085 [G/A] chr1 2176085 Cc01_g01400:1196 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 GG GG GA GG -chr1:2176089 [A/G] chr1 2176089 Cc01_g01400:1200 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AG AA -chr1:2176098 [C/T] chr1 2176098 Cc01_g01400:1209 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC -chr1:2176099 [G/A] chr1 2176099 Cc01_g01400:1210 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG AG GG GG -chr1:2176255 [G/A] chr1 2176255 Cc01_g01400:1285 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GA GG GG -chr1:2176279 [T/A] chr1 2176279 Cc01_g01400:1309 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TT TT TA -chr1:2176311 [C/A] chr1 2176311 Cc01_g01400:1341 exon SYNONYMOUS_CODING atC/atA I/I 12.5% 4 CC CA CC CC -chr1:2176321 [G/A] chr1 2176321 Cc01_g01400:1351 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG AA AA GA -chr1:2176345 [C/G] chr1 2176345 Cc01_g01400:1375 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 12.5% 4 CC CG CC CC -chr1:2176383 [A/G] chr1 2176383 Cc01_g01400:1413 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA -chr1:2176387 [A/T] chr1 2176387 Cc01_g01400:1417 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AT AA AA -chr1:2177071 [T/G] chr1 2177071 Cc01_g01410:37 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT GG NN TT -chr1:2177072 [G/T] chr1 2177072 Cc01_g01410:38 exon NON_SYNONYMOUS_CODING tGt/tTt C/F 33.3% 3 GG GG NN TT -chr1:2177953 [T/C] chr1 2177953 Cc01_g01410:198 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 2 TT NN NN CC -chr1:2185597 [C/A] chr1 2185597 Cc01_g01420:45 exon SYNONYMOUS_CODING tcG/tcT S/S 25.0% 4 CC CA CC CA -chr1:2185587 [T/C] chr1 2185587 Cc01_g01420:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TC TT TT -chr1:2185534 [T/C] chr1 2185534 Cc01_g01420:108 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 TT TT TC TT -chr1:2185452 [G/C] chr1 2185452 Cc01_g01420:190 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 12.5% 4 GG GG GC GG -chr1:2185431 [T/C] chr1 2185431 Cc01_g01420:211 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 TT TT TT TC -chr1:2185418 [T/C] chr1 2185418 Cc01_g01420:224 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 12.5% 4 TT TT CT TT -chr1:2185408 [C/T] chr1 2185408 Cc01_g01420:234 exon SYNONYMOUS_CODING agG/agA R/R 37.5% 4 CC TT TT CT -chr1:2185315 [A/C] chr1 2185315 Cc01_g01420:327 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 AA AA AA AC -chr1:2185281 [A/G] chr1 2185281 Cc01_g01420:361 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA -chr1:2185274 [G/T] chr1 2185274 Cc01_g01420:368 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 25.0% 4 GG GG TT GG -chr1:2185232 [C/T] chr1 2185232 Cc01_g01420:410 exon NON_SYNONYMOUS_CODING gGg/gAg G/E 12.5% 4 CC CC CT CC -chr1:2185228 [A/T] chr1 2185228 Cc01_g01420:414 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA TA AA -chr1:2185186 [A/G] chr1 2185186 Cc01_g01420:456 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 AA AG AA AA -chr1:2185185 [T/A] chr1 2185185 Cc01_g01420:457 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 25.0% 4 TT AT TT TA -chr1:2185150 [A/G] chr1 2185150 Cc01_g01420:492 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 AA GA AA AG -chr1:2185136 [T/G] chr1 2185136 Cc01_g01420:506 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 12.5% 4 TT TG TT TT -chr1:2185131 [A/T] chr1 2185131 Cc01_g01420:511 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 4 AA TT AT AT -chr1:2185130 [C/G] chr1 2185130 Cc01_g01420:512 exon NON_SYNONYMOUS_CODING tGg/tCg W/S 50.0% 4 CC GG CG CG -chr1:2185056 [C/T] chr1 2185056 Cc01_g01420:586 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CT CC CC -chr1:2185024 [C/G] chr1 2185024 Cc01_g01420:618 exon SYNONYMOUS_CODING cgG/cgC R/R 12.5% 4 CC CC CG CC -chr1:2184985 [C/T] chr1 2184985 Cc01_g01420:657 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC -chr1:2184978 [A/G] chr1 2184978 Cc01_g01420:664 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 AA AA AG AA -chr1:2184967 [C/T] chr1 2184967 Cc01_g01420:675 exon SYNONYMOUS_CODING agG/agA R/R 12.5% 4 CC CC CT CC -chr1:2184923 [T/C] chr1 2184923 Cc01_g01420:719 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT -chr1:2184900 [G/A] chr1 2184900 Cc01_g01420:742 exon NON_SYNONYMOUS_CODING Ctc/Ttc L/F 12.5% 4 GG GG GA GG -chr1:2184858 [C/T] chr1 2184858 Cc01_g01420:784 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC -chr1:2184847 [T/G] chr1 2184847 Cc01_g01420:795 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 12.5% 4 TT TT TG TT -chr1:2184843 [A/G] chr1 2184843 Cc01_g01420:799 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 AA GG GG GG -chr1:2184715 [A/G] chr1 2184715 Cc01_g01420:927 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA -chr1:2184631 [A/G] chr1 2184631 Cc01_g01420:1011 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA AG AA AA -chr1:2184436 [C/T] chr1 2184436 Cc01_g01420:1087 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC TT CT TT -chr1:2184420 [C/T] chr1 2184420 Cc01_g01420:1103 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC TC CC -chr1:2184375 [A/C] chr1 2184375 Cc01_g01420:1148 exon NON_SYNONYMOUS_CODING tTt/tGt F/C 25.0% 4 AA CC CC CC -chr1:2184365 [C/T] chr1 2184365 Cc01_g01420:1158 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 CC CC CC CT -chr1:2184361 [T/C] chr1 2184361 Cc01_g01420:1162 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 50.0% 4 TT CC CC TT -chr1:2184164 [T/A] chr1 2184164 Cc01_g01420:1280 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 37.5% 4 TT AA AA AT -chr1:2184085 [C/T] chr1 2184085 Cc01_g01420:1359 exon SYNONYMOUS_CODING aaG/aaA K/K 25.0% 4 CC CC TT CC -chr1:2184069 [A/G] chr1 2184069 Cc01_g01420:1375 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA GG GG GG -chr1:2184058 [T/A] chr1 2184058 Cc01_g01420:1386 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA AA AA -chr1:2184010 [T/C] chr1 2184010 Cc01_g01420:1434 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TT TC -chr1:2183902 [T/C] chr1 2183902 Cc01_g01420:1542 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT CC CC CC -chr1:2191614 [T/C] chr1 2191614 Cc01_g01430:14 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 TT TC TC TC -chr1:2190583 [G/T] chr1 2190583 Cc01_g01430:511 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG GT GG GT -chr1:2190560 [C/G] chr1 2190560 Cc01_g01430:534 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CC CC GC -chr1:2190508 [A/G] chr1 2190508 Cc01_g01430:586 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AG AA AA -chr1:2190494 [A/G] chr1 2190494 Cc01_g01430:600 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 AA AG AG AA -chr1:2189807 [A/T] chr1 2189807 Cc01_g01430:897 exon SYNONYMOUS_CODING gcT/gcA A/A 25.0% 4 AA AT AT AA -chr1:2189651 [T/C] chr1 2189651 Cc01_g01430:1053 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 TT CC TC CC -chr1:2189636 [A/G] chr1 2189636 Cc01_g01430:1068 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG -chr1:2189634 [A/T] chr1 2189634 Cc01_g01430:1070 exon NON_SYNONYMOUS_CODING aTt/aAt I/N 12.5% 4 AA AA TA AA -chr1:2188570 [T/C] chr1 2188570 Cc01_g01430:1166 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT -chr1:2188551 [A/G] chr1 2188551 Cc01_g01430:1185 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AA AG AA -chr1:2196422 [A/G] chr1 2196422 Cc01_g01440:36 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 AA AG AA AG -chr1:2196341 [T/C] chr1 2196341 Cc01_g01440:117 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT TC TC TC -chr1:2196333 [G/C] chr1 2196333 Cc01_g01440:125 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG CG GG GG -chr1:2196286 [C/A] chr1 2196286 Cc01_g01440:172 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 37.5% 4 CC AA CC CA -chr1:2196284 [T/G] chr1 2196284 Cc01_g01440:174 exon SYNONYMOUS_CODING gcA/gcC A/A 12.5% 4 TT GT TT TT -chr1:2196257 [A/G] chr1 2196257 Cc01_g01440:201 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA -chr1:2196212 [A/G] chr1 2196212 Cc01_g01440:246 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AG AA -chr1:2196172 [A/G] chr1 2196172 Cc01_g01440:286 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 AA AA GG AA -chr1:2196160 [A/G] chr1 2196160 Cc01_g01440:298 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 AA GG AA AG -chr1:2196140 [A/G] chr1 2196140 Cc01_g01440:318 exon SYNONYMOUS_CODING gcT/gcC A/A 25.0% 4 AA AA GG AA -chr1:2196134 [G/C] chr1 2196134 Cc01_g01440:324 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GC GG GG -chr1:2196132 [C/T] chr1 2196132 Cc01_g01440:326 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 CC CT CC CC -chr1:2196068 [T/A] chr1 2196068 Cc01_g01440:390 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 37.5% 4 TT TA TA TA -chr1:2196065 [T/C] chr1 2196065 Cc01_g01440:393 exon SYNONYMOUS_CODING gtA/gtG V/V 37.5% 4 TT TC TC TC -chr1:2195449 [A/G] chr1 2195449 Cc01_g01440:536 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 12.5% 4 AA AA AA AG -chr1:2195438 [T/A] chr1 2195438 Cc01_g01440:547 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 37.5% 4 TT TA TA TA -chr1:2195424 [C/A] chr1 2195424 Cc01_g01440:561 exon SYNONYMOUS_CODING ctG/ctT L/L 25.0% 4 CC CA CA CC -chr1:2195362 [G/A] chr1 2195362 Cc01_g01440:623 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 GG AG GG GA -chr1:2195350 [A/G] chr1 2195350 Cc01_g01440:635 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AA AG -chr1:2195327 [T/C] chr1 2195327 Cc01_g01440:658 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 TT CT TT TC -chr1:2195242 [C/G] chr1 2195242 Cc01_g01440:743 exon NON_SYNONYMOUS_CODING gGa/gCa G/A 12.5% 4 CC CG CC CC -chr1:2195189 [A/G] chr1 2195189 Cc01_g01440:796 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA GA AA AA -chr1:2195153 [T/C] chr1 2195153 Cc01_g01440:832 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT TT TC CC -chr1:2195139 [A/G] chr1 2195139 Cc01_g01440:846 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 AA AG AA AA -chr1:2194136 [C/T] chr1 2194136 Cc01_g01440:878 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC TC CC CC -chr1:2194114 [G/A] chr1 2194114 Cc01_g01440:900 exon SYNONYMOUS_CODING cgC/cgT R/R 25.0% 4 GG AA AA AA -chr1:2194101 [G/T] chr1 2194101 Cc01_g01440:913 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG TG GG GG -chr1:2194096 [T/G] chr1 2194096 Cc01_g01440:918 exon SYNONYMOUS_CODING tcA/tcC S/S 12.5% 4 TT TG TT TT -chr1:2194092 [C/T] chr1 2194092 Cc01_g01440:922 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC -chr1:2194052 [T/A] chr1 2194052 Cc01_g01440:962 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 12.5% 4 TT TT TA TT -chr1:2193981 [A/G] chr1 2193981 Cc01_g01440:1033 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 12.5% 4 AA AG AA AA -chr1:2193975 [T/C] chr1 2193975 Cc01_g01440:1039 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TT TC TT -chr1:2193955 [C/A] chr1 2193955 Cc01_g01440:1059 exon SYNONYMOUS_CODING gcG/gcT A/A 37.5% 4 CC AA CC CA -chr1:2209238 [C/T] chr1 2209238 Cc01_g01450:478 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 25.0% 4 CC CC CC TT -chr1:2209206 [G/T] chr1 2209206 Cc01_g01450:510 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG GG TT NN -chr1:2208545 [T/C] chr1 2208545 Cc01_g01450:868 exon NON_SYNONYMOUS_CODING Agc/Ggc S/G 12.5% 4 TT TC TT TT -chr1:2208543 [G/T] chr1 2208543 Cc01_g01450:870 exon NON_SYNONYMOUS_CODING agC/agA S/R 12.5% 4 GG GT GG GG -chr1:2208524 [T/A] chr1 2208524 Cc01_g01450:889 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 12.5% 4 TT TA TT TT -chr1:2208480 [C/T] chr1 2208480 Cc01_g01450:933 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CT CC CC -chr1:2208471 [A/G] chr1 2208471 Cc01_g01450:942 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 AA GA AA AA -chr1:2208398 [C/T] chr1 2208398 Cc01_g01450:1015 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 33.3% 3 CC TT NN TT -chr1:2208295 [T/G] chr1 2208295 Cc01_g01450:1118 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 12.5% 4 TT TG TT TT -chr1:2208265 [G/A] chr1 2208265 Cc01_g01450:1148 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GA GG GG -chr1:2208247 [G/T] chr1 2208247 Cc01_g01450:1166 exon NON_SYNONYMOUS_CODING cCa/cAa P/Q 25.0% 4 GG GT GG GT -chr1:2208199 [T/A] chr1 2208199 Cc01_g01450:1214 exon NON_SYNONYMOUS_CODING aAc/aTc N/I 12.5% 4 TT TT TA TT -chr1:2208185 [C/T] chr1 2208185 Cc01_g01450:1228 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC TC CC -chr1:2208178 [T/C] chr1 2208178 Cc01_g01450:1235 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 12.5% 4 TT TT TC TT -chr1:2208133 [G/A] chr1 2208133 Cc01_g01450:1280 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 GG GA GG GG -chr1:2274354 [C/T] chr1 2274354 Cc01_g01460:831 exon SYNONYMOUS_CODING atC/atT I/I 33.3% 3 CC TT NN TT -chr1:2274363 [T/C] chr1 2274363 Cc01_g01460:840 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT CC NN CC -chr1:2274385 [G/C] chr1 2274385 Cc01_g01460:862 exon NON_SYNONYMOUS_CODING Gac/Cac D/H 33.3% 3 GG CC NN CC -chr1:2274390 [A/T] chr1 2274390 Cc01_g01460:867 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT -chr1:2274408 [A/C] chr1 2274408 Cc01_g01460:885 exon SYNONYMOUS_CODING atA/atC I/I 50.0% 2 AA NN NN CC -chr1:2274417 [C/T] chr1 2274417 Cc01_g01460:894 exon SYNONYMOUS_CODING tgC/tgT C/C 33.3% 3 CC TT NN TT -chr1:2300221 [C/T] chr1 2300221 Cc01_g01470:1228 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 CC NN NN TT -chr1:2300215 [T/C] chr1 2300215 Cc01_g01470:1234 exon NON_SYNONYMOUS_CODING Act/Gct T/A 50.0% 2 TT NN NN CC -chr1:2300214 [G/A] chr1 2300214 Cc01_g01470:1235 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 50.0% 2 GG NN NN AA -chr1:2343380 [T/C] chr1 2343380 Cc01_g01490:11 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 TT TT TT TC -chr1:2343353 [T/C] chr1 2343353 Cc01_g01490:38 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT CC CC CC -chr1:2343351 [G/C] chr1 2343351 Cc01_g01490:40 exon NON_SYNONYMOUS_CODING Ccc/Gcc P/A 25.0% 4 GG CC CC CC -chr1:2343348 [T/C] chr1 2343348 Cc01_g01490:43 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT CC CC CC -chr1:2343347 [A/G] chr1 2343347 Cc01_g01490:44 exon NON_SYNONYMOUS_CODING aTg/aCg M/T 25.0% 4 AA GG GG GG -chr1:2343346 [C/T] chr1 2343346 Cc01_g01490:45 exon NON_SYNONYMOUS_CODING atG/atA M/I 37.5% 4 CC CC TT TC -chr1:2343313 [A/G] chr1 2343313 Cc01_g01490:78 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 AA AA GG GA -chr1:2343300 [G/A] chr1 2343300 Cc01_g01490:91 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 GG GG GG AG -chr1:2343296 [C/T] chr1 2343296 Cc01_g01490:95 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 25.0% 4 CC TT TT TT -chr1:2343283 [A/G] chr1 2343283 Cc01_g01490:108 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 AA AG AG GG -chr1:2343280 [T/G] chr1 2343280 Cc01_g01490:111 exon SYNONYMOUS_CODING acA/acC T/T 50.0% 4 TT TG TG GG -chr1:2343274 [A/C] chr1 2343274 Cc01_g01490:117 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 AA AA AC CA -chr1:2343261 [C/A] chr1 2343261 Cc01_g01490:130 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 37.5% 4 CC CA CC AA -chr1:2343259 [C/G] chr1 2343259 Cc01_g01490:132 exon SYNONYMOUS_CODING gtG/gtC V/V 37.5% 4 CC CG CC GG -chr1:2343244 [G/T] chr1 2343244 Cc01_g01490:147 exon NON_SYNONYMOUS_CODING caC/caA H/Q 25.0% 4 GG GG GG TT -chr1:2343241 [T/G] chr1 2343241 Cc01_g01490:150 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 TT TT TG GG -chr1:2343235 [G/C] chr1 2343235 Cc01_g01490:156 exon SYNONYMOUS_CODING tcC/tcG S/S 37.5% 4 GG GG GC CC -chr1:2343232 [A/C] chr1 2343232 Cc01_g01490:159 exon SYNONYMOUS_CODING ggT/ggG G/G 37.5% 4 AA AA AC CC -chr1:2343229 [A/T] chr1 2343229 Cc01_g01490:162 exon SYNONYMOUS_CODING tcT/tcA S/S 37.5% 4 AA AA AT TT -chr1:2343225 [T/C] chr1 2343225 Cc01_g01490:166 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 TT TT TC CC -chr1:2343092 [T/C] chr1 2343092 Cc01_g01490:299 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 25.0% 4 TT TT TT CC -chr1:2342875 [G/A] chr1 2342875 Cc01_g01490:516 exon SYNONYMOUS_CODING ttC/ttT F/F 33.3% 3 GG AA NN AA -chr1:2342772 [C/T] chr1 2342772 Cc01_g01490:619 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 CC TT CC CC -chr1:2342382 [C/T] chr1 2342382 Cc01_g01490:636 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC TT NN CC -chr1:2342352 [A/T] chr1 2342352 Cc01_g01490:666 exon SYNONYMOUS_CODING atT/atA I/I 37.5% 4 AA TT TT AT -chr1:2342154 [T/G] chr1 2342154 Cc01_g01490:774 exon SYNONYMOUS_CODING gcA/gcC A/A 37.5% 4 TT TT TG GG -chr1:2342153 [A/G] chr1 2342153 Cc01_g01490:775 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 37.5% 4 AA AA AG GG -chr1:2342152 [C/T] chr1 2342152 Cc01_g01490:776 exon STOP_GAINED tGg/tAg W/9 37.5% 4 CC CC CT TT -chr1:2342133 [G/A] chr1 2342133 Cc01_g01490:795 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 4 GG GA GA AA -chr1:2342078 [G/A] chr1 2342078 Cc01_g01490:850 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA AA AA -chr1:2342048 [C/A] chr1 2342048 Cc01_g01490:880 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 25.0% 4 CC AA AA AA -chr1:2342034 [A/G] chr1 2342034 Cc01_g01490:894 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 AA GG GG GG -chr1:2342013 [T/G] chr1 2342013 Cc01_g01490:915 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT GG GG GG -chr1:2342007 [T/A] chr1 2342007 Cc01_g01490:921 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 TT TT TT TA -chr1:2342001 [G/T] chr1 2342001 Cc01_g01490:927 exon SYNONYMOUS_CODING atC/atA I/I 37.5% 4 GG TT GT TT -chr1:2341971 [A/G] chr1 2341971 Cc01_g01490:957 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AA AG AA -chr1:2341944 [T/C] chr1 2341944 Cc01_g01490:984 exon SYNONYMOUS_CODING ggA/ggG G/G 50.0% 4 TT TC TC CC -chr1:2341934 [C/T] chr1 2341934 Cc01_g01490:994 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 50.0% 4 CC CT CT TT -chr1:2341930 [A/C] chr1 2341930 Cc01_g01490:998 exon NON_SYNONYMOUS_CODING gTc/gGc V/G 37.5% 4 AA AC AA CC -chr1:2341921 [C/T] chr1 2341921 Cc01_g01490:1007 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 37.5% 4 CC CT CC TT -chr1:2341915 [G/A] chr1 2341915 Cc01_g01490:1013 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 37.5% 4 GG GA GG AA -chr1:2341914 [T/G] chr1 2341914 Cc01_g01490:1014 exon SYNONYMOUS_CODING acA/acC T/T 37.5% 4 TT TG TT GG -chr1:2341905 [G/A] chr1 2341905 Cc01_g01490:1023 exon SYNONYMOUS_CODING agC/agT S/S 50.0% 4 GG GA GA AA -chr1:2341899 [A/G] chr1 2341899 Cc01_g01490:1029 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 4 AA AG AG GG -chr1:2341885 [G/A] chr1 2341885 Cc01_g01490:1043 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 25.0% 4 GG AA AA AA -chr1:2341855 [C/T] chr1 2341855 Cc01_g01490:1073 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 CC TT TT TT -chr1:2341853 [A/G] chr1 2341853 Cc01_g01490:1075 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 AA GG GG GG -chr1:2341843 [T/G] chr1 2341843 Cc01_g01490:1085 exon NON_SYNONYMOUS_CODING aAt/aCt N/T 25.0% 4 TT GG GG GG -chr1:2341816 [C/T] chr1 2341816 Cc01_g01490:1112 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 25.0% 4 CC TT TT TT -chr1:2341814 [G/C] chr1 2341814 Cc01_g01490:1114 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 4 GG CC CC CC -chr1:2341761 [A/G] chr1 2341761 Cc01_g01490:1167 exon SYNONYMOUS_CODING aaT/aaC N/N 25.0% 4 AA GG GG GG -chr1:2341752 [T/G] chr1 2341752 Cc01_g01490:1176 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 25.0% 4 TT GG GG GG -chr1:2341742 [G/A] chr1 2341742 Cc01_g01490:1186 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA -chr1:2341734 [T/C] chr1 2341734 Cc01_g01490:1194 exon SYNONYMOUS_CODING agA/agG R/R 50.0% 4 TT TC TC CC -chr1:2341733 [G/T] chr1 2341733 Cc01_g01490:1195 exon NON_SYNONYMOUS_CODING Cat/Aat H/N 50.0% 4 GG GT GT TT -chr1:2341731 [A/C] chr1 2341731 Cc01_g01490:1197 exon NON_SYNONYMOUS_CODING caT/caG H/Q 50.0% 4 AA AC AC CC -chr1:2341728 [G/A] chr1 2341728 Cc01_g01490:1200 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 4 GG GA GA AA -chr1:2341719 [C/G] chr1 2341719 Cc01_g01490:1209 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 25.0% 4 CC GG GG GG -chr1:2341697 [T/C] chr1 2341697 Cc01_g01490:1231 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TT TC -chr1:2341685 [C/G] chr1 2341685 Cc01_g01490:1243 exon NON_SYNONYMOUS_CODING Gta/Cta V/L 12.5% 4 CC CG CC CC -chr1:2340685 [G/A] chr1 2340685 Cc01_g01490:1261 exon SYNONYMOUS_CODING Ctg/Ttg L/L 25.0% 4 GG AA AA AA -chr1:2340667 [T/C] chr1 2340667 Cc01_g01490:1279 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC CC CC -chr1:2334881 [A/G] chr1 2334881 Cc01_g01490:1362 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 AA AA AG AA -chr1:2334835 [T/C] chr1 2334835 Cc01_g01490:1408 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 37.5% 4 TT CC CT CC -chr1:2334831 [G/T] chr1 2334831 Cc01_g01490:1412 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 50.0% 4 GG GT TG TT -chr1:2334799 [A/C] chr1 2334799 Cc01_g01490:1444 exon NON_SYNONYMOUS_CODING Tta/Gta L/V 25.0% 4 AA AC AA AC -chr1:2334780 [A/T] chr1 2334780 Cc01_g01490:1463 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 12.5% 4 AA TA AA AA -chr1:2334662 [A/T] chr1 2334662 Cc01_g01490:1581 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 12.5% 4 AA AA AT AA -chr1:2334642 [G/T] chr1 2334642 Cc01_g01490:1601 exon NON_SYNONYMOUS_CODING aCt/aAt T/N 37.5% 4 GG TT GT TT -chr1:2334620 [A/C] chr1 2334620 Cc01_g01490:1623 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AA AA AC -chr1:2334584 [G/A] chr1 2334584 Cc01_g01490:1659 exon SYNONYMOUS_CODING atC/atT I/I 37.5% 4 GG AA GA AA -chr1:2334185 [G/A] chr1 2334185 Cc01_g01490:1719 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA -chr1:2334144 [C/G] chr1 2334144 Cc01_g01490:1760 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 50.0% 4 CC GG CC GG -chr1:2334140 [A/C] chr1 2334140 Cc01_g01490:1764 exon NON_SYNONYMOUS_CODING atT/atG I/M 12.5% 4 AA AC AA AA -chr1:2334026 [T/C] chr1 2334026 Cc01_g01490:1878 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TC TT TC -chr1:2333864 [T/C] chr1 2333864 Cc01_g01490:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 50.0% 4 TT CC TC TC -chr1:2360212 [G/A] chr1 2360212 Cc01_g01510:67 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 33.3% 3 GG AA NN GG -chr1:2360304 [G/T] chr1 2360304 Cc01_g01510:159 exon SYNONYMOUS_CODING ggG/ggT G/G 33.3% 3 GG TT NN GG -chr1:2360308 [C/T] chr1 2360308 Cc01_g01510:163 exon SYNONYMOUS_CODING Cta/Tta L/L 33.3% 3 CC TT NN CC -chr1:2360310 [A/G] chr1 2360310 Cc01_g01510:165 exon SYNONYMOUS_CODING ctA/ctG L/L 33.3% 3 AA GG NN AA -chr1:2360316 [A/G] chr1 2360316 Cc01_g01510:171 exon SYNONYMOUS_CODING aaA/aaG K/K 33.3% 3 AA AA NN GG -chr1:2360324 [G/A] chr1 2360324 Cc01_g01510:179 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 50.0% 2 GG AA NN NN -chr1:2360326 [G/A] chr1 2360326 Cc01_g01510:181 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN -chr1:2360328 [C/A] chr1 2360328 Cc01_g01510:183 exon NON_SYNONYMOUS_CODING gaC/gaA D/E 50.0% 2 CC AA NN NN -chr1:2361074 [C/T] chr1 2361074 Cc01_g01510:929 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 16.7% 3 CC CC NN CT -chr1:2361629 [A/G] chr1 2361629 Cc01_g01510:1263 exon SYNONYMOUS_CODING gtA/gtG V/V 50.0% 2 AA NN NN GG -chr1:2361636 [T/C] chr1 2361636 Cc01_g01510:1270 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT NN NN CC -chr1:2361659 [G/A] chr1 2361659 Cc01_g01510:1293 exon SYNONYMOUS_CODING gaG/gaA E/E 50.0% 2 GG NN NN AA -chr1:2361716 [G/A] chr1 2361716 Cc01_g01510:1350 exon NON_SYNONYMOUS_CODING atG/atA M/I 50.0% 2 GG NN NN AA -chr1:2383654 [G/A] chr1 2383654 Cc01_g01520:42 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GA GG GG -chr1:2383674 [T/C] chr1 2383674 Cc01_g01520:62 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 25.0% 4 TT CC TT TT -chr1:2383681 [C/T] chr1 2383681 Cc01_g01520:69 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 CC TT CC CC -chr1:2383712 [G/A] chr1 2383712 Cc01_g01520:100 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GG GG GA -chr1:2383714 [T/C] chr1 2383714 Cc01_g01520:102 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC -chr1:2383758 [T/C] chr1 2383758 Cc01_g01520:146 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 TT CC CC CC -chr1:2383785 [A/G] chr1 2383785 Cc01_g01520:173 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA GG AA AA -chr1:2383795 [C/A] chr1 2383795 Cc01_g01520:183 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 50.0% 4 CC AA CC AA -chr1:2383839 [G/A] chr1 2383839 Cc01_g01520:227 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 25.0% 4 GG GG AA GG -chr1:2383851 [A/T] chr1 2383851 Cc01_g01520:239 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AT AA AA -chr1:2383866 [C/T] chr1 2383866 Cc01_g01520:254 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 12.5% 4 CC CT CC CC -chr1:2383874 [T/A] chr1 2383874 Cc01_g01520:262 exon NON_SYNONYMOUS_CODING Tgc/Agc C/S 12.5% 4 TT TA TT TT -chr1:2383920 [G/T] chr1 2383920 Cc01_g01520:308 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG GG TT GG -chr1:2383927 [T/C] chr1 2383927 Cc01_g01520:315 exon SYNONYMOUS_CODING ttT/ttC F/F 25.0% 4 TT CC TT TT -chr1:2384077 [T/G] chr1 2384077 Cc01_g01520:465 exon NON_SYNONYMOUS_CODING agT/agG S/R 25.0% 4 TT TT TT GG -chr1:2384181 [A/G] chr1 2384181 Cc01_g01520:569 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 AA AA AA AG -chr1:2384200 [C/T] chr1 2384200 Cc01_g01520:588 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CC TT CC -chr1:2384756 [T/G] chr1 2384756 Cc01_g01520:1041 exon NON_SYNONYMOUS_CODING agT/agG S/R 12.5% 4 TT TG TT TT -chr1:2385308 [T/C] chr1 2385308 Cc01_g01520:1470 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 TT TC TT TT -chr1:2409054 [C/A] chr1 2409054 Cc01_g01530:78 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA CC CC -chr1:2409092 [T/C] chr1 2409092 Cc01_g01530:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 25.0% 4 TT CC TT TT -chr1:2409231 [A/C] chr1 2409231 Cc01_g01530:255 exon SYNONYMOUS_CODING tcA/tcC S/S 16.7% 3 AA AC NN AA -chr1:2409249 [C/T] chr1 2409249 Cc01_g01530:273 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 3 CC CT NN TT -chr1:2409678 [A/G] chr1 2409678 Cc01_g01530:702 exon SYNONYMOUS_CODING ctA/ctG L/L 16.7% 3 AA NN AA AG -chr1:2409702 [T/C] chr1 2409702 Cc01_g01530:726 exon SYNONYMOUS_CODING taT/taC Y/Y 37.5% 4 TT TC CC CC -chr1:2409721 [T/A] chr1 2409721 Cc01_g01530:745 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 12.5% 4 TT TT TT TA -chr1:2409726 [C/T] chr1 2409726 Cc01_g01530:750 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 CC CC CC CT -chr1:2425980 [A/G] chr1 2425980 Cc01_g01540:231 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AG AA -chr1:2426360 [G/A] chr1 2426360 Cc01_g01540:397 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG AA GA GG -chr1:2426489 [T/C] chr1 2426489 Cc01_g01540:526 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 12.5% 4 TT TC TT TT -chr1:2427186 [G/A] chr1 2427186 Cc01_g01540:843 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GA GG GG -chr1:2427440 [T/C] chr1 2427440 Cc01_g01540:936 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC TT -chr1:2428201 [A/G] chr1 2428201 Cc01_g01540:1375 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 AA GG AG AA -chr1:2428270 [A/G] chr1 2428270 Cc01_g01540:1444 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AA AG AA -chr1:2429289 [T/A] chr1 2429289 Cc01_g01540:1547 exon NON_SYNONYMOUS_CODING aTg/aAg M/K 12.5% 4 TT TA TT TT -chr1:2431687 [G/A] chr1 2431687 Cc01_g01540:1638 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG -chr1:2432530 [C/T] chr1 2432530 Cc01_g01540:1850 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC -chr1:2432737 [A/G] chr1 2432737 Cc01_g01540:1942 exon NON_SYNONYMOUS_CODING Act/Gct T/A 12.5% 4 AA AA AG AA -chr1:2433099 [T/C] chr1 2433099 Cc01_g01540:2141 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT -chr1:2434119 [T/A] chr1 2434119 Cc01_g01540:2374 exon NON_SYNONYMOUS_CODING Tct/Act S/T 12.5% 4 TT TA TT TT -chr1:2434512 [A/G] chr1 2434512 Cc01_g01540:2553 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AG AA AA -chr1:2436532 [A/G] chr1 2436532 Cc01_g01550:172 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 12.5% 4 AA AG AA AA -chr1:2436544 [G/A] chr1 2436544 Cc01_g01550:184 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG -chr1:2436558 [G/A] chr1 2436558 Cc01_g01550:198 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG -chr1:2436572 [G/A] chr1 2436572 Cc01_g01550:212 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 12.5% 4 GG GA GG GG -chr1:2439858 [T/C] chr1 2439858 Cc01_g01550:505 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 25.0% 4 TT TC TT TC -chr1:2440047 [T/C] chr1 2440047 Cc01_g01550:597 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT -chr1:2440153 [C/G] chr1 2440153 Cc01_g01550:703 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CG CC CG -chr1:2440191 [A/G] chr1 2440191 Cc01_g01550:741 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 AA AA AA AG -chr1:2440206 [A/G] chr1 2440206 Cc01_g01550:756 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AG AA AG -chr1:2444991 [C/G] chr1 2444991 Cc01_g01560:39 exon SYNONYMOUS_CODING gcC/gcG A/A 25.0% 4 CC CC GG CC -chr1:2445037 [C/T] chr1 2445037 Cc01_g01560:85 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC CC CT -chr1:2445130 [G/A] chr1 2445130 Cc01_g01560:178 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 GG GG GG GA -chr1:2445144 [G/C] chr1 2445144 Cc01_g01560:192 exon SYNONYMOUS_CODING tcG/tcC S/S 25.0% 4 GG CC CC CC -chr1:2445153 [C/T] chr1 2445153 Cc01_g01560:201 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT CC TT -chr1:2445246 [G/A] chr1 2445246 Cc01_g01560:294 exon SYNONYMOUS_CODING ttG/ttA L/L 37.5% 4 GG GA GG AA -chr1:2445335 [G/T] chr1 2445335 Cc01_g01560:383 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 GG TT TT TT -chr1:2445435 [T/C] chr1 2445435 Cc01_g01560:483 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT CC CC CC -chr1:2445449 [C/G] chr1 2445449 Cc01_g01560:497 exon NON_SYNONYMOUS_CODING aCc/aGc T/S 16.7% 3 CC CG CC NN -chr1:2445473 [A/G] chr1 2445473 Cc01_g01560:521 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 16.7% 3 AA AA AG NN -chr1:2445488 [G/A] chr1 2445488 Cc01_g01560:536 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 33.3% 3 GG GG AA NN -chr1:2445537 [A/T] chr1 2445537 Cc01_g01560:585 exon SYNONYMOUS_CODING atA/atT I/I 16.7% 3 AA AT AA NN -chr1:2445552 [C/G] chr1 2445552 Cc01_g01560:600 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC -chr1:2445610 [G/C] chr1 2445610 Cc01_g01560:658 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 12.5% 4 GG GC GG GG -chr1:2445684 [G/A] chr1 2445684 Cc01_g01560:732 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 GG AA AA AA -chr1:2445697 [C/G] chr1 2445697 Cc01_g01560:745 exon NON_SYNONYMOUS_CODING Ctt/Gtt L/V 37.5% 4 CC CG CC GG -chr1:2445722 [T/G] chr1 2445722 Cc01_g01560:770 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 37.5% 4 TT TG TT GG -chr1:2445747 [A/T] chr1 2445747 Cc01_g01560:795 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 12.5% 4 AA TA AA AA -chr1:2445750 [T/C] chr1 2445750 Cc01_g01560:798 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TT TT CC -chr1:2445796 [A/T] chr1 2445796 Cc01_g01560:844 exon NON_SYNONYMOUS_CODING Act/Tct T/S 37.5% 4 AA AT AA TT -chr1:2445815 [A/G] chr1 2445815 Cc01_g01560:863 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 16.7% 3 AA AG AA NN -chr1:2445816 [G/A] chr1 2445816 Cc01_g01560:864 exon SYNONYMOUS_CODING gaG/gaA E/E 16.7% 3 GG AG GG NN -chr1:2445827 [G/T] chr1 2445827 Cc01_g01560:875 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 16.7% 3 GG GT GG NN -chr1:2483851 [A/G] chr1 2483851 Cc01_g01570:110 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 50.0% 2 AA GG NN NN -chr1:2483849 [A/G] chr1 2483849 Cc01_g01570:112 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 50.0% 2 AA GG NN NN -chr1:2483845 [A/G] chr1 2483845 Cc01_g01570:116 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 50.0% 2 AA GG NN NN -chr1:2524880 [C/T] chr1 2524880 Cc01_g01600:173 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 12.5% 4 CC CT CC CC -chr1:2523795 [C/T] chr1 2523795 Cc01_g01600:1189 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CT CC -chr1:2523742 [G/A] chr1 2523742 Cc01_g01600:1242 exon SYNONYMOUS_CODING ttC/ttT F/F 16.7% 3 GG NN GG GA -chr1:2522662 [T/C] chr1 2522662 Cc01_g01600:2133 exon SYNONYMOUS_CODING ggA/ggG G/G 25.0% 4 TT TT CC TT -chr1:2522423 [T/A] chr1 2522423 Cc01_g01600:2279 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 TT TT TT TA -chr1:2522420 [A/G] chr1 2522420 Cc01_g01600:2282 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AG AA AA -chr1:2522274 [T/C] chr1 2522274 Cc01_g01600:2428 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 37.5% 4 TT CC TT TC -chr1:2522265 [A/G] chr1 2522265 Cc01_g01600:2437 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 16.7% 3 AA NN AA GA -chr1:2522182 [G/C] chr1 2522182 Cc01_g01600:2439 exon SYNONYMOUS_CODING tcC/tcG S/S 33.3% 3 GG NN CC GG -chr1:2522124 [G/A] chr1 2522124 Cc01_g01600:2497 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 25.0% 4 GG AA GG GG -chr1:2522105 [T/C] chr1 2522105 Cc01_g01600:2516 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 12.5% 4 TT TT TT TC -chr1:2522103 [C/T] chr1 2522103 Cc01_g01600:2518 exon NON_SYNONYMOUS_CODING Gta/Ata V/I 12.5% 4 CC CC CT CC -chr1:2522070 [G/A] chr1 2522070 Cc01_g01600:2551 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 4 GG AA GG GG -chr1:2522006 [C/A] chr1 2522006 Cc01_g01600:2615 exon NON_SYNONYMOUS_CODING cGg/cTg R/L 12.5% 4 CC CC CC CA -chr1:2521969 [T/C] chr1 2521969 Cc01_g01600:2652 exon SYNONYMOUS_CODING ttA/ttG L/L 12.5% 4 TT TT TT TC -chr1:2521892 [T/C] chr1 2521892 Cc01_g01600:2729 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT -chr1:2521826 [G/A] chr1 2521826 Cc01_g01600:2795 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 37.5% 4 GG GG AA GA -chr1:2521810 [G/C] chr1 2521810 Cc01_g01600:2811 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GG GC -chr1:2521773 [A/G] chr1 2521773 Cc01_g01600:2848 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 25.0% 4 AA GG GG GG -chr1:2521725 [G/C] chr1 2521725 Cc01_g01600:2896 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 50.0% 4 GG CC GC GC -chr1:2521724 [T/A] chr1 2521724 Cc01_g01600:2897 exon NON_SYNONYMOUS_CODING cAg/cTg Q/L 12.5% 4 TT TA TT TT -chr1:2521694 [C/A] chr1 2521694 Cc01_g01600:2927 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 12.5% 4 CC AC CC CC -chr1:2521672 [T/C] chr1 2521672 Cc01_g01600:2949 exon SYNONYMOUS_CODING ggA/ggG G/G 12.5% 4 TT TT CT TT -chr1:2521665 [G/A] chr1 2521665 Cc01_g01600:2956 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 37.5% 4 GG GA GA GA -chr1:2521659 [T/C] chr1 2521659 Cc01_g01600:2962 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 12.5% 4 TT TC TT TT -chr1:2521567 [C/T] chr1 2521567 Cc01_g01600:3054 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC -chr1:2521560 [A/T] chr1 2521560 Cc01_g01600:3061 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT -chr1:2521545 [G/A] chr1 2521545 Cc01_g01600:3076 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GA GG GG -chr1:2521544 [C/G] chr1 2521544 Cc01_g01600:3077 exon NON_SYNONYMOUS_CODING cGt/cCt R/P 12.5% 4 CC CC CG CC -chr1:2521538 [G/A] chr1 2521538 Cc01_g01600:3083 exon NON_SYNONYMOUS_CODING aCg/aTg T/M 12.5% 4 GG GG GA GG -chr1:2521522 [G/A] chr1 2521522 Cc01_g01600:3099 exon SYNONYMOUS_CODING caC/caT H/H 12.5% 4 GG GG AG GG -chr1:2521518 [G/A] chr1 2521518 Cc01_g01600:3103 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 12.5% 4 GG GG AG GG -chr1:2521434 [C/T] chr1 2521434 Cc01_g01600:3187 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 12.5% 4 CC CC CC CT -chr1:2521424 [T/C] chr1 2521424 Cc01_g01600:3197 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 12.5% 4 TT TT TT TC -chr1:2521409 [A/C] chr1 2521409 Cc01_g01600:3212 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 37.5% 4 AA AA CC CA -chr1:2521377 [C/A] chr1 2521377 Cc01_g01600:3244 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 CC CA CC CA -chr1:2521375 [T/C] chr1 2521375 Cc01_g01600:3246 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 TT TC TT CT -chr1:2521230 [G/A] chr1 2521230 Cc01_g01600:3301 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 GG GA AA GG -chr1:2520587 [T/C] chr1 2520587 Cc01_g01600:3322 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 TT CC CC CC -chr1:2520583 [C/T] chr1 2520583 Cc01_g01600:3326 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CT CC CC -chr1:2520561 [A/G] chr1 2520561 Cc01_g01600:3348 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA AA AA AG -chr1:2520556 [G/T] chr1 2520556 Cc01_g01600:3353 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 25.0% 4 GG TT TT TT -chr1:2520547 [A/G] chr1 2520547 Cc01_g01600:3362 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 25.0% 4 AA GG GG GG -chr1:2520537 [T/C] chr1 2520537 Cc01_g01600:3372 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC TC -chr1:2520525 [C/T] chr1 2520525 Cc01_g01600:3384 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 CC CC CT CC -chr1:2520511 [A/G] chr1 2520511 Cc01_g01600:3398 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 AA GG GG GG -chr1:2526140 [A/T] chr1 2526140 Cc01_g01610:233 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 25.0% 4 AA AA TT AA -chr1:2528701 [G/C] chr1 2528701 Cc01_g01610:265 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 33.3% 3 GG GG NN CC -chr1:2528783 [T/C] chr1 2528783 Cc01_g01610:347 exon NON_SYNONYMOUS_CODING gTc/gCc V/A 12.5% 4 TT TT TT TC -chr1:2528803 [T/C] chr1 2528803 Cc01_g01610:367 exon SYNONYMOUS_CODING Tta/Cta L/L 25.0% 4 TT TT TT CC -chr1:2528813 [T/C] chr1 2528813 Cc01_g01610:377 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TC TT -chr1:2528941 [T/G] chr1 2528941 Cc01_g01610:433 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG -chr1:2528952 [C/G] chr1 2528952 Cc01_g01610:444 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC CG CC CG -chr1:2529568 [A/G] chr1 2529568 Cc01_g01610:557 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 2 AA NN NN GG -chr1:2530078 [A/G] chr1 2530078 Cc01_g01610:1067 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 37.5% 4 AA AG AG AG -chr1:2551182 [G/A] chr1 2551182 Cc01_g01620:26 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG AA GG GG -chr1:2551151 [G/T] chr1 2551151 Cc01_g01620:57 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG TT NN GG -chr1:2551113 [C/T] chr1 2551113 Cc01_g01620:95 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 37.5% 4 CC TT CC CT -chr1:2551100 [G/A] chr1 2551100 Cc01_g01620:108 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 GG AA GG GG -chr1:2551069 [T/A] chr1 2551069 Cc01_g01620:139 exon NON_SYNONYMOUS_CODING Agc/Tgc S/C 25.0% 4 TT AA TT TT -chr1:2551068 [C/A] chr1 2551068 Cc01_g01620:140 exon NON_SYNONYMOUS_CODING aGc/aTc S/I 25.0% 4 CC AA CC CC -chr1:2551000 [T/A] chr1 2551000 Cc01_g01620:208 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 12.5% 4 TT TT TT TA -chr1:2550995 [T/C] chr1 2550995 Cc01_g01620:213 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC -chr1:2550979 [G/A] chr1 2550979 Cc01_g01620:229 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 GG GG GG GA -chr1:2550929 [G/C] chr1 2550929 Cc01_g01620:279 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GG CG -chr1:2550905 [G/A] chr1 2550905 Cc01_g01620:303 exon SYNONYMOUS_CODING ttC/ttT F/F 37.5% 4 GG AA GG GA -chr1:2550878 [T/C] chr1 2550878 Cc01_g01620:330 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TT TT TC -chr1:2550853 [G/A] chr1 2550853 Cc01_g01620:355 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 GG AA NN AA -chr1:2550817 [C/T] chr1 2550817 Cc01_g01620:391 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 CC CC CC CT -chr1:2550788 [A/G] chr1 2550788 Cc01_g01620:420 exon SYNONYMOUS_CODING caT/caC H/H 37.5% 4 AA GG AA AG -chr1:2550718 [C/A] chr1 2550718 Cc01_g01620:490 exon NON_SYNONYMOUS_CODING Gtc/Ttc V/F 33.3% 3 CC AA NN AA -chr1:2550703 [A/G] chr1 2550703 Cc01_g01620:505 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 AA AA NN GG -chr1:2550656 [A/C] chr1 2550656 Cc01_g01620:552 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 AA AC AA AA -chr1:2550608 [A/G] chr1 2550608 Cc01_g01620:600 exon SYNONYMOUS_CODING ctT/ctC L/L 50.0% 3 AA GG NN AG -chr1:2550457 [A/C] chr1 2550457 Cc01_g01620:751 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 AA CC AA NN -chr1:2550455 [A/T] chr1 2550455 Cc01_g01620:753 exon STOP_GAINED tgT/tgA C/1 33.3% 3 AA TT AA NN -chr1:2550410 [G/A] chr1 2550410 Cc01_g01620:798 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 GG AA NN AA -chr1:2550352 [A/C] chr1 2550352 Cc01_g01620:856 exon STOP_LOST Taa/Gaa 2/E 33.3% 3 AA CC AA NN -chr1:2565722 [C/G] chr1 2565722 Cc01_g01630:400 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 12.5% 4 CC CG CC CC -chr1:2565615 [C/T] chr1 2565615 Cc01_g01630:437 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC TC CC CC -chr1:2558672 [A/G] chr1 2558672 Cc01_g01630:759 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 AA AA AA AG -chr1:2558633 [T/C] chr1 2558633 Cc01_g01630:798 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 TT TT TC CT -chr1:2558434 [T/C] chr1 2558434 Cc01_g01630:859 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 37.5% 4 TT TC CT CT -chr1:2558347 [C/A] chr1 2558347 Cc01_g01630:946 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 12.5% 4 CC CA CC CC -chr1:2558280 [T/G] chr1 2558280 Cc01_g01630:1013 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TG TT TT -chr1:2558276 [G/A] chr1 2558276 Cc01_g01630:1017 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GA GG GG -chr1:2558203 [G/A] chr1 2558203 Cc01_g01630:1090 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 12.5% 4 GG GA GG GG -chr1:2558132 [G/C] chr1 2558132 Cc01_g01630:1161 exon SYNONYMOUS_CODING acC/acG T/T 12.5% 4 GG GC GG GG -chr1:2558129 [G/A] chr1 2558129 Cc01_g01630:1164 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG -chr1:2558028 [G/A] chr1 2558028 Cc01_g01630:1265 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 12.5% 4 GG GA GG GG -chr1:2557954 [G/C] chr1 2557954 Cc01_g01630:1339 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 12.5% 4 GG GC GG GG -chr1:2557932 [A/T] chr1 2557932 Cc01_g01630:1361 exon NON_SYNONYMOUS_CODING aTa/aAa I/K 12.5% 4 AA AT AA AA -chr1:2557907 [G/A] chr1 2557907 Cc01_g01630:1386 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG -chr1:2557619 [T/C] chr1 2557619 Cc01_g01630:1575 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TC TT TT -chr1:2557277 [T/C] chr1 2557277 Cc01_g01630:1917 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 TT TC TT TT -chr1:2557173 [A/G] chr1 2557173 Cc01_g01630:2021 exon NON_SYNONYMOUS_CODING cTg/cCg L/P 12.5% 4 AA AG AA AA -chr1:2557145 [T/C] chr1 2557145 Cc01_g01630:2049 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TC TT TT -chr1:2557074 [C/A] chr1 2557074 Cc01_g01630:2120 exon NON_SYNONYMOUS_CODING gGa/gTa G/V 12.5% 4 CC CA CC CC -chr1:2557055 [G/A] chr1 2557055 Cc01_g01630:2139 exon SYNONYMOUS_CODING ggC/ggT G/G 12.5% 4 GG GA GG GG -chr1:2557019 [T/C] chr1 2557019 Cc01_g01630:2175 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT -chr1:2557016 [A/G] chr1 2557016 Cc01_g01630:2178 exon SYNONYMOUS_CODING acT/acC T/T 12.5% 4 AA AG AA AA -chr1:2610598 [G/T] chr1 2610598 Cc01_g01650:233 exon NON_SYNONYMOUS_CODING gGt/gTt G/V 12.5% 4 GG GT GG GG -chr1:2611238 [T/C] chr1 2611238 Cc01_g01650:279 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TC TT TT -chr1:2612873 [T/C] chr1 2612873 Cc01_g01650:375 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 TT TC TT TT -chr1:2612964 [C/T] chr1 2612964 Cc01_g01650:466 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 CC CC CC CT -chr1:2613791 [G/C] chr1 2613791 Cc01_g01650:835 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GG GG GC -chr1:2613877 [G/A] chr1 2613877 Cc01_g01650:921 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GG GA -chr1:2613943 [C/T] chr1 2613943 Cc01_g01650:987 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 CC CC CT CC -chr1:2615356 [A/T] chr1 2615356 Cc01_g01650:1179 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 AA AA AT AA -chr1:2618568 [T/C] chr1 2618568 Cc01_g01650:1693 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TC TT TT -chr1:2618665 [C/T] chr1 2618665 Cc01_g01650:1790 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC -chr1:2618850 [C/T] chr1 2618850 Cc01_g01650:1886 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CC CT -chr1:2618880 [A/G] chr1 2618880 Cc01_g01650:1916 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 AA AA AG AA -chr1:2619302 [A/G] chr1 2619302 Cc01_g01650:2224 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 12.5% 4 AA AG AA AA -chr1:2619373 [C/T] chr1 2619373 Cc01_g01650:2295 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CT CC CC -chr1:2622083 [C/T] chr1 2622083 Cc01_g01650:2580 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 CC CT CC CC -chr1:2622084 [A/C] chr1 2622084 Cc01_g01650:2581 exon NON_SYNONYMOUS_CODING Aac/Cac N/H 12.5% 4 AA AC AA AA -chr1:2622099 [C/G] chr1 2622099 Cc01_g01650:2596 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC GC CC CC -chr1:2623353 [A/C] chr1 2623353 Cc01_g01650:2974 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AA AA AC -chr1:2624213 [G/T] chr1 2624213 Cc01_g01650:3039 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 25.0% 4 GG GT GG TG -chr1:2624222 [T/A] chr1 2624222 Cc01_g01650:3048 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 25.0% 4 TT TA TT AT -chr1:2624249 [T/C] chr1 2624249 Cc01_g01650:3075 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TC TT TT -chr1:2624263 [T/A] chr1 2624263 Cc01_g01650:3089 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 TT TA TT TT -chr1:2624270 [T/A] chr1 2624270 Cc01_g01650:3096 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 TT TA TT TT -chr1:2624289 [G/T] chr1 2624289 Cc01_g01650:3115 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG GG GG TG -chr1:2624433 [C/T] chr1 2624433 Cc01_g01650:3173 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC CT -chr1:2668103 [C/G] chr1 2668103 Cc01_g01670:315 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 CC GG GG GG -chr1:2668636 [A/G] chr1 2668636 Cc01_g01670:848 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 25.0% 4 AA AA AA GG -chr1:2668660 [G/A] chr1 2668660 Cc01_g01670:872 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 GG GA GG GG -chr1:2668692 [T/C] chr1 2668692 Cc01_g01670:904 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN TT -chr1:2668715 [T/G] chr1 2668715 Cc01_g01670:927 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT NN TT GG -chr1:2668739 [T/A] chr1 2668739 Cc01_g01670:951 exon SYNONYMOUS_CODING ccT/ccA P/P 50.0% 2 TT NN AA NN -chr1:2668764 [A/T] chr1 2668764 Cc01_g01670:976 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 50.0% 2 AA NN TT NN -chr1:2668782 [C/T] chr1 2668782 Cc01_g01670:994 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC NN TT TT -chr1:2668811 [G/A] chr1 2668811 Cc01_g01670:1023 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 GG NN AA AA -chr1:2669258 [A/C] chr1 2669258 Cc01_g01670:1470 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 33.3% 3 AA NN CC CC -chr1:2669279 [T/A] chr1 2669279 Cc01_g01670:1491 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 2 TT NN AA NN -chr1:2669349 [A/G] chr1 2669349 Cc01_g01670:1519 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN GG AA -chr1:2669357 [T/A] chr1 2669357 Cc01_g01670:1527 exon SYNONYMOUS_CODING cgT/cgA R/R 33.3% 3 TT NN AA AA -chr1:2669424 [A/G] chr1 2669424 Cc01_g01670:1594 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 33.3% 3 AA NN GG GG -chr1:2669466 [G/T] chr1 2669466 Cc01_g01670:1636 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 33.3% 3 GG NN TT GG -chr1:2669497 [A/G] chr1 2669497 Cc01_g01670:1667 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 33.3% 3 AA NN GG AA -chr1:2669523 [T/C] chr1 2669523 Cc01_g01670:1693 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TC TT TT -chr1:2669527 [G/T] chr1 2669527 Cc01_g01670:1697 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 25.0% 4 GG GG TT GG -chr1:2669572 [G/A] chr1 2669572 Cc01_g01670:1742 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 GG GG AA GG -chr1:2669581 [C/A] chr1 2669581 Cc01_g01670:1751 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 25.0% 4 CC CC AA CC -chr1:2669627 [T/C] chr1 2669627 Cc01_g01670:1797 exon SYNONYMOUS_CODING tgT/tgC C/C 25.0% 4 TT CC CC CC -chr1:2669629 [A/G] chr1 2669629 Cc01_g01670:1799 exon NON_SYNONYMOUS_CODING gAc/gGc D/G 50.0% 4 AA GG GG AA -chr1:2669742 [A/C] chr1 2669742 Cc01_g01670:1912 exon NON_SYNONYMOUS_CODING Aca/Cca T/P 25.0% 4 AA CC CC CC -chr1:2669750 [T/C] chr1 2669750 Cc01_g01670:1920 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT CC TT TT -chr1:2669752 [A/T] chr1 2669752 Cc01_g01670:1922 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 25.0% 4 AA TT AA AA -chr1:2669754 [G/A] chr1 2669754 Cc01_g01670:1924 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 4 GG AA GG AA -chr1:2669766 [G/T] chr1 2669766 Cc01_g01670:1936 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 50.0% 4 GG GG TT TT -chr1:2669787 [A/G] chr1 2669787 Cc01_g01670:1957 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA GG AA AA -chr1:2669788 [T/C] chr1 2669788 Cc01_g01670:1958 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 25.0% 4 TT CC CC CC -chr1:2669790 [C/A] chr1 2669790 Cc01_g01670:1960 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 33.3% 3 CC AA NN AA -chr1:2669868 [C/T] chr1 2669868 Cc01_g01670:2038 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 33.3% 3 CC TT NN CC -chr1:2670063 [C/T] chr1 2670063 Cc01_g01670:2233 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 33.3% 3 CC NN CC TT -chr1:2670072 [C/T] chr1 2670072 Cc01_g01670:2242 exon STOP_GAINED Cga/Tga R/8 25.0% 4 CC CC CC TT -chr1:2670078 [G/A] chr1 2670078 Cc01_g01670:2248 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG AA GG GG -chr1:2670084 [T/A] chr1 2670084 Cc01_g01670:2254 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 50.0% 4 TT AA AA TT -chr1:2670086 [A/G] chr1 2670086 Cc01_g01670:2256 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA GG GG NN -chr1:2672520 [A/G] chr1 2672520 Cc01_g01670:2295 exon SYNONYMOUS_CODING agA/agG R/R 33.3% 3 AA AA NN GG -chr1:2672522 [C/G] chr1 2672522 Cc01_g01670:2297 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 33.3% 3 CC CC NN GG -chr1:2672529 [A/T] chr1 2672529 Cc01_g01670:2304 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 33.3% 3 AA AA NN TT -chr1:2672531 [T/C] chr1 2672531 Cc01_g01670:2306 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 33.3% 3 TT TT NN CC -chr1:2672554 [T/A] chr1 2672554 Cc01_g01670:2329 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 33.3% 3 TT TT NN AA -chr1:2672699 [C/T] chr1 2672699 Cc01_g01670:2474 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 25.0% 2 CC CT NN NN -chr1:2672995 [T/C] chr1 2672995 Cc01_g01670:2770 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 50.0% 2 TT CC NN NN -chr1:2672999 [C/T] chr1 2672999 Cc01_g01670:2774 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 2 CC CT NN NN -chr1:2673033 [A/G] chr1 2673033 Cc01_g01670:2808 exon SYNONYMOUS_CODING tcA/tcG S/S 37.5% 4 AA AG AA GG -chr1:2673073 [A/T] chr1 2673073 Cc01_g01670:2848 exon NON_SYNONYMOUS_CODING Atc/Ttc I/F 33.3% 3 AA TT TT NN -chr1:2673080 [T/C] chr1 2673080 Cc01_g01670:2855 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 TT CC TT NN -chr1:2673111 [G/T] chr1 2673111 Cc01_g01670:2886 exon NON_SYNONYMOUS_CODING agG/agT R/S 25.0% 4 GG GG TT GG -chr1:2673117 [A/T] chr1 2673117 Cc01_g01670:2892 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 AA AA AA TT -chr1:2673163 [T/G] chr1 2673163 Cc01_g01670:2938 exon NON_SYNONYMOUS_CODING Ttc/Gtc F/V 25.0% 4 TT TT GG TT -chr1:2673186 [G/C] chr1 2673186 Cc01_g01670:2961 exon NON_SYNONYMOUS_CODING atG/atC M/I 33.3% 3 GG GG NN CC -chr1:2673191 [G/A] chr1 2673191 Cc01_g01670:2966 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 2 GG GA NN NN -chr1:2673238 [C/G] chr1 2673238 Cc01_g01670:3013 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 25.0% 2 CC CG NN NN -chr1:2673525 [G/A] chr1 2673525 Cc01_g01670:3300 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG GA GG GA -chr1:2673526 [G/T] chr1 2673526 Cc01_g01670:3301 exon STOP_GAINED Gag/Tag E/1 25.0% 4 GG GT GG GT -chr1:2673538 [T/G] chr1 2673538 Cc01_g01670:3313 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GG TG -chr1:2673541 [C/T] chr1 2673541 Cc01_g01670:3316 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 25.0% 4 CC TC CC CT -chr1:2673542 [C/T] chr1 2673542 Cc01_g01670:3317 exon NON_SYNONYMOUS_CODING cCg/cTg P/L 25.0% 4 CC TC CC CT -chr1:2673543 [G/T] chr1 2673543 Cc01_g01670:3318 exon SYNONYMOUS_CODING ccG/ccT P/P 25.0% 4 GG TG GG GT -chr1:2674163 [G/A] chr1 2674163 Cc01_g01670:3319 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 37.5% 4 GG AG GA GA -chr1:2674174 [G/C] chr1 2674174 Cc01_g01670:3330 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 37.5% 4 GG CG GC GC -chr1:2674189 [A/C] chr1 2674189 Cc01_g01670:3345 exon SYNONYMOUS_CODING ggA/ggC G/G 25.0% 4 AA CA AA AC -chr1:2674276 [C/T] chr1 2674276 Cc01_g01680:15 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CT CC CC -chr1:2674294 [G/A] chr1 2674294 Cc01_g01680:33 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA AA AA -chr1:2674295 [C/G] chr1 2674295 Cc01_g01680:34 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 25.0% 4 CC GG GG GG -chr1:2674297 [G/T] chr1 2674297 Cc01_g01680:36 exon NON_SYNONYMOUS_CODING caG/caT Q/H 25.0% 4 GG GG GG TT -chr1:2674941 [A/G] chr1 2674941 Cc01_g01680:48 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 AA AA AG AA -chr1:2674945 [C/T] chr1 2674945 Cc01_g01680:52 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CC TC CC -chr1:2674962 [G/A] chr1 2674962 Cc01_g01680:69 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG -chr1:2674964 [G/T] chr1 2674964 Cc01_g01680:71 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 37.5% 4 GG GT GG TT -chr1:2674973 [T/A] chr1 2674973 Cc01_g01680:80 exon STOP_GAINED tTg/tAg L/7 37.5% 4 TT TA AA AA -chr1:2674983 [G/T] chr1 2674983 Cc01_g01680:90 exon NON_SYNONYMOUS_CODING ttG/ttT L/F 25.0% 4 GG TT TT TT -chr1:2675001 [T/C] chr1 2675001 Cc01_g01680:108 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 2 TT TC NN NN -chr1:2675015 [T/A] chr1 2675015 Cc01_g01680:122 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 16.7% 3 TT TA NN TT -chr1:2675040 [T/A] chr1 2675040 Cc01_g01680:147 exon SYNONYMOUS_CODING ccT/ccA P/P 33.3% 3 TT AA NN AA -chr1:2675043 [C/T] chr1 2675043 Cc01_g01680:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT -chr1:2675048 [G/A] chr1 2675048 Cc01_g01680:155 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG AG NN GG -chr1:2675053 [A/T] chr1 2675053 Cc01_g01680:160 exon NON_SYNONYMOUS_CODING Att/Ttt I/F 50.0% 3 AA AT NN TT -chr1:2732265 [A/G] chr1 2732265 Cc01_g01700:720 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 2 AA NN NN AG -chr1:2836390 [A/T] chr1 2836390 Cc01_g01710:126 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 AA TT NN NN -chr1:2836415 [G/C] chr1 2836415 Cc01_g01710:151 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 2 GG GC NN NN -chr1:2836420 [G/C] chr1 2836420 Cc01_g01710:156 exon SYNONYMOUS_CODING gcG/gcC A/A 50.0% 2 GG CC NN NN -chr1:2836423 [C/T] chr1 2836423 Cc01_g01710:159 exon SYNONYMOUS_CODING gaC/gaT D/D 25.0% 2 CC CT NN NN -chr1:2836441 [C/A] chr1 2836441 Cc01_g01710:177 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 CC AA CC NN -chr1:2836445 [G/A] chr1 2836445 Cc01_g01710:181 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN -chr1:2836460 [G/A] chr1 2836460 Cc01_g01710:196 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN -chr1:2836484 [A/G] chr1 2836484 Cc01_g01710:220 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 16.7% 3 AA AG AA NN -chr1:2836488 [C/T] chr1 2836488 Cc01_g01710:224 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 16.7% 3 CC CT CC NN -chr1:2836561 [A/G] chr1 2836561 Cc01_g01710:297 exon SYNONYMOUS_CODING aaA/aaG K/K 50.0% 2 AA GG NN NN -chr1:2837031 [G/A] chr1 2837031 Cc01_g01720:58 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 50.0% 2 GG AA NN NN -chr1:2837037 [A/G] chr1 2837037 Cc01_g01720:64 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 50.0% 2 AA GG NN NN -chr1:2837164 [A/G] chr1 2837164 Cc01_g01720:191 exon NON_SYNONYMOUS_CODING gAa/gGa E/G 25.0% 4 AA AA AA GG -chr1:2837166 [A/G] chr1 2837166 Cc01_g01720:193 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA GG AA AA -chr1:2837171 [A/G] chr1 2837171 Cc01_g01720:198 exon SYNONYMOUS_CODING aaA/aaG K/K 25.0% 4 AA GG AA AA -chr1:2837187 [G/C] chr1 2837187 Cc01_g01720:214 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 50.0% 4 GG GG CC CC -chr1:2837200 [T/G] chr1 2837200 Cc01_g01720:227 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 37.5% 4 TT TT TG GG -chr1:2837207 [A/G] chr1 2837207 Cc01_g01720:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA -chr1:2837244 [G/A] chr1 2837244 Cc01_g01720:271 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 25.0% 4 GG GG GA GA -chr1:2837245 [A/G] chr1 2837245 Cc01_g01720:272 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 25.0% 4 AA GG GG GG -chr1:2837246 [T/C] chr1 2837246 Cc01_g01720:273 exon SYNONYMOUS_CODING gaT/gaC D/D 37.5% 4 TT TT CC TC -chr1:2837248 [G/A] chr1 2837248 Cc01_g01720:275 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 37.5% 4 GG GG AA GA -chr1:2837259 [T/C] chr1 2837259 Cc01_g01720:286 exon SYNONYMOUS_CODING Tta/Cta L/L 37.5% 4 TT CC TT CT -chr1:2837266 [A/G] chr1 2837266 Cc01_g01720:293 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 37.5% 4 AA GG AA GA -chr1:2837271 [C/T] chr1 2837271 Cc01_g01720:298 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 CC CC TT CT -chr1:2837287 [G/T] chr1 2837287 Cc01_g01720:314 exon NON_SYNONYMOUS_CODING tGg/tTg W/L 33.3% 3 GG TT NN GG -chr1:2837295 [T/C] chr1 2837295 Cc01_g01720:322 exon SYNONYMOUS_CODING Ttg/Ctg L/L 33.3% 3 TT CC NN CC -chr1:2837310 [A/C] chr1 2837310 Cc01_g01720:337 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 50.0% 3 AA AC NN CC -chr1:2837316 [G/A] chr1 2837316 Cc01_g01720:343 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 50.0% 3 GG GA NN AA -chr1:2837318 [G/C] chr1 2837318 Cc01_g01720:345 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 GG GG NN CC -chr1:2837319 [G/C] chr1 2837319 Cc01_g01720:346 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG GG NN CC -chr1:2837348 [A/G] chr1 2837348 Cc01_g01720:375 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA AG NN AG -chr1:2837391 [G/A] chr1 2837391 Cc01_g01720:418 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 50.0% 3 GG GA NN AA -chr1:2837393 [A/T] chr1 2837393 Cc01_g01720:420 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA TA NN AA -chr1:2837420 [C/T] chr1 2837420 Cc01_g01720:447 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT -chr1:2837423 [T/G] chr1 2837423 Cc01_g01720:450 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 TT GG NN GG -chr1:2837425 [T/G] chr1 2837425 Cc01_g01720:452 exon NON_SYNONYMOUS_CODING gTa/gGa V/G 33.3% 3 TT GG NN GG -chr1:2837433 [A/G] chr1 2837433 Cc01_g01720:460 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 AA GG NN GG -chr1:2837480 [T/C] chr1 2837480 Cc01_g01720:507 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC -chr1:2837519 [G/A] chr1 2837519 Cc01_g01720:546 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG AA NN AA -chr1:2837526 [G/T] chr1 2837526 Cc01_g01720:553 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 33.3% 3 GG TT NN TT -chr1:2837537 [G/A] chr1 2837537 Cc01_g01720:564 exon SYNONYMOUS_CODING aaG/aaA K/K 33.3% 3 GG AA NN AA -chr1:2837615 [T/C] chr1 2837615 Cc01_g01720:642 exon SYNONYMOUS_CODING gcT/gcC A/A 50.0% 2 TT NN CC NN -chr1:2837629 [T/A] chr1 2837629 Cc01_g01720:656 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 50.0% 2 TT NN AA NN -chr1:2837640 [A/G] chr1 2837640 Cc01_g01720:667 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 50.0% 2 AA NN GG NN -chr1:2901565 [C/A] chr1 2901565 Cc01_g01730:118 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 12.5% 4 CC CA CC CC -chr1:2901573 [A/T] chr1 2901573 Cc01_g01730:126 exon SYNONYMOUS_CODING gcA/gcT A/A 16.7% 3 AA AT NN AA -chr1:2901666 [T/C] chr1 2901666 Cc01_g01730:219 exon SYNONYMOUS_CODING ttT/ttC F/F 16.7% 3 TT TC NN TT -chr1:2902604 [C/T] chr1 2902604 Cc01_g01730:618 exon SYNONYMOUS_CODING aaC/aaT N/N 50.0% 3 CC CT NN TT -chr1:2902609 [A/G] chr1 2902609 Cc01_g01730:623 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 3 AA AG NN GG -chr1:2902632 [G/A] chr1 2902632 Cc01_g01730:646 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 33.3% 3 GG AA NN AA -chr1:2902646 [A/C] chr1 2902646 Cc01_g01730:660 exon NON_SYNONYMOUS_CODING caA/caC Q/H 33.3% 3 AA CC NN CC -chr1:2902650 [G/A] chr1 2902650 Cc01_g01730:664 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG AA NN AA -chr1:2902664 [T/C] chr1 2902664 Cc01_g01730:678 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 TT CC NN CC -chr1:2902673 [T/G] chr1 2902673 Cc01_g01730:687 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG NN GG -chr1:2902849 [T/G] chr1 2902849 Cc01_g01730:863 exon NON_SYNONYMOUS_CODING aTa/aGa I/R 25.0% 2 TT NN NN TG -chr1:2902856 [G/C] chr1 2902856 Cc01_g01730:870 exon SYNONYMOUS_CODING ggG/ggC G/G 50.0% 2 GG NN NN CC -chr1:2902865 [G/A] chr1 2902865 Cc01_g01730:879 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 GG GG NN AA -chr1:2902892 [A/G] chr1 2902892 Cc01_g01730:906 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 2 AA GG NN NN -chr1:2903083 [G/A] chr1 2903083 Cc01_g01730:1097 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG AA NN AA -chr1:2903094 [G/A] chr1 2903094 Cc01_g01730:1108 exon NON_SYNONYMOUS_CODING Gct/Act A/T 33.3% 3 GG AA NN AA -chr1:2903117 [A/G] chr1 2903117 Cc01_g01730:1131 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA AA GG AA -chr1:2903173 [T/G] chr1 2903173 Cc01_g01730:1187 exon NON_SYNONYMOUS_CODING aTc/aGc I/S 25.0% 4 TT GG GG GG -chr1:2903230 [C/G] chr1 2903230 Cc01_g01730:1244 exon NON_SYNONYMOUS_CODING aCa/aGa T/R 16.7% 3 CC NN CC CG -chr1:2903240 [A/G] chr1 2903240 Cc01_g01730:1254 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA -chr1:2903273 [A/G] chr1 2903273 Cc01_g01730:1287 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AG AA AA -chr1:2903283 [G/A] chr1 2903283 Cc01_g01730:1297 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 GG GA GG GG -chr1:2903292 [G/A] chr1 2903292 Cc01_g01730:1306 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 GG AG GG GG -chr1:2903341 [A/G] chr1 2903341 Cc01_g01730:1355 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 2 AA GG NN NN -chr1:2903558 [C/T] chr1 2903558 Cc01_g01730:1572 exon SYNONYMOUS_CODING ttC/ttT F/F 50.0% 2 CC TT NN NN -chr1:2903571 [C/T] chr1 2903571 Cc01_g01730:1585 exon SYNONYMOUS_CODING Ctg/Ttg L/L 50.0% 2 CC TT NN NN -chr1:2903610 [G/A] chr1 2903610 Cc01_g01730:1624 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 50.0% 2 GG AA NN NN -chr1:2903621 [T/C] chr1 2903621 Cc01_g01730:1635 exon SYNONYMOUS_CODING aaT/aaC N/N 50.0% 2 TT CC NN NN -chr1:2903627 [T/G] chr1 2903627 Cc01_g01730:1641 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 TT GG TT NN -chr1:2903770 [G/A] chr1 2903770 Cc01_g01730:1784 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 50.0% 2 GG NN AA NN -chr1:2903814 [G/A] chr1 2903814 Cc01_g01730:1828 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG NN AA GG -chr1:2903816 [G/T] chr1 2903816 Cc01_g01730:1830 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 33.3% 3 GG NN GG TT -chr1:2903820 [G/T] chr1 2903820 Cc01_g01730:1834 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 33.3% 3 GG NN TT GG -chr1:2903823 [A/G] chr1 2903823 Cc01_g01730:1837 exon NON_SYNONYMOUS_CODING Aga/Gga R/G 33.3% 3 AA NN AA GG -chr1:2904055 [G/T] chr1 2904055 Cc01_g01730:1910 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN -chr1:2904064 [A/G] chr1 2904064 Cc01_g01730:1919 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 50.0% 2 AA GG NN NN -chr1:2904368 [T/C] chr1 2904368 Cc01_g01730:2163 exon SYNONYMOUS_CODING acT/acC T/T 50.0% 2 TT NN CC NN -chr1:2904423 [C/T] chr1 2904423 Cc01_g01730:2218 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 3 CC CT TT NN -chr1:2986926 [T/C] chr1 2986926 Cc01_g01750:549 exon SYNONYMOUS_CODING ggT/ggC G/G 50.0% 2 TT CC NN NN -chr1:2986947 [A/C] chr1 2986947 Cc01_g01750:570 exon SYNONYMOUS_CODING acA/acC T/T 25.0% 2 AA AC NN NN -chr1:2988225 [A/G] chr1 2988225 Cc01_g01750:1848 exon SYNONYMOUS_CODING cgA/cgG R/R 50.0% 2 AA GG NN NN -chr1:2988245 [A/G] chr1 2988245 Cc01_g01750:1868 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 50.0% 2 AA GG NN NN -chr1:2989009 [G/A] chr1 2989009 Cc01_g01750:2542 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 50.0% 2 GG AA NN NN -chr1:2989157 [G/T] chr1 2989157 Cc01_g01750:2690 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 50.0% 2 GG NN NN TT -chr1:2989172 [A/G] chr1 2989172 Cc01_g01750:2705 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 50.0% 2 AA NN NN GG -chr1:2989569 [T/C] chr1 2989569 Cc01_g01750:3021 exon SYNONYMOUS_CODING taT/taC Y/Y 33.3% 3 TT NN CC CC -chr1:2989571 [T/G] chr1 2989571 Cc01_g01750:3023 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT GG GG GG -chr1:2989664 [A/G] chr1 2989664 Cc01_g01750:3116 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 33.3% 3 AA GG NN GG -chr1:2989678 [G/C] chr1 2989678 Cc01_g01750:3130 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC NN CC -chr1:2989702 [G/A] chr1 2989702 Cc01_g01750:3154 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GA NN GG -chr1:2989705 [A/G] chr1 2989705 Cc01_g01750:3157 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 50.0% 4 AA GG GG AA -chr1:2989708 [G/A] chr1 2989708 Cc01_g01750:3160 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 12.5% 4 GG GG GG GA -chr1:2989742 [A/G] chr1 2989742 Cc01_g01750:3194 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 37.5% 4 AA AG AG AG -chr1:2989743 [A/T] chr1 2989743 Cc01_g01750:3195 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 37.5% 4 AA TA TA TA -chr1:2989751 [G/A] chr1 2989751 Cc01_g01750:3203 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 12.5% 4 GG GG AG GG -chr1:2989752 [G/T] chr1 2989752 Cc01_g01750:3204 exon SYNONYMOUS_CODING cgG/cgT R/R 12.5% 4 GG GG TG GG -chr1:2989766 [G/A] chr1 2989766 Cc01_g01750:3218 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 4 GG AA GA AG -chr1:2989770 [A/G] chr1 2989770 Cc01_g01750:3222 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 AA GG AA GA -chr1:2989771 [C/T] chr1 2989771 Cc01_g01750:3223 exon STOP_GAINED Cga/Tga R/5 12.5% 4 CC CC CT CC -chr1:2989797 [C/T] chr1 2989797 Cc01_g01750:3249 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CC CT -chr1:2989804 [T/G] chr1 2989804 Cc01_g01750:3256 exon STOP_LOST Tag/Gag 1/E 50.0% 2 TT GG NN NN -chr1:2996368 [A/C] chr1 2996368 Cc01_g01760:9 exon SYNONYMOUS_CODING cgA/cgC R/R 33.3% 3 AA CC NN CC -chr1:2996399 [G/A] chr1 2996399 Cc01_g01760:40 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 33.3% 3 GG GA NN GA -chr1:2996415 [G/A] chr1 2996415 Cc01_g01760:56 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 16.7% 3 GG GG NN AG -chr1:2996419 [A/G] chr1 2996419 Cc01_g01760:60 exon SYNONYMOUS_CODING caA/caG Q/Q 16.7% 3 AA AA NN AG -chr1:2996421 [A/G] chr1 2996421 Cc01_g01760:62 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 33.3% 3 AA GG NN GG -chr1:2996436 [G/T] chr1 2996436 Cc01_g01760:77 exon NON_SYNONYMOUS_CODING aGa/aTa R/I 25.0% 4 GG GG GG TT -chr1:2997079 [G/A] chr1 2997079 Cc01_g01760:118 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GA GG GA -chr1:2997084 [T/C] chr1 2997084 Cc01_g01760:123 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC TT CC -chr1:2997085 [A/C] chr1 2997085 Cc01_g01760:124 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 25.0% 4 AA AA CC AA -chr1:2997097 [G/C] chr1 2997097 Cc01_g01760:136 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 25.0% 4 GG CG GG CG -chr1:2997102 [A/T] chr1 2997102 Cc01_g01760:141 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 12.5% 4 AA AA AA AT -chr1:2997106 [A/G] chr1 2997106 Cc01_g01760:145 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AG AA AA -chr1:2997108 [T/C] chr1 2997108 Cc01_g01760:147 exon SYNONYMOUS_CODING atT/atC I/I 50.0% 4 TT CC TT CC -chr1:2997111 [T/C] chr1 2997111 Cc01_g01760:150 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT TT TT TC -chr1:2997112 [G/A] chr1 2997112 Cc01_g01760:151 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 12.5% 4 GG GG GG GA -chr1:2997122 [T/A] chr1 2997122 Cc01_g01760:161 exon NON_SYNONYMOUS_CODING cTa/cAa L/Q 25.0% 4 TT TA TT AT -chr1:2997125 [C/T] chr1 2997125 Cc01_g01760:164 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 12.5% 4 CC CC CT CC -chr1:2997133 [A/G] chr1 2997133 Cc01_g01760:172 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 37.5% 4 AA AG GA AG -chr1:2997137 [G/A] chr1 2997137 Cc01_g01760:176 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG -chr1:2997152 [T/C] chr1 2997152 Cc01_g01760:191 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT CT TT -chr1:2997154 [G/C] chr1 2997154 Cc01_g01760:193 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 GG CG GG GC -chr1:2997157 [A/G] chr1 2997157 Cc01_g01760:196 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 AA GA AA AG -chr1:2997163 [G/C] chr1 2997163 Cc01_g01760:202 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 GG CC CG GC -chr1:2997173 [C/T] chr1 2997173 Cc01_g01760:212 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CC CT CC -chr1:2997174 [T/G] chr1 2997174 Cc01_g01760:213 exon SYNONYMOUS_CODING gcT/gcG A/A 12.5% 4 TT TT TG TT -chr1:2997191 [C/T] chr1 2997191 Cc01_g01760:230 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 CC CC CC TC -chr1:2997196 [T/C] chr1 2997196 Cc01_g01760:235 exon SYNONYMOUS_CODING Ttg/Ctg L/L 37.5% 4 TT TC CT CT -chr1:2997204 [A/G] chr1 2997204 Cc01_g01760:243 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 AA AG GA AG -chr1:2997206 [G/A] chr1 2997206 Cc01_g01760:245 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 GG AA AA AA -chr1:2997213 [C/G] chr1 2997213 Cc01_g01760:252 exon NON_SYNONYMOUS_CODING agC/agG S/R 37.5% 4 CC GC GC CG -chr1:2997215 [C/T] chr1 2997215 Cc01_g01760:254 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC CT TC TC -chr1:2997227 [T/G] chr1 2997227 Cc01_g01760:266 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 25.0% 4 TT TT TG GT -chr1:2997231 [C/T] chr1 2997231 Cc01_g01760:270 exon SYNONYMOUS_CODING tgC/tgT C/C 12.5% 4 CC CT CC CC -chr1:2997233 [G/C] chr1 2997233 Cc01_g01760:272 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 25.0% 4 GG GG GC CG -chr1:2997243 [T/A] chr1 2997243 Cc01_g01760:282 exon SYNONYMOUS_CODING atT/atA I/I 25.0% 4 TT AA AA AA -chr1:2997247 [C/G] chr1 2997247 Cc01_g01760:286 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 CC CG CC CC -chr1:2997250 [C/T] chr1 2997250 Cc01_g01760:289 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 12.5% 4 CC CC TC CC -chr1:2997252 [T/C] chr1 2997252 Cc01_g01760:291 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT TT TC CT -chr1:2997275 [C/A] chr1 2997275 Cc01_g01760:314 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 12.5% 4 CC CA CC CC -chr1:2997294 [G/T] chr1 2997294 Cc01_g01760:333 exon STOP_LOST taG/taT 1/Y 25.0% 4 GG GG GG TT -chr1:3052579 [G/A] chr1 3052579 Cc01_g01770:91 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 50.0% 2 GG NN NN AA -chr1:3052586 [C/T] chr1 3052586 Cc01_g01770:98 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 33.3% 3 CC NN TT TT -chr1:3052603 [G/A] chr1 3052603 Cc01_g01770:115 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 50.0% 2 GG NN NN AA -chr1:3052725 [G/A] chr1 3052725 Cc01_g01770:237 exon SYNONYMOUS_CODING ctG/ctA L/L 50.0% 4 GG AA GA GA -chr1:3052735 [C/A] chr1 3052735 Cc01_g01770:247 exon NON_SYNONYMOUS_CODING Cac/Aac H/N 25.0% 4 CC AA AA AA -chr1:3052737 [C/A] chr1 3052737 Cc01_g01770:249 exon NON_SYNONYMOUS_CODING caC/caA H/Q 12.5% 4 CC CC CC CA -chr1:3052781 [T/C] chr1 3052781 Cc01_g01770:293 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 33.3% 3 TT NN CC TT -chr1:3052796 [G/A] chr1 3052796 Cc01_g01770:308 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 50.0% 2 GG NN AA NN -chr1:3052819 [G/A] chr1 3052819 Cc01_g01770:331 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 16.7% 3 GG GG GA NN -chr1:3052820 [C/A] chr1 3052820 Cc01_g01770:332 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 16.7% 3 CC CC CA NN -chr1:3052827 [T/C] chr1 3052827 Cc01_g01770:339 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 TT CC TT NN -chr1:3052878 [C/G] chr1 3052878 Cc01_g01770:390 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 33.3% 3 CC GG GG NN -chr1:3053184 [T/A] chr1 3053184 Cc01_g01770:696 exon NON_SYNONYMOUS_CODING caT/caA H/Q 16.7% 3 TT NN TA TT -chr1:3053253 [T/C] chr1 3053253 Cc01_g01770:765 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT CC CC CC -chr1:3053284 [A/G] chr1 3053284 Cc01_g01770:796 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 4 AA AA GG GG -chr1:3053300 [A/G] chr1 3053300 Cc01_g01770:812 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 50.0% 4 AA AA GG GG -chr1:3053448 [T/A] chr1 3053448 Cc01_g01770:886 exon NON_SYNONYMOUS_CODING Tct/Act S/T 50.0% 2 TT NN NN AA -chr1:3053505 [C/T] chr1 3053505 Cc01_g01770:943 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 CC TT TT NN -chr1:3053568 [T/C] chr1 3053568 Cc01_g01770:1006 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 TT TT TC TT -chr1:3053590 [A/C] chr1 3053590 Cc01_g01770:1028 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 50.0% 4 AA AC CA CC -chr1:3053591 [T/C] chr1 3053591 Cc01_g01770:1029 exon SYNONYMOUS_CODING gaT/gaC D/D 12.5% 4 TT CT TT TT -chr1:3053592 [T/G] chr1 3053592 Cc01_g01770:1030 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 50.0% 4 TT TG GT GG -chr1:3053593 [A/G] chr1 3053593 Cc01_g01770:1031 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 50.0% 4 AA AG GA GG -chr1:3053596 [A/C] chr1 3053596 Cc01_g01770:1034 exon NON_SYNONYMOUS_CODING gAa/gCa E/A 12.5% 4 AA AA AC AA -chr1:3053597 [A/C] chr1 3053597 Cc01_g01770:1035 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 37.5% 4 AA AA CA CC -chr1:3053608 [G/A] chr1 3053608 Cc01_g01770:1046 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 12.5% 4 GG GG GA GG -chr1:3053622 [A/C] chr1 3053622 Cc01_g01770:1060 exon NON_SYNONYMOUS_CODING Atg/Ctg M/L 16.7% 3 AA NN CA AA -chr1:3053627 [C/T] chr1 3053627 Cc01_g01770:1065 exon SYNONYMOUS_CODING agC/agT S/S 33.3% 3 CC NN CC TT -chr1:3053887 [T/C] chr1 3053887 Cc01_g01770:1325 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 50.0% 2 TT NN NN CC -chr1:3054011 [A/G] chr1 3054011 Cc01_g01770:1449 exon SYNONYMOUS_CODING ccA/ccG P/P 16.7% 3 AA AA AG NN -chr1:3054042 [G/A] chr1 3054042 Cc01_g01770:1480 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN -chr1:3054054 [G/T] chr1 3054054 Cc01_g01770:1492 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 25.0% 4 GG TT GG GG -chr1:3054055 [T/A] chr1 3054055 Cc01_g01770:1493 exon NON_SYNONYMOUS_CODING gTa/gAa V/E 37.5% 4 TT TT TA AA -chr1:3054103 [C/T] chr1 3054103 Cc01_g01770:1541 exon NON_SYNONYMOUS_CODING tCc/tTc S/F 25.0% 4 CC CC TT CC -chr1:3054112 [T/G] chr1 3054112 Cc01_g01770:1550 exon NON_SYNONYMOUS_CODING aTt/aGt I/S 33.3% 3 TT NN GG TT -chr1:3054118 [T/C] chr1 3054118 Cc01_g01770:1556 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 33.3% 3 TT NN CC TT -chr1:3054218 [G/T] chr1 3054218 Cc01_g01770:1605 exon SYNONYMOUS_CODING ggG/ggT G/G 50.0% 2 GG NN NN TT -chr1:3054264 [C/T] chr1 3054264 Cc01_g01770:1651 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 50.0% 2 CC TT NN NN -chr1:3054265 [G/A] chr1 3054265 Cc01_g01770:1652 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 50.0% 2 GG AA NN NN -chr1:3054271 [G/T] chr1 3054271 Cc01_g01770:1658 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 50.0% 2 GG TT NN NN -chr1:3054274 [T/A] chr1 3054274 Cc01_g01770:1661 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 50.0% 2 TT AA NN NN -chr1:3054279 [G/A] chr1 3054279 Cc01_g01770:1666 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN -chr1:3054354 [G/A] chr1 3054354 Cc01_g01770:1741 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GA GG -chr1:3054370 [A/G] chr1 3054370 Cc01_g01770:1757 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA GG AA NN -chr1:3054389 [G/A] chr1 3054389 Cc01_g01770:1776 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 GG AA GG NN -chr1:3054402 [C/G] chr1 3054402 Cc01_g01770:1789 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 33.3% 3 CC CC GG NN -chr1:3054406 [G/A] chr1 3054406 Cc01_g01770:1793 exon NON_SYNONYMOUS_CODING tGc/tAc C/Y 33.3% 3 GG GG AA NN -chr1:3054411 [T/G] chr1 3054411 Cc01_g01770:1798 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 33.3% 3 TT TT GG NN -chr1:3054417 [A/T] chr1 3054417 Cc01_g01770:1804 exon NON_SYNONYMOUS_CODING Agt/Tgt S/C 33.3% 3 AA AA TT NN -chr1:3054423 [C/G] chr1 3054423 Cc01_g01770:1810 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 33.3% 3 CC CC NN GG -chr1:3054432 [A/T] chr1 3054432 Cc01_g01770:1819 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 16.7% 3 AA AT NN AA -chr1:3054439 [A/G] chr1 3054439 Cc01_g01770:1826 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 AA AG NN AA -chr1:3054447 [A/T] chr1 3054447 Cc01_g01770:1834 exon NON_SYNONYMOUS_CODING Aca/Tca T/S 33.3% 3 AA AA NN TT -chr1:3054480 [G/A] chr1 3054480 Cc01_g01770:1867 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 33.3% 3 GG AA NN GG -chr1:3054501 [C/T] chr1 3054501 Cc01_g01770:1888 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 33.3% 3 CC TT NN CC -chr1:3054566 [C/G] chr1 3054566 Cc01_g01770:1953 exon SYNONYMOUS_CODING acC/acG T/T 33.3% 3 CC CC NN GG -chr1:3054570 [A/C] chr1 3054570 Cc01_g01770:1957 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 33.3% 3 AA AA NN CC -chr1:3054575 [G/C] chr1 3054575 Cc01_g01770:1962 exon NON_SYNONYMOUS_CODING agG/agC R/S 16.7% 3 GG GC NN GG -chr1:3054596 [A/G] chr1 3054596 Cc01_g01770:1983 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 3 AA AG NN GG -chr1:3054734 [C/G] chr1 3054734 Cc01_g01770:2121 exon SYNONYMOUS_CODING ccC/ccG P/P 12.5% 4 CC CG CC CC -chr1:3054743 [A/G] chr1 3054743 Cc01_g01770:2130 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AG AA AA -chr1:3054746 [A/G] chr1 3054746 Cc01_g01770:2133 exon SYNONYMOUS_CODING tcA/tcG S/S 12.5% 4 AA AG AA AA -chr1:3054764 [G/C] chr1 3054764 Cc01_g01770:2151 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 GG GG GG CC -chr1:3054783 [C/A] chr1 3054783 Cc01_g01770:2170 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CC CC AA -chr1:3054800 [A/T] chr1 3054800 Cc01_g01770:2187 exon NON_SYNONYMOUS_CODING gaA/gaT E/D 25.0% 4 AA AA AA TT -chr1:3054820 [A/G] chr1 3054820 Cc01_g01770:2207 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA -chr1:3054956 [A/C] chr1 3054956 Cc01_g01770:2238 exon SYNONYMOUS_CODING cgA/cgC R/R 50.0% 2 AA NN NN CC -chr1:3054966 [T/C] chr1 3054966 Cc01_g01770:2248 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN CC CC -chr1:3054968 [A/G] chr1 3054968 Cc01_g01770:2250 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 AA NN GG GG -chr1:3054987 [C/G] chr1 3054987 Cc01_g01770:2269 exon NON_SYNONYMOUS_CODING Cca/Gca P/A 25.0% 4 CC CC CC GG -chr1:3055134 [T/C] chr1 3055134 Cc01_g01770:2416 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 TT TT CC TT -chr1:3055136 [C/T] chr1 3055136 Cc01_g01770:2418 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 CC CT CC CC -chr1:3055137 [G/A] chr1 3055137 Cc01_g01770:2419 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG -chr1:3055144 [C/A] chr1 3055144 Cc01_g01770:2426 exon NON_SYNONYMOUS_CODING gCc/gAc A/D 25.0% 4 CC CC AA CC -chr1:3055154 [C/A] chr1 3055154 Cc01_g01770:2436 exon SYNONYMOUS_CODING cgC/cgA R/R 25.0% 4 CC CA CC CA -chr1:3055178 [A/G] chr1 3055178 Cc01_g01770:2460 exon SYNONYMOUS_CODING gaA/gaG E/E 37.5% 4 AA AG GG AA -chr1:3055254 [T/G] chr1 3055254 Cc01_g01770:2470 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 25.0% 4 TT GT TG TT -chr1:3055255 [A/T] chr1 3055255 Cc01_g01770:2471 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 AA AT AA AA -chr1:3055257 [T/C] chr1 3055257 Cc01_g01770:2473 exon NON_SYNONYMOUS_CODING Ttt/Ctt F/L 25.0% 4 TT TC TC TT -chr1:3055258 [T/C] chr1 3055258 Cc01_g01770:2474 exon NON_SYNONYMOUS_CODING tTt/tCt F/S 25.0% 4 TT TC TC TT -chr1:3055259 [T/G] chr1 3055259 Cc01_g01770:2475 exon NON_SYNONYMOUS_CODING ttT/ttG F/L 12.5% 4 TT TT TG TT -chr1:3076176 [T/C] chr1 3076176 Cc01_g01770:2481 exon SYNONYMOUS_CODING agT/agC S/S 37.5% 4 TT CT CC CC -chr1:3076177 [G/A] chr1 3076177 Cc01_g01770:2482 exon NON_SYNONYMOUS_CODING Ggt/Agt G/S 37.5% 4 GG GA GG AA -chr1:3076201 [A/G] chr1 3076201 Cc01_g01770:2506 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 12.5% 4 AA AG AA AA -chr1:3076211 [A/T] chr1 3076211 Cc01_g01770:2516 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 AA AA AT AA -chr1:3076217 [C/T] chr1 3076217 Cc01_g01770:2522 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 37.5% 4 CC TC CT CT -chr1:3076219 [G/A] chr1 3076219 Cc01_g01770:2524 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG GA AG GG -chr1:3076221 [C/T] chr1 3076221 Cc01_g01770:2526 exon SYNONYMOUS_CODING gtC/gtT V/V 37.5% 4 CC TT CT TT -chr1:3076224 [A/G] chr1 3076224 Cc01_g01770:2529 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG GA AA -chr1:3076239 [G/A] chr1 3076239 Cc01_g01770:2544 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG GA GG GA -chr1:3076622 [T/G] chr1 3076622 Cc01_g01770:2572 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 12.5% 4 TT TT GT TT -chr1:3080563 [C/T] chr1 3080563 Cc01_g01780:14 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 CC TT NN NN -chr1:3080566 [T/A] chr1 3080566 Cc01_g01780:17 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 50.0% 2 TT AA NN NN -chr1:3080588 [T/C] chr1 3080588 Cc01_g01780:39 exon SYNONYMOUS_CODING tgT/tgC C/C 33.3% 3 TT TT CC NN -chr1:3080607 [C/T] chr1 3080607 Cc01_g01780:58 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 37.5% 4 CC CT TT TT -chr1:3080619 [G/A] chr1 3080619 Cc01_g01780:70 exon NON_SYNONYMOUS_CODING Gct/Act A/T 37.5% 4 GG GA AA AA -chr1:3080771 [T/C] chr1 3080771 Cc01_g01780:138 exon SYNONYMOUS_CODING atT/atC I/I 25.0% 4 TT TT TT CC -chr1:3080777 [A/G] chr1 3080777 Cc01_g01780:144 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA -chr1:3080789 [T/C] chr1 3080789 Cc01_g01780:156 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 TT TC TT TC -chr1:3080803 [T/A] chr1 3080803 Cc01_g01780:170 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 25.0% 4 TT TA TT TA -chr1:3080819 [C/A] chr1 3080819 Cc01_g01780:186 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 CC CC CC AC -chr1:3080919 [C/A] chr1 3080919 Cc01_g01780:200 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC AA CC CC -chr1:3080921 [C/T] chr1 3080921 Cc01_g01780:202 exon NON_SYNONYMOUS_CODING Ccc/Tcc P/S 37.5% 4 CC CC TT TC -chr1:3080927 [C/G] chr1 3080927 Cc01_g01780:208 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 25.0% 4 CC CC CG CG -chr1:3080944 [G/A] chr1 3080944 Cc01_g01780:225 exon SYNONYMOUS_CODING gcG/gcA A/A 37.5% 4 GG AA AA GA -chr1:3080947 [A/G] chr1 3080947 Cc01_g01780:228 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 AA AA GG AG -chr1:3080956 [T/A] chr1 3080956 Cc01_g01780:237 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 TT AA AA AA -chr1:3081805 [A/T] chr1 3081805 Cc01_g01780:415 exon STOP_GAINED Aga/Tga R/9 50.0% 3 AA TT NN AT -chr1:3081884 [T/A] chr1 3081884 Cc01_g01780:494 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 25.0% 4 TT TA TA TT -chr1:3081885 [T/A] chr1 3081885 Cc01_g01780:495 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 37.5% 4 TT AT TT AA -chr1:3081886 [T/A] chr1 3081886 Cc01_g01780:496 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 25.0% 4 TT TA TA TT -chr1:3081887 [T/A] chr1 3081887 Cc01_g01780:497 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TT TA -chr1:3081888 [T/A] chr1 3081888 Cc01_g01780:498 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 12.5% 4 TT TA TT TT -chr1:3100066 [G/C] chr1 3100066 Cc01_g01790:442 exon NON_SYNONYMOUS_CODING Cga/Gga R/G 37.5% 4 GG GC GG CC -chr1:3100063 [C/T] chr1 3100063 Cc01_g01790:445 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 37.5% 4 CC CT CC TT -chr1:3099861 [T/C] chr1 3099861 Cc01_g01790:647 exon NON_SYNONYMOUS_CODING gAt/gGt D/G 16.7% 3 TT TC TT NN -chr1:3099819 [A/G] chr1 3099819 Cc01_g01790:689 exon NON_SYNONYMOUS_CODING tTc/tCc F/S 16.7% 3 AA AG AA NN -chr1:3099817 [A/G] chr1 3099817 Cc01_g01790:691 exon SYNONYMOUS_CODING Tta/Cta L/L 16.7% 3 AA AG AA NN -chr1:3099361 [C/T] chr1 3099361 Cc01_g01790:921 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT -chr1:3099178 [C/T] chr1 3099178 Cc01_g01790:1104 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC -chr1:3098863 [C/T] chr1 3098863 Cc01_g01790:1419 exon SYNONYMOUS_CODING caG/caA Q/Q 50.0% 2 CC NN TT NN -chr1:3098710 [T/G] chr1 3098710 Cc01_g01790:1572 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 33.3% 3 TT NN GG TT -chr1:3098694 [C/T] chr1 3098694 Cc01_g01790:1588 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC TT CC -chr1:3098670 [C/T] chr1 3098670 Cc01_g01790:1612 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 25.0% 4 CC CC CC TT -chr1:3098669 [A/T] chr1 3098669 Cc01_g01790:1613 exon NON_SYNONYMOUS_CODING gTg/gAg V/E 25.0% 4 AA AA AA TT -chr1:3098646 [G/A] chr1 3098646 Cc01_g01790:1636 exon NON_SYNONYMOUS_CODING Cgg/Tgg R/W 33.3% 3 GG NN GG AA -chr1:3098643 [C/T] chr1 3098643 Cc01_g01790:1639 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 CC NN TT CC -chr1:3098575 [T/A] chr1 3098575 Cc01_g01790:1707 exon SYNONYMOUS_CODING gtA/gtT V/V 33.3% 3 TT TT NN AA -chr1:3098545 [C/T] chr1 3098545 Cc01_g01790:1737 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 2 CC NN NN CT -chr1:3098445 [T/G] chr1 3098445 Cc01_g01790:1837 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 33.3% 3 TT GG TT NN -chr1:3098439 [A/C] chr1 3098439 Cc01_g01790:1843 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA AC AC NN -chr1:3098433 [C/T] chr1 3098433 Cc01_g01790:1849 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 CC CC TC NN -chr1:3098416 [A/G] chr1 3098416 Cc01_g01790:1866 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 AA AA GA NN -chr1:3098249 [T/G] chr1 3098249 Cc01_g01790:1982 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN GG NN -chr1:3098236 [T/G] chr1 3098236 Cc01_g01790:1995 exon SYNONYMOUS_CODING gcA/gcC A/A 25.0% 4 TT TG TG TT -chr1:3098217 [T/C] chr1 3098217 Cc01_g01790:2014 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 TT TT TT CC -chr1:3098210 [C/A] chr1 3098210 Cc01_g01790:2021 exon NON_SYNONYMOUS_CODING aGg/aTg R/M 25.0% 4 CC AC AC CC -chr1:3098185 [G/T] chr1 3098185 Cc01_g01790:2046 exon SYNONYMOUS_CODING ccC/ccA P/P 25.0% 4 GG GG GG TT -chr1:3098182 [C/T] chr1 3098182 Cc01_g01790:2049 exon SYNONYMOUS_CODING caG/caA Q/Q 37.5% 4 CC CC TC TT -chr1:3098175 [C/T] chr1 3098175 Cc01_g01790:2056 exon NON_SYNONYMOUS_CODING Gct/Act A/T 25.0% 4 CC CC TC CT -chr1:3098148 [A/G] chr1 3098148 Cc01_g01790:2083 exon NON_SYNONYMOUS_CODING Tac/Cac Y/H 25.0% 4 AA GG GG GG -chr1:3098140 [C/G] chr1 3098140 Cc01_g01790:2091 exon NON_SYNONYMOUS_CODING caG/caC Q/H 25.0% 4 CC CC GC CG -chr1:3098133 [C/A] chr1 3098133 Cc01_g01790:2098 exon NON_SYNONYMOUS_CODING Gat/Tat D/Y 37.5% 4 CC AA CA CC -chr1:3098100 [T/C] chr1 3098100 Cc01_g01790:2131 exon NON_SYNONYMOUS_CODING Act/Gct T/A 25.0% 4 TT TT TC TC -chr1:3098097 [C/T] chr1 3098097 Cc01_g01790:2134 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CC TC -chr1:3098083 [C/G] chr1 3098083 Cc01_g01790:2148 exon NON_SYNONYMOUS_CODING gaG/gaC E/D 12.5% 4 CC CC CG CC -chr1:3098073 [G/C] chr1 3098073 Cc01_g01790:2158 exon NON_SYNONYMOUS_CODING Cac/Gac H/D 37.5% 4 GG CC CG GG -chr1:3098015 [T/C] chr1 3098015 Cc01_g01790:2216 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC -chr1:3097800 [C/T] chr1 3097800 Cc01_g01790:2431 exon NON_SYNONYMOUS_CODING Gcg/Acg A/T 50.0% 2 CC NN NN TT -chr1:3130398 [G/A] chr1 3130398 Cc01_g01800:5 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG GA GA GA -chr1:3130394 [G/A] chr1 3130394 Cc01_g01800:9 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG AG GG -chr1:3130389 [G/A] chr1 3130389 Cc01_g01800:14 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 37.5% 4 GG AG GA AG -chr1:3130367 [A/G] chr1 3130367 Cc01_g01800:36 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 AA GA AG GA -chr1:3130332 [C/T] chr1 3130332 Cc01_g01800:71 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 12.5% 4 CC CC TC CC -chr1:3130320 [A/G] chr1 3130320 Cc01_g01800:83 exon NON_SYNONYMOUS_CODING gTt/gCt V/A 12.5% 4 AA GA AA AA -chr1:3130313 [C/T] chr1 3130313 Cc01_g01800:90 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC TT TT TT -chr1:3130268 [G/C] chr1 3130268 Cc01_g01800:135 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG CC GC GG -chr1:3130244 [G/A] chr1 3130244 Cc01_g01800:159 exon SYNONYMOUS_CODING gaC/gaT D/D 12.5% 4 GG GG GG GA -chr1:3130238 [G/T] chr1 3130238 Cc01_g01800:165 exon NON_SYNONYMOUS_CODING aaC/aaA N/K 37.5% 4 GG TT GT GG -chr1:3130227 [T/C] chr1 3130227 Cc01_g01800:176 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 50.0% 4 TT CC TC TC -chr1:3130205 [T/C] chr1 3130205 Cc01_g01800:198 exon SYNONYMOUS_CODING aaA/aaG K/K 37.5% 4 TT CC TC TT -chr1:3130073 [A/C] chr1 3130073 Cc01_g01800:276 exon NON_SYNONYMOUS_CODING aaT/aaG N/K 33.3% 3 AA CC CC NN -chr1:3130016 [G/T] chr1 3130016 Cc01_g01800:333 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 3 GG NN TT GT -chr1:3129989 [G/C] chr1 3129989 Cc01_g01800:360 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 12.5% 4 GG GC GG GG -chr1:3129968 [G/C] chr1 3129968 Cc01_g01800:381 exon NON_SYNONYMOUS_CODING caC/caG H/Q 12.5% 4 GG GG GC GG -chr1:3129955 [C/T] chr1 3129955 Cc01_g01800:394 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 37.5% 4 CC TT TC CC -chr1:3129939 [G/C] chr1 3129939 Cc01_g01800:410 exon NON_SYNONYMOUS_CODING aCg/aGg T/R 12.5% 4 GG GG GG GC -chr1:3129936 [G/A] chr1 3129936 Cc01_g01800:413 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 12.5% 4 GG GG GG GA -chr1:3129931 [T/G] chr1 3129931 Cc01_g01800:418 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG -chr1:3129930 [C/T] chr1 3129930 Cc01_g01800:419 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 12.5% 4 CC CC CC TC -chr1:3129911 [A/G] chr1 3129911 Cc01_g01800:438 exon SYNONYMOUS_CODING gtT/gtC V/V 12.5% 4 AA AA AA GA -chr1:3129147 [T/C] chr1 3129147 Cc01_g01800:481 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 50.0% 2 TT CC NN NN -chr1:3129110 [C/T] chr1 3129110 Cc01_g01800:518 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 50.0% 2 CC TT NN NN -chr1:3129103 [G/A] chr1 3129103 Cc01_g01800:525 exon SYNONYMOUS_CODING gtC/gtT V/V 50.0% 2 GG AA NN NN -chr1:3128596 [C/T] chr1 3128596 Cc01_g01800:1032 exon SYNONYMOUS_CODING ttG/ttA L/L 33.3% 3 CC NN TT CC -chr1:3128592 [T/C] chr1 3128592 Cc01_g01800:1036 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 33.3% 3 TT NN CC TT -chr1:3128555 [A/G] chr1 3128555 Cc01_g01800:1073 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 16.7% 3 AA NN AG AA -chr1:3128551 [T/C] chr1 3128551 Cc01_g01800:1077 exon SYNONYMOUS_CODING gcA/gcG A/A 16.7% 3 TT NN TC TT -chr1:3128512 [A/C] chr1 3128512 Cc01_g01800:1116 exon NON_SYNONYMOUS_CODING gaT/gaG D/E 33.3% 3 AA NN CC CC -chr1:3128013 [A/T] chr1 3128013 Cc01_g01800:1525 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN TT AA -chr1:3127995 [T/A] chr1 3127995 Cc01_g01800:1543 exon NON_SYNONYMOUS_CODING Aat/Tat N/Y 33.3% 3 TT NN TT AA -chr1:3127863 [C/T] chr1 3127863 Cc01_g01800:1675 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 CC NN TT CC -chr1:3127784 [G/T] chr1 3127784 Cc01_g01800:1754 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 33.3% 3 GG NN GG TT -chr1:3127444 [C/G] chr1 3127444 Cc01_g01800:2094 exon NON_SYNONYMOUS_CODING caG/caC Q/H 50.0% 2 CC NN NN GG -chr1:3127440 [C/A] chr1 3127440 Cc01_g01800:2098 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 33.3% 3 CC NN CC AA -chr1:3127337 [C/T] chr1 3127337 Cc01_g01800:2201 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 33.3% 3 CC TT CC NN -chr1:3127308 [G/A] chr1 3127308 Cc01_g01800:2230 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 50.0% 3 GG GA AA NN -chr1:3127296 [T/C] chr1 3127296 Cc01_g01800:2242 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 33.3% 3 TT CC CC NN -chr1:3127276 [C/T] chr1 3127276 Cc01_g01800:2262 exon SYNONYMOUS_CODING gtG/gtA V/V 33.3% 3 CC CC TT NN -chr1:3127267 [C/T] chr1 3127267 Cc01_g01800:2271 exon SYNONYMOUS_CODING caG/caA Q/Q 33.3% 3 CC TT TT NN -chr1:3127260 [A/C] chr1 3127260 Cc01_g01800:2278 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 AA CC AA NN -chr1:3127254 [T/G] chr1 3127254 Cc01_g01800:2284 exon SYNONYMOUS_CODING Agg/Cgg R/R 50.0% 2 TT NN GG NN -chr1:3127253 [C/T] chr1 3127253 Cc01_g01800:2285 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 CC TT TT NN -chr1:3127252 [C/T] chr1 3127252 Cc01_g01800:2286 exon SYNONYMOUS_CODING agG/agA R/R 33.3% 3 CC TT TT NN -chr1:3127234 [G/A] chr1 3127234 Cc01_g01800:2304 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 2 GG NN GA NN -chr1:3127034 [G/A] chr1 3127034 Cc01_g01800:2411 exon NON_SYNONYMOUS_CODING gCa/gTa A/V 50.0% 2 GG AA NN NN -chr1:3127033 [T/A] chr1 3127033 Cc01_g01800:2412 exon SYNONYMOUS_CODING gcA/gcT A/A 50.0% 2 TT AA NN NN -chr1:3126983 [A/G] chr1 3126983 Cc01_g01800:2462 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 25.0% 4 AA AA AA GG -chr1:3126979 [A/G] chr1 3126979 Cc01_g01800:2466 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 AA GG AA AA -chr1:3126953 [A/C] chr1 3126953 Cc01_g01800:2492 exon NON_SYNONYMOUS_CODING cTc/cGc L/R 33.3% 3 AA NN AA CC -chr1:3126937 [G/T] chr1 3126937 Cc01_g01800:2508 exon SYNONYMOUS_CODING ccC/ccA P/P 33.3% 3 GG NN GG TT -chr1:3126913 [C/T] chr1 3126913 Cc01_g01800:2532 exon SYNONYMOUS_CODING tcG/tcA S/S 16.7% 3 CC NN CT CC -chr1:3126816 [G/A] chr1 3126816 Cc01_g01800:2569 exon NON_SYNONYMOUS_CODING Cac/Tac H/Y 33.3% 3 GG NN GG AA -chr1:3126795 [C/T] chr1 3126795 Cc01_g01800:2590 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC CC CC TT -chr1:3126780 [A/T] chr1 3126780 Cc01_g01800:2605 exon NON_SYNONYMOUS_CODING Tcg/Acg S/T 25.0% 4 AA AA AA TT -chr1:3126751 [G/A] chr1 3126751 Cc01_g01800:2634 exon SYNONYMOUS_CODING gaC/gaT D/D 33.3% 3 GG AA AA NN -chr1:3126700 [G/T] chr1 3126700 Cc01_g01800:2685 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT -chr1:3126699 [G/A] chr1 3126699 Cc01_g01800:2686 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 25.0% 4 GG GA GG GA -chr1:3126690 [C/G] chr1 3126690 Cc01_g01800:2695 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 50.0% 4 CC GG CC GG -chr1:3126637 [A/G] chr1 3126637 Cc01_g01800:2748 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 4 AA GG AA GG -chr1:3126626 [C/T] chr1 3126626 Cc01_g01800:2759 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 33.3% 3 CC TT CC NN -chr1:3126612 [G/A] chr1 3126612 Cc01_g01800:2773 exon SYNONYMOUS_CODING Ctg/Ttg L/L 33.3% 3 GG AA GG NN -chr1:3126600 [A/T] chr1 3126600 Cc01_g01800:2785 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 33.3% 3 AA TT AA NN -chr1:3126553 [T/A] chr1 3126553 Cc01_g01800:2832 exon SYNONYMOUS_CODING ccA/ccT P/P 33.3% 3 TT TT AA NN -chr1:3126547 [G/T] chr1 3126547 Cc01_g01800:2838 exon SYNONYMOUS_CODING ctC/ctA L/L 33.3% 3 GG GG TT NN -chr1:3126532 [T/A] chr1 3126532 Cc01_g01800:2853 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 33.3% 3 TT TT AA NN -chr1:3126528 [T/C] chr1 3126528 Cc01_g01800:2857 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT CC TT NN -chr1:3126526 [T/A] chr1 3126526 Cc01_g01800:2859 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 25.0% 4 TT TT TT AA -chr1:3126503 [C/T] chr1 3126503 Cc01_g01800:2882 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CC CT CC -chr1:3126400 [T/C] chr1 3126400 Cc01_g01800:2985 exon SYNONYMOUS_CODING ttA/ttG L/L 33.3% 3 TT CC TT NN -chr1:3126397 [C/T] chr1 3126397 Cc01_g01800:2988 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC TT TT TT -chr1:3126364 [G/T] chr1 3126364 Cc01_g01800:3021 exon SYNONYMOUS_CODING cgC/cgA R/R 50.0% 4 GG TT GG TT -chr1:3126267 [A/G] chr1 3126267 Cc01_g01800:3118 exon NON_SYNONYMOUS_CODING Tcg/Ccg S/P 33.3% 3 AA GG GG NN -chr1:3126189 [T/C] chr1 3126189 Cc01_g01800:3196 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 TT NN CC NN -chr1:3126120 [T/G] chr1 3126120 Cc01_g01800:3265 exon SYNONYMOUS_CODING Aga/Cga R/R 33.3% 3 TT GG GG NN -chr1:3148320 [G/C] chr1 3148320 Cc01_g01810:19 exon NON_SYNONYMOUS_CODING Cat/Gat H/D 25.0% 4 GG CC CC CC -chr1:3148319 [T/G] chr1 3148319 Cc01_g01810:20 exon NON_SYNONYMOUS_CODING cAt/cCt H/P 12.5% 4 TT TT TT TG -chr1:3148309 [A/T] chr1 3148309 Cc01_g01810:30 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 25.0% 4 AA TT TT TT -chr1:3148308 [A/C] chr1 3148308 Cc01_g01810:31 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 25.0% 4 AA CC CC CC -chr1:3148305 [G/A] chr1 3148305 Cc01_g01810:34 exon NON_SYNONYMOUS_CODING Cat/Tat H/Y 25.0% 4 GG AA AA AA -chr1:3148268 [G/T] chr1 3148268 Cc01_g01810:71 exon NON_SYNONYMOUS_CODING aCg/aAg T/K 12.5% 4 GG GG GT GG -chr1:3148255 [A/T] chr1 3148255 Cc01_g01810:84 exon SYNONYMOUS_CODING acT/acA T/T 12.5% 4 AA AA AT AA -chr1:3148238 [A/G] chr1 3148238 Cc01_g01810:101 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 37.5% 4 AA GG GA GG -chr1:3148222 [G/C] chr1 3148222 Cc01_g01810:117 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 12.5% 4 GG GG CG GG -chr1:3148212 [A/G] chr1 3148212 Cc01_g01810:127 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 12.5% 4 AA AG AA AA -chr1:3148211 [C/T] chr1 3148211 Cc01_g01810:128 exon NON_SYNONYMOUS_CODING tGt/tAt C/Y 37.5% 4 CC TT TC TT -chr1:3148184 [T/C] chr1 3148184 Cc01_g01810:155 exon NON_SYNONYMOUS_CODING tAc/tGc Y/C 12.5% 4 TT CT TT TT -chr1:3148162 [G/A] chr1 3148162 Cc01_g01810:177 exon SYNONYMOUS_CODING agC/agT S/S 12.5% 4 GG AG GG GG -chr1:3148147 [C/T] chr1 3148147 Cc01_g01810:192 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 CC TT TT TT -chr1:3148104 [T/C] chr1 3148104 Cc01_g01810:202 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 TT TT TC TT -chr1:3148094 [G/T] chr1 3148094 Cc01_g01810:212 exon STOP_GAINED tCa/tAa S/1 12.5% 4 GG GG GG GT -chr1:3148091 [G/T] chr1 3148091 Cc01_g01810:215 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 GG GG GG GT -chr1:3191460 [A/G] chr1 3191460 Cc01_g01820:313 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 25.0% 4 AA GG AA AA -chr1:3191468 [T/G] chr1 3191468 Cc01_g01820:321 exon SYNONYMOUS_CODING ctT/ctG L/L 12.5% 4 TT TG TT TT -chr1:3191469 [G/A] chr1 3191469 Cc01_g01820:322 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 25.0% 4 GG AA AA AA -chr1:3191497 [A/G] chr1 3191497 Cc01_g01820:350 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AA AA AG -chr1:3191499 [G/A] chr1 3191499 Cc01_g01820:352 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG GA -chr1:3191505 [C/G] chr1 3191505 Cc01_g01820:358 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC CC GG -chr1:3191507 [A/G] chr1 3191507 Cc01_g01820:360 exon SYNONYMOUS_CODING ctA/ctG L/L 37.5% 4 AA GA AA GG -chr1:3191521 [C/A] chr1 3191521 Cc01_g01820:374 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 12.5% 4 CC CC CA CC -chr1:3191526 [G/T] chr1 3191526 Cc01_g01820:379 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GG GT GG -chr1:3191552 [T/C] chr1 3191552 Cc01_g01820:405 exon SYNONYMOUS_CODING gtT/gtC V/V 37.5% 4 TT CC CC TC -chr1:3191561 [A/G] chr1 3191561 Cc01_g01820:414 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA GA -chr1:3191576 [T/C] chr1 3191576 Cc01_g01820:429 exon SYNONYMOUS_CODING acT/acC T/T 25.0% 4 TT TT TC TC -chr1:3191774 [T/C] chr1 3191774 Cc01_g01820:627 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT -chr1:3191801 [A/G] chr1 3191801 Cc01_g01820:654 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AA AG -chr1:3191814 [A/G] chr1 3191814 Cc01_g01820:667 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 12.5% 4 AA AA AA AG -chr1:3191835 [G/A] chr1 3191835 Cc01_g01820:688 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 12.5% 4 GG GG GG AG -chr1:3191836 [G/A] chr1 3191836 Cc01_g01820:689 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 12.5% 4 GG GG GA GG -chr1:3191840 [A/G] chr1 3191840 Cc01_g01820:693 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AG AA -chr1:3191846 [A/C] chr1 3191846 Cc01_g01820:699 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 12.5% 4 AA AA AC AA -chr1:3191856 [C/A] chr1 3191856 Cc01_g01820:709 exon SYNONYMOUS_CODING Cgg/Agg R/R 25.0% 4 CC CA CC AC -chr1:3191872 [G/A] chr1 3191872 Cc01_g01820:725 exon NON_SYNONYMOUS_CODING gGa/gAa G/E 25.0% 4 GG GA GG AG -chr1:3191876 [A/C] chr1 3191876 Cc01_g01820:729 exon NON_SYNONYMOUS_CODING gaA/gaC E/D 25.0% 4 AA AC AA CA -chr1:3191881 [A/G] chr1 3191881 Cc01_g01820:734 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 25.0% 4 AA AG AG AA -chr1:3191888 [A/C] chr1 3191888 Cc01_g01820:741 exon NON_SYNONYMOUS_CODING caA/caC Q/H 12.5% 4 AA AA CA AA -chr1:3191897 [G/A] chr1 3191897 Cc01_g01820:750 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GG GA -chr1:3191902 [A/G] chr1 3191902 Cc01_g01820:755 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG -chr1:3191903 [G/A] chr1 3191903 Cc01_g01820:756 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 GG GG GG GA -chr1:3191912 [T/A] chr1 3191912 Cc01_g01820:765 exon SYNONYMOUS_CODING ctT/ctA L/L 50.0% 4 TT TT AA AA -chr1:3192960 [A/G] chr1 3192960 Cc01_g01820:1688 exon NON_SYNONYMOUS_CODING cAt/cGt H/R 50.0% 2 AA NN GG NN -chr1:3192995 [G/T] chr1 3192995 Cc01_g01820:1723 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 25.0% 2 GG NN GT NN -chr1:3193034 [T/A] chr1 3193034 Cc01_g01820:1762 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 50.0% 3 TT AA TA NN -chr1:3193036 [G/T] chr1 3193036 Cc01_g01820:1764 exon NON_SYNONYMOUS_CODING tgG/tgT W/C 50.0% 3 GG TT GT NN -chr1:3193095 [A/G] chr1 3193095 Cc01_g01820:1823 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 2 AA NN NN AG -chr1:3193128 [G/A] chr1 3193128 Cc01_g01820:1856 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG AA GG NN -chr1:3193178 [T/C] chr1 3193178 Cc01_g01820:1906 exon NON_SYNONYMOUS_CODING Tgc/Cgc C/R 33.3% 3 TT CC TT NN -chr1:3193205 [G/A] chr1 3193205 Cc01_g01820:1933 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN -chr1:3193208 [C/G] chr1 3193208 Cc01_g01820:1936 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 33.3% 3 CC GG GG NN -chr1:3193232 [G/A] chr1 3193232 Cc01_g01820:1960 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA GG NN -chr1:3193249 [T/A] chr1 3193249 Cc01_g01820:1977 exon NON_SYNONYMOUS_CODING ttT/ttA F/L 33.3% 3 TT AA TT NN -chr1:3193250 [A/G] chr1 3193250 Cc01_g01820:1978 exon NON_SYNONYMOUS_CODING Agg/Ggg R/G 33.3% 3 AA GG AA NN -chr1:3193251 [G/A] chr1 3193251 Cc01_g01820:1979 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 33.3% 3 GG AA GG NN -chr1:3193257 [A/T] chr1 3193257 Cc01_g01820:1985 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 33.3% 3 AA TT AA NN -chr1:3193258 [A/T] chr1 3193258 Cc01_g01820:1986 exon NON_SYNONYMOUS_CODING caA/caT Q/H 33.3% 3 AA TT AA NN -chr1:3193262 [G/A] chr1 3193262 Cc01_g01820:1990 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 33.3% 3 GG AA GG NN -chr1:3193330 [T/C] chr1 3193330 Cc01_g01820:2058 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 2 TT NN CC NN -chr1:3193551 [A/C] chr1 3193551 Cc01_g01820:2279 exon NON_SYNONYMOUS_CODING tAt/tCt Y/S 50.0% 4 AA CC AA CC -chr1:3193556 [A/G] chr1 3193556 Cc01_g01820:2284 exon NON_SYNONYMOUS_CODING Acc/Gcc T/A 25.0% 4 AA AA AA GG -chr1:3193561 [T/C] chr1 3193561 Cc01_g01820:2289 exon SYNONYMOUS_CODING tcT/tcC S/S 25.0% 4 TT TT TT CC -chr1:3193565 [C/A] chr1 3193565 Cc01_g01820:2293 exon NON_SYNONYMOUS_CODING Cag/Aag Q/K 25.0% 4 CC AA CC CC -chr1:3193580 [A/T] chr1 3193580 Cc01_g01820:2308 exon NON_SYNONYMOUS_CODING Act/Tct T/S 25.0% 4 AA AA AA TT -chr1:3193581 [C/T] chr1 3193581 Cc01_g01820:2309 exon NON_SYNONYMOUS_CODING aCt/aTt T/I 25.0% 4 CC CC CC TT -chr1:3193590 [G/A] chr1 3193590 Cc01_g01820:2318 exon NON_SYNONYMOUS_CODING gGc/gAc G/D 25.0% 4 GG AA GG GG -chr1:3193598 [G/A] chr1 3193598 Cc01_g01820:2326 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 GG AA GG GG -chr1:3193621 [A/G] chr1 3193621 Cc01_g01820:2349 exon SYNONYMOUS_CODING caA/caG Q/Q 33.3% 3 AA NN AA GG -chr1:3193623 [G/A] chr1 3193623 Cc01_g01820:2351 exon NON_SYNONYMOUS_CODING cGa/cAa R/Q 33.3% 3 GG NN GG AA -chr1:3193638 [T/C] chr1 3193638 Cc01_g01820:2366 exon NON_SYNONYMOUS_CODING tTg/tCg L/S 33.3% 3 TT NN TT CC -chr1:3193642 [G/T] chr1 3193642 Cc01_g01820:2370 exon NON_SYNONYMOUS_CODING gaG/gaT E/D 12.5% 4 GG GG GT GG -chr1:3193647 [A/T] chr1 3193647 Cc01_g01820:2375 exon NON_SYNONYMOUS_CODING gAa/gTa E/V 37.5% 4 AA TT AT AA -chr1:3193825 [G/T] chr1 3193825 Cc01_g01820:2553 exon SYNONYMOUS_CODING tcG/tcT S/S 16.7% 3 GG GG GT NN -chr1:3193843 [A/G] chr1 3193843 Cc01_g01820:2571 exon SYNONYMOUS_CODING gaA/gaG E/E 33.3% 3 AA GG AA NN -chr1:3193848 [A/G] chr1 3193848 Cc01_g01820:2576 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA AG AG NN -chr1:3193868 [G/A] chr1 3193868 Cc01_g01820:2596 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 16.7% 3 GG GA GG NN -chr1:3193975 [T/C] chr1 3193975 Cc01_g01820:2703 exon SYNONYMOUS_CODING gcT/gcC A/A 33.3% 3 TT NN TT CC -chr1:3194001 [G/A] chr1 3194001 Cc01_g01820:2729 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 33.3% 3 GG NN GG AA -chr1:3197392 [A/G] chr1 3197392 Cc01_g01830:128 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 AA AG AA AA -chr1:3197403 [C/T] chr1 3197403 Cc01_g01830:139 exon SYNONYMOUS_CODING Ctg/Ttg L/L 37.5% 4 CC CT TT CC -chr1:3197417 [A/G] chr1 3197417 Cc01_g01830:153 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 AA AG GG AG -chr1:3197423 [A/G] chr1 3197423 Cc01_g01830:159 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AA AG -chr1:3197426 [A/G] chr1 3197426 Cc01_g01830:162 exon SYNONYMOUS_CODING tcA/tcG S/S 25.0% 4 AA AG AA AG -chr1:3197433 [T/A] chr1 3197433 Cc01_g01830:169 exon NON_SYNONYMOUS_CODING Ttg/Atg L/M 50.0% 4 TT TA AA TA -chr1:3197457 [T/C] chr1 3197457 Cc01_g01830:193 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 25.0% 4 TT CT TT CT -chr1:3197458 [C/T] chr1 3197458 Cc01_g01830:194 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CC CT CC -chr1:3197465 [T/G] chr1 3197465 Cc01_g01830:201 exon SYNONYMOUS_CODING gcT/gcG A/A 25.0% 4 TT TT TG TG -chr1:3197474 [C/T] chr1 3197474 Cc01_g01830:210 exon SYNONYMOUS_CODING ctC/ctT L/L 37.5% 4 CC CT TC CT -chr1:3197478 [T/C] chr1 3197478 Cc01_g01830:214 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 TT TT TC TT -chr1:3197482 [T/C] chr1 3197482 Cc01_g01830:218 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 37.5% 4 TT CT TC CT -chr1:3197490 [G/A] chr1 3197490 Cc01_g01830:226 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG -chr1:3197494 [T/C] chr1 3197494 Cc01_g01830:230 exon NON_SYNONYMOUS_CODING aTc/aCc I/T 12.5% 4 TT CT TT TT -chr1:3197498 [C/T] chr1 3197498 Cc01_g01830:234 exon SYNONYMOUS_CODING ttC/ttT F/F 12.5% 4 CC TC CC CC -chr1:3197500 [T/C] chr1 3197500 Cc01_g01830:236 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 25.0% 4 TT CT TC TT -chr1:3197504 [C/T] chr1 3197504 Cc01_g01830:240 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC -chr1:3197513 [G/T] chr1 3197513 Cc01_g01830:249 exon SYNONYMOUS_CODING gtG/gtT V/V 12.5% 4 GG GG GT GG -chr1:3197514 [C/A] chr1 3197514 Cc01_g01830:250 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 CC CA AC CC -chr1:3197516 [T/G] chr1 3197516 Cc01_g01830:252 exon SYNONYMOUS_CODING ctT/ctG L/L 25.0% 4 TT GT TG TT -chr1:3197529 [G/A] chr1 3197529 Cc01_g01830:265 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 50.0% 4 GG GA GA AA -chr1:3197531 [C/T] chr1 3197531 Cc01_g01830:267 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 CC CC CC CT -chr1:3197533 [A/T] chr1 3197533 Cc01_g01830:269 exon NON_SYNONYMOUS_CODING gAt/gTt D/V 12.5% 4 AA AA AA AT -chr1:3197544 [T/G] chr1 3197544 Cc01_g01830:280 exon NON_SYNONYMOUS_CODING Tgt/Ggt C/G 12.5% 4 TT TT TT GT -chr1:3197558 [C/T] chr1 3197558 Cc01_g01830:294 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CT CC -chr1:3293623 [C/T] chr1 3293623 Cc01_g01840:150 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC TT NN TT -chr1:3293672 [A/C] chr1 3293672 Cc01_g01840:199 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 12.5% 4 AA AA AC AA -chr1:3293717 [G/A] chr1 3293717 Cc01_g01840:244 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GG GA GG -chr1:3294121 [G/C] chr1 3294121 Cc01_g01840:555 exon NON_SYNONYMOUS_CODING aaG/aaC K/N 25.0% 4 GG CC GG GG -chr1:3294122 [A/C] chr1 3294122 Cc01_g01840:556 exon NON_SYNONYMOUS_CODING Aag/Cag K/Q 25.0% 4 AA AA CC AA -chr1:3294138 [T/A] chr1 3294138 Cc01_g01840:572 exon NON_SYNONYMOUS_CODING cTc/cAc L/H 33.3% 3 TT TT AA NN -chr1:3294175 [A/G] chr1 3294175 Cc01_g01840:609 exon SYNONYMOUS_CODING aaA/aaG K/K 16.7% 3 AA AA NN AG -chr1:3294278 [G/A] chr1 3294278 Cc01_g01840:655 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 33.3% 3 GG AA NN AA -chr1:3294351 [C/T] chr1 3294351 Cc01_g01840:728 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 25.0% 4 CC CC TT CC -chr1:3294386 [A/G] chr1 3294386 Cc01_g01840:763 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 AA GG NN GG -chr1:3294489 [G/T] chr1 3294489 Cc01_g01840:866 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 25.0% 4 GG TT TT TT -chr1:3294543 [C/T] chr1 3294543 Cc01_g01840:920 exon NON_SYNONYMOUS_CODING tCt/tTt S/F 12.5% 4 CC CT CC CC -chr1:3295343 [G/C] chr1 3295343 Cc01_g01840:1501 exon NON_SYNONYMOUS_CODING Gaa/Caa E/Q 33.3% 3 GG CC GG NN -chr1:3295400 [G/A] chr1 3295400 Cc01_g01840:1558 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 37.5% 4 GG GA GG AA -chr1:3295407 [C/A] chr1 3295407 Cc01_g01840:1565 exon NON_SYNONYMOUS_CODING gCt/gAt A/D 25.0% 4 CC CC AA CC -chr1:3295410 [T/A] chr1 3295410 Cc01_g01840:1568 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 25.0% 4 TT TT TT AA -chr1:3295411 [T/G] chr1 3295411 Cc01_g01840:1569 exon SYNONYMOUS_CODING gtT/gtG V/V 50.0% 4 TT GG TT GG -chr1:3295423 [G/T] chr1 3295423 Cc01_g01840:1581 exon SYNONYMOUS_CODING ccG/ccT P/P 12.5% 4 GG TG GG GG -chr1:3295466 [G/A] chr1 3295466 Cc01_g01840:1624 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA NN AA -chr1:3295709 [T/C] chr1 3295709 Cc01_g01840:1867 exon NON_SYNONYMOUS_CODING Tgt/Cgt C/R 50.0% 2 TT NN NN CC -chr1:3295750 [A/G] chr1 3295750 Cc01_g01840:1908 exon SYNONYMOUS_CODING ttA/ttG L/L 50.0% 2 AA NN NN GG -chr1:3295781 [G/A] chr1 3295781 Cc01_g01840:1939 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 16.7% 3 GG GG NN GA -chr1:3295793 [T/A] chr1 3295793 Cc01_g01840:1951 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 25.0% 4 TT TT TT AA -chr1:3295794 [G/A] chr1 3295794 Cc01_g01840:1952 exon STOP_GAINED tGg/tAg W/1 50.0% 4 GG AA GG AA -chr1:3295796 [T/G] chr1 3295796 Cc01_g01840:1954 exon NON_SYNONYMOUS_CODING Tat/Gat Y/D 33.3% 3 TT TT NN GG -chr1:3295811 [C/G] chr1 3295811 Cc01_g01840:1969 exon NON_SYNONYMOUS_CODING Caa/Gaa Q/E 37.5% 4 CC CG CC GG -chr1:3295832 [G/C] chr1 3295832 Cc01_g01840:1990 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 50.0% 3 GG CC NN GC -chr1:3295834 [T/A] chr1 3295834 Cc01_g01840:1992 exon NON_SYNONYMOUS_CODING gaT/gaA D/E 50.0% 3 TT AA NN TA -chr1:3295846 [A/G] chr1 3295846 Cc01_g01840:2004 exon SYNONYMOUS_CODING acA/acG T/T 33.3% 3 AA AG NN GA -chr1:3295852 [T/C] chr1 3295852 Cc01_g01840:2010 exon SYNONYMOUS_CODING ccT/ccC P/P 33.3% 3 TT CC NN CC -chr1:3295877 [T/A] chr1 3295877 Cc01_g01840:2035 exon NON_SYNONYMOUS_CODING Tac/Aac Y/N 33.3% 3 TT TT AA NN -chr1:3295893 [G/A] chr1 3295893 Cc01_g01840:2051 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 33.3% 3 GG NN AA GG -chr1:3323377 [T/C] chr1 3323377 Cc01_g01850:669 exon SYNONYMOUS_CODING ccA/ccG P/P 12.5% 4 TT TT TT TC -chr1:3323201 [C/T] chr1 3323201 Cc01_g01850:845 exon NON_SYNONYMOUS_CODING aGc/aAc S/N 16.7% 3 CC CT NN CC -chr1:3337218 [C/A] chr1 3337218 Cc01_g01860:15 exon SYNONYMOUS_CODING acG/acT T/T 12.5% 4 CC CA CC CC -chr1:3337216 [G/A] chr1 3337216 Cc01_g01860:17 exon NON_SYNONYMOUS_CODING tCg/tTg S/L 12.5% 4 GG GG GG GA -chr1:3337209 [G/C] chr1 3337209 Cc01_g01860:24 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GG GC GG -chr1:3337191 [C/T] chr1 3337191 Cc01_g01860:42 exon SYNONYMOUS_CODING ctG/ctA L/L 37.5% 4 CC TT TC CC -chr1:3337176 [G/T] chr1 3337176 Cc01_g01860:57 exon SYNONYMOUS_CODING ctC/ctA L/L 50.0% 4 GG TT TT GG -chr1:3337167 [C/T] chr1 3337167 Cc01_g01860:66 exon SYNONYMOUS_CODING ggG/ggA G/G 37.5% 4 CC TT TC CC -chr1:3337129 [C/T] chr1 3337129 Cc01_g01860:104 exon NON_SYNONYMOUS_CODING aGa/aAa R/K 25.0% 4 CC TT TT TT -chr1:3336284 [G/A] chr1 3336284 Cc01_g01860:213 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 GG GG GA GG -chr1:3336266 [G/A] chr1 3336266 Cc01_g01860:231 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 GG GA GA AA -chr1:3336239 [T/C] chr1 3336239 Cc01_g01860:258 exon SYNONYMOUS_CODING gaA/gaG E/E 50.0% 4 TT TC CC TC -chr1:3333450 [A/T] chr1 3333450 Cc01_g01860:400 exon NON_SYNONYMOUS_CODING Tta/Ata L/I 12.5% 4 AA AA AT AA -chr1:3333413 [G/C] chr1 3333413 Cc01_g01860:437 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 GG GC GG GG -chr1:3333326 [G/A] chr1 3333326 Cc01_g01860:524 exon NON_SYNONYMOUS_CODING tCa/tTa S/L 12.5% 4 GG GG GG GA -chr1:3333322 [T/C] chr1 3333322 Cc01_g01860:528 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 TT TT TC TT -chr1:3333297 [C/T] chr1 3333297 Cc01_g01860:553 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC TC CC -chr1:3333229 [G/A] chr1 3333229 Cc01_g01860:621 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG GA GG GA -chr1:3333223 [C/T] chr1 3333223 Cc01_g01860:627 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 CC CC CT CC -chr1:3332599 [C/T] chr1 3332599 Cc01_g01860:669 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 CC CC CT CC -chr1:3332597 [C/G] chr1 3332597 Cc01_g01860:671 exon NON_SYNONYMOUS_CODING cGa/cCa R/P 12.5% 4 CC CC GC CC -chr1:3332395 [T/C] chr1 3332395 Cc01_g01860:775 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TC TT -chr1:3332371 [G/C] chr1 3332371 Cc01_g01860:799 exon NON_SYNONYMOUS_CODING Cag/Gag Q/E 12.5% 4 GG GG CG GG -chr1:3332350 [T/C] chr1 3332350 Cc01_g01860:820 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT CC TT TT -chr1:3332348 [T/C] chr1 3332348 Cc01_g01860:822 exon SYNONYMOUS_CODING acA/acG T/T 37.5% 4 TT CC CC TC -chr1:3332316 [A/G] chr1 3332316 Cc01_g01860:854 exon NON_SYNONYMOUS_CODING cTa/cCa L/P 12.5% 4 AA AG AA AA -chr1:3332250 [A/G] chr1 3332250 Cc01_g01860:920 exon NON_SYNONYMOUS_CODING cTt/cCt L/P 12.5% 4 AA AA AA AG -chr1:3332219 [G/A] chr1 3332219 Cc01_g01860:951 exon SYNONYMOUS_CODING tcC/tcT S/S 12.5% 4 GG GA GG GG -chr1:3332209 [T/C] chr1 3332209 Cc01_g01860:961 exon NON_SYNONYMOUS_CODING Act/Gct T/A 37.5% 4 TT CC CC TC -chr1:3338434 [G/T] chr1 3338434 Cc01_g01870:20 exon NON_SYNONYMOUS_CODING cGa/cTa R/L 16.7% 3 GG GG GT NN -chr1:3338449 [A/G] chr1 3338449 Cc01_g01870:35 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 25.0% 2 AA NN AG NN -chr1:3338455 [C/G] chr1 3338455 Cc01_g01870:41 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 50.0% 2 CC NN GG NN -chr1:3338489 [T/G] chr1 3338489 Cc01_g01870:75 exon SYNONYMOUS_CODING gcT/gcG A/A 16.7% 3 TT TT TG NN -chr1:3338523 [A/G] chr1 3338523 Cc01_g01870:109 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 2 AA NN AG NN -chr1:3338527 [C/G] chr1 3338527 Cc01_g01870:113 exon NON_SYNONYMOUS_CODING cCg/cGg P/R 25.0% 2 CC NN CG NN -chr1:3338584 [C/A] chr1 3338584 Cc01_g01870:170 exon NON_SYNONYMOUS_CODING cCg/cAg P/Q 25.0% 4 CC CC AA CC -chr1:3338618 [G/A] chr1 3338618 Cc01_g01870:204 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 GG GG AA GG -chr1:3338682 [A/G] chr1 3338682 Cc01_g01870:268 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 12.5% 4 AA AG AA AA -chr1:3340569 [G/C] chr1 3340569 Cc01_g01870:341 exon NON_SYNONYMOUS_CODING gGt/gCt G/A 12.5% 4 GG GG GC GG -chr1:3340586 [C/A] chr1 3340586 Cc01_g01870:358 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 25.0% 4 CC CA CA CC -chr1:3340636 [A/T] chr1 3340636 Cc01_g01870:408 exon SYNONYMOUS_CODING ccA/ccT P/P 25.0% 4 AA AT AT AA -chr1:3341154 [G/A] chr1 3341154 Cc01_g01870:609 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 GG AA GG GG -chr1:3341373 [A/G] chr1 3341373 Cc01_g01870:828 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA AG AG AA -chr1:3341763 [C/A] chr1 3341763 Cc01_g01870:1039 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC CA CA CC -chr1:3341885 [T/G] chr1 3341885 Cc01_g01870:1161 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TT GG TT -chr1:3341925 [G/T] chr1 3341925 Cc01_g01870:1201 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 25.0% 4 GG GG TT GG -chr1:3341957 [C/T] chr1 3341957 Cc01_g01870:1233 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC CT CC -chr1:3342026 [A/G] chr1 3342026 Cc01_g01870:1302 exon SYNONYMOUS_CODING ttA/ttG L/L 25.0% 4 AA AA GG AA -chr1:3342047 [T/C] chr1 3342047 Cc01_g01870:1323 exon SYNONYMOUS_CODING gcT/gcC A/A 12.5% 4 TT TT TC TT -chr1:3342053 [G/A] chr1 3342053 Cc01_g01870:1329 exon NON_SYNONYMOUS_CODING atG/atA M/I 25.0% 4 GG GG AA GG -chr1:3342122 [T/G] chr1 3342122 Cc01_g01870:1398 exon SYNONYMOUS_CODING ccT/ccG P/P 25.0% 4 TT TG TG TT -chr1:3342260 [C/G] chr1 3342260 Cc01_g01870:1441 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC -chr1:3342603 [G/A] chr1 3342603 Cc01_g01870:1728 exon SYNONYMOUS_CODING aaG/aaA K/K 16.7% 3 GG GG GA NN -chr1:3342762 [T/C] chr1 3342762 Cc01_g01870:1887 exon SYNONYMOUS_CODING ggT/ggC G/G 25.0% 4 TT TC TC TT -chr1:3342780 [C/T] chr1 3342780 Cc01_g01870:1905 exon SYNONYMOUS_CODING taC/taT Y/Y 12.5% 4 CC CC TC CC -chr1:3342870 [C/T] chr1 3342870 Cc01_g01870:1995 exon SYNONYMOUS_CODING ggC/ggT G/G 25.0% 4 CC CT CT CC -chr1:3342879 [T/C] chr1 3342879 Cc01_g01870:2004 exon SYNONYMOUS_CODING ttT/ttC F/F 12.5% 4 TT TT TC TT -chr1:3342996 [C/T] chr1 3342996 Cc01_g01870:2121 exon SYNONYMOUS_CODING gtC/gtT V/V 33.3% 3 CC CT CT NN -chr1:3342999 [A/T] chr1 3342999 Cc01_g01870:2124 exon SYNONYMOUS_CODING gcA/gcT A/A 33.3% 3 AA AT AT NN -chr1:3343053 [T/A] chr1 3343053 Cc01_g01870:2178 exon SYNONYMOUS_CODING gcT/gcA A/A 16.7% 3 TT TT TA NN -chr1:3343056 [T/C] chr1 3343056 Cc01_g01870:2181 exon SYNONYMOUS_CODING gcT/gcC A/A 16.7% 3 TT TT TC NN -chr1:3343080 [C/T] chr1 3343080 Cc01_g01870:2205 exon SYNONYMOUS_CODING gcC/gcT A/A 16.7% 3 CC NN CT CC -chr1:3343146 [T/C] chr1 3343146 Cc01_g01870:2271 exon SYNONYMOUS_CODING cgT/cgC R/R 16.7% 3 TT NN TC TT -chr1:3343149 [C/T] chr1 3343149 Cc01_g01870:2274 exon SYNONYMOUS_CODING tgC/tgT C/C 16.7% 3 CC NN CT CC -chr1:3343251 [C/T] chr1 3343251 Cc01_g01870:2376 exon SYNONYMOUS_CODING gtC/gtT V/V 12.5% 4 CC CC CT CC -chr1:3343348 [G/A] chr1 3343348 Cc01_g01870:2473 exon NON_SYNONYMOUS_CODING Gca/Aca A/T 25.0% 4 GG GG AA GG -chr1:3343425 [A/T] chr1 3343425 Cc01_g01870:2550 exon SYNONYMOUS_CODING acA/acT T/T 16.7% 3 AA NN AT AA -chr1:3343449 [A/G] chr1 3343449 Cc01_g01870:2574 exon SYNONYMOUS_CODING tcA/tcG S/S 16.7% 3 AA NN AG AA -chr1:3343557 [G/A] chr1 3343557 Cc01_g01870:2682 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 2 GG NN GA NN -chr1:3343584 [G/C] chr1 3343584 Cc01_g01870:2709 exon NON_SYNONYMOUS_CODING ttG/ttC L/F 12.5% 4 GG GG GC GG -chr1:3343605 [T/C] chr1 3343605 Cc01_g01870:2730 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT -chr1:3343713 [G/A] chr1 3343713 Cc01_g01870:2838 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 GG GG GA GG -chr1:3343793 [A/G] chr1 3343793 Cc01_g01870:2918 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 33.3% 3 AA NN GG AA -chr1:3343946 [T/A] chr1 3343946 Cc01_g01870:3071 exon NON_SYNONYMOUS_CODING tTt/tAt F/Y 12.5% 4 TT TT TA TT -chr1:3343980 [T/A] chr1 3343980 Cc01_g01870:3105 exon SYNONYMOUS_CODING ctT/ctA L/L 12.5% 4 TT TT TA TT -chr1:3344061 [T/C] chr1 3344061 Cc01_g01870:3186 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 TT TT TC TT -chr1:3344094 [C/G] chr1 3344094 Cc01_g01870:3219 exon SYNONYMOUS_CODING ctC/ctG L/L 25.0% 4 CC CC GG CC -chr1:3344225 [A/C] chr1 3344225 Cc01_g01870:3350 exon NON_SYNONYMOUS_CODING aAc/aCc N/T 25.0% 4 AA AC AC AA -chr1:3344291 [A/G] chr1 3344291 Cc01_g01870:3416 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 AA AG AG AA -chr1:3344304 [A/G] chr1 3344304 Cc01_g01870:3429 exon SYNONYMOUS_CODING gaA/gaG E/E 25.0% 4 AA AG AG AA -chr1:3344335 [A/T] chr1 3344335 Cc01_g01870:3460 exon NON_SYNONYMOUS_CODING Act/Tct T/S 12.5% 4 AA AA AT AA -chr1:3344340 [A/G] chr1 3344340 Cc01_g01870:3465 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AA AG AA -chr1:3344367 [G/A] chr1 3344367 Cc01_g01870:3492 exon NON_SYNONYMOUS_CODING atG/atA M/I 12.5% 4 GG GG GA GG -chr1:3344610 [A/G] chr1 3344610 Cc01_g01870:3646 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 25.0% 4 AA AG AG AA -chr1:3344615 [C/T] chr1 3344615 Cc01_g01870:3651 exon SYNONYMOUS_CODING taC/taT Y/Y 25.0% 4 CC CT CT CC -chr1:3344705 [T/C] chr1 3344705 Cc01_g01870:3741 exon SYNONYMOUS_CODING agT/agC S/S 50.0% 4 TT CC CC TT -chr1:3344765 [C/T] chr1 3344765 Cc01_g01870:3801 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 CC CT CT CC -chr1:3344998 [C/G] chr1 3344998 Cc01_g01870:3928 exon NON_SYNONYMOUS_CODING Cta/Gta L/V 25.0% 4 CC CC GG CC -chr1:3345023 [C/G] chr1 3345023 Cc01_g01870:3953 exon NON_SYNONYMOUS_CODING aCt/aGt T/S 12.5% 4 CC CC CG CC -chr1:3345239 [G/A] chr1 3345239 Cc01_g01870:4077 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 GG GA AA GG -chr1:3345251 [G/A] chr1 3345251 Cc01_g01870:4089 exon SYNONYMOUS_CODING ggG/ggA G/G 12.5% 4 GG GG GA GG -chr1:3345257 [A/G] chr1 3345257 Cc01_g01870:4095 exon SYNONYMOUS_CODING ctA/ctG L/L 12.5% 4 AA AA AG AA -chr1:3345539 [A/G] chr1 3345539 Cc01_g01870:4290 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 AA AA GG AA -chr1:3346036 [G/A] chr1 3346036 Cc01_g01870:4488 exon SYNONYMOUS_CODING acG/acA T/T 12.5% 4 GG GA GG GG -chr1:3346713 [T/C] chr1 3346713 Cc01_g01870:4716 exon SYNONYMOUS_CODING cgT/cgC R/R 25.0% 4 TT TC TC TT -chr1:3346848 [C/T] chr1 3346848 Cc01_g01870:4851 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 4 CC CT CT CC -chr1:3346851 [T/G] chr1 3346851 Cc01_g01870:4854 exon SYNONYMOUS_CODING cgT/cgG R/R 12.5% 4 TT TT TG TT -chr1:3346917 [G/A] chr1 3346917 Cc01_g01870:4920 exon SYNONYMOUS_CODING gaG/gaA E/E 33.3% 3 GG GA GA NN -chr1:3346920 [T/G] chr1 3346920 Cc01_g01870:4923 exon SYNONYMOUS_CODING ctT/ctG L/L 16.7% 3 TT TT GT NN -chr1:3347106 [T/C] chr1 3347106 Cc01_g01870:5109 exon SYNONYMOUS_CODING gaT/gaC D/D 25.0% 4 TT TC TC TT -chr1:3347181 [C/A] chr1 3347181 Cc01_g01870:5184 exon SYNONYMOUS_CODING acC/acA T/T 25.0% 4 CC CA CA CC -chr1:3347198 [T/C] chr1 3347198 Cc01_g01870:5201 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 TT TT TC TT -chr1:3347363 [C/T] chr1 3347363 Cc01_g01870:5280 exon SYNONYMOUS_CODING ccC/ccT P/P 25.0% 4 CC CT CT CC -chr1:3347553 [A/G] chr1 3347553 Cc01_g01870:5361 exon NON_SYNONYMOUS_CODING atA/atG I/M 12.5% 4 AA AA AG AA -chr1:3347739 [C/T] chr1 3347739 Cc01_g01870:5547 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CT CC -chr1:3347754 [A/G] chr1 3347754 Cc01_g01870:5562 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AG AA -chr1:3347884 [T/C] chr1 3347884 Cc01_g01870:5616 exon SYNONYMOUS_CODING cgT/cgC R/R 12.5% 4 TT TT TC TT -chr1:3347890 [A/C] chr1 3347890 Cc01_g01870:5622 exon SYNONYMOUS_CODING ggA/ggC G/G 12.5% 4 AA AA AC AA -chr1:3348120 [T/A] chr1 3348120 Cc01_g01870:5852 exon NON_SYNONYMOUS_CODING gTc/gAc V/D 25.0% 4 TT AA AA AA -chr1:3348121 [C/A] chr1 3348121 Cc01_g01870:5853 exon SYNONYMOUS_CODING gtC/gtA V/V 25.0% 4 CC AA AA AA -chr1:3348167 [A/G] chr1 3348167 Cc01_g01870:5899 exon NON_SYNONYMOUS_CODING Att/Gtt I/V 12.5% 4 AA AA AG AA -chr1:3348225 [A/G] chr1 3348225 Cc01_g01870:5957 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 12.5% 4 AA AG AA AA -chr1:3348593 [G/A] chr1 3348593 Cc01_g01870:6109 exon NON_SYNONYMOUS_CODING Gtg/Atg V/M 12.5% 4 GG GG GG GA -chr1:3348598 [C/T] chr1 3348598 Cc01_g01870:6114 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CT CC CC -chr1:3348607 [G/A] chr1 3348607 Cc01_g01870:6123 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GA GG -chr1:3348689 [G/T] chr1 3348689 Cc01_g01870:6205 exon NON_SYNONYMOUS_CODING Gtt/Ttt V/F 12.5% 4 GG GG GT GG -chr1:3348691 [T/C] chr1 3348691 Cc01_g01870:6207 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT -chr1:3348799 [C/T] chr1 3348799 Cc01_g01870:6219 exon SYNONYMOUS_CODING gcC/gcT A/A 25.0% 4 CC CT CT CC -chr1:3348886 [T/C] chr1 3348886 Cc01_g01870:6306 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT -chr1:3348950 [T/C] chr1 3348950 Cc01_g01870:6370 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 12.5% 4 TT TT TC TT -chr1:3349098 [C/A] chr1 3349098 Cc01_g01870:6441 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CC CA CC -chr1:3349159 [A/T] chr1 3349159 Cc01_g01870:6502 exon NON_SYNONYMOUS_CODING Atg/Ttg M/L 12.5% 4 AA AA AT AA -chr1:3349258 [T/C] chr1 3349258 Cc01_g01870:6601 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 12.5% 4 TT TT TC TT -chr1:3349275 [T/C] chr1 3349275 Cc01_g01870:6618 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TT TC TT -chr1:3349309 [A/G] chr1 3349309 Cc01_g01870:6652 exon NON_SYNONYMOUS_CODING Atg/Gtg M/V 25.0% 4 AA AA AA GG -chr1:3349550 [A/G] chr1 3349550 Cc01_g01870:6731 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AA AG -chr1:3349635 [A/G] chr1 3349635 Cc01_g01870:6816 exon SYNONYMOUS_CODING ccA/ccG P/P 37.5% 4 AA AG GG AA -chr1:3349684 [A/C] chr1 3349684 Cc01_g01870:6865 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 AA AC AC AA -chr1:3349692 [T/C] chr1 3349692 Cc01_g01870:6873 exon SYNONYMOUS_CODING taT/taC Y/Y 12.5% 4 TT TT TC TT -chr1:3349701 [G/A] chr1 3349701 Cc01_g01870:6882 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 GG GG GA GA -chr1:3349725 [T/C] chr1 3349725 Cc01_g01870:6906 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TT TC TT -chr1:3349872 [T/A] chr1 3349872 Cc01_g01870:6942 exon SYNONYMOUS_CODING ccT/ccA P/P 25.0% 4 TT TA TA TT -chr1:3349938 [A/G] chr1 3349938 Cc01_g01870:7008 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 AA AA AG AA -chr1:3349953 [T/G] chr1 3349953 Cc01_g01870:7023 exon SYNONYMOUS_CODING ccT/ccG P/P 12.5% 4 TT TT TG TT -chr1:3349955 [A/G] chr1 3349955 Cc01_g01870:7025 exon NON_SYNONYMOUS_CODING aAg/aGg K/R 12.5% 4 AA AA AG AA -chr1:3349959 [C/G] chr1 3349959 Cc01_g01870:7029 exon NON_SYNONYMOUS_CODING gaC/gaG D/E 25.0% 4 CC GG GG GG -chr1:3349968 [T/C] chr1 3349968 Cc01_g01870:7038 exon SYNONYMOUS_CODING caT/caC H/H 25.0% 4 TT CC TT TT -chr1:3350026 [A/G] chr1 3350026 Cc01_g01870:7096 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 37.5% 4 AA AG GG AA -chr1:3350040 [C/T] chr1 3350040 Cc01_g01870:7110 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 CC CT CC CC -chr1:3362501 [A/T] chr1 3362501 Cc01_g01900:15 exon SYNONYMOUS_CODING atT/atA I/I 33.3% 3 AA NN TT TT -chr1:3362493 [G/C] chr1 3362493 Cc01_g01900:23 exon STOP_GAINED tCa/tGa S8* 25.0% 4 GG CC CC CC -chr1:3362488 [C/T] chr1 3362488 Cc01_g01900:28 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 25.0% 4 CC TT TT TT -chr1:3362464 [C/G] chr1 3362464 Cc01_g01900:52 exon NON_SYNONYMOUS_CODING Gtc/Ctc V/L 25.0% 4 CC GG GG GG -chr1:3362461 [C/G] chr1 3362461 Cc01_g01900:55 exon NON_SYNONYMOUS_CODING Gat/Cat D/H 25.0% 4 CC GG GG GG -chr1:3362423 [T/G] chr1 3362423 Cc01_g01900:93 exon NON_SYNONYMOUS_CODING aaA/aaC K/N 50.0% 4 TT TT GG GG -chr1:3383330 [A/T] chr1 3383330 Cc01_g01910:149 exon NON_SYNONYMOUS_CODING aTc/aAc I/N 50.0% 2 AA TT NN NN -chr1:3383254 [C/T] chr1 3383254 Cc01_g01910:225 exon SYNONYMOUS_CODING aaG/aaA K/K 50.0% 2 CC NN NN TT -chr1:3383250 [A/C] chr1 3383250 Cc01_g01910:229 exon NON_SYNONYMOUS_CODING Tca/Gca S/A 50.0% 2 AA NN NN CC -chr1:3383240 [T/G] chr1 3383240 Cc01_g01910:239 exon NON_SYNONYMOUS_CODING cAa/cCa Q/P 50.0% 2 TT NN NN GG -chr1:3543339 [T/C] chr1 3543339 Cc01_g01950:133 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 37.5% 4 TT CC TT TC -chr1:3543344 [T/C] chr1 3543344 Cc01_g01950:138 exon SYNONYMOUS_CODING ctT/ctC L/L 12.5% 4 TT TC TT TT -chr1:3543798 [C/T] chr1 3543798 Cc01_g01950:592 exon SYNONYMOUS_CODING Ctg/Ttg L/L 12.5% 4 CC CT CC CC -chr1:3544052 [T/C] chr1 3544052 Cc01_g01950:846 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 TT TC TT TT -chr1:3563539 [T/A] chr1 3563539 Cc01_g01960:208 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 TT AA TT NN -chr1:3563667 [G/A] chr1 3563667 Cc01_g01960:336 exon SYNONYMOUS_CODING gcG/gcA A/A 16.7% 3 GG GG NN GA -chr1:3563754 [G/C] chr1 3563754 Cc01_g01960:423 exon SYNONYMOUS_CODING acG/acC T/T 25.0% 4 GG GC GG GC -chr1:3563771 [A/G] chr1 3563771 Cc01_g01960:440 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 AA GG AG AG -chr1:3563793 [T/C] chr1 3563793 Cc01_g01960:462 exon SYNONYMOUS_CODING gtT/gtC V/V 25.0% 4 TT TC TC TT -chr1:3574473 [G/C] chr1 3574473 Cc01_g01970:51 exon SYNONYMOUS_CODING gcC/gcG A/A 33.3% 3 GG NN CC GG -chr1:3574458 [A/G] chr1 3574458 Cc01_g01970:66 exon SYNONYMOUS_CODING ctT/ctC L/L 33.3% 3 AA NN AA GG -chr1:3574326 [A/T] chr1 3574326 Cc01_g01970:198 exon NON_SYNONYMOUS_CODING aaT/aaA N/K 33.3% 3 AA NN TT TT -chr1:3574296 [A/G] chr1 3574296 Cc01_g01970:228 exon SYNONYMOUS_CODING gaT/gaC D/D 33.3% 3 AA NN AA GG -chr1:3574115 [T/C] chr1 3574115 Cc01_g01970:409 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 33.3% 3 TT NN CC CC -chr1:3574063 [G/A] chr1 3574063 Cc01_g01970:461 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 25.0% 4 GG GG AA GG -chr1:3574027 [A/T] chr1 3574027 Cc01_g01970:497 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT -chr1:3573800 [C/T] chr1 3573800 Cc01_g01970:724 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 CC TT TT TT -chr1:3573759 [A/G] chr1 3573759 Cc01_g01970:765 exon SYNONYMOUS_CODING ggT/ggC G/G 33.3% 3 AA NN AA GG -chr1:3573736 [C/T] chr1 3573736 Cc01_g01970:788 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 50.0% 4 CC TT CC TT -chr1:3573699 [G/C] chr1 3573699 Cc01_g01970:825 exon NON_SYNONYMOUS_CODING ttC/ttG F/L 25.0% 4 GG GG CC GG -chr1:3573693 [A/G] chr1 3573693 Cc01_g01970:831 exon SYNONYMOUS_CODING gtT/gtC V/V 50.0% 4 AA GG AA GG -chr1:3573559 [A/T] chr1 3573559 Cc01_g01970:965 exon NON_SYNONYMOUS_CODING gTt/gAt V/D 33.3% 3 AA NN AA TT -chr1:3573509 [A/T] chr1 3573509 Cc01_g01970:1015 exon NON_SYNONYMOUS_CODING Ttt/Att F/I 33.3% 3 AA NN AA TT -chr1:3573370 [C/T] chr1 3573370 Cc01_g01970:1053 exon SYNONYMOUS_CODING ccG/ccA P/P 33.3% 3 CC NN CC TT -chr1:3573336 [C/A] chr1 3573336 Cc01_g01970:1087 exon NON_SYNONYMOUS_CODING Ggc/Tgc G/C 50.0% 4 CC AA CC AA -chr1:3573271 [C/G] chr1 3573271 Cc01_g01970:1152 exon SYNONYMOUS_CODING ggG/ggC G/G 33.3% 3 CC NN GG CC -chr1:3573239 [G/C] chr1 3573239 Cc01_g01970:1184 exon NON_SYNONYMOUS_CODING tCg/tGg S/W 33.3% 3 GG NN CC CC -chr1:3573098 [G/T] chr1 3573098 Cc01_g01970:1251 exon SYNONYMOUS_CODING ccC/ccA P/P 50.0% 4 GG TT GG TT -chr1:3573097 [T/G] chr1 3573097 Cc01_g01970:1252 exon NON_SYNONYMOUS_CODING Ata/Cta I/L 50.0% 4 TT GG TT GG -chr1:3572965 [G/A] chr1 3572965 Cc01_g01970:1384 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 33.3% 3 GG NN AA AA -chr1:3572931 [A/G] chr1 3572931 Cc01_g01970:1418 exon NON_SYNONYMOUS_CODING tTa/tCa L/S 33.3% 3 AA NN GG GG -chr1:3572899 [T/C] chr1 3572899 Cc01_g01970:1450 exon NON_SYNONYMOUS_CODING Ata/Gta I/V 25.0% 4 TT CC CC CC -chr1:3572885 [C/G] chr1 3572885 Cc01_g01970:1464 exon SYNONYMOUS_CODING gcG/gcC A/A 25.0% 4 CC GG GG GG -chr1:3572859 [C/T] chr1 3572859 Cc01_g01970:1490 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT -chr1:3572854 [G/T] chr1 3572854 Cc01_g01970:1495 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 25.0% 4 GG TT TT TT -chr1:3572835 [T/A] chr1 3572835 Cc01_g01970:1514 exon NON_SYNONYMOUS_CODING aAg/aTg K/M 25.0% 4 TT TT AA TT -chr1:3649364 [A/T] chr1 3649364 Cc01_g01980:156 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 AA AA AA AT -chr1:3649391 [C/T] chr1 3649391 Cc01_g01980:183 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC CT -chr1:3649422 [C/G] chr1 3649422 Cc01_g01980:214 exon NON_SYNONYMOUS_CODING Cgc/Ggc R/G 25.0% 4 CC GG CC CC -chr1:3649490 [G/A] chr1 3649490 Cc01_g01980:282 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA GG GG -chr1:3649502 [T/C] chr1 3649502 Cc01_g01980:294 exon SYNONYMOUS_CODING gcT/gcC A/A 37.5% 4 TT CC TC CC -chr1:3649727 [T/C] chr1 3649727 Cc01_g01980:519 exon SYNONYMOUS_CODING tgT/tgC C/C 12.5% 4 TT TC TT TT -chr1:3649746 [G/T] chr1 3649746 Cc01_g01980:538 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 25.0% 4 GG TT TT TT -chr1:3661555 [G/C] chr1 3661555 Cc01_g01990:23 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 33.3% 3 GG CC GG NN -chr1:3661523 [T/C] chr1 3661523 Cc01_g01990:55 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 33.3% 3 TT CC CC NN -chr1:3661511 [C/G] chr1 3661511 Cc01_g01990:67 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 33.3% 3 CC GG NN CC -chr1:3661507 [A/C] chr1 3661507 Cc01_g01990:71 exon NON_SYNONYMOUS_CODING cTg/cGg L/R 33.3% 3 AA CC NN AA -chr1:3661453 [T/C] chr1 3661453 Cc01_g01990:125 exon NON_SYNONYMOUS_CODING aAa/aGa K/R 25.0% 4 TT CC TT TT -chr1:3661403 [A/T] chr1 3661403 Cc01_g01990:175 exon NON_SYNONYMOUS_CODING Tgg/Agg W/R 33.3% 3 AA TT AA NN -chr1:3661345 [G/T] chr1 3661345 Cc01_g01990:233 exon NON_SYNONYMOUS_CODING tCt/tAt S/Y 33.3% 3 GG GG NN TT -chr1:3661344 [A/G] chr1 3661344 Cc01_g01990:234 exon SYNONYMOUS_CODING tcT/tcC S/S 16.7% 3 AA AG NN AA -chr1:3660894 [T/C] chr1 3660894 Cc01_g01990:273 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 TT CC NN TT -chr1:3660770 [C/T] chr1 3660770 Cc01_g01990:319 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 33.3% 3 CC NN TT CC -chr1:3660756 [A/C] chr1 3660756 Cc01_g01990:333 exon NON_SYNONYMOUS_CODING caT/caG H/Q 25.0% 4 AA CC AA AA -chr1:3660584 [T/C] chr1 3660584 Cc01_g01990:379 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 25.0% 4 TT TT TT CC -chr1:3660566 [G/A] chr1 3660566 Cc01_g01990:397 exon NON_SYNONYMOUS_CODING Cca/Tca P/S 37.5% 4 GG GA AA GG -chr1:3660548 [C/T] chr1 3660548 Cc01_g01990:415 exon NON_SYNONYMOUS_CODING Gga/Aga G/R 37.5% 4 CC CT TT CC -chr1:3660530 [C/T] chr1 3660530 Cc01_g01990:433 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 25.0% 4 CC TT TT TT -chr1:3660529 [C/A] chr1 3660529 Cc01_g01990:434 exon NON_SYNONYMOUS_CODING gGc/gTc G/V 50.0% 4 CC AA AA CC -chr1:3660523 [C/T] chr1 3660523 Cc01_g01990:440 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 50.0% 4 CC TT TT CC -chr1:3660509 [T/C] chr1 3660509 Cc01_g01990:454 exon NON_SYNONYMOUS_CODING Aat/Gat N/D 25.0% 4 TT CC TT TT -chr1:3660489 [T/G] chr1 3660489 Cc01_g01990:474 exon SYNONYMOUS_CODING gcA/gcC A/A 50.0% 4 TT GG GG TT -chr1:3660392 [T/G] chr1 3660392 Cc01_g01990:571 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 25.0% 4 TT GG GG GG -chr1:3660382 [T/A] chr1 3660382 Cc01_g01990:581 exon NON_SYNONYMOUS_CODING aAa/aTa K/I 25.0% 4 TT AA TT TT -chr1:3660368 [T/C] chr1 3660368 Cc01_g01990:595 exon NON_SYNONYMOUS_CODING Agt/Ggt S/G 25.0% 4 TT CC CC CC -chr1:3663378 [T/A] chr1 3663378 Cc01_g02000:123 exon SYNONYMOUS_CODING tcA/tcT S/S 12.5% 4 TT TA TT TT -chr1:3663363 [C/T] chr1 3663363 Cc01_g02000:138 exon SYNONYMOUS_CODING aaG/aaA K/K 12.5% 4 CC TC CC CC -chr1:3663324 [G/A] chr1 3663324 Cc01_g02000:177 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 GG AG GG GG -chr1:3663323 [C/T] chr1 3663323 Cc01_g02000:178 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 12.5% 4 CC CC CT CC -chr1:3663308 [A/T] chr1 3663308 Cc01_g02000:193 exon STOP_LOST Tag/Aag 6/K 37.5% 4 AA TT AT AA -chr1:3704574 [A/T] chr1 3704574 Cc01_g02010:179 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 25.0% 4 AA TT TT TT -chr1:3704558 [T/A] chr1 3704558 Cc01_g02010:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT -chr1:3704537 [A/G] chr1 3704537 Cc01_g02010:216 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AG AA -chr1:3704524 [A/T] chr1 3704524 Cc01_g02010:229 exon NON_SYNONYMOUS_CODING Tat/Aat Y/N 12.5% 4 AA AA AA AT -chr1:3704520 [G/C] chr1 3704520 Cc01_g02010:233 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG -chr1:3704494 [C/T] chr1 3704494 Cc01_g02010:259 exon NON_SYNONYMOUS_CODING Gcc/Acc A/T 25.0% 4 CC TT TT TT -chr1:3702641 [A/T] chr1 3702641 Cc01_g02010:350 exon NON_SYNONYMOUS_CODING cTt/cAt L/H 12.5% 4 AA AT AA AA -chr1:3702616 [T/A] chr1 3702616 Cc01_g02010:375 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TA TT TT -chr1:3702601 [T/C] chr1 3702601 Cc01_g02010:390 exon SYNONYMOUS_CODING agA/agG R/R 12.5% 4 TT TT TT TC -chr1:3702599 [T/A] chr1 3702599 Cc01_g02010:392 exon NON_SYNONYMOUS_CODING cAa/cTa Q/L 12.5% 4 TT TT TT AT -chr1:3702582 [C/T] chr1 3702582 Cc01_g02010:409 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC TC CC CC -chr1:3702367 [T/C] chr1 3702367 Cc01_g02010:534 exon SYNONYMOUS_CODING gcA/gcG A/A 25.0% 4 TT TT TT CC -chr1:3702346 [A/T] chr1 3702346 Cc01_g02010:555 exon SYNONYMOUS_CODING tcT/tcA S/S 12.5% 4 AA AA AT AA -chr1:3702331 [G/A] chr1 3702331 Cc01_g02010:570 exon SYNONYMOUS_CODING gcC/gcT A/A 37.5% 4 GG GA AA GG -chr1:3702283 [G/A] chr1 3702283 Cc01_g02010:618 exon SYNONYMOUS_CODING agC/agT S/S 25.0% 4 GG AA AA AA -chr1:3702270 [A/G] chr1 3702270 Cc01_g02010:631 exon NON_SYNONYMOUS_CODING Tgg/Cgg W/R 12.5% 4 AA AG AA AA -chr1:3702235 [A/G] chr1 3702235 Cc01_g02010:666 exon SYNONYMOUS_CODING agT/agC S/S 12.5% 4 AA GA AA AA -chr1:3702233 [T/C] chr1 3702233 Cc01_g02010:668 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 37.5% 4 TT TC CC TT -chr1:3702222 [T/G] chr1 3702222 Cc01_g02010:679 exon SYNONYMOUS_CODING Aga/Cga R/R 12.5% 4 TT TT TT TG -chr1:3702218 [T/C] chr1 3702218 Cc01_g02010:683 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 12.5% 4 TT TT TT CT -chr1:3701396 [C/T] chr1 3701396 Cc01_g02010:708 exon SYNONYMOUS_CODING gtG/gtA V/V 12.5% 4 CC CC CC CT -chr1:3701386 [A/G] chr1 3701386 Cc01_g02010:718 exon SYNONYMOUS_CODING Ttg/Ctg L/L 25.0% 4 AA AA AA GG -chr1:3701243 [T/C] chr1 3701243 Cc01_g02010:861 exon SYNONYMOUS_CODING gcA/gcG A/A 12.5% 4 TT TT TC TT -chr1:3701240 [G/A] chr1 3701240 Cc01_g02010:864 exon SYNONYMOUS_CODING acC/acT T/T 25.0% 4 GG GG GG AA -chr1:3701237 [C/T] chr1 3701237 Cc01_g02010:867 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CC CT CC -chr1:3700510 [C/T] chr1 3700510 Cc01_g02010:931 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 16.7% 3 CC CC CT NN -chr1:3699429 [C/T] chr1 3699429 Cc01_g02010:1020 exon SYNONYMOUS_CODING agG/agA R/R 25.0% 4 CC CC CC TT -chr1:3699397 [G/C] chr1 3699397 Cc01_g02010:1052 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 16.7% 3 GG GG GC NN -chr1:3699002 [C/A] chr1 3699002 Cc01_g02010:1192 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 37.5% 4 CC CA CC AA -chr1:3698979 [A/G] chr1 3698979 Cc01_g02010:1215 exon SYNONYMOUS_CODING caT/caC H/H 12.5% 4 AA AA AA AG -chr1:3698964 [T/C] chr1 3698964 Cc01_g02010:1230 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 TT TT TC TT -chr1:3698934 [C/T] chr1 3698934 Cc01_g02010:1260 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC CT CT TT -chr1:3698922 [C/T] chr1 3698922 Cc01_g02010:1272 exon SYNONYMOUS_CODING gcG/gcA A/A 25.0% 4 CC CC CC TT -chr1:3698901 [C/T] chr1 3698901 Cc01_g02010:1293 exon SYNONYMOUS_CODING tcG/tcA S/S 37.5% 4 CC CC CT TT -chr1:3698886 [A/G] chr1 3698886 Cc01_g02010:1308 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 AA AA AG AA -chr1:3698880 [T/C] chr1 3698880 Cc01_g02010:1314 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TC TT -chr1:3698871 [T/A] chr1 3698871 Cc01_g02010:1323 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 TT TT TT AA -chr1:3698841 [T/A] chr1 3698841 Cc01_g02010:1353 exon NON_SYNONYMOUS_CODING ttA/ttT L/F 25.0% 4 TT AA AA AA -chr1:3698450 [C/T] chr1 3698450 Cc01_g02010:1477 exon NON_SYNONYMOUS_CODING Gct/Act A/T 12.5% 4 CC CC CT CC -chr1:3698412 [G/A] chr1 3698412 Cc01_g02010:1515 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 GG GG GG AA -chr1:3698398 [T/A] chr1 3698398 Cc01_g02010:1529 exon NON_SYNONYMOUS_CODING tAc/tTc Y/F 12.5% 4 TT TA TT TT -chr1:3698247 [A/G] chr1 3698247 Cc01_g02010:1680 exon SYNONYMOUS_CODING taT/taC Y/Y 25.0% 4 AA AA AA GG -chr1:3697989 [T/C] chr1 3697989 Cc01_g02010:1692 exon SYNONYMOUS_CODING caA/caG Q/Q 12.5% 4 TT TT TC TT -chr1:3696904 [A/T] chr1 3696904 Cc01_g02010:1866 exon NON_SYNONYMOUS_CODING caT/caA H/Q 50.0% 2 AA NN TT NN -chr1:3696445 [A/G] chr1 3696445 Cc01_g02010:1945 exon NON_SYNONYMOUS_CODING Tat/Cat Y/H 25.0% 4 AA AA AA GG -chr1:3696441 [C/T] chr1 3696441 Cc01_g02010:1949 exon NON_SYNONYMOUS_CODING gGt/gAt G/D 25.0% 4 CC TT TT TT -chr1:3696389 [C/T] chr1 3696389 Cc01_g02010:2001 exon SYNONYMOUS_CODING ccG/ccA P/P 37.5% 4 CC CC CT TT -chr1:3696380 [C/T] chr1 3696380 Cc01_g02010:2010 exon SYNONYMOUS_CODING ttG/ttA L/L 25.0% 4 CC TT TT TT -chr1:3696362 [T/C] chr1 3696362 Cc01_g02010:2028 exon SYNONYMOUS_CODING ctA/ctG L/L 25.0% 4 TT TT TT CC -chr1:3696314 [T/G] chr1 3696314 Cc01_g02010:2076 exon SYNONYMOUS_CODING tcA/tcC S/S 25.0% 4 TT TT TT GG -chr1:3696312 [C/G] chr1 3696312 Cc01_g02010:2078 exon NON_SYNONYMOUS_CODING aGa/aCa R/T 37.5% 4 CC GG CG CC -chr1:3695395 [A/G] chr1 3695395 Cc01_g02010:2114 exon NON_SYNONYMOUS_CODING gTa/gCa V/A 12.5% 4 AA AA AA AG -chr1:3695358 [T/C] chr1 3695358 Cc01_g02010:2151 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT CT -chr1:3695350 [T/C] chr1 3695350 Cc01_g02010:2159 exon NON_SYNONYMOUS_CODING aAc/aGc N/S 50.0% 4 TT CC CC TT -chr1:3695299 [G/A] chr1 3695299 Cc01_g02010:2210 exon NON_SYNONYMOUS_CODING aCa/aTa T/I 25.0% 4 GG GG GG AA -chr1:3725796 [T/C] chr1 3725796 Cc01_g02020:642 exon SYNONYMOUS_CODING atT/atC I/I 16.7% 3 TT NN TT TC -chr1:3725964 [A/G] chr1 3725964 Cc01_g02020:810 exon NON_SYNONYMOUS_CODING atA/atG I/M 33.3% 3 AA NN GG GG -chr1:3727454 [C/T] chr1 3727454 Cc01_g02020:1724 exon NON_SYNONYMOUS_CODING gCc/gTc A/V 50.0% 2 CC NN NN TT -chr1:3727458 [A/T] chr1 3727458 Cc01_g02020:1728 exon NON_SYNONYMOUS_CODING aaA/aaT K/N 50.0% 2 AA NN NN TT -chr1:3727501 [G/A] chr1 3727501 Cc01_g02020:1771 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 37.5% 4 GG AA AA GA -chr1:3727517 [T/C] chr1 3727517 Cc01_g02020:1787 exon NON_SYNONYMOUS_CODING aTt/aCt I/T 12.5% 4 TT TT TT TC -chr1:3727787 [T/A] chr1 3727787 Cc01_g02020:2057 exon NON_SYNONYMOUS_CODING tTc/tAc F/Y 33.3% 3 TT NN AA TT -chr1:3727789 [A/G] chr1 3727789 Cc01_g02020:2059 exon NON_SYNONYMOUS_CODING Aag/Gag K/E 50.0% 2 AA NN NN GG -chr1:3727802 [T/G] chr1 3727802 Cc01_g02020:2072 exon NON_SYNONYMOUS_CODING tTg/tGg L/W 50.0% 2 TT NN NN GG -chr1:3727809 [C/T] chr1 3727809 Cc01_g02020:2079 exon SYNONYMOUS_CODING gcC/gcT A/A 50.0% 2 CC NN NN TT -chr1:3727827 [T/C] chr1 3727827 Cc01_g02020:2097 exon SYNONYMOUS_CODING ttT/ttC F/F 50.0% 2 TT NN NN CC -chr1:3727876 [T/G] chr1 3727876 Cc01_g02020:2146 exon NON_SYNONYMOUS_CODING Tac/Gac Y/D 50.0% 2 TT NN NN GG -chr1:3727959 [G/A] chr1 3727959 Cc01_g02020:2229 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 2 GG NN NN GA -chr1:3727969 [T/C] chr1 3727969 Cc01_g02020:2239 exon NON_SYNONYMOUS_CODING Tca/Cca S/P 33.3% 3 TT TT NN CC -chr1:3728011 [C/T] chr1 3728011 Cc01_g02020:2281 exon SYNONYMOUS_CODING Cta/Tta L/L 25.0% 2 CC NN NN CT -chr1:3728022 [C/T] chr1 3728022 Cc01_g02020:2292 exon SYNONYMOUS_CODING ttC/ttT F/F 25.0% 2 CC NN NN CT -chr1:3728064 [G/A] chr1 3728064 Cc01_g02020:2334 exon SYNONYMOUS_CODING gcG/gcA A/A 50.0% 2 GG NN NN AA -chr1:3728080 [T/A] chr1 3728080 Cc01_g02020:2350 exon NON_SYNONYMOUS_CODING Ttc/Atc F/I 50.0% 2 TT NN NN AA -chr1:3740570 [G/A] chr1 3740570 Cc01_g02030:19 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 33.3% 3 GG AA AA NN -chr1:3740594 [G/A] chr1 3740594 Cc01_g02030:43 exon NON_SYNONYMOUS_CODING Gac/Aac D/N 33.3% 3 GG AA GG NN -chr1:3740608 [G/T] chr1 3740608 Cc01_g02030:57 exon SYNONYMOUS_CODING tcG/tcT S/S 50.0% 2 GG TT NN NN -chr1:3740686 [G/A] chr1 3740686 Cc01_g02030:135 exon SYNONYMOUS_CODING gaG/gaA E/E 25.0% 4 GG AA GG GG -chr1:3740718 [C/T] chr1 3740718 Cc01_g02030:167 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 12.5% 4 CC CT CC CC -chr1:3740764 [C/T] chr1 3740764 Cc01_g02030:213 exon SYNONYMOUS_CODING gcC/gcT A/A 33.3% 3 CC NN TT CC -chr1:3740817 [C/A] chr1 3740817 Cc01_g02030:266 exon NON_SYNONYMOUS_CODING gCa/gAa A/E 33.3% 3 CC NN AA CC -chr1:3750735 [C/T] chr1 3750735 Cc01_g02040:6 exon SYNONYMOUS_CODING ggG/ggA G/G 25.0% 4 CC CT CC CT -chr1:3750711 [C/G] chr1 3750711 Cc01_g02040:30 exon SYNONYMOUS_CODING gtG/gtC V/V 12.5% 4 CC CG CC CC -chr1:3750587 [C/T] chr1 3750587 Cc01_g02040:154 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 12.5% 4 CC CC CC CT -chr1:3750577 [C/T] chr1 3750577 Cc01_g02040:164 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 12.5% 4 CC CT CC CC -chr1:3750569 [T/C] chr1 3750569 Cc01_g02040:172 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 TT TT TT TC -chr1:3750546 [T/A] chr1 3750546 Cc01_g02040:195 exon SYNONYMOUS_CODING ccA/ccT P/P 12.5% 4 TT TT TA TT -chr1:3750522 [A/G] chr1 3750522 Cc01_g02040:219 exon SYNONYMOUS_CODING caT/caC H/H 50.0% 4 AA AA GG GG -chr1:3750505 [G/C] chr1 3750505 Cc01_g02040:236 exon NON_SYNONYMOUS_CODING tCt/tGt S/C 12.5% 4 GG GG GC GG -chr1:3748656 [T/C] chr1 3748656 Cc01_g02040:302 exon NON_SYNONYMOUS_CODING cAg/cGg Q/R 50.0% 2 TT NN NN CC -chr1:3748610 [C/T] chr1 3748610 Cc01_g02040:348 exon SYNONYMOUS_CODING ccG/ccA P/P 12.5% 4 CC CC CC CT -chr1:3748546 [C/T] chr1 3748546 Cc01_g02040:412 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC -chr1:3748306 [A/G] chr1 3748306 Cc01_g02040:562 exon SYNONYMOUS_CODING Ttg/Ctg L/L 12.5% 4 AA AA AA AG -chr1:3748282 [C/T] chr1 3748282 Cc01_g02040:586 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 25.0% 4 CC TT TT TT -chr1:3748213 [T/C] chr1 3748213 Cc01_g02040:655 exon NON_SYNONYMOUS_CODING Aac/Gac N/D 25.0% 4 TT TT TT CC -chr1:3748170 [A/C] chr1 3748170 Cc01_g02040:698 exon NON_SYNONYMOUS_CODING cTa/cGa L/R 12.5% 4 AA AA AA AC -chr1:3747303 [G/A] chr1 3747303 Cc01_g02040:777 exon SYNONYMOUS_CODING gcC/gcT A/A 12.5% 4 GG GG GA GG -chr1:3747255 [G/A] chr1 3747255 Cc01_g02040:825 exon SYNONYMOUS_CODING gtC/gtT V/V 25.0% 4 GG AA AA AA -chr1:3747226 [T/G] chr1 3747226 Cc01_g02040:854 exon NON_SYNONYMOUS_CODING cAg/cCg Q/P 12.5% 4 TT TT TT TG -chr1:3745743 [G/A] chr1 3745743 Cc01_g02040:1024 exon NON_SYNONYMOUS_CODING Cgc/Tgc R/C 50.0% 4 GG GG AA AA -chr1:3745742 [C/T] chr1 3745742 Cc01_g02040:1025 exon NON_SYNONYMOUS_CODING cGc/cAc R/H 25.0% 4 CC TT CC CC -chr1:3745322 [A/T] chr1 3745322 Cc01_g02040:1191 exon SYNONYMOUS_CODING atT/atA I/I 12.5% 4 AA AA AA AT -chr1:3745225 [G/T] chr1 3745225 Cc01_g02040:1288 exon NON_SYNONYMOUS_CODING Ctc/Atc L/I 12.5% 4 GG GG GG GT -chr1:3745223 [G/A] chr1 3745223 Cc01_g02040:1290 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GG AG -chr1:3745208 [T/C] chr1 3745208 Cc01_g02040:1305 exon SYNONYMOUS_CODING ctA/ctG L/L 50.0% 4 TT CC TT CC -chr1:3745196 [T/C] chr1 3745196 Cc01_g02040:1317 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 TT TT TC CT -chr1:3745187 [T/A] chr1 3745187 Cc01_g02040:1326 exon SYNONYMOUS_CODING ctA/ctT L/L 12.5% 4 TT TT TT TA -chr1:3745165 [G/A] chr1 3745165 Cc01_g02040:1348 exon NON_SYNONYMOUS_CODING Cgt/Tgt R/C 12.5% 4 GG GG GG AG -chr1:3745164 [C/T] chr1 3745164 Cc01_g02040:1349 exon NON_SYNONYMOUS_CODING cGt/cAt R/H 12.5% 4 CC CC CT CC -chr1:3744647 [G/C] chr1 3744647 Cc01_g02040:1598 exon NON_SYNONYMOUS_CODING cCt/cGt P/R 12.5% 4 GG GG GG GC -chr1:3744596 [C/T] chr1 3744596 Cc01_g02040:1649 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CC CT -chr1:3744575 [T/C] chr1 3744575 Cc01_g02040:1670 exon NON_SYNONYMOUS_CODING aAt/aGt N/S 12.5% 4 TT TT TC TT -chr1:3744299 [T/A] chr1 3744299 Cc01_g02040:1698 exon SYNONYMOUS_CODING gcA/gcT A/A 12.5% 4 TT TT TA TT -chr1:3742967 [T/C] chr1 3742967 Cc01_g02040:1935 exon SYNONYMOUS_CODING gtA/gtG V/V 12.5% 4 TT TT TC TT -chr1:3742922 [G/A] chr1 3742922 Cc01_g02040:1980 exon SYNONYMOUS_CODING agC/agT S/S 37.5% 4 GG AA GG GA -chr1:3742793 [C/T] chr1 3742793 Cc01_g02040:2109 exon SYNONYMOUS_CODING ttG/ttA L/L 50.0% 4 CC TT TT CC -chr1:3741865 [T/G] chr1 3741865 Cc01_g02040:2131 exon NON_SYNONYMOUS_CODING Att/Ctt I/L 12.5% 4 TT TG TT TT -chr1:3741857 [A/G] chr1 3741857 Cc01_g02040:2139 exon SYNONYMOUS_CODING ccT/ccC P/P 12.5% 4 AA AA AA AG -chr1:3741842 [T/C] chr1 3741842 Cc01_g02040:2154 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 TT TT TT TC -chr1:3741793 [C/T] chr1 3741793 Cc01_g02040:2203 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 CC CC CC CT -chr1:3759622 [T/A] chr1 3759622 Cc01_g02050:54 exon SYNONYMOUS_CODING ggT/ggA G/G 25.0% 4 TT TT TA TA -chr1:3762484 [A/G] chr1 3762484 Cc01_g02050:82 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 AA AA AA AG -chr1:3762723 [A/G] chr1 3762723 Cc01_g02050:202 exon NON_SYNONYMOUS_CODING Aca/Gca T/A 12.5% 4 AA AA AA AG -chr1:3762755 [A/G] chr1 3762755 Cc01_g02050:234 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG GG GG -chr1:3762781 [A/C] chr1 3762781 Cc01_g02050:260 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA -chr1:3762848 [G/A] chr1 3762848 Cc01_g02050:327 exon SYNONYMOUS_CODING acG/acA T/T 37.5% 4 GG AA GG GA -chr1:3763034 [A/G] chr1 3763034 Cc01_g02050:411 exon SYNONYMOUS_CODING ccA/ccG P/P 25.0% 4 AA GG AA AA -chr1:3763038 [C/A] chr1 3763038 Cc01_g02050:415 exon NON_SYNONYMOUS_CODING Cta/Ata L/I 25.0% 4 CC AA CC CC -chr1:3763049 [G/A] chr1 3763049 Cc01_g02050:426 exon SYNONYMOUS_CODING caG/caA Q/Q 25.0% 4 GG AA GG GG -chr1:3763055 [A/T] chr1 3763055 Cc01_g02050:432 exon SYNONYMOUS_CODING ccA/ccT P/P 37.5% 4 AA AA TT AT -chr1:3763064 [A/G] chr1 3763064 Cc01_g02050:441 exon SYNONYMOUS_CODING acA/acG T/T 25.0% 4 AA GG AA AA -chr1:3763079 [G/A] chr1 3763079 Cc01_g02050:456 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GG AA GA -chr1:3766634 [T/G] chr1 3766634 Cc01_g02060:471 exon SYNONYMOUS_CODING ccT/ccG P/P 33.3% 3 TT GG NN TT -chr1:3766695 [T/C] chr1 3766695 Cc01_g02060:532 exon SYNONYMOUS_CODING Tta/Cta L/L 33.3% 3 TT NN TT CC -chr1:3920385 [G/T] chr1 3920385 Cc01_g02110:211 exon NON_SYNONYMOUS_CODING Gca/Tca A/S 50.0% 2 GG NN TT NN -chr1:3920402 [T/C] chr1 3920402 Cc01_g02110:228 exon SYNONYMOUS_CODING tcT/tcC S/S 50.0% 2 TT NN CC NN -chr1:3923592 [A/T] chr1 3923592 Cc01_g02120:176 exon NON_SYNONYMOUS_CODING gAg/gTg E/V 12.5% 4 AA AA AA AT -chr1:3923713 [C/T] chr1 3923713 Cc01_g02120:207 exon SYNONYMOUS_CODING ccC/ccT P/P 12.5% 4 CC CC CT CC -chr1:3923759 [C/T] chr1 3923759 Cc01_g02120:253 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 CC CC CT CC -chr1:3923905 [C/T] chr1 3923905 Cc01_g02120:399 exon SYNONYMOUS_CODING tcC/tcT S/S 50.0% 4 CC TT CT CT -chr1:3923938 [T/A] chr1 3923938 Cc01_g02120:432 exon SYNONYMOUS_CODING cgT/cgA R/R 12.5% 4 TT TA TT TT -chr1:3923947 [C/T] chr1 3923947 Cc01_g02120:441 exon SYNONYMOUS_CODING gaC/gaT D/D 50.0% 4 CC TT CT CT -chr1:3924037 [G/A] chr1 3924037 Cc01_g02120:531 exon SYNONYMOUS_CODING tcG/tcA S/S 12.5% 4 GG GG GA GG -chr1:3924086 [C/T] chr1 3924086 Cc01_g02120:580 exon NON_SYNONYMOUS_CODING Cct/Tct P/S 12.5% 4 CC CT CC CC -chr1:3924307 [T/C] chr1 3924307 Cc01_g02120:801 exon SYNONYMOUS_CODING tcT/tcC S/S 12.5% 4 TT TC TT TT -chr1:3924337 [G/A] chr1 3924337 Cc01_g02120:831 exon SYNONYMOUS_CODING tcG/tcA S/S 25.0% 4 GG AA AA AA -chr1:3924341 [C/G] chr1 3924341 Cc01_g02120:835 exon NON_SYNONYMOUS_CODING Cct/Gct P/A 12.5% 4 CC CC CG CC -chr1:3924368 [C/A] chr1 3924368 Cc01_g02120:862 exon NON_SYNONYMOUS_CODING Cct/Act P/T 12.5% 4 CC AC CC CC -chr1:3924378 [A/G] chr1 3924378 Cc01_g02120:872 exon NON_SYNONYMOUS_CODING cAc/cGc H/R 12.5% 4 AA AG AA AA -chr1:3924397 [G/A] chr1 3924397 Cc01_g02120:891 exon SYNONYMOUS_CODING ttG/ttA L/L 12.5% 4 GG GA GG GG -chr1:3924554 [A/C] chr1 3924554 Cc01_g02120:1048 exon SYNONYMOUS_CODING Agg/Cgg R/R 12.5% 4 AA AC AA AA -chr1:3924566 [T/C] chr1 3924566 Cc01_g02120:1060 exon NON_SYNONYMOUS_CODING Tct/Cct S/P 12.5% 4 TT TT TT TC -chr1:3924571 [C/A] chr1 3924571 Cc01_g02120:1065 exon SYNONYMOUS_CODING ccC/ccA P/P 12.5% 4 CC CA CC CC -chr1:3924632 [G/T] chr1 3924632 Cc01_g02120:1126 exon NON_SYNONYMOUS_CODING Gct/Tct A/S 12.5% 4 GG TG GG GG -chr1:3924644 [G/A] chr1 3924644 Cc01_g02120:1138 exon NON_SYNONYMOUS_CODING Gag/Aag E/K 12.5% 4 GG GA GG GG -chr1:3924648 [A/C] chr1 3924648 Cc01_g02120:1142 exon NON_SYNONYMOUS_CODING gAg/gCg E/A 12.5% 4 AA AA AC AA -chr1:3924703 [A/G] chr1 3924703 Cc01_g02120:1197 exon SYNONYMOUS_CODING gaA/gaG E/E 12.5% 4 AA AG AA AA -chr1:3924857 [G/C] chr1 3924857 Cc01_g02120:1351 exon NON_SYNONYMOUS_CODING Gag/Cag E/Q 12.5% 4 GG GC GG GG -chr1:3924860 [G/A] chr1 3924860 Cc01_g02120:1354 exon NON_SYNONYMOUS_CODING Ggc/Agc G/S 12.5% 4 GG AG GG GG -chr1:3924877 [A/C] chr1 3924877 Cc01_g02120:1371 exon SYNONYMOUS_CODING ccA/ccC P/P 12.5% 4 AA CA AA AA -chr1:3925027 [T/C] chr1 3925027 Cc01_g02120:1521 exon SYNONYMOUS_CODING ggT/ggC G/G 12.5% 4 TT TC TT TT -chr1:3925086 [C/T] chr1 3925086 Cc01_g02120:1580 exon NON_SYNONYMOUS_CODING gCg/gTg A/V 12.5% 4 CC TC CC CC -chr1:3925308 [G/A] chr1 3925308 Cc01_g02120:1650 exon SYNONYMOUS_CODING aaG/aaA K/K 37.5% 4 GG GA GA GA -chr1:3925317 [T/C] chr1 3925317 Cc01_g02120:1659 exon SYNONYMOUS_CODING ttT/ttC F/F 37.5% 4 TT TC TC TC -chr1:3925320 [G/T] chr1 3925320 Cc01_g02120:1662 exon NON_SYNONYMOUS_CODING aaG/aaT K/N 37.5% 4 GG GT GT GT -chr1:3925346 [A/G] chr1 3925346 Cc01_g02120:1688 exon NON_SYNONYMOUS_CODING gAg/gGg E/G 25.0% 4 AA AG AA AG -chr1:3930848 [G/T] chr1 3930848 Cc01_g02130:14 exon NON_SYNONYMOUS_CODING tGc/tTc C/F 12.5% 4 GG GT GG GG -chr1:3930877 [G/T] chr1 3930877 Cc01_g02130:43 exon NON_SYNONYMOUS_CODING Ggt/Tgt G/C 12.5% 4 GG GG GG GT -chr1:3930883 [G/T] chr1 3930883 Cc01_g02130:49 exon NON_SYNONYMOUS_CODING Gta/Tta V/L 50.0% 4 GG TT GT GT -chr1:3930897 [T/A] chr1 3930897 Cc01_g02130:63 exon SYNONYMOUS_CODING gtT/gtA V/V 12.5% 4 TT TA TT TT -chr1:3931056 [C/T] chr1 3931056 Cc01_g02130:222 exon SYNONYMOUS_CODING ctC/ctT L/L 25.0% 4 CC CT CT CC -chr1:3931087 [C/A] chr1 3931087 Cc01_g02130:253 exon SYNONYMOUS_CODING Cga/Aga R/R 37.5% 4 CC AA CA CC -chr1:3931218 [A/G] chr1 3931218 Cc01_g02130:267 exon SYNONYMOUS_CODING agA/agG R/R 25.0% 4 AA GA AA AG -chr1:3931281 [T/C] chr1 3931281 Cc01_g02130:330 exon SYNONYMOUS_CODING gaT/gaC D/D 50.0% 4 TT CC TC CT -chr1:3931307 [C/T] chr1 3931307 Cc01_g02130:356 exon NON_SYNONYMOUS_CODING gCt/gTt A/V 50.0% 4 CC TT CT TC -chr1:3932233 [C/T] chr1 3932233 Cc01_g02130:381 exon SYNONYMOUS_CODING acC/acT T/T 37.5% 4 CC CT CT CT -chr1:3932286 [G/A] chr1 3932286 Cc01_g02130:434 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 37.5% 4 GG GA GA GA -chr1:3932490 [A/G] chr1 3932490 Cc01_g02130:492 exon SYNONYMOUS_CODING aaA/aaG K/K 12.5% 4 AA AA AA GA -chr1:3933113 [G/T] chr1 3933113 Cc01_g02130:592 exon NON_SYNONYMOUS_CODING Gtg/Ttg V/L 12.5% 4 GG GT GG GG -chr1:3933131 [G/A] chr1 3933131 Cc01_g02130:610 exon NON_SYNONYMOUS_CODING Gaa/Aaa E/K 25.0% 4 GG GG GA GA -chr1:3933913 [C/T] chr1 3933913 Cc01_g02130:645 exon SYNONYMOUS_CODING taC/taT Y/Y 50.0% 4 CC TT CT CT -chr1:3933970 [T/C] chr1 3933970 Cc01_g02130:702 exon SYNONYMOUS_CODING ctT/ctC L/L 25.0% 4 TT TC TC TT -chr1:3933994 [C/T] chr1 3933994 Cc01_g02130:726 exon SYNONYMOUS_CODING aaC/aaT N/N 12.5% 4 CC CC CC CT -chr1:3934095 [A/G] chr1 3934095 Cc01_g02130:733 exon NON_SYNONYMOUS_CODING Aaa/Gaa K/E 25.0% 4 AA AG AG AA -chr1:3934103 [C/T] chr1 3934103 Cc01_g02130:741 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 CC CC CC TC -chr1:3934155 [G/A] chr1 3934155 Cc01_g02130:793 exon NON_SYNONYMOUS_CODING Ggg/Agg G/R 25.0% 4 GG AG GG GA -chr1:3935070 [A/G] chr1 3935070 Cc01_g02130:858 exon SYNONYMOUS_CODING gtA/gtG V/V 25.0% 4 AA AG AG AA -chr1:3935127 [A/G] chr1 3935127 Cc01_g02130:915 exon SYNONYMOUS_CODING ttA/ttG L/L 37.5% 4 AA GG AG GG -chr1:3935145 [A/T] chr1 3935145 Cc01_g02130:933 exon SYNONYMOUS_CODING ctA/ctT L/L 25.0% 4 AA AT AT AA -chr1:3935149 [G/C] chr1 3935149 Cc01_g02130:937 exon NON_SYNONYMOUS_CODING Gct/Cct A/P 12.5% 4 GG GG GG GC -chr1:3935722 [A/C] chr1 3935722 Cc01_g02130:949 exon SYNONYMOUS_CODING Aga/Cga R/R 25.0% 4 AA AC AC AA -chr1:3935742 [A/G] chr1 3935742 Cc01_g02130:969 exon SYNONYMOUS_CODING caA/caG Q/Q 25.0% 4 AA AG AG AA -chr1:3935757 [G/A] chr1 3935757 Cc01_g02130:984 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG AG -chr1:3935791 [T/G] chr1 3935791 Cc01_g02130:1018 exon NON_SYNONYMOUS_CODING Tct/Gct S/A 37.5% 4 TT GG TG GG -chr1:3935805 [T/G] chr1 3935805 Cc01_g02130:1032 exon SYNONYMOUS_CODING gtT/gtG V/V 12.5% 4 TT TT TT TG -chr1:3935956 [A/C] chr1 3935956 Cc01_g02130:1061 exon NON_SYNONYMOUS_CODING gAt/gCt D/A 12.5% 4 AA AA AA AC -chr1:3935975 [G/A] chr1 3935975 Cc01_g02130:1080 exon SYNONYMOUS_CODING gcG/gcA A/A 12.5% 4 GG GG GG GA -chr1:3936792 [A/G] chr1 3936792 Cc01_g02130:1125 exon SYNONYMOUS_CODING acA/acG T/T 12.5% 4 AA AA AA AG -chr1:3936831 [A/G] chr1 3936831 Cc01_g02130:1164 exon SYNONYMOUS_CODING caA/caG Q/Q 50.0% 4 AA AG AG GG -chr1:3936971 [G/C] chr1 3936971 Cc01_g02130:1222 exon NON_SYNONYMOUS_CODING Gtt/Ctt V/L 37.5% 4 GG CC GC CC -chr1:3942733 [G/A] chr1 3942733 Cc01_g02140:62 exon NON_SYNONYMOUS_CODING cCc/cTc P/L 25.0% 4 GG AA GG GG -chr1:3942723 [T/A] chr1 3942723 Cc01_g02140:72 exon SYNONYMOUS_CODING gcA/gcT A/A 25.0% 4 TT AA TT TT -chr1:3940926 [G/A] chr1 3940926 Cc01_g02140:213 exon SYNONYMOUS_CODING ctC/ctT L/L 12.5% 4 GG GG GA GG -chr1:3940777 [C/A] chr1 3940777 Cc01_g02140:362 exon NON_SYNONYMOUS_CODING aGt/aTt S/I 25.0% 4 CC AA CC CC -chr1:3940686 [A/G] chr1 3940686 Cc01_g02140:453 exon SYNONYMOUS_CODING aaT/aaC N/N 12.5% 4 AA AG AA AA -chr1:3940475 [A/G] chr1 3940475 Cc01_g02140:664 exon NON_SYNONYMOUS_CODING Ttc/Ctc F/L 12.5% 4 AA AA AA AG -chr1:3940287 [C/T] chr1 3940287 Cc01_g02140:852 exon SYNONYMOUS_CODING acG/acA T/T 25.0% 4 CC TT CC CC -chr1:3940278 [G/A] chr1 3940278 Cc01_g02140:861 exon SYNONYMOUS_CODING aaC/aaT N/N 25.0% 4 GG AA GG GG -chr1:3940190 [T/C] chr1 3940190 Cc01_g02140:949 exon NON_SYNONYMOUS_CODING Atc/Gtc I/V 12.5% 4 TT TT TC TT -chr1:3940062 [G/A] chr1 3940062 Cc01_g02140:1077 exon SYNONYMOUS_CODING aaC/aaT N/N 37.5% 4 GG AA GA AA -chr1:3939962 [C/A] chr1 3939962 Cc01_g02140:1177 exon NON_SYNONYMOUS_CODING Gcc/Tcc A/S 12.5% 4 CC CA CC CC -chr1:3939959 [G/T] chr1 3939959 Cc01_g02140:1180 exon NON_SYNONYMOUS_CODING Ctt/Att L/I 25.0% 4 GG TT GG GG -chr1:3939916 [C/T] chr1 3939916 Cc01_g02140:1223 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 25.0% 4 CC TT CC CC -chr1:3938977 [G/C] chr1 3938977 Cc01_g02140:1335 exon SYNONYMOUS_CODING tcC/tcG S/S 12.5% 4 GG GC GG GG -chr1:3938798 [T/G] chr1 3938798 Cc01_g02140:1369 exon NON_SYNONYMOUS_CODING Agt/Cgt S/R 37.5% 4 TT GG TG TT -chr1:3938797 [C/G] chr1 3938797 Cc01_g02140:1370 exon NON_SYNONYMOUS_CODING aGt/aCt S/T 12.5% 4 CC CC CC CG -chr1:3938792 [G/A] chr1 3938792 Cc01_g02140:1375 exon SYNONYMOUS_CODING Cta/Tta L/L 12.5% 4 GG GG GG AG -chr1:3938784 [C/T] chr1 3938784 Cc01_g02140:1383 exon SYNONYMOUS_CODING ccG/ccA P/P 25.0% 4 CC TC CT CC -chr1:3938738 [C/T] chr1 3938738 Cc01_g02140:1429 exon NON_SYNONYMOUS_CODING Gtt/Att V/I 12.5% 4 CC CC CT CC -chr1:3938734 [T/C] chr1 3938734 Cc01_g02140:1433 exon NON_SYNONYMOUS_CODING cAa/cGa Q/R 25.0% 4 TT TT TC CT -chr1:3938731 [A/G] chr1 3938731 Cc01_g02140:1436 exon NON_SYNONYMOUS_CODING gTg/gCg V/A 12.5% 4 AA AA AG AA -chr1:3938674 [C/T] chr1 3938674 Cc01_g02140:1493 exon NON_SYNONYMOUS_CODING aGt/aAt S/N 12.5% 4 CC CC CT CC -chr1:3950327 [A/C] chr1 3950327 Cc01_g02150:300 exon NON_SYNONYMOUS_CODING caT/caG H/Q 37.5% 4 AA CC AC AA -chr1:3949508 [G/T] chr1 3949508 Cc01_g02150:438 exon SYNONYMOUS_CODING tcC/tcA S/S 12.5% 4 GG GT GG GG -chr1:3949500 [T/C] chr1 3949500 Cc01_g02150:446 exon NON_SYNONYMOUS_CODING tAt/tGt Y/C 12.5% 4 TT TT TC TT -chr1:3949478 [G/A] chr1 3949478 Cc01_g02150:468 exon SYNONYMOUS_CODING cgC/cgT R/R 12.5% 4 GG GG GA GG -chr1:3949470 [C/T] chr1 3949470 Cc01_g02150:476 exon NON_SYNONYMOUS_CODING aGg/aAg R/K 25.0% 4 CC TT CC CC -chr1:3949465 [C/G] chr1 3949465 Cc01_g02150:481 exon NON_SYNONYMOUS_CODING Ggt/Cgt G/R 37.5% 4 CC GG CG CC -chr1:3949086 [C/T] chr1 3949086 Cc01_g02150:541 exon NON_SYNONYMOUS_CODING Gtc/Atc V/I 12.5% 4 CC CC CT CC -chr1:3967535 [C/T] chr1 3967535 Cc01_g02160:57 exon SYNONYMOUS_CODING cgG/cgA R/R 12.5% 4 CC CT CC CC -chr1:3967530 [A/T] chr1 3967530 Cc01_g02160:62 exon NON_SYNONYMOUS_CODING cTg/cAg L/Q 12.5% 4 AA AA AA AT -chr1:3967524 [G/A] chr1 3967524 Cc01_g02160:68 exon NON_SYNONYMOUS_CODING cCa/cTa P/L 37.5% 4 GG AG GA AG -chr1:3967512 [A/G] chr1 3967512 Cc01_g02160:80 exon NON_SYNONYMOUS_CODING aTa/aCa I/T 12.5% 4 AA AA AG AA -chr1:3967435 [A/G] chr1 3967435 Cc01_g02160:157 exon NON_SYNONYMOUS_CODING Tcc/Ccc S/P 25.0% 4 AA AG AA AG -chr1:3967421 [G/A] chr1 3967421 Cc01_g02160:171 exon SYNONYMOUS_CODING acC/acT T/T 12.5% 4 GG AG GG GG -chr1:3967412 [A/C] chr1 3967412 Cc01_g02160:180 exon STOP_GAINED taT/taG Y/0 37.5% 4 AA AC AC AC -chr1:3967382 [A/G] chr1 3967382 Cc01_g02160:210 exon SYNONYMOUS_CODING ccT/ccC P/P 25.0% 4 AA GA GA AA -chr1:3967354 [G/T] chr1 3967354 Cc01_g02160:238 exon NON_SYNONYMOUS_CODING Caa/Aaa Q/K 12.5% 4 GG GG GG GT -chr1:3967352 [T/C] chr1 3967352 Cc01_g02160:240 exon SYNONYMOUS_CODING caA/caG Q/Q 37.5% 4 TT CC CT CC -chr1:3967310 [G/C] chr1 3967310 Cc01_g02160:282 exon NON_SYNONYMOUS_CODING atC/atG I/M 37.5% 4 GG GC GC GC -chr1:3967300 [C/T] chr1 3967300 Cc01_g02160:292 exon NON_SYNONYMOUS_CODING Gat/Aat D/N 12.5% 4 CC CC CC TC -chr1:3967295 [G/A] chr1 3967295 Cc01_g02160:297 exon SYNONYMOUS_CODING atC/atT I/I 12.5% 4 GG GG GA GG -chr1:3966909 [T/A] chr1 3966909 Cc01_g02160:683 exon NON_SYNONYMOUS_CODING tAt/tTt Y/F 12.5% 4 TT TA TT TT -chr1:3966784 [G/A] chr1 3966784 Cc01_g02160:808 exon NON_SYNONYMOUS_CODING Ctt/Ttt L/F 16.7% 3 GG NN GA GG
--- a/SNP_density/test-data/result.txt Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -Chromosome Position SNPs -chr1 200000 355 -chr1 400000 228 -chr1 600000 63 -chr1 800000 191 -chr1 1000000 88 -chr1 1200000 90 -chr1 1400000 190 -chr1 1600000 267 -chr1 1800000 226 -chr1 2000000 163 -chr1 2200000 357 -chr1 2400000 132 -chr1 2600000 158 -chr1 2800000 104 -chr1 3000000 146 -chr1 3200000 331 -chr1 3400000 181 -chr1 3600000 36 -chr1 3800000 167 -chr1 4000000 110
--- a/SNP_density/test-data/result_bysample.txt Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -Chromosome BA58 BA59 BD54 -chr1 220 197 225 -chr1 130 119 133 -chr1 43 43 40 -chr1 139 167 141 -chr1 62 72 78 -chr1 35 76 38 -chr1 98 123 82 -chr1 133 205 135 -chr1 94 141 151 -chr1 112 116 117 -chr1 228 238 204 -chr1 86 95 96 -chr1 60 106 82 -chr1 60 74 64 -chr1 106 112 115 -chr1 199 220 228 -chr1 151 94 64 -chr1 18 32 27 -chr1 87 90 100 -chr1 54 75 47
--- a/VCF2Hapmap/VCF2FastaAndHapmap.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,525 +0,0 @@ - -#!/usr/bin/perl - -use strict; -use Getopt::Long; - -my $usage = qq~Usage:$0 <args> [<opts>] - -where <args> are: - - -v, --vcf <VCF input> - -o, --out <Output basename> - -<opts> are: - - -r, --reference <Reference fasta file> - -g, --gff <GFF input file to create alignments of genes> -~; -$usage .= "\n"; - -my ($input,$out,$reference,$gff); - - - -GetOptions( - "vcf=s" => \$input, - "out=s" => \$out, - "reference=s" => \$reference, - "gff=s" => \$gff -); - - -die $usage - if ( !$input || !$out); - -if ($gff && !$reference) -{ - die "You must provide a Fasta reference file when providing GFF annotation\n"; -} - - -my %ref_sequences; -if ($reference) -{ - my $id; - my $sequence = ""; - open(my $R,$reference) or die "cannot open file: $reference"; - while(<$R>) - { - my $line =$_; - $line =~s/\n//g; - $line =~s/\r//g; - if ($line =~ />([^\s]+)/){ - $ref_sequences{$id} = $sequence; - $id=$1;$sequence=""; - } - else - { - $sequence .= $line; - } - } - close($R); - $ref_sequences{$id} = $sequence; -} - - -my %chr_of_gene; -my %ann; -if ($gff) -{ - open(my $G,$gff) or die "cannot open file: $gff"; - while(<$G>) - { - my $line =$_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\t/,$line); - my $chr = $i[0]; - my $feature = $i[2]; - my $strand = $i[6]; - my $start = $i[3]; - my $stop = $i[4]; - my $inf = $i[8]; - if ($feature eq 'gene') - { - if ($inf =~/Name=([\w\-\.]+)[;\s]*/){$inf = $1;} - $ann{$inf}{"start"}=$start; - $ann{$inf}{"stop"}=$stop; - $ann{$inf}{"strand"}=$strand; - $chr_of_gene{$inf} = $chr; - } - } - close($G); -} - - - -my %IUPAC = -( - '[A/G]'=> "R", - '[G/A]'=> "R", - '[C/T]'=> "Y", - '[T/C]'=> "Y", - '[T/G]'=> "K", - '[G/T]'=> "K", - '[C/G]'=> "S", - '[G/C]'=> "S", - '[A/T]'=> "W", - '[T/A]'=> "W", - '[A/C]'=> "M", - '[C/A]'=> "M", - '[C/A/T]'=> "H", - '[A/T/C]'=> "H", - '[A/C/T]'=> "H", - '[C/T/A]'=> "H", - '[T/C/A]'=> "H", - '[T/A/C]'=> "H", - '[C/A/G]'=> "V", - '[A/G/C]'=> "V", - '[A/C/G]'=> "V", - '[C/G/A]'=> "V", - '[G/C/A]'=> "V", - '[G/A/C]'=> "V", - '[C/T/G]'=> "B", - '[T/G/C]'=> "B", - '[T/C/G]'=> "B", - '[C/G/T]'=> "B", - '[G/C/T]'=> "B", - '[G/T/C]'=> "B", - '[T/A/G]'=> "D", - '[A/G/T]'=> "D", - '[A/T/G]'=> "D", - '[T/G/A]'=> "D", - '[G/T/A]'=> "D", - '[G/A/T]'=> "D", -); - -my %snps_of_gene; -my %snps_of_gene2; -my %indiv_order; -my $indiv_list; -my %genotyping_infos; -my $num_line = 0; -my $genename_rank_in_snpeff = 4; - -my $find_annotations = `grep -c 'EFF=' $input`; - -open(my $HAPMAP,">$out.hapmap"); -print $HAPMAP "rs# alleles chrom pos gene feature effect codon_change amino_acid_change MAF missing_data"; -open(my $VCF,$input); -while(<$VCF>) -{ - my $line = $_; - chomp($line); - my @infos = split(/\t/,$line); - - if (/^##INFO=\<ID=EFF/ && /Amino_Acid_length \| Gene_Name \| Transcript_BioType \| Gene_Coding/) - { - $genename_rank_in_snpeff = 8; - } - - if (scalar @infos > 9) - { - if (/#CHROM/) - { - for (my $j=9;$j<=$#infos;$j++) - { - my $individu = $infos[$j]; - $indiv_list .= " $individu"; - $indiv_order{$j} = $individu; - } - print $HAPMAP "$indiv_list\n"; - } - elsif (!/^#/) - { - $num_line++; - - my $chromosome = $infos[0]; - my $chromosome_position = $infos[1]; - my $ref_allele = $infos[3]; - my $alt_allele = $infos[4]; - - if ($ref_allele =~/\w\w+/) - { - $ref_allele = "A"; - $alt_allele = "T"; - } - elsif ($alt_allele =~/\w\w+/) - { - $ref_allele = "T"; - $alt_allele = "A"; - } - - my $info = $infos[7]; - my $is_in_exon = "#"; - my $is_synonyme = "#"; - my $gene; - if ($find_annotations > 1) - { - $gene = "intergenic"; - } - else - { - $gene = $chromosome; - } - my $modif_codon = "#"; - my $modif_aa = "#"; - my $geneposition; - if ($info =~/EFF=(.*)/) - { - my @annotations = split(",",$1); - foreach my $annotation(@annotations) - { - my ($syn, $additional) = split(/\(/,$annotation); - - if ($syn =~/STREAM/){next;} - - $is_in_exon = "exon"; - if ($syn =~/UTR/) - { - $is_in_exon = $syn; - } - else - { - $is_synonyme = $syn; - } - my @infos_additional = split(/\|/,$additional); - $gene = $infos_additional[$genename_rank_in_snpeff]; - $modif_codon = $infos_additional[2]; - $modif_aa = $infos_additional[3]; - - if ($syn =~/INTERGENIC/) - { - $is_synonyme = "#"; - $gene = "intergenic"; - $is_in_exon = "#"; - } - elsif ($syn =~/SYNONYM/) - { - $is_in_exon = "exon"; - } - elsif ($syn =~/INTRON/ or $syn =~/SPLICE_SITE_DONOR/) - { - $is_in_exon = "intron"; - $is_synonyme = "#"; - } - - - if ($modif_aa =~/(\w)(\d+)$/) - { - $modif_aa = "$1/$1"; - } - elsif ($modif_aa =~/(\w)(\d+)(\w)/) - { - $modif_aa = "$1/$3"; - } - if ($infos_additional[8] =~/Exon/) - { - $is_in_exon = "exon"; - } - - if (!$modif_aa){$modif_aa="#";} - if (!$modif_codon){$modif_codon="#";} - } - } - $gene =~s/\.\d//g; - if ($ann{$gene}{"start"}) - { - my $strand = $ann{$gene}{"strand"}; - if ($strand eq '-') - { - $geneposition = $ann{$gene}{"stop"} - $chromosome_position; - } - else - { - $geneposition = $chromosome_position - $ann{$gene}{"start"}; - } - } - #if ($info =~/GenePos=(\d+);/) - #{ - # $geneposition = $1; - #} - my $ratio_missing_data; - my $snp_frequency; - my $genotyping = ""; - - if (2 > 1) - { - - $genotyping_infos{"ref"} = "$ref_allele$ref_allele"; - - my %alleles_found; - my $nb_readable_ind = 0; - for (my $i = 9;$i <= $#infos;$i++) - { - my $dnasample = $indiv_order{$i}; - my @infos_alleles = split(":",$infos[$i]); - my $genotype = $infos_alleles[0]; - $genotype =~s/0/$ref_allele/g; - - if ($alt_allele =~/,/) - { - my @alt_alleles = split(",",$alt_allele); - my $num_all = 1; - foreach my $alt_al(@alt_alleles) - { - $genotype =~s/$num_all/$alt_al/g; - $num_all++; - } - } - else - { - $genotype =~s/1/$alt_allele/g; - } - if ($genotype eq '.'){$genotype = "./.";} - $genotype =~s/\./N/g; - if ($genotype !~/N\/N/) - { - $nb_readable_ind++; - } - my @alleles; - if ($genotype =~/\//) - { - @alleles = split(/\//,$genotype); - } - else - { - @alleles = split(/\|/,$genotype); - } - $genotyping .= join("",@alleles) . " "; - $genotyping_infos{$dnasample} = join("",@alleles); - - foreach my $al(@alleles) - { - if ($al ne 'N'){$alleles_found{$al}++;} - } - } - chop($genotyping); - - $snp_frequency = 0; - - my $max = 0; - my $min = 10000000; - my $total = 0; - foreach my $al(keys(%alleles_found)) - { - my $nb = $alleles_found{$al}; - $total+= $nb; - if ($nb > $max) - { - $max = $nb; - } - if ($nb < $min) - { - $min = $nb; - } - } - if ($total > 0) - { - $snp_frequency = sprintf("%.1f",($min/$total)*100); - } - - $ratio_missing_data = 100 - ($nb_readable_ind / ($#infos - 8)) * 100; - $ratio_missing_data = sprintf("%.1f",$ratio_missing_data); - - foreach my $dna(keys(%genotyping_infos)) - { - $snps_of_gene{$gene}{$geneposition}{$dna} = $genotyping_infos{$dna}; - } - } - my $snp_type = "[$ref_allele/$alt_allele]"; - $snps_of_gene2{$chromosome}{$chromosome_position} = $snp_type; - #print $HAPMAP "$chromosome:$chromosome_position\t$snp_type\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$nb_readable_ind\t$genotyping\n"; - print $HAPMAP "$chromosome:$chromosome_position\t$ref_allele/$alt_allele\t$chromosome\t$chromosome_position\t$gene:$geneposition\t$is_in_exon\t$is_synonyme\t$modif_codon\t$modif_aa\t$snp_frequency%\t$ratio_missing_data%\t$genotyping\n"; - } - } -} -close($VCF); -close($HAPMAP); - - -if (!$reference){exit;} - -################################################################# -# generate flanking sequences for Illumina VeraCode technology -################################################################# -open(my $FLANKING,">$out.flanking.txt"); -foreach my $seq(keys(%ref_sequences)) -{ - if ($snps_of_gene2{$seq}) - { - my $refhash = $snps_of_gene2{$seq}; - my %hashreal = %$refhash; - - # create consensus - my $refseq = $ref_sequences{$seq}; - my $consensus = ""; - my $previous = 0; - foreach my $pos(sort {$a<=>$b} keys(%hashreal)) - { - my $length = $pos - $previous - 1; - $consensus .= substr($refseq,$previous,$length); - my $iupac_code = $IUPAC{$snps_of_gene2{$seq}{$pos}}; - $consensus .= $iupac_code; - $previous = $pos; - } - my $length = length($refseq) - $previous; - $consensus .= substr($refseq,$previous,$length); - - foreach my $pos(sort {$a<=>$b} keys(%hashreal)) - { - my $snp_name = "$seq-$pos"; - my $flanking_length = 60; - my $length = $flanking_length; - my $start = $pos - $flanking_length - 1; - if ($pos <= $flanking_length) - { - $length = $pos - 1; - $start = 0; - } - my $sequence = substr($consensus,$start,$length); - - $sequence .= $snps_of_gene2{$seq}{$pos}; - $sequence .= substr($consensus,$pos,$flanking_length); - print $FLANKING "$snp_name,$sequence,0,0,0,Project_name,0,diploid,Other,Forward\n"; - } - } - } - - close($FLANKING); - - if (!$gff){exit;} - - my @individuals_list = split(/\t/,$indiv_list); - if ((scalar @individuals_list * scalar keys(%snps_of_gene)) > 800000) - { - print "Sorry, too many sequences to manage ...\n"; - exit; - } - - open(my $ALIGN_EGGLIB,">$out.gene_alignment.fas"); - my %alignments_ind; - foreach my $seq(keys(%snps_of_gene)) - { - if ($snps_of_gene{$seq}) - { - my $refhash = $snps_of_gene{$seq}; - my %hashreal = %$refhash; - - # get flanking sequences - my %flanking5; - my $start = $ann{$seq}{"start"}; - my $stop = $ann{$seq}{"stop"}; - my $strand = $ann{$seq}{"strand"}; - my $genelength = $stop - $start+1; - my $chr = $chr_of_gene{$seq}; - my $refseq = substr($ref_sequences{$chr},$start-1,$genelength); - if ($strand eq '-') - { - $refseq =~ tr /atcgATCG/tagcTAGC/; $refseq = reverse($refseq); - } - #print "$seq $chr $start $stop $refseq \n"; - my $previous = 0; - foreach my $pos(sort {$a<=>$b} keys(%hashreal)) - { - my $length = $pos - $previous - 1; - $flanking5{$pos} = substr($refseq,$previous,$length); - $previous = $pos; - } - my $length = length($refseq) - $previous; - my $flanking3 = substr($refseq,$previous,$length); - foreach my $ind(@individuals_list) - { - my $nb_missing_data_for_this_individual = 0; - if ($ind) - { - my $alignment_for_ind = ""; - my $seq_without_underscore = $seq; - $seq_without_underscore =~s/_//g; - $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_1\n"; - foreach my $pos(sort {$a<=>$b} keys(%hashreal)) - { - $alignment_for_ind .= $flanking5{$pos}; - my $geno = $snps_of_gene{$seq}{$pos}{$ind}; - $geno =~s/N/?/g; - if ($geno =~/\?/){$nb_missing_data_for_this_individual++;} - my @alleles = split("",$geno); - $alignment_for_ind .= $alleles[0]; - if ($alleles[0] eq $alleles[1]) - { - $alignments_ind{$ind} .= $alleles[1]; - } - else - { - my $snp_type = "[" . $alleles[0] . "/" . $alleles[1] . "]"; - $alignments_ind{$ind} .= $IUPAC{$snp_type}; - } - } - $alignment_for_ind .= $flanking3; - $alignment_for_ind .= "\n"; - - - $alignment_for_ind .= ">$seq_without_underscore" . "_$ind" . "_2\n"; - foreach my $pos(sort {$a<=>$b} keys(%hashreal)) - { - $alignment_for_ind .= $flanking5{$pos}; - my $geno = $snps_of_gene{$seq}{$pos}{$ind}; - $geno =~s/N/?/g; - my @alleles = split("",$geno); - $alignment_for_ind .= $alleles[1]; - } - $alignment_for_ind .= $flanking3; - $alignment_for_ind .= "\n"; - if (keys(%hashreal) != $nb_missing_data_for_this_individual) - { - print $ALIGN_EGGLIB $alignment_for_ind; - } - } - } - } -} -close($ALIGN_EGGLIB); - - -
--- a/VCF2Hapmap/vcf2FastaAndHapmap.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -#!/bin/bash - -tool_path=$(dirname $0) - - - -filein=$1 -fileout_label=$2 -fileout=$3 -option=$4 - -option_text='' - - -if [ "$option" != "none" ] -then fileout_seq=$5 - fileout_fa1=$6 - filefasta=$7 - if [ "$option" == "fasta_gff" ] - then filegff=$8 - fi -fi - -if [ "$option" == "fasta" ] -then option_text="--reference $filefasta" -fi - -if [ "$option" == "fasta_gff" ] -then option_text="--reference $filefasta --gff $filegff" -fi - - -perl $tool_path/VCF2FastaAndHapmap.pl --vcf $filein --out $fileout_label $option_text - - -cp $fileout_label.hapmap $fileout ; rm $fileout_label.hapmap - -if [ "$option" == "fasta_gff" ] -then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; cp $fileout_label.gene_alignment.fas $fileout_fa1 ; rm $fileout_label.gene_alignment.fas ; -fi - -if [ "$option" == "fasta" ] -then cp $fileout_label.flanking.txt $fileout_seq ; rm $fileout_label.flanking.txt ; -fi -
--- a/VCF2Hapmap/vcf2FastaAndHapmap.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,251 +0,0 @@ -<tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0"> - - <!-- [REQUIRED] Tool description displayed after the tool name --> - <description> Convert VCF to Hapmap </description> - - <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> - <requirements> - <requirement type="binary">perl</requirement> - </requirements> - - <!-- [OPTIONAL] Command to be executed to get the tool's version string --> - <version_command> -<!-- - tool_binary -v ---> - </version_command> - - <!-- [REQUIRED] The command to execute --> - <command interpreter="bash"> - vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt - #if str( $optional.file_opt ) != "none": - $fileout_seq $fileout_fa1 $filefasta - #if str( $optional.file_opt ) == "fasta_gff": - $filegff - #end if - #end if - </command> - - <!-- [REQUIRED] Input files and tool parameters --> - <inputs> - <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> - <param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/> - <conditional name="optional" > - <param name="file_opt" type="select" label="Optional files" > - <option value="none" selected="true">No</option> - <option value="fasta">Fasta</option> - <option value="fasta_gff">Fasta and GFF</option> - </param> - <when value="none" /> - <when value="fasta"> - <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" /> - </when> - <when value="fasta_gff"> - <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" /> - <param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" /> - </when> - </conditional> - </inputs> - - <!-- [REQUIRED] Output files --> - <outputs> - <data name="fileout" format="txt" label="${fileout_label}.hapmap" /> - <data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt"> - <filter>(optional['file_opt'] != 'none')</filter> - </data> - <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas"> - <filter>(optional['file_opt'] == 'fasta_gff')</filter> - </data> - </outputs> - - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <test> - <param name="filein" value="sample.vcf" /> - <param name="otpional.file_opt" value="none" /> - <output name="fileout" file="result1.hapmap" /> - </test> - <test> - <param name="filein" value="sample.vcf" /> - <param name="otpional.file_opt" value="fasta" /> - <param name="filefasta" value="reference.fa" /> - <output name="fileout" file="result2.hapmap" /> - <output name="fileout_seq" file="result2.flanking.txt" /> - <output name="fileout_fa1" file="result2.gene_alignment.fas" /> - </test> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> - - -.. class:: infomark - -**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - -.. class:: infomark - -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. - -.. class:: infomark - -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr - ---------------------------------------------------- - -======================= -VCF to Hapmap -======================= - ------------ -Description ------------ - - | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided. - | Furthermore it also creates fasta alignment of genes if GFF annotation is provided - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -VCFtools Filter VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=============== ========================== =========== -Name input file(s) format -=============== ========================== =========== -SNP density Hapmap file tabular -=============== ========================== =========== - - ----------- -Input file ----------- - -VCF file - VCF file with all SNPs - ----------- -Parameters ----------- - -Output file basename - Prefix for the output VCF file - -Optional files - To add additional files fasta file and GFF file. - ------------- -Output files ------------- - -Hapmap file - Hapmap converted file - -Additional files - If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -VCF file ---------- - -:: - - #fileformat=VCFv4.1 - #FILTER=<ID=LowQual,Description="Low quality"> - #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> - [...] - CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 - chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 - -Fasta file ----------- - - -:: - - >chr1 - CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT - -Parameters -========== - -Output name -> input - -Optional files -> Fasta - - -Output files -============ - -input.hapmap ------------- - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1 - chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT - chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC - -input.flanking.txt ------------------- - -:: - - chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward - chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward - -input.gene_alignment.fas ------------------------- - -:: - - >chr1_CATB1_1 - TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT - - - </help> - - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - }</citation> - - </citations> - -</tool>
--- a/check_gwas_inputs/CheckGWASInputs.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,184 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -h, --hapmap <Hapmap input file> - -t, --trait <Trait input file> - -o, --out <Output base name> -~; -$usage .= "\n"; - -my ($hapmap,$trait,$out); - - -GetOptions( - "trait=s" => \$trait, - "out=s" => \$out, - "hapmap=s" => \$hapmap -); - - -die $usage - if ( !$trait || !$out || !$hapmap); - -my %inds; - -####################################### -# get individuals in trait file -####################################### -my %traits; -my $head_trait = `head -1 $trait`; -open(my $T,$trait); -<$T>; -while(<$T>) -{ - my @infos = split(/\t/,$_); - my $ind = $infos[0]; - $inds{$ind}++; - $traits{$ind} = $_; -} -close($T); -my $nb_ind_trait = scalar keys(%traits); - -####################################### -# get individuals in hapmap file -####################################### -my $line_ind = `head -1 $hapmap`; -chomp($line_ind); -my @infos = split(/\t/,$line_ind); -for (my $i = 11; $i <= $#infos; $i++) -{ - my $ind = $infos[$i]; - $inds{$ind}++; -} -my $nb_ind_hapmap = scalar @infos - 11; - -################################################################# -# create trait output by keeping individuals found in both files -################################################################# -open(my $O,">$out.trait"); -print $O $head_trait; -my $nb_common = 0; -foreach my $ind(keys(%inds)) -{ - my $nb_found = $inds{$ind}; - if ($nb_found == 2) - { - $nb_common++; - print $O $traits{$ind}; - } -} -close($O); - - -##################################################################### -# create hapmap output after keeping individuals found in both files -# and removing monomorphic positions -##################################################################### -open(my $O2,">$out.hapmap"); -my $numline = 0; -my %genotypes; -my %columns_to_keep; -my $nb_monomorphic = 0; -my $not_biallelic = 0; -my $diff_variation = 0; -open(my $H,$hapmap); -while(<$H>) -{ - $numline++; - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @infos = split(/\t/,$line); - if ($numline == 1) - { - my @titles; - for (my $i = 0; $i <= 10; $i++) - { - my $title = $infos[$i]; - push(@titles,$title); - } - print $O2 join("\t",@titles); - for (my $i = 11; $i <= $#infos; $i++) - { - my $ind = $infos[$i]; - my $nb_found = $inds{$ind}; - if ($nb_found == 2) - { - print $O2 " $ind"; - $columns_to_keep{$i} = 1; - } - } - print $O2 "\n"; - } - else - { - my $to_be_printed = ""; - my $variation = $infos[1]; - for (my $i = 0; $i <= 10; $i++) - { - my $title = $infos[$i]; - $to_be_printed .= "$title "; - } - my %letters; - for (my $i = 11; $i <= $#infos; $i++) - { - if ($columns_to_keep{$i}) - { - my $genotype = $infos[$i]; - if ($genotype ne 'NN') - { - my ($allele1,$allele2) = split(//,$genotype); - $letters{$allele1}=1; - $letters{$allele2}=1; - } - $to_be_printed .= "$genotype "; - } - } - chop($to_be_printed); - - my $variation_obs = join("/",sort keys(%letters)); - - # print only if polymorphic - if (scalar keys(%letters) < 2) - { - $nb_monomorphic++; - } - elsif (scalar keys(%letters) > 2) - { - $not_biallelic++; - } - else - { - if ($variation ne $variation_obs) - { - $to_be_printed =~s/$variation/$variation_obs/; - $diff_variation++; - } - - print $O2 $to_be_printed . "\n"; - } - } -} -close($H); -close($O2); - -print "==============================================\n"; -print "Individuals\n"; -print "==============================================\n"; -print "Individuals in hapmap file: $nb_ind_hapmap\n"; -print "Individuals in trait file: $nb_ind_trait\n"; -print "Individuals found in both files: $nb_common\n"; -print "==============================================\n"; -print "Markers\n"; -print "==============================================\n"; -print "Discarded markers:\n"; -print "Monomorphic: $nb_monomorphic\n"; -print "Not biallelic: $not_biallelic\n"; -print "Modified markers:\n"; -print "Difference in variation: $diff_variation\n"; -
--- a/check_gwas_inputs/CheckGWASInputs.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -#!/bin/bash -hapmap=$1 -trait=$2 -out_hapmap=$3 -out_trait=$4 -stats=$5 - -directory=`dirname $0` -mkdir tmpdir$$ -#cp -rf $input tmpdir$$/input - -perl $directory/CheckGWASInputs.pl -h $hapmap -t $trait -o tmpdir$$/out >>$stats 2>&1 - -mv tmpdir$$/out.hapmap $out_hapmap -mv tmpdir$$/out.trait $out_trait - -
--- a/check_gwas_inputs/CheckGWASInputs.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,184 +0,0 @@ -<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0"> - <description>checks concordance between input files for GWAS analysis</description> - <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats - </command> - <inputs> - <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> - <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/> - </inputs> - <outputs> - <data format="txt" name="out_hapmap" label="Hapmap output"/> - <data format="txt" name="out_trait" label="Trait output"/> - <data format="txt" name="stats" label="Logfile and statistics"/> - </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - <help> - - <![CDATA[ - - -.. class:: infomark - -**Authors** South Green - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - -.. class:: infomark - -**Galaxy integration** South Green. - ---------------------------------------------------- - - -=============== -CheckGWASInputs -=============== - ------------ -Description ------------ - - | CheckGWASInputs checks concordance between input files for GWAS analysis. - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Hapmap file hapmap -=============== ====================== =========== - - - - ----------- -Input file ----------- - -Hapmap file - Allelic file in Hapmap format - -Trait file - Phenotypic file - ------------- -Output files ------------- - -Hapmap output - -Trait output - -Logfile and statistics - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -Hapmap file ------------ - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 - SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA - SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA - -Trait file ----------- - -:: - - <Trait> Test - Ind1 -2.9985936006411 - Ind2 -2.68669426456267 - -Output files -============ - -Hapmap output -------------- - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4 - SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA - SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT - - -Trait output ------------- - -:: - - <Trait> Test - Ind429 -26.2142525264157 - Ind373 12.0306115988504 - Ind81 1.98118654229534 - -Logfile and statistics ----------------------- - -:: - - - ============================================== - Individuals - ============================================== - Individuals in hapmap file: 500 - Individuals in trait file: 500 - Individuals found in both files: 500 - ============================================== - Markers - ============================================== - Discarded markers: - Monomorphic: 0 - Not biallelic: 0 - Modified markers: - Difference in variation: 0 - - ]]> - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_gwas_inputs/CheckGWASInputs.xml~ Fri Jul 10 10:38:11 2015 -0400 @@ -0,0 +1,184 @@ +<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0"> + <description>checks concordance between input files for GWAS analysis</description> + <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats + </command> + <inputs> + <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> + <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/> + </inputs> + <outputs> + <data format="txt" name="out_hapmap" label="Hapmap output"/> + <data format="txt" name="out_trait" label="Trait output"/> + <data format="txt" name="stats" label="Logfile and statistics"/> + </outputs> + <!-- [STRONGLY RECOMMANDED] Exit code rules --> + <stdio> + <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> + <exit_code range="1:" level="fatal" /> + </stdio> + + <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> + <!-- [HELP] Test files have to be in the ~/test-data directory --> + <!-- [HELP] Multiple tests can be defined with different parameters --> +<!-- + <test> + </test> +--> + </tests> + <help> + + <![CDATA[ + + +.. class:: infomark + +**Authors** South Green + + | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). + +.. class:: infomark + +**Galaxy integration** South Green. + +--------------------------------------------------- + + +=============== +CheckGWASInputs +=============== + +----------- +Description +----------- + + | CheckGWASInputs checks concordance between input files for GWAS analysis. + + +----------------- +Workflow position +----------------- + +**Upstream tool** + +=============== ====================== =========== +Name output file(s) format +=============== ====================== =========== +VCF to Hapmap Hapmap file hapmap +=============== ====================== =========== + + + + +---------- +Input file +---------- + +Hapmap file + Allelic file in Hapmap format + +Trait file + Phenotypic file + +------------ +Output files +------------ + +Hapmap output + +Trait output + +Logfile and statistics + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +=========== + +Hapmap file +----------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA + +Trait file +---------- + +:: + + <Trait> Test + Ind1 -2.9985936006411 + Ind2 -2.68669426456267 + +Output files +============ + +Hapmap output +------------- + +:: + + rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4 + SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA + SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT + + +Trait output +------------ + +:: + + <Trait> Test + Ind429 -26.2142525264157 + Ind373 12.0306115988504 + Ind81 1.98118654229534 + +Logfile and statistics +---------------------- + +:: + + + ============================================== + Individuals + ============================================== + Individuals in hapmap file: 500 + Individuals in trait file: 500 + Individuals found in both files: 500 + ============================================== + Markers + ============================================== + Discarded markers: + Monomorphic: 0 + Not biallelic: 0 + Modified markers: + Difference in variation: 0 + + ]]> + + + </help> + <citations> + <!-- [HELP] As DOI or BibTex entry --> + <citation type="bibtex">@article{Dereeper03062015, +author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, +title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, +year = {2015}, +doi = {10.1093/nar/gkv351}, +abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, +URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, +eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, +journal = {Nucleic Acids Research} +} + + </citation> + + </citations> +</tool>
--- a/egglib/CalculateDiversityIndexes.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <FASTA input> - -o, --output <output filename> - -d, --directory <directory of egglib package> -~; -$usage .= "\n"; - -my ($infile,$outfile,$dir_exe); - - -GetOptions( - "input=s" => \$infile, - "output=s" => \$outfile, - "directory=s"=> \$dir_exe -); - - -die $usage - if ( !$infile || !$outfile || !$dir_exe); - - -my $EGGSTATS_EXE = "$dir_exe/egglib-2.1.5/bin/eggstats"; - -my %gene_alignments; -my $in = Bio::SeqIO->new(-file => $infile , '-format' => 'Fasta'); -while ( my $seq = $in->next_seq() ) -{ - my $id = $seq -> id(); - my $sequence = $seq -> seq(); - my ($gene,$ind,$num_allele) = split("_",$id); - $gene_alignments{$gene}.= ">$id\n$sequence\n"; -} - -open(OUT,">$outfile"); -foreach my $gene(keys(%gene_alignments)) -{ - open(F,">$gene.egglib_input.fa"); - print F $gene_alignments{$gene}; - close(F); - - my $results_egglib = `$EGGSTATS_EXE $gene.egglib_input.fa`; - - # parse Seqlib output - if ($results_egglib) - { - my %egglig_stats; - my @eggstats = split(/^/,$results_egglib); - foreach my $eggstat(@eggstats) - { - my ($desc,$value) = split(/: /,$eggstat); - chomp($value); - $egglig_stats{$desc} = $value; - } - print OUT "$gene;"; - print OUT $egglig_stats{"Total number of sequences"} . ";"; - print OUT $egglig_stats{"Total number of sites"} . ";"; - print OUT $egglig_stats{"Number of analyzed sites"} . ";"; - print OUT $egglig_stats{"S"} . ";"; - print OUT $egglig_stats{"thetaW"} . ";"; - print OUT $egglig_stats{"Pi"} . ";"; - print OUT $egglig_stats{"D"} . ";"; - print OUT $egglig_stats{"number of haplotypes"} . ";"; - print OUT $egglig_stats{"haplotypes diversity"} . ";"; - print OUT $egglig_stats{"Fay and Wu H"} . ";"; - print OUT $egglig_stats{"Fst"} . ";"; - print OUT $egglig_stats{"Snn"} . ";"; - print OUT "\n"; - unlink("$gene.egglib_input.fa"); - } -} -close(OUT); -
--- a/egglib/CalculateDiversityIndexes.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -#!/bin/bash -input=$1 -output=$2 -log=$3 - -directory=`dirname $0` - -perl $directory/CalculateDiversityIndexes.pl -i $input -o $output -d $directory >>$log 2>&1 - - -
--- a/egglib/CalculateDiversityIndexes.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,175 +0,0 @@ -<tool id="calculate_diversity" name="Diversity by gene" version="2.1.6"> - <description>calculates various diversity indexes with EggLib.</description> - <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log - </command> - <inputs> - <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/> - </inputs> - <outputs> - <data format="txt" name="output" label="Diversity"/> - <data format="txt" name="log" label="Logfile"/> - </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - <help> - - - -.. class:: infomark - -**Authors** EggLib_ - -.. _EggLib: http://egglib.sourceforge.net/ - - | "EggLib: processing, analysis and simulation tools for population genetics and genomics.", **De Mita S. and M. Siol.**, BMC Genet. 2012. 13:27. - -.. class:: infomark - -**Galaxy integration** South Green. - -.. class:: infomark - -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - ---------------------------------------------------- - - - -================== -Diversity by genes -================== - ------------ -Description ------------ - - | Provides various diversity indexes using EggLib library. - | For further informations, please visite the EggLib website_. - -.. _website: http://egglib.sourceforge.net/ - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Fasta alignment fasta -=============== ====================== =========== - - - ----------- -Input file ----------- - -Fasta file - Fasta alignment - - - ------------- -Output files ------------- - -Diversity - -Log file - - ------------- -Dependencies ------------- -EggLib - version 2.1.5 - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -Fasta file ----------- - -:: - - >LOCOs11g09160_AZUCENA_1 - ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA - CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG - GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT - GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA - TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC - >LOCOs11g09160_AZUCENA_2 - ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA - CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG - GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT - GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA - TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC - >LOCOs11g09160_BULUPANDAK_1 - ATGTGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGCGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA - CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG - GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCTGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT - GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA - TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC - >LOCOs11g09160_BULUPANDAK_2 - ATGAGGCGGGCGAGGCGGTGGCCGTGGCCGTGGCGGTCGCAGCGGCGAGCGGCGAGGATGCTCTCGTCGGGTGAGCCAGCGGCGGGGCGGCGGAGGGTGGCGGCGCTGTGGGGGAACGGGGA - CTACGGGCGGCTGGGGATGGGGGCGCTGGAGTCGCGGTGGAGCCCCACGGCGTGCCCCTTCTTCCTCACCGGCCGCCCCGGCGACGACGACGACGACCCGCCCGCCTCCCTCGCCTGCGGCG - GCGCCCACACCCTCTTCCTCACCGGTACTCCTGAATTGAAATCGCCAGCTTGTGTAATTACTCGAGCGAGAGAGAGATTGTGTTGAATCGAGATTAATGTGGGAGTATGTGATTTTTGGCCT - GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA - TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC - >LOCOs07g23169_AZUCENA_1 - ACTAGTGAAGTGTTGCCCGTTGGGTTTGGTGGAGTTTGAAGAGCTCTGTCGCCGTCTTCACTCCTCGCAGTCAGACGGGAGTGGACTACTGGAGGGAGAGAGAGGGTGAGCGAGGTGTGGGA - GCTGGTTTTGCTCAGAGAGCGGGCGCGTGTTCGCCGCGGGTCTCAACGACTTCGGGCAGCTCGGGATAGGCTCCTCCGTGACTCATTCCCTGGTACTGAGCTTCTTGTACATCATGCCTCCA - TGTGAAATTTTCATCTACATTGTGAGCCAGCCTACTTTTACACAGTAAGCGAAAGCTGGCTGGACATATCAGAGTTGCAATGGGGATTGACCAAATCAATTCTGACTCCTGTTACATGTTGC - -Output files -============ - -Diversity ---------- - -:: - - LOCOs07g23169;8;10494;10494;2;7.35039e-05;8.16793e-05;0.414213;2;0.428571;0.857143;0;1; - LOCOs11g09160;8;6577;6577;2;0.00011728;0.000130324;0.414213;2;0.428571;0.857143;0;1; - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Align.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,378 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_ALIGN_HPP -#define EGGLIB_ALIGN_HPP - -#include "Container.hpp" -#include "CharMatrix.hpp" -#include <vector> - -/** \mainpage Summary - * - * This is the automatically-generated reference manual of the C++ - * egglib-cpp library. The library is presented as several modules, but - * note that they are only used to structure the documentation. - * - * There is a single namespace (egglib) in which all classes are - * defined. See an example of programming with egglib-cpp in the - * EggLib package main documentation. Use "Modules" or "Classes" above - * to navigate in the library reference manual. - * - */ - - -/** \defgroup core core - * - * \brief Central core of the C++ library of Egglib - * - * Data storage classes, parsers/formatters and tools, plus exception - * types. - * - */ - -namespace egglib { - - - /** \brief Handles a sequence alignment - * - * \ingroup core - * - * Creation from a file or string stream should be performed using - * the class Fasta. Align objects can be created by deep copy from - * both Align and Container type. In the latter case, the length are - * artificially equalized by "?" characters. Align objects can be - * created from a DataMatrix object (and all the way arround) using - * the specific class DMAConverter. - * - * Sequences are represented by two strings (name and sequence) and - * an integer (group) that can be accessed or modified by index.The - * order of sequences is guaranteed to be conserved, as if Align was - * a list of triplets (name, sequence, group). - * - * The data matrix is implemented as continuous array (char**) and - * allows efficient access and modification of data. For very large - * data matrices you might claim immediately the required memory - * using the constructor Align(unsigned int, char**). - * - */ - class Align : public Container, public CharMatrix { - public: - - /** \brief Creates an empty alignment - * - */ - Align(); - - - /** \brief Creates an alignment from a data matrix. - * - * Allows you to create an object from data stored in a char* - * array. The array's dimensions must be passed to the - * constructor, and as a result there is not need to - * terminate each sequence by a NULL character. - * - * \param number_of_sequences the number of sequences (the - * length of the first dimension of the array). - * - * \param alignment_length the length of sequences (the - * length of all lines of the array). - * - * \param cstring_array the pointer to the data matrix. - * - */ - Align(unsigned int number_of_sequences, unsigned int alignment_length, char const * const * const cstring_array); - - - /** \brief Creates an alignment with given dimensions - * - * Allows you to allocate directly a data matrix of a given - * size. Names are empty strings, groups 0, and all - * characters are ?. - * - * \param number_of_sequences the number of sequences (the - * length of the first dimension of the array). - * - * \param alignment_length the length of sequences (the - * length of all lines of the array). - * - */ - Align(unsigned int number_of_sequences, unsigned int alignment_length); - - - /** \brief Copy constructor - * - */ - Align(const Align& align); - - - /** \brief Copy constructor accepting a Container object - * - * All but the longest sequences are padded with ? to match - * the longest sequence's length. - * - */ - Align(const Container& container); - - - /** \brief Copy operator - * - */ - Align& operator=(const Align& align); - - - /** \brief Copy operator accepting a Container object - * - * All but the longest sequences are padded with ? to match - * the longest sequence's length. - * - */ - Align& operator=(const Container& container); - - - /** \brief Destructor - * - */ - virtual ~Align(); - - - /** \brief Adds a sequence - * - * If the object already contains at least one sequence, the - * new sequence must have the same length. Otherwise, a - * EggUnalignedError is raised. - * - * \param name the name of the sequence. - * \param sequence the sequence string. - * \param group the group index of the sequence. - * \return The new number of sequences. - * - */ - virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0); - - - /** \brief Removes a position (column) of the alignment - * - * \param pos the position to remove in the alignment. - * \return The new length of the alignment. - * - */ - virtual unsigned int removePosition(unsigned int pos); - - - /** \brief Removes a sequence from the alignment - * - * \param pos the index of the sequence to remove. - * \return The new number of sequences. - * - */ - virtual unsigned int remove(unsigned int pos); - - - /** \brief Replace a sequence string - * - * The new sequence must have the same length than the - * alignment. Otherwise, a EggUnalignedError is raised. - * - * \param seq the index of the sequence to change. - * \param sequence the new sequence. - * - */ - virtual void sequence(unsigned int seq, const char* sequence); - - - /** \brief Gets the name of a given sequence - * - * \param pos the index of the sequence. - * - * \return The sequence string for that particular sequence. - * - */ - virtual inline const char* sequence(unsigned int pos) const { return Container::sequence(pos); } - - - /** \brief Alignment length - * - * Returns 0 if the alignment is empty. - * - */ - virtual unsigned int ls() const; - - - /** \brief Length of a given sequence - * - * Calling this function is exactly the same as calling ls() - * (without arguments), regardless of the index provided, - * except that an exception is thrown if the index is out of - * bounds. Provided for compatibility with Container. - * - * \param pos the index of the sequence. - * \return the length of the alignment. - * - */ - virtual unsigned int ls(unsigned int pos) const; - - - /** \brief Fast and unsecure accessor - * - * This accessor doesn't perform out-of-bound checking! - * - * \param s the index of the sequence (line). - * \param p the position in the alignment (column). - * \return The character at the given position. - * - */ - inline char character(unsigned int s, unsigned int p) const { return sequences[s][p]; } - - - /** \brief Gets a nucleotide - * - * This modifier does perform out-of-bound checking. - * The specified position must exist. - * - * \param sequence the index of the sequence (line). - * \param position the position in the alignment (column). - * \return the character at the given position. - * - */ - virtual char get(unsigned int sequence, unsigned int position) const; - - - /** \brief Sets a matrix position to a new character - * - * This modifier does perform out-of-bound checking. - * The specified position must exist. - * - * \param sequence the index of the sequence (line). - * \param position the position in the alignment (column). - * \param ch the new character value. - */ - virtual void set(unsigned int sequence, unsigned position, char ch); - - - /** \brief Reverse a given column in binary data - * - * The specified column must contain only "0" ans "1" characters. - * "0" is replaced by "1" and all the way around - * - */ - void binSwitch(unsigned int pos); - - - /** \brief Extracts specified positions (columns) of the alignment - * - * All the specified sites are extracted in the specified - * order. This function is suitable for bootstrap (resample - * allowing redrawing the same site) and permutations. - * - * This function doesn't perform out-of-bound checking. - * - * \param list_of_sites a vector containing alignment - * positions. - * - * \return A copy of the object containing the specified - * set of positions. - * - */ - Align vslice(std::vector<unsigned int> list_of_sites); - - - /** \brief Extracts a range of positions (columns) - * - * \param a the first position. - * - * \param b the index immediately passed the last sequence to - * extract. - * - * \return A copy of the object containing the specified - * range of sequences. - * - * Positions a to b-1 are extracted, provided that the - * indices fit in the current length of sequences. To extract - * all sequences, use align.vslice(0, align.ls()). - * - * Note: invalid ranges will be silently supported. If - * a>=ls or b<=a, an empty object is returned. If b>ns, - * ls will be substituted to a. - */ - Align vslice(unsigned int a, unsigned int b); - - - /** \brief Deletes all the content of the object - * - */ - virtual void clear(); - - - /** \brief Same as ns() - * - */ - inline unsigned int numberOfSequences() const { - return _ns; - } - - - /** \brief Same as ls() - * - */ - inline unsigned int numberOfSites() const { - return _ls; - } - - - /** \brief Gets a group label (insecure) - * - */ - inline unsigned int populationLabel(unsigned int sequenceIndex) const { - return groups[sequenceIndex]; - } - - - /** \brief Just return the passed value - * - */ - inline double sitePosition(unsigned int position) const { - return (double) position; - } - - - protected: - - /// This function is not available for alignments - virtual void appendSequence(unsigned int pos, const char* sequence) {} - - // Initializer (creates a valid empty alignment) - virtual void init(); - - // Makes a deep copy of the specified data matrix - if cstring_array is NULL, then ignores it and pads with ?'s - virtual void setFromSource(unsigned int number_of_sequences, unsigned int alignment_length, const char* const * const cstring_array); - - // Copies from a Container - virtual void copyObject(const Container&); - - // Copies from an Align - virtual void copyObject(const Align&); - - // Alignment length - unsigned int _ls; - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,300 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_ARG_HPP -#define EGGLIB_ARG_HPP - - -#include "Current.hpp" -#include "Edge.hpp" -#include <string> - - -/** \defgroup coalesce coalesce - * - * \brief Coalescent simulator - * - * The set of classes implements a three-scale coalescent simulator with - * recombination, and a flexible mutation model. The main classes are - * Controller (the starting point for generating genealogies), ParamSet - * (that centralizes parameter specification), the Change hierarchy - * (that implements demographic change specifications), Arg (ancestral - * recombination graph; the result of generation a genealogy) and - * Mutator (that generates genotype data from an ARG). - * - */ - - -namespace egglib { - - class Random; - - /** \brief Ancestral recombination graph - * - * \ingroup coalesce - * - * This class stores the ARG (genealogical information). It is - * progressively built by appropriate (especially regarding to the - * timing) calls to coal() and recomb() methods. Then it can be - * used by a mutator class to generates data, or it can also - * generate newick trees (one tree by non-recombining segment). - * - */ - class Arg { - - public: - - /** \brief Default constructor - * - * Creates a null, useless, object. - * - */ - Arg(); - - - /** \brief Object initialization - * - * \param current address of the Current instance used by - * the simulator. - * - * \param numberOfSegments number of recombining segments. - * - */ - void set(Current* current, unsigned int numberOfSegments); - - - /** \brief Object reset method - * - * This method doesn't reset all parameters (the number of - * segments and associated tables are retained, as well as - * the Edge object pool). - * - * \param current address of the Current instance used by - * the simulator. - * - */ - void reset(Current* current); - - - /** \brief Standard constructor - * - * \param current address of the Current instance used by - * the simulator. - * - * \param numberOfSegments number of recombining segments - * - */ - Arg(Current* current, unsigned int numberOfSegments); - - - /** \brief Destructor - * - * Clears all Edge instances referenced in the object. - * - */ - virtual ~Arg(); - - - /** \brief Gets the current value of the time counter - * - */ - double time() const; - - - /** \brief Increments the time counter - * - */ - void addTime(double increment); - - - /** \brief Performs a coalescence event - * - * For this version, the two lineages to coalesce are - * predefined. - * - * \param incr increment of the time counter. - * \param pop index of the population. - * \param index1 first lineage to coalesce. - * \param index2 second lineage to coalesce. - * - */ - void coalescence(double incr, unsigned int pop, unsigned int index1, unsigned int index2); - - - /** \brief Performs a coalescence event - * - * For this version, the two lineages to coalesce are - * randomly picked in the given population - * - * \param incr increment of the time counter. - * \param pop index of the population. - * \param random pointer to simulator's random generator - * instance. - * - */ - void coalescence(double incr, unsigned int pop, Random* random); - - - /** \brief Performs a recombination event - * - * \param incr increment of the time counter. - * \param random pointer to simulator's random generator - * instance. - * - */ - void recombination(double incr, Random* random); - - - /** \brief Places a mutation - * - * \param segment index of the segment affected. - * - * \param treePosition a random number placed on the - * interval defined by the tree length at this position. - * - * \return the concerned Edge's address. - * - * \todo why this is not encapsulated? - * - * Another nerve-taking point: calling this method assume - * that all Edge of have previously undergone a call of - * branchLength(position) with intervalPosition - what - * should be done by the called (that is, Mutator) through - * my (Arg's) treeLength of something. BEWARE WHEN MODIFYING - * (enhancements should be directed to Edge in my view) - * - */ - Edge* mute(unsigned int segment, double treePosition); - - - /** \brief Age of the uMRCA - * - * The uMRCA is the ultimate Most Recent Common Ancestor, - * that is the point where the last segment finds its most - * recent common ancestor. This member will have a meaningful - * value only if the coalescent process is completed. - * - */ - inline double ageUltimateMRCA() const { - return _time; - } - - - /** \brief Age of the MRCA for a given segment - * - * The MRCA is the Most Recent Common Ancestor, that is the - * point where the coalescent process is over (all lineages - * have coalesced). This member will have a meaningful - * value only if the coalescent process is completed. - * - * Note that the value is cached; it is computed only one - * upon first call and no again, even if the Arg is modified< - * - */ - inline double ageMRCA(unsigned int segmentIndex) { - return _MRCA[segmentIndex]->bottom; - } - - /** \brief MRCA for each segment - * - * The MRCA is the Most Recent Common Ancestor, that is the - * point where the coalescent process is over (all lineages - * have coalesced). This member will have a meaningful - * value only if the coalescent process is completed. - * - * Note that the value is cached; it is computed only one - * upon first call and no again, even if the Arg is modified - * - */ - inline const Edge* MRCA(unsigned int segmentIndex) { - return _MRCA[segmentIndex]; - } - - /// Ultimate MRCA - - inline const Edge* uMRCA() { - return edges[numberOfEdges-1]; - } - - - /// the number of recombining segments - unsigned int numberOfSegments; - - /** \brief Formats the newick-formatted tree for a segment - * - */ - std::string newick(unsigned int segment); - - - /// Number of initial lineages - unsigned int numberOfSamples; - - - /** \brief Total tree length (summed over all segments) - * - */ - double totalLength; - - /** \brief Segment-specific tree length - * - */ - double* segmentLengths; - - /// Current number of Edges in the tree (including the MRCA node) - unsigned int numberOfEdges; - - /// Total number of recombination events that occurred - unsigned int numberOfRecombinationEvents; - - /// Set the number of actual sites in all branches - void set_actualNumberOfSites(unsigned int actualNumberOfSites); - - - private: - - /// Copy constructor not available - Arg(const Arg&) { } - - /// Assignment operator not available - Arg& operator=(const Arg&) { return *this; } - - void init_stable_parameters(); - void init_variable_parameters(); - void clear(); - void addEdge(Edge*); - std::string rnewick(Edge* edge, unsigned int segment, double cache); - - Current* current; - double _time; - Edge** edges; - - void findMRCA(unsigned int segmentIndex); - void computeTotalLength(); - void computeSegmentLength(unsigned int segmentIndex); - - unsigned int* numberOfEdgesPerSegment; - Edge** _MRCA; - - EdgePool edgePool; - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/BaseDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,169 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_BASEDIVERSITY_HPP -#define EGGLIB_BASEDIVERSITY_HPP - -#include "CharMatrix.hpp" -#include "SitePolymorphism.hpp" -#include <string> - -/** \defgroup polymorphism polymorphism - * - * \brief Diversity analyses - * - * Two classes are contained in this module: NucleotideDiversity, that - * performs site-centered polymorphism analyses, and HaplotypeDiversity, - * that performs haplotype-centered analyses. The detection of - * polymorphic sites is common to both, through the base class - * BaseDiversity. However this phase must be repeated when stats from - * the two classes are needed. To reduce the computational burden, the - * function reserve() can be use, that directly allocates needed memory - * when the eventual number of polymorphic sites is known prior to - * analysis (even if not precisely). For both classes, a set of - * statistics are computed immediately upon load of a data set. For - * NucleotideDiversity, additional statistics are computed per group - * upon use of the corresponding accessors. This number of operations - * performed several times is strictly limited. This is particularly - * useful when different statistics are needed for a given alignment. - * However, this system allows not computing unnecessary statistics to - * a certain extend. - * - */ - -namespace egglib { - - /** \brief Base class of diversity classes - * - * Mutualizes the analysis of polymorphic sites through the method - * importSites() and related accessors. - * - * \ingroup polymorphism - * - */ - class BaseDiversity { - - public: - - /** \brief Constructor - * - */ - BaseDiversity(); - - /** \brief Destructor - * - */ - virtual ~BaseDiversity(); - - /** \brief Reserve sufficient memory for a given number of - * polymorphic sites. - * - * This method makes importSite function faster when you - * already know how many polymorphic sites to expect, since - * the necessary memory will be allocated prior the screening - * of data. It is possible to use reserve() even if with a - * number of sites that is not matching what importSites() - * will find. - * - * \param numberOfSites a strictly positive integer. - * - */ - virtual void reserve(unsigned int numberOfSites); - - /// Gets a site - const SitePolymorphism* get_site(unsigned int index) const; - - /// Gets a site position - unsigned int get_position(unsigned int index) const; - - /** \brief Predefined mapping string for DNA data - * - */ - static const std::string dnaMapping; - - - /** \brief Predefined mapping string for RNA data - * - */ - static const std::string rnaMapping; - - - /** \brief Predefined mapping string for amino acid data - * - */ - static const std::string aaMapping; - - - /// Clears and re-initializes object - virtual void reset(); - - - protected: - - virtual void init(); - virtual void clear(); - - // - void importSites(CharMatrix& data, bool allowMultipleMutations, - double minimumExploitableData, unsigned int ignoreFrequency, - std::string characterMapping, bool useZeroAsAncestral, - bool ignoreOutgroup); - - // - void analyzeSite(CharMatrix& data, unsigned int index, double maxMissingData, bool ignoreOutgroup); // analyzes a site, adds a Site to the Site container if the site is polymorphic - unsigned int getPopIndex(unsigned int label) const; // returns v_npop if not found - - SitePolymorphism** v_sites; // holder of polymorphic site addresses - bool* v_orientables; // stores whether the sites are orientable or not - unsigned int* v_sitePositions; // stores position of sites - - unsigned int v_reserved; - unsigned int v_ns; // maximum number of sequences analyzed (max of sites' ns) - unsigned int v_S; // number of polymorphic sites - unsigned int v_So; // number of orientable sites - unsigned int v_eta; // number of mutation (whatever multiple) - double v_nseff; // average number of analyzed sequence - unsigned int v_lseff; // number of analyzed sites - double v_nseffo; // average number of analyzed sequences for analyzes with outgroup - unsigned int v_lseffo; // number of analyzed sites for analyzes with outgroup - unsigned int v_npop; // number of populations - unsigned int *v_popLabel; // label of each pop - - // options - bool p_allowMultipleMutations; - double p_minimumExploitableData; - std::string p_characterMapping; - unsigned int p_pos_sep_mapping; - bool p_useZeroAsAncestral; - unsigned int p_ignoreFrequency; - - - - private: - - BaseDiversity(const BaseDiversity& source) { } - - BaseDiversity& operator=(const BaseDiversity& source) { - return *this; - } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,428 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_CHANGETYPES_HPP -#define EGGLIB_CHANGETYPES_HPP - -#include "ParamSet.hpp" -#include "Controller.hpp" - -namespace egglib { - -/**********************************************************************/ - - /** \brief Pure virtual base class for parameter changes - * - * \ingroup coalesce - * - */ - class Change { - public: - - /** \brief Default constructor - * - * The default date is 0. - * - */ - Change(); - - /** \brief Standard constructor - * - * \param date the event date. - * - */ - Change(double date); - - /// Gets the event date value - double date() const; - - /// Sets the event date value - void date(double value); - - /** \brief Applies the event - * - * \param paramSet the ParamSet instance to which the Change - * instance is attached. - * \param controller the Controller instance of the - * simulation. - * - */ - virtual void apply(ParamSet* paramSet, Controller* controller) const = 0; - - protected: - double _date; - - }; - -/**********************************************************************/ - - /** \brief Pure virtual base class for single parameter changes - * - * \ingroup coalesce - * - */ - class SingleParamChange : public Change { - public: - - /** \brief Default constructor - * - * The default date is 0., the default parameter value is 0. - * - */ - SingleParamChange(); - - /** \brief Standard constructor - * - * \param date the event date. - * \param value the parameter value. - * - */ - SingleParamChange(double date, double value); - - /// Gets the parameter value - double value() const; - - /// Sets the parameter value - void value(double value); - - protected: - double _value; - - }; - -/**********************************************************************/ - - /** \brief Single parameter changes applied to a single population - * - * \ingroup coalesce - * - */ - class PopulationParamChange : public SingleParamChange { - public: - - /** \brief Default constructor - * - * The default date is 0., the default parameter value is 0., - * the default population is 0 - * - */ - PopulationParamChange(); - - /** \brief Standard constructor - * - * \param date the event date. - * \param population the population index. - * \param value the parameter value. - * - */ - PopulationParamChange(double date, unsigned int population, double value); - - /// Gets the population index - unsigned int population() const; - - /// Sets the population index - void population(unsigned int value); - - protected: - - unsigned int _population; - - }; - - -/**********************************************************************/ - - /** \brief Bottleneck event - * - * \ingroup coalesce - * - * The bottleneck parameter is its strength, corresponding to an - * amount of time where time is locked and only coalescences are - * allowed (resulting in a given - and random - number of - * instantaneous coalescence with branches). - * - */ - class Bottleneck : public SingleParamChange { - public: - Bottleneck(double date, double param) : SingleParamChange(date, param) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - -/**********************************************************************/ - - /** \brief Population-specific bottleneck event - * - * \ingroup coalesce - * - */ - class PopulationBottleneck : public PopulationParamChange { - public: - PopulationBottleneck(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - - -/**********************************************************************/ - - /** \brief Change of the size of all populations - * - * The parameter is the new size (applied to all populations) - * - * \ingroup coalesce - * - */ - class AllPopulationSizeChange : public SingleParamChange { - public: - AllPopulationSizeChange(double date, double value) : SingleParamChange(date, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - - -/**********************************************************************/ - - /** \brief Change of a single population size - * - * \ingroup coalesce - * - */ - class SinglePopulationSizeChange : public PopulationParamChange { - public: - SinglePopulationSizeChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - - - -/**********************************************************************/ - - /** \brief Change of the growth rate of all populations - * - * The parameter is the new rate (applied to all populations) - * - * \ingroup coalesce - * - */ - class GrowthRateChange : public SingleParamChange { - public: - GrowthRateChange(double date, double value) : SingleParamChange(date, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - - -/**********************************************************************/ - - /** \brief Change of a single population's growth rate - * - * \ingroup coalesce - * - */ - class PopulationGrowthRateChange : public PopulationParamChange { - public: - PopulationGrowthRateChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - -/**********************************************************************/ - - /** \brief Change of the selfing rate - * - * The parameter is the new rate - * - * \ingroup coalesce - * - */ - class SelfingRateChange : public SingleParamChange { - public: - SelfingRateChange(double date, double value) : SingleParamChange(date, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - -/**********************************************************************/ - - /** \brief Fusion of two populations - * - * \ingroup coalesce - * - */ - class PopulationFusion : public Change { - public: - /** \brief Default constructor - * - * The default date is 0., the default mother is 0, the - * default daughter is 0. - * - */ - PopulationFusion(); - - /** \brief Standard constructor - * - * \param date the date of the event. - * \param mother first population to merge. - * \param daughter second population to merge. - * - * A time date, all the lineages from the daughter population - * are moved to the mother population and all mutation rates - * to the daughter population are cancelled. This functions - * emulates a population split (forward in time). - * - */ - PopulationFusion(double date, unsigned int mother, unsigned int daughter); - - void apply(ParamSet* paramSet, Controller* controller) const; - - /// Sets the daughter population - void daughter(unsigned int); - - /// Gets the daughter population - unsigned int daughter() const; - - /// Sets the mother population - void mother(unsigned int); - - /// Gets the mother population - unsigned int mother() const; - - protected: - unsigned int _mother; - unsigned int _daughter; - }; - - -/**********************************************************************/ - - /** \brief Split of a population - * - * \ingroup coalesce - * - */ - class PopulationSplit : public Change { - public: - /** \brief Default constructor - * - * The default date is 0., the default population is 0, the - * default probability is 0.5. - * - */ - PopulationSplit(); - - /** \brief Standard constructor - * - * A the time given by date, the specified population is - * split in two. An additional population (whose index is - * incremented from the current total number of population) - * is created and lineages are randomly picked and moved to - * the new population. The parameter proba gives the - * probability that a lineage from the population number pop - * moves instantly to the new population. If proba is 0, - * the program emulates the creation of an empty population - * (thinking forward in time, this is a population - * extinction). In general, forward in time, this is a - * population fusion. - * - * \param date the date of the event. - * \param pop population index. - * \param proba the probability that lineages move to the - * new population. - * - */ - PopulationSplit(double date, unsigned int pop, double proba); - - void apply(ParamSet* paramSet, Controller* controller) const; - - /// Gets the population index - unsigned int population() const; - - /// Sets the population index - void population(unsigned int); - - /// Gets the probability of instant migration - double probability() const; - - /// Sets the probability of instant migration - void probability(double); - - protected: - unsigned int _population; - double _probability; - }; - -/**********************************************************************/ - - /** \brief Change of the migration rate of all population pairs - * - * The parameter is the new rate (applied to all population pairs) - * - * \ingroup coalesce - * - */ - class AllMigrationRateChange : public SingleParamChange { - public: - AllMigrationRateChange(double date, double value) : SingleParamChange(date, value) {} - void apply(ParamSet* paramSet, Controller* controller) const; - }; - -/**********************************************************************/ - - /** \brief Change of a single migration rate - * - * \ingroup coalesce - * - */ - class SingleMigrationRateChange : public SingleParamChange { - public: - /** \brief Default constructor - * - * The default date is 0., the default parameter value is 0., - * the default source population is 0, the default - * destination population 1. - * - */ - SingleMigrationRateChange(); - - /** \brief Standard constructor - * - * \param date the date of the event. - * \param source index of the source population. - * \param dest index of the destination population. - * \param migr new value of the pairwise migration rate. - * - */ - SingleMigrationRateChange(double date, unsigned int source, unsigned int dest, double migr); - - /// Gets the source population index - unsigned source() const; - - /// Sets the source population index - void source(unsigned int); - - /// Gets the dest population index - unsigned dest() const; - - /// Sets the dest population index - void dest(unsigned int); - - void apply(ParamSet* paramSet, Controller* controller) const; - - protected: - unsigned int _source; - unsigned int _dest; - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/CharMatrix.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,70 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_CHARMATRIX_HPP -#define EGGLIB_CHARMATRIX_HPP - - -namespace egglib { - - /** \brief Interface for classes usable as a square matrix of characters - * - * \ingroup core - * - */ - class CharMatrix { - - public: - - /** \brief Gets number of rows or sequences - * - */ - virtual unsigned int numberOfSequences() const = 0; - - - /** \brief Gets number of columns or sites - * - */ - virtual unsigned int numberOfSites() const = 0; - - - /** \brief Gets the character at a given position - * - * The accessor should be "fast" and does not guarantee to - * perform out-of-bounds checks - * - */ - virtual char character(unsigned int sequence, unsigned int site) const = 0; - - - /** \brief Gets population index - * - */ - virtual unsigned int populationLabel(unsigned int row) const = 0; - - - /** \brief Get site position - * - */ - virtual double sitePosition(unsigned int column) const = 0; - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Consensus.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,421 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_CONSENSUS_HPP -#define EGGLIB_CONSENSUS_HPP - -#include "Align.hpp" -#include <sstream> -#include <string> -#include <vector> - -namespace egglib { - - /** \brief Generates consensus sequences - * - * \ingroup polymorphism - * - * - * A consensus is generated when two sequences have the same name, - * ignoring everything after the first separator character (by - * default, "_"). Hence, the names "foo", "foo_goo" and "foo_third" - * will be treated as identical and the root will be "foo". The root - * will be used to name the resulting sequence. Note that the - * class works only for DNA sequences. - * - * Symbol convention: - * - A: adenosine - * - C: cytosine - * - G: guanine - * - T: thymine - * - M: A or C - * - R: A or G - * - W: A or T (weak) - * - S: C or G (strong) - * - Y: C or T - * - K: G or T - * - B: C or G or T(not A) - * - D: A or G or T (not C) - * - H: A or C or T (not G) - * - V: A or C or G (not T) - * - N: A or C or G or T - * - ?: nonsequenced position - * - * Other symbols will be treated as ? (lowercase are supported). - * - * Rigorous (alias liberal or strong) mode: - * - If two characters are the same, it is retained whatever it is - * (A + A = A) - * - Otherwise: - * - If one is the missing character (?) the other is retained - * whatever it is (A + ? = A). - * - If characters are consistent, that is one contains - * more information, that one is retained (A + M = A). - * - If characters are not consistent, the closest - * generic symbol is retained (A + C = M). - * . - * Note that the feedback of inconsistent characters in the - * outcome is not garanteed. - * In fact, (A + A + G) will result in R (as expected) but (A + - * G + A) will result in A, masking the problem. - * However, the position will indeed be counted as inconsistent. - * - * Not rigorous (conservative/weak) mode: - * - If two characters are the same, it is retained whatever it - * is (A + A = A). - * - Otherwise: - * - If one is ? the other is retained whatever it is (A + ? - * = A). - * - Otherwise an inconsistent character (by default, Z) is - * retained (A + C = Z). - * - * Iterative process of consensus: - * - Each sequence is taken in turn. - * - Each pair involving the focus sequence is processed and a - * consensus is generated. - * - When all pair have been processsed, the consensus already - * generated are themselves iteratively processed until only one - * remains. - * - Note that at each time the last two are taken first. - * - * A transparent interface gives access to the data for all steps of - * the consensus process, as vectors that covers all pairs (including - * intermediate steps of the iterative procedure described above) as - * well as singleton sequences. For the latter, the second name is - * not filled and all counts are set to 0. Note also that the name of - * such singleton sequence is shortened to the separator as well. - * - */ - class Consensus { - public: - /** \brief Constructor - * - */ - Consensus(); - - /** \brief Destructor - * - */ - virtual ~Consensus() {} - - /// Sets the character interpreted as missing (default: ?) - void setMissing(char); - - /// Sets the character used to point to disagreements (default: Z) - void setDisagreement(char); - - /// Checks all the characters - bool check_sequences(Align& align); - - /** \brief Reduces the sequence alignment by making consensus sequences - * - * \param align the original alignment. - * - * \param separator the character used to separated the root - * name of sequences to the variable part, as in (for the - * default value: "sequence_read1". - * - * \param rigorous consensus mode. - * - * \return An Align instance with duplicated sequences consensed. - * - */ - Align consensus(Align& align, char separator='_', bool rigorous=true); - - /// First name of consensed pairs - const std::vector<std::string>& firstSequenceNames(); - - /// Second names of consensed pairs - const std::vector<std::string>& secondSequenceNames(); - - /// Root names of consensed pairs - const std::vector<std::string>& roots(); - - /// Number of consistent positions for all consensed pairs - const std::vector<int>& consistentPositions(); - - /// Number of complementary positions for all consensed pairs - const std::vector<int>& complementaryPositions(); - - /// Number of uninformative positions for all consensed pairs - const std::vector<int>& uninformativePositions(); - - /// Number of ambiguous positions for all consensed pairs - const std::vector<int>& ambiguousPositions(); - - /// Number of at least partially resolved ambiguities for all consensed pairs - const std::vector<int>& atLeastPartiallyResolvedAmbiguities(); - - /// Vector of inconsistent positions ofr all consensed pairs - const std::vector<std::vector<int> >& inconsistentPositions(); - - - private: - - /** \brief Copying this class is not allowed - * - */ - Consensus(const Consensus& source) { } - - /** \brief Copying this class is not allowed - * - */ - Consensus& operator=(const Consensus& source) { return *this; } - - // A private helper - class PairwiseConsensus; - - // report data - std::vector<std::string> t_firstSequenceNames; - std::vector<std::string> t_secondSequenceNames; - std::vector<std::string> t_roots; - std::vector<int> t_consistentPositions; - std::vector<int> t_complementaryPositions; - std::vector<int> t_uninformativePositions; - std::vector<int> t_ambiguousPositions; - std::vector<int> t_atLeastPartiallyResolvedAmbiguities; - std::vector<std::vector<int> > t_inconsistentPositions; - - // Code for missing data (usually ?) - char MISSING; - - // Code for disgrement - char DISAGREEMENT; - - // Helper class managing a single pair - class PairwiseConsensus { - public: - // Default object creation - PairwiseConsensus(); - - // Object destruction - virtual ~PairwiseConsensus() {} - - // Usual object creation - PairwiseConsensus(std::string, std::string); - - // Fills an object created with the default constructor - void load(std::string,std::string); - - // Changes the MISSING character - void setUndeterminedCharacter(char); - - // Changes the DISAGREEMENT character - void setDisagreementCharacter(char); - - /* Uses the conservative mode of consensus - * - * Tries to avoid to make decisions, and adds the - * character set by DISAGREEMENT upon inconsistencies - * - * return The number of inconsistencies. - */ - int generateSoftConsensus(); - - /* Strict mode of consensus - * - * The number of inconsistencies. - */ - int generateHardConsensus(); - - // Two fully resolved (including gap) and identical characters - int getConsistentPositions(); - - // One informative (including gap) and one missing - int getComplementaryPositions(); - - // None missing, but different and incompatible - int getInconsistentPositions(); - - // Both are missing - int getUninformativePositions(); - - // Both identical or one missing, but not fully resolved - int getAmbiguousPositions(); - - // Different, not missing, complementary. - int getAtLeastPartiallyResolvedAmbiguities(); - - // Accessor - int getThisInconsistentPosition(unsigned int); - - // Generates the consensus sequence - std::string getConsensus(); - - private: - - inline bool isValid(char c) { - switch (c) { - case 'A': case 'a': - case 'C': case 'c': - case 'G': case 'g': - case 'T': case 't': - return true; - default: - return false; - } - } - - // This initiates a series of embedded objects - void setCharacterContainers(); - - // The first sequence - std::string seqA; - - // The second sequence - std::string seqB; - - // The resulting consensus - std::string cons; - - // The vecotr storing the inconsistent positions - std::vector<int> posIncons; - - // The length of the sequences - unsigned int ls; - - // Counter - int cntConsistentPositions; - - // Counter - int cntComplementaryPositions; - - // Counter - int cntAmbiguousPositions; - - // Counter - int cntInconsistentPositions; - - // Counter - int cntUninformativePositions; - - // Counter - int cntAtLeastPartiallyResolvedAmbiguities; - - // Code for missing data (usually ?) - char MISSING; - - // Code for disgrement - char DISAGREEMENT; - - public: - // This class manages relationships different symbols - class CharacterContainer { - public: - // Default value: @ - CharacterContainer(); - - // Initiates to a given symbol - CharacterContainer(const char&); - - // Assignment operator - CharacterContainer& operator=(const char&); - - // Sets the symbol - void setValue(char); - - // Set the descendants - void setSons(std::vector<CharacterContainer>); - - // Tests whether the symbol is the same - bool is(CharacterContainer); - - // Tests if the query is contained amongst the sons - bool has(CharacterContainer); - - // Tests if the query is contained amongst the sons - bool has(char); - - /* Tests whether the left character has the left one - * Should be called on the N object only. - */ - char lhas(CharacterContainer,CharacterContainer); - - /* Creates the object with the proper sons - * Should be called on the N object only. - */ - CharacterContainer init(char); - - // The symbol - char value; - - // The descendants - std::vector<CharacterContainer> sons; - }; - - private: - // Symbol ? - CharacterContainer ccQ; - - // Symbol A - CharacterContainer ccA; - - // Symbol C - CharacterContainer ccC; - - // Symbol G - CharacterContainer ccG; - - // Symbol T - CharacterContainer ccT; - - // Symbol U - CharacterContainer ccU; - - // Symbol M - CharacterContainer ccM; - - // Symbol R - CharacterContainer ccR; - - // Symbol W - CharacterContainer ccW; - - // Symbol S - CharacterContainer ccS; - - // Symbol Y - CharacterContainer ccY; - - // Symbol K - CharacterContainer ccK; - - // Symbol B - CharacterContainer ccB; - - // Symbol D - CharacterContainer ccD; - - // Symbol H - CharacterContainer ccH; - - // Symbol V - CharacterContainer ccV; - - // Symbol N - CharacterContainer ccN; - - // Symbol - - CharacterContainer ccGAP; - }; - }; -} - -#endif -
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Container.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,326 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_CONTAINER_HPP -#define EGGLIB_CONTAINER_HPP - - -namespace egglib { - - /** \brief Handles a set of sequence alignment (aligned or not) - * - * \ingroup core - * - * Creation from a file or string stream should be performed using - * the class Fasta. - * - * Sequences are represented by two strings (name and sequence) and - * an integer (group) that can be accessed or modified by index.The - * order of sequences is guaranteed to be conserved, as if Container - * was a list of triplets (name, sequence, group). - * - * The data matrix is implemented as continuous arrays (char**) and - * allows efficient access and modification of data. For very large - * data matrices you might claim immediately the required memory - * using the constructor Container(unsigned int, char**). - * - */ - class Container { - - public: - - /** \brief Creates an empty object - * - */ - Container(); - - - /** \brief Copy constructor - * - */ - Container(const Container& source); - - - /** \brief Assignment operator - * - */ - Container& operator= (const Container& source); - - - /** \brief Creates an object from a data matrix - * - * Allows you to create an object from data stored in a char* - * array. The array's size must be passed to the constructor. - * Since sequences can have different lengths, you need to - * terminate each sequence by a NULL character. This constructor - * is dedicated to very performance-critical tasks. For usual - * tasks, using the default constructor and subsequently adding - * sequences with addSeq should be enough. - * - * \param number_of_sequences the number of sequences (the length - * of the first dimension of the array). - * - * \param cstring_array the pointer to the data matrix. - * - */ - Container(unsigned int number_of_sequences, char const* const* const cstring_array); - - - /** \brief Destructor - * - */ - virtual ~Container(); - - - /** \brief Clears all content of the object - * - */ - virtual void clear(); - - - /** \brief Adds a sequence to the object - * - * \param name the name of the sequence, as a c-string. - * \param sequence the sequence string, as a c-string. - * \param group the group index of the sequence. - * - * \return The new number of sequences. - * - */ - virtual unsigned int append(const char* name, const char* sequence, unsigned int group=0); - - - /** \brief Removes a sequence from the object - * - * \param pos the index of the sequence to remove. - * - * \return The new number of sequences. - */ - virtual unsigned int remove(unsigned int pos); - - - /** \brief Changes the name of a given sequence - * - * \param pos the sequence index. - * \param name the new name as a C-like string. - * - */ - virtual void name(unsigned int pos, const char* name); - - - /** \brief Changes the sequence string of a given sequence - * - * \param pos the sequence index. - * \param sequence the new sequence as a C-like string. - * - */ - virtual void sequence(unsigned int pos, const char* sequence); - - - /** \brief Appends a string to the a given sequence - * - * \param pos the sequence index. - * \param sequence the sequence to append at the end of the - * current one. - * - */ - virtual void appendSequence(unsigned int pos, const char* sequence); - - - /** \brief Changes a character - * - * \param sequence the sequence index. - * \param position the character index. - * \param ch the new character value. - * - * The positions must fit in the current ranges. - * - */ - virtual void set(unsigned int sequence, unsigned position, char ch); - - - /** \brief Gets a given character - * - * \param s the sequence index. - * \param p the character index. - * - * \return the character value. - * - * The positions must fit in the current ranges. - * - */ - virtual char get(unsigned int s, unsigned int p) const; - - - /** \brief Changes the group index of a given sequence - * - * \param pos the sequence index. - * \param group the new group index value. - * - */ - virtual void group(unsigned int pos, unsigned int group); - - - /** \brief Extracts a range of sequences - * - * \param a the index of the first sequence. - * - * \param b the index immediately passed the last sequence to - * extract. - * - * \return A copy of the object containing the specified - * range of sequences. - * - * Sequences a to b-1 are extracted, provided that the - * indices fit in the current number of sequences. To extract - * all sequences, use container.hslice(0, container.ns()). - * - * Note: invalid ranges will be silently supported. If - * a>=ls or b<=a, an empty object is returned. If b>ns, - * ls will be substituted to a. - * - */ - Container hslice(unsigned int a, unsigned int b) const; - - - /** \brief Gets the number of sequences - * - */ - unsigned int ns() const; - - - /** \brief Gets the length of a given sequence - * - * \param pos the index of the sequence. - * - * \return The length of that particular sequence. - * - */ - virtual unsigned int ls(unsigned int pos) const ; - - - /** \brief Gets the name of the a given sequence - * - * \param pos the index of the sequence. - * - * \return The name of that particular sequence. - * - */ - virtual const char* name(unsigned int pos) const; - - - /** \brief Gets the name of a given sequence - * - * \param pos the index of the sequence. - * - * \return The sequence string for that particular sequence. - * - */ - virtual const char* sequence(unsigned int pos) const; - - - - /** \brief Gets the group index of a given sequence - * - * \param pos the index of the sequence. - * - * \return The group index of that particular sequence. - * - */ - virtual unsigned int group(unsigned int pos) const; - - - /** \brief Checks if all lengths are equal - * - * Returns true if the length of all sequences are equal or - * if there is less thant two sequences. - * - */ - bool isEqual() const; - - - /** \brief Equalizes sequence lengths - * - * Extends sequences as need to ensure that all sequences - * have the same length. - * - * \param ch the character to use for padding. - * - * \return The final length obtained, which is the length of - * the longest sequence before the operation. - * - */ - unsigned int equalize(char ch='?'); - - - /** \brief Finds a sequence by its name - * - * Gets the position of the first sequence with the specified - * name. - * - * \param string a sequence name. - * - * \param strict if true, seeks an exact match. If false, - * compares only until the end of the requested name (for - * example: ATCFF will match ATCFF_01 if strict is false). - * - * \return The lowest index where the name matches, -1 if no - * sequence has such name. - * - */ - int find(const char* string, bool strict=true) const; - - - protected: - // The number of sequences - unsigned int _ns; - - // The array of name lengths - unsigned int* lnames; - - // The array of names - char** names; - - // The array of sequences (as c-strings) - char** sequences; - - // The array of groups - unsigned int* groups; - - // Imports an array of c-strings - virtual void setFromSource(unsigned int number_of_sequences, const char* const* const cstring_array); - - // Constructor helper - virtual void copyObject(const Container&); - - // Constructor partial helper - virtual void getNamesAndGroups(const Container&); - - private: - - // The array of sequence lengths - unsigned int* lsequences; - - // Setup a valid empty object - virtual void init(); - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,156 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_CONTROLLER_HPP -#define EGGLIB_CONTROLLER_HPP - -#include "Current.hpp" -#include "Arg.hpp" -#include "ParamSet.hpp" - -namespace egglib { - - class Random; - - /** \brief Controls a coalescent simulation - * - * \ingroup coalesce - * - * This class generates the gene genealogy, based on the parameters - * stocked in a ParamSet object. - * - */ - class Controller { - - public: - - /** \brief Default constructor - * - * Uses a default ParamSet object that will not allow - * performing simulations. - * - */ - Controller(); - - /** \brief Destructor - * - */ - ~Controller(); - - /** \brief Standard constructor - * - * \param paramSet a ParamSet object containing run - * parameters (it is taken as a reference and stored as this - * so it must not be modified during simulations). - * - * \param random the address of the random number generator. - * - */ - Controller(const ParamSet* paramSet, Random* random); - - /** \brief Reset for a new simulation - * - * Object is reinitiliazed for a new simulation. - * - */ - void reset(); - - /** \brief Increments the coalescent model - * - * \return The number of lineages. - * - */ - unsigned int step(); - - /** \brief Gets the Ancestral Recombination Graph - * - * \return The address of the ARG contained in the object. - * - */ - Arg* getArg(); - - /** \brief Applies a bottleneck to a given population - * - * The bottleneck is applied following Galtier, Depaulis and - * Barton (Genetics, 2000): the general time counter is - * stopped, and coalescence events are performed during a - * time (of normal coalescent process) given by the parameter - * strength. All coalescent events are instantaneous. - * - * \param populationIndex index of the population concerned - * by the event. - * - * \param strength strength of the bottleneck given by a - * number of time units (2N generations times the size of - * the population). - * - */ - void bottleneck(unsigned int populationIndex, double strength); - - /** \brief Migrate a complete population - * - * Takes all the lineages currently present in the population - * source to the population dest. - * - */ - void moveAllLineages(unsigned int source, unsigned int dest); - - /** \brief Migrate a complete population - * - * Takes all the lineages currently present in the population - * source to the population dest. - * - * \param source source population. - * \param dest destination population. - * \param probability the probability that a lineage of - * source migrates to dest. - * - */ - void moveSomeLineages(unsigned int source, unsigned int dest, double probability); - - /// Adds an empty population - void addPopulation(); - - private: - - /// The copy constructor is disabled - Controller(const Controller& source) {} - - /// The assignment operator is disabled - Controller& operator=(const Controller& source) {return *this;} - - void diploids(); - double getMigrationTime(double& migrationParameterDestination); - void getCoalescenceTime(double& destTime, unsigned int& destPopIndex); - double getCoalescenceTimeForPopulation(unsigned int populationIndex); - double getRecombinationTime() const; - void migrate(double migrationParameter); - - const ParamSet* initialParamSet; - ParamSet paramSet; - Current current; - Arg arg; - - Random* random; - - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Convert.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,234 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_CONVERT_HPP -#define EGGLIB_CONVERT_HPP - - -#include "DataMatrix.hpp" -#include "Align.hpp" -#include "EggException.hpp" -#include "Random.hpp" -#include <string> - -#include "config.h" - -#ifdef HAVE_LIBBPP_SEQ -#include <Bpp/Seq/Alphabet.all> -#include <Bpp/Seq/Sequence.h> -#include <Bpp/Seq/Container.all> -#endif - - - -namespace egglib { - - - /** \brief Performs conversion between sequence holder types - * - * \ingroup core - * - * Static methods of this class allows conversion between sequence - * holder types implying parametrizable modifications. - * - */ - class Convert { - - public: - - /** \brief DataMatrix to Align conversion - * - * By defaut, this method generates an Align instance - * containing only the polymorphic sites. The integers of - * the DataMatrix will be converted as follow: 0 to A, 1 to - * C, 2 to G and 3 to T. This behaviour can be largely - * modified using options. - * - * \param dataMatrix DataMatrix instance. - * - * \param length length of the desired alignment. Non-varying - * stretches of data will be introduced to reach the - * specified length. By default the positions of segregating - * sites will be determined from the positions given by the - * DataMatrix object. Those positions are expressed in a - * continuous range, and will be discretized. Mutations - * falling on the same site will be moved of one position - * left or right (always preserving the order of mutation - * sites). If positions are all zero (the default of the - * DataMatrix class) and if length is larger than the number - * of segregating sites, then all segregating sites will - * cluster on the left-hand side of the alignment. - * - * \param random the address to a Random object allowing to - * draw random numbers (for randomizing positions and/or - * non-varying states). If an address is provided but no - * random numbers are required, it is ignored. If no address - * if provided and random numbers are required, a Random - * instance is built internally. - * - * \param randomizePositions if true, the positions specified - * in the DataMatrix objects are ignored and the positions of - * mutations are drawn randomly along the interval (only if - * the specified length is larger than the number of - * segregating sites). If randomizePositions and false and - * positions are not - * - * \param enforceLength specify whether a - * EggRuntimeError should be thrown when the number of - * polymorphic sites is larger than the specified length. If - * false (the default) and in cases where the specified - * length is too short to harbor all polymorphic sites, the - * alignment length will be increased as needed. - * - * \param randomizeNonVaryingStates if true, the stretches of - * conserved positions (between segregating sites) will be - * randomly drawn from the current symbol mapping. Otherwise, - * the symbol given by fixed will be used. - * - * \param randomizeAlleles if true, alleles will be drawn - * randomly from the mapped characters. Note that if a - * genotype value is larger than the size of the mapping, it - * will be replaced by the character given by unknown, - * without randomization. In other words, with the mapping - * "ACGT", alleles 0, 1, 2 and 3 will be randomly assigned - * to these four characters, but larger and negative alleles - * will be assigned to the unknown character. - * - * \param mapping a string given the character to assign to - * different character values read from the DataMatrix. If - * the read value is 0, the first character of the string - * will used, the the value is 1, the second character will - * be used, and so on. If the integer read is out of range - * (in particular, for any negative value), then the - * character given by unknown will be used. An empty string - * will always lead to alignments containing only the - * character given by unknown. The string "01" is suitable - * for binary data. - * - * \param unknown the character to use if an integer genotype - * value is not mapped in the mapping string (that is, if - * the mapping string is too short). - * - * \param nonVaryingState character to use for conserved - * stretches of data. It doesn't have to be included in the - * mapping. If randomizeNonVaryingState is true, this - * argument is ignored. - * - * \return The resulting Align object. - * - */ - static Align align( - DataMatrix& dataMatrix, - unsigned int length=0, - Random* random=NULL, - bool randomizePositions=false, - bool randomizeNonVaryingStates=false, - bool randomizeAlleles=false, - bool enforceLength=false, - std::string mapping="ACGT", - char unknown='?', - char nonVaryingState='A' - ); - - -#ifdef HAVE_LIBBPP_SEQ - - /** \brief Converts an alignment to the equivalent Bio++ type - * - * During conversion, name information is lost (arbitrary - * names are generated in order toprevent duplicate names). - * The object is attached to an alphabet matching the passed - * integer. The names are bare rank integers (starting at the - * value giving by *offset*). - * - * \param align the source alignment object. - * - * \param alphabetID an integer indicating which alphabet to - * use: - * - 1 for DNA - * - 2 for RNA - * - 3 for proteins - * - 4 for standard codon - * - 5 for vertebrate mitochondrial codon - * - 6 for invertebrate mitochondrial codon - * - 7 for echinoderm mitochondrial codon - * . - * Other values will result in an exception. - * - * \param outgroupFlag an integer indicating whether to - * include outgroup sequences: - * - 0 use all sequences - * - 1 use only sequences without 999 label (ingroup) - * - 2 use only sequences with 999 label (outgroup) - * . - * Other values will result in an exception. - * - * \param offset enter an integer to shift the names of the - * resulting alignment (useful to merge alignment and ensure - * that names are not duplicated). - * - * \return A Bio++ alignment. - * - */ - static bpp::AlignedSequenceContainer egglib2bpp(Align& align, unsigned int alphabetID, unsigned int outgroupFlag, unsigned int offset=0); - -#endif - - - - protected: - - /** \brief This class cannot be instantiated - * - */ - Convert() { } - - - /** \brief This class cannot be instantiated - * - */ - Convert(const Convert& source) { } - - - /** \brief This class cannot be instantiated - * - */ - Convert& operator=(const Convert& source) { return *this; } - - - /** \brief This class cannot be instantiated - * - */ - virtual ~Convert() { } - -#ifdef HAVE_LIBBPP_SEQ - static bpp::DNA dnaAlphabet; - static bpp::RNA rnaAlphabet; - static bpp::ProteicAlphabet proteicAlphabet; - static bpp::StandardCodonAlphabet standardCodonAlphabet; - static bpp::VertebrateMitochondrialCodonAlphabet vertebrateMitochondrialCodonAlphabet; - static bpp::InvertebrateMitochondrialCodonAlphabet invertebrateMitochondrialCodonAlphabet; - static bpp::EchinodermMitochondrialCodonAlphabet echinodermMitochondrialCodonAlphabet; -#endif - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Current.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,128 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_CURRENT_HPP -#define EGGLIB_CURRENT_HPP - - -namespace egglib { - - class Population; - class ParamSet; - - /** \brief Represents the current set of populations - * - * \ingroup coalesce - * - */ - class Current { - - public: - - /** \brief Default constructor - * - */ - Current(); - - /** \brief Standard constructor - * - * \param paramSet allows to initiate the correct structure - * of populations. - * - */ - Current(ParamSet* paramSet); - - /** \brief Rebuilds the object - * - * \param paramSet allows to initiate the correct structure - * of populations. - * - */ - void reset(ParamSet* paramSet); - - /** \brief Destructor - * - */ - virtual ~Current(); - - /** \brief Copy constructor - * - */ - Current(const Current&); - - /** \brief Assignment operator - * - */ - Current& operator=(const Current&); - - /** \brief Gets the current number of populations - * - */ - unsigned int numberOfPopulations() const; - - - /** \brief Adds an empty population to the system - * - */ - void addPopulation(); - - - /** \brief Gets the number of lineages contained by a given - * population - * - */ - unsigned int populationNumberOfLineages(unsigned int populationIndex) const; - - - /** \brief Provides access to a given population - * - * The returned pointer can be used to modify the object. - * - */ - Population* population(unsigned int populationIndex); - - - /** \brief Total number of lineages - * - */ - unsigned int totalNumberOfLineages() const; - - - /** \brief Efficient number of lineages - * - * This sums the number of covered segments of each lineage. - * - */ - unsigned int efficientNumberOfLineages() const; - - - private: - - void setPopulationArray(); - void copy(const Current&); - void clear(); - - unsigned int _numberOfPopulations; - unsigned int _numberOfSegments; - Population** populations; - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/DataMatrix.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,219 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_DATAMATRIX_HPP -#define EGGLIB_DATAMATRIX_HPP - - -#include "CharMatrix.hpp" - - -namespace egglib { - - /** \brief Data table - * - * \ingroup core - * - * Holds a data matrix representing genotype data from simulations. - * Data are stored as integers, to each site is associated a - * position, and to each sequence is associated a group index (any - * integer labelling, for example, a subpopulation). Supports the - * CharMatrix interface with the condition that allele genotype - * datum is >=0 and <=9. - * - */ - class DataMatrix : public CharMatrix { - - public: - - /** \brief Default constructor - * - * The data table default dimensions are {0,0} - * - */ - DataMatrix(); - - - /** \brief Standard constructor - * - * The data table dimensions must be given. - * Each cell default default is 0, and each site position is 0.. - * - * \param numberOfSequences number of lines of the data table. - * \param numberOfSites number of columns of the data table. - * - */ - DataMatrix(unsigned int numberOfSequences, unsigned int numberOfSites); - - - /** \brief Copy constructor - * - */ - DataMatrix(const DataMatrix&); - - - /** \brief Copy constructor - * - */ - DataMatrix(const CharMatrix&); - - - /** \brief Assignment operator - * - */ - virtual DataMatrix& operator=(const DataMatrix&); - - - /** \brief Assignment operator - * - */ - virtual DataMatrix& operator=(const CharMatrix&); - - - /** \brief Destructor - * - */ - virtual ~DataMatrix(); - - - /** \brief Gets number of sites - * - */ - unsigned int numberOfSites() const; - - - /** \brief Gets number of sequences - * - */ - unsigned int numberOfSequences() const; - - - /** \brief Sets a value of the data table - * - */ - void set(unsigned int sequence, unsigned int site, int value); - - - /** \brief Gets a value from the data table - * - */ - int get(unsigned int sequence, unsigned int site) const; - - - /** \brief Faster and unsecure version of get - * - */ - inline int fget(unsigned int sequence, unsigned int site) const { - return dataMatrix[sequence][site]; - } - - - /** \brief Sets the position of a site - * - */ - void sitePosition(unsigned int site, double value); - - - /** \brief Gets the position of a site - * - */ - double sitePosition(unsigned int site) const; - - - /** \brief Sets the group label of a sequence - * - */ - void populationLabel(unsigned int sequence, unsigned int value); - - - /** \brief Gets the group label of a sequence - * - */ - unsigned int populationLabel(unsigned int sequence) const; - - - /** \brief Removes all information from the object - * - */ - void clear(); - - - /** \brief Resizes the data matrix - * - * \param newNumberOfSequences number of sequences (rows) - * \param newNumberOfSites number of sites (columns) - * - * If new values are larger, data already set is left unchanged. - * New data are set to zero. - * - */ - void resize(unsigned int newNumberOfSequences, unsigned int newNumberOfSites); - - - /** \brief Shifts allele value - * - * \param minimum the minimum allele value. - * - * Shifts all alleles at all sites to ensure that alleles alleles - * are equal to or larger than minimum. The shifting is specific - * to each site. - * - */ - void shift(int minimum); - - /** \brief Gets the character at a given position - * - * An exception is generated if the allele value at this - * position is not >=0 and <=9. Not out-of-bound check is - * performed. - * - */ - char character(unsigned int sequence, unsigned int site) const; - - - - private: - - // Initializes to default values (for empty object) - void init(); - - // Copies from a source object - virtual void copy(const CharMatrix&); - - // Copies from a source object - virtual void copy(const DataMatrix&); - - // Number of lines of the data matrix - unsigned int _numberOfSequences; - - // Number of columns of the data matrix - unsigned int _numberOfSites; - - // Data matrix - int **dataMatrix; - - // Vector of site positions - double *positions; - - // Vector of group indices - unsigned int *groups; - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Edge.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,331 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_EDGE_HPP -#define EGGLIB_EDGE_HPP - -#include <vector> -#include <climits> -#include "EggException.hpp" - -namespace egglib { - - class Random; - - /** \brief Edge of the ancestral recombination graph - * - * \ingroup coalesce - * - * Each Edge instance provides access to its 0, 1 or 2 descendants - * (the former holds for a terminal node, the middle for the parent - * of a recombined node and the latter for the parent of a coalesced - * node (most classical node in the coalescent).The Edge also - * provides to the edge length. Note that the Edge instance must be - * understood as an ARG node and the branch above it (latter in the - * coalescence process). Edge instances also keep track of the list - * of descendants descending from this node (which may differ along - * recombining segment). Edge instances *must* be created through one - * of the "default" and "coalescence" constructors or through the - * recombination method. Edge instances should never be copied but - * manipulated by references. - * - */ - class Edge { - - public: - - /// Destructor - virtual ~Edge(); - - /** \brief Constructor - * - * \param numberOfSegments the number of recombining segments - * (one for a non-recombining region). - * - * Use the Pool, instead. Objects are delivered with a - * complete coverage. - * - */ - Edge(unsigned int numberOfSegments); - - - /// Restore object to `factory` state - void reset(); - - - /** \brief Builds for internal node - * - * \param date the date of creation of the edge. - * \param son1 first edge descending from this edge. - * \param son2 second edge descending from this edge. - * \param edgesPerSegments counts the current number of - * (non-coalesced lineages for each lineages); must have the - * appropriate size and will be updated. - * \param MRCA the list where to place the address of segment - * MRCA, if it occurs. - * \param totalLength the total length of the tree. - * \param segmentLengths the table of tree lengths per - * segment. - * - * Assumes the current object has the correct number of - * segments. - * - */ - void coalescence(double date, Edge* son1, Edge* son2, - unsigned int* edgesPerSegments, Edge** MRCA, - double& totalLength, double* segmentLengths); - - - /** \brief Generates a recombination event - * - * \param date the date of the event. - * \param dest1 destination for the first resulting edge. - * \param dest2 destination for the second resulting edge. - * \param random pointer to the Random instance used by the - * simulator. - * \param totalLength the total length of the tree. - * \param segmentLengths the table of tree lengths per - * segment. - * - * dest1 and dest2 must be Edge address initialized with the - * appropriate number of segments. - * - */ - void recombination(double date, - Edge* dest1, Edge* dest2, Random* random, - double& totalLength, double* segmentLengths); - - - /** \brief Define this edge to be terminal - * - * The edge have only non-covered segments - * - */ - void set_terminal(unsigned int leaf_index); - - /// Branch's raw length (doesn't take account segment coverage) - double length; - - /// Number of covered segments - unsigned int coverage; - - /// Time position of the branch's bottom - double bottom; - - /// Time position of the branch's top - double top; - - /// Address of the first son - Edge* son1; - - /// Address of the second son - Edge* son2; - - /// Number of sons (0, 1 or 2) - unsigned int numberOfSons; - - /// Checks if a given segment is covered - inline bool segment(unsigned int segmentIndex) const { - //while(segments[segmentIndex]==0) segmentIndex--; - if (segments[segmentIndex]==0) return false; - if (segments[segmentIndex]==UINT_MAX) return true; - return segbools[segmentIndex]; - } - - /// leaf index (0 for internal nodes) - inline unsigned int label() const { - return _label; - } - - /// Number of mutations per segment - unsigned int* numberOfMutationsPerActualSite; - - /// Sets the actual number of sites - void set_actualNumberOfSites(unsigned int actualNumberOfSites); - - - private: - - unsigned int _label; - - /// Default constructor is not available - Edge(); - - /// Copy constructor is not available - Edge(const Edge& edge) {} - - /// Assignment operator is not available - Edge& operator=(const Edge& edge) { return *this; } - - void init(unsigned int numberOfSegments); - - unsigned int numberOfSegments; - unsigned int* segments; - bool* segbools; - - /// complete the covered ranges with UINT_MAX's and the non-covered by 0's - inline void fill() { - coverage=0.; - unsigned int i=0,j; - while (i<numberOfSegments) { - if (segbools[i]==true) { - coverage += segments[i]; - for (j=1; j<segments[i]; j++) { - segments[i+j] = UINT_MAX; - } - } - i+=segments[i]; - } - } - - - - /// update containing Arg's branch lengths - inline void update_lengths(double& totalLength, double* segmentLengths) { - unsigned int i=0,j; - while (i<numberOfSegments) { - if (segbools[i]==true) { - totalLength += segments[i]*length; - for (j=0; j<segments[i]; j++) { - segmentLengths[i+j] += length; - } - } - i+=segments[i]; - } - } - - - }; - - - - - - - - - - - - - /** \brief Pool of Edge objects - * - * \ingroup coalesce - * - * Holds a pool of Edge objects that can be recycled to spare the - * building burden. A construction time, a number of Edge objects - * equals to the predicted number of needed instances should be - * requested. The Edge's will be prebuilt immediately and delivered - * upon request. After use, the Edge's should be released. It is only - * possible to release the last issued Edge instance or all of them - * at once. - * - */ - class EdgePool { - - public: - - /// Default constructor (nothing allocated) - EdgePool(); - - - /// Destructor - virtual ~EdgePool(); - - - /** \brief Configure pool - * - * Pre-allocates a given number of Edge objects. The objects - * will be immediately available. - * - * Data previously allocated (by a previous call of this - * function or by the deliver() method) will be lost so it - * can be required to use clear() before. - * - * \param numberOfSegments the number of segments of the - * simulation; all Edge instances will use this value. - * - * \param numberOfPreAllocated the number of Edge that should - * be kept ready for immediate use. - * - */ - void set(unsigned int numberOfSegments, unsigned numberOfPreAllocated); - - - /** \brief Frees internally stored memory - * - * This invalidate all points that have been delivered - * previously. However, any previously set number of segments - * (0, by default) is retained. - * - */ - void clear(); - - - /** \brief Deliver an Edge - * - * The object must not be freed by the client! This object is - * allocated on the heap if the cache is not large enough, - * only reset if it was previously released, or just delivered - * if it is one of the initially allocated instances. - * - */ - Edge* deliver(); - - - /** \brief Release an Edge - * - * Release the last delivered Edge. The instance is only - * cached for a potential future use; it is not freed nor - * reset immediately. If no Edge's are in use, nothing is - * done. - * - */ - void releaseLast(); - - - /** \brief Release all Edge's - * - * Release all delivered Edges. The instances are only - * cached for a potential future use; they are not freed nor - * reset immediately. If no Edge's are in use, nothing is - * done. - * - */ - void releaseAll(); - - private: - - /// Not available - EdgePool(const EdgePool& ep) {} - - /// Not available - EdgePool& operator=(const EdgePool& ep) { return *this; } - - unsigned int numberOfSegments; - unsigned int used; - unsigned int released; - unsigned int ready; - Edge** cache; - - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/EggException.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,173 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_EGGEXCEPTION_HPP -#define EGGLIB_EGGEXCEPTION_HPP - -#include <string> -#include <exception> - -namespace egglib { - - /** \brief Base exception type for errors occurring in this library - * - * \ingroup core - * - */ - class EggException : public std::exception { - public: - /// Constructor with empty error message - EggException(); - /// Creates the exception - EggException(const char* message); - /// Destructor - ~EggException() throw() {} - /// Gets error message - virtual const char* what() const throw(); - - protected: - std::string message; - - }; - - - /** \brief Exception type for memory errors - * - * \ingroup core - * - */ - class EggMemoryError : public EggException { - public: - /// Creates the exception - EggMemoryError(); - /// Destructor - ~EggMemoryError() throw() {} - }; - - - /** \brief Exception type for argument value errors - * - * \ingroup core - * - */ - class EggArgumentValueError : public EggException { - public: - /// Creates the exception - EggArgumentValueError(const char* m ); - /// Destructor - ~EggArgumentValueError() throw() {} - }; - - - /** \brief Exception type for runtime errors - * - * Runtime error definition is rather large. Includes bugs as well - * as logical errors. - * - * \ingroup core - * - */ - class EggRuntimeError : public EggException { - public: - /// Creates the exception - EggRuntimeError(const char* m ); - /// Destructor - ~EggRuntimeError() throw() {} - }; - - - /** \brief Exception type for file/string formatting errors - * - * \ingroup core - * - */ - class EggFormatError : public EggException { - public: - /// Creates the exception - EggFormatError(const char* fileName, const char* expectedFormat, const char* m); - /// Destructor - ~EggFormatError() throw() {} - /// Gets the file name - std::string fileName() const; - /// Gets the expected format - std::string expectedFormat() const; - /// Formats a longer string - virtual const char* what_more() const; - - protected: - std::string fname; - std::string eformat; - }; - - - /** \brief Exception type for errors while opening a file - * - * \ingroup core - * - */ - class EggOpenFileError : public EggException { - public: - /// Creates the exception - EggOpenFileError(const char* fileName ); - /// Destructor - ~EggOpenFileError() throw() {} - }; - - - /** \brief Exception type for unaligned sequences - * - * \ingroup core - * - */ - class EggUnalignedError : public EggException { - public: - /** \brief Creates the exception - * - */ - EggUnalignedError(); - - /** \brief Destructor - * - */ - ~EggUnalignedError() throw() {} - }; - - /** \brief Exception type for invalid character - * - * \ingroup core - * - */ - class EggInvalidCharacterError : public EggException { - public: - /** \brief Creates the exception - * - */ - EggInvalidCharacterError(char c, unsigned int seqIndex, unsigned int posIndex); - - /** \brief Destructor - * - */ - ~EggInvalidCharacterError() throw() {} - }; - -} - - - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/FStatistics.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,288 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_FSTATISTICS_HPP -#define EGGLIB_FSTATISTICS_HPP - - - -namespace egglib { - - - /** \brief Computes Fis, Fst and Fit from diploid data - * - * The class requires loading data. Data are loaded by individual - * (two genotypes per individual). The analyses are cached: they are - * performed upon the first call to statistics accessors. The cache - * is emptied whenever a datum is loaded. - * - * The computations are performed after Weir and Cockerham. The - * statistics F, theta and f are generalized for multiple alleles. - * To allow computation of multi-locus statistics, variance - * components are also available. The three components of the - * variance are Vpopulation (between-population), Vindividual - * (within-population, between-individual) and Vallele (within- - * individual). The formulas to compute the F-statistics are as - * follows: - * - 1-F = Vallele/(Vpopulation+Vindividual+Vallele) - * - theta = Vpopulation/(Vpopulation+Vindividual+Vallele) - * - 1-f = Vallele/(Vindividual+Vallele). - * - * \ingroup polymorphism - * - */ - class FStatistics { - - public: - - /** \brief Constructor - * - */ - FStatistics(); - - - /** \brief Destructor - * - */ - virtual ~FStatistics(); - - - /** \brief Reserve sufficient memory for a given number of - * individuals. - * - * This method makes the load function faster by allocating - * all required memory at once. - * - * \param numberOfIndividuals a strictly positive integer. - * - */ - void reserve(unsigned int numberOfIndividuals); - - - /** \brief Loads the data for one individual - * - * \param genotype1 an integer giving the first allele. - * \param genotype2 an integer giving the second allele. - * \param populationLabel an integer indication belonging to - * a population. - * - * Genotypes and population labels are not required to be - * consecutive (both are labels, not indices). They are - * internally mapped to indices (the mapping can be obtained - * by accessors populationLabel and allele). - * - * All genotypes are considered to be valid (no missing data). - * If statistics were computed previous to call to this - * function, all data will be erase. - * - */ - void loadIndividual(unsigned int genotype1, - unsigned int genotype2, unsigned int populationLabel); - - - /** \brief Label of a population - * - * The index corresponds to the local mapping of populations - * regardless of the ranking of population labels. (No out - * of bound checking.) - * - */ - unsigned int populationLabel(unsigned int populationIndex); - - - /** \brief Value of an allele - * - * The index corresponds to the local mapping of alleles - * regardless of the ranking of allele values. (No out of - * bound checking.) - * - */ - unsigned int alleleValue(unsigned int alleleIndex); - - - /// First allele of a given individual (no checking) - unsigned int firstAllele(unsigned int individualIndex) const; - - /// Second allele of a given individual (no checking) - unsigned int secondAllele(unsigned int individualIndex) const; - - /// Population label of a given individual (no checking) - unsigned int individualLabel(unsigned int individualIndex) const; - - - /** \brief Number of alleles - * - */ - unsigned int numberOfAlleles(); - - - /** \brief Number of populations - * - */ - unsigned int numberOfPopulations(); - - - /** \brief Number of loaded genotypes - * - */ - unsigned int numberOfGenotypes() const; - - - /** \brief Absolute total allele frequency - * - */ - unsigned int alleleFrequencyTotal(unsigned int alleleIndex); - - - /** \brief Absolute allele frequency in a population - * - */ - unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex); - - - /** \brief Absolute genotype frequency - * - * Note that allele AB is considered different to BA (this - * means that values can be accessed both sides of the - * diagonal. - * - */ - unsigned int genotypeFrequencyTotal(unsigned int alleleIndex1, unsigned int alleleIndex2); - - - /** \brief Absolute genotype frequency in a population - * - * Note that allele AB is considered different to BA (this - * means that values can be accessed both sides of the - * diagonal. - * - */ - unsigned int genotypeFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex1, unsigned int alleleIndex2); - - - /** \brief Sample size of a population - * - */ - unsigned int populationFrequency(unsigned int populationIndex); - - - /** \brief Weir-Cockerham F-statistic - * - * Note: equivalent to Fit. - * - */ - double F(); - - - /** \brief Weir-Cockerham theta-statistic - * - * Note: equivalent to Fst. - * - */ - double theta(); - - - /** \brief Weir-Cockerham f-statistic - * - * Note: equivalent to Fis. - * - */ - double f(); - - - /** \brief Between-population component of variance - * - */ - double Vpopulation(); - - - /** \brief Within-population, between-individual component of variance - * - */ - double Vindividual(); - - - /** \brief Within-individual component of variance - * - */ - double Vallele(); - - - protected: - - bool d_flag; - void d_init(); - void d_clear(); - unsigned int d_reserved; - unsigned int d_numberOfGenotypes; - unsigned int *d_genotypes; - unsigned int *d_populationLabels; - - bool s_flag; - void s_init(); - void s_clear(); - void s_compute(); - void processPopulations(); - void processAlleles(); - unsigned int getPopulationIndex(unsigned int) const; - unsigned int getAlleleIndex(unsigned int) const; - unsigned int s_numberOfAlleles; - unsigned int *s_alleleValueMapping; - unsigned int s_numberOfPopulations; - unsigned int *s_populationLabelMapping; - unsigned int *s_populationFrequencies; - unsigned int *s_alleleFrequenciesTotal; - unsigned int **s_alleleFrequenciesPerPopulation; - unsigned int **s_genotypeFrequenciesTotal; - unsigned int ***s_genotypeFrequenciesPerPopulation; - - bool w_flag; - void w_init(); - void w_clear(); - void w_compute(); - double w_F; - double w_T; - double w_f; - double *w_a; - double *w_b; - double *w_c; - double w_nbar; - double w_nc; - double *w_pbar; - double *w_ssquare; - double *w_hbar; - double w_sum_a; - double w_sum_b; - double w_sum_c; - double w_sum_abc; - double w_sum_bc; - - - private: - - FStatistics(const FStatistics& source) { } - - FStatistics& operator=(const FStatistics& source) { - return *this; - } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Fasta.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,278 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_FASTA_HPP -#define EGGLIB_FASTA_HPP - -#include <istream> -#include <iostream> -#include <string> -#include "Container.hpp" - -namespace egglib { - - /** \brief Fasta parser/formatted - * - * \ingroup core - * - * Reads a multifasta sequence file from a string, a stream or a file - * and returns a Container. See the description of the format below. - * Formats a fasta string from a sequence container object and places - * it in a string, a stream of a file. All methods are static and the - * class cannot be instantiated. The methods parsef and formatf will - * open the file for you while the others will read/write directly - * in a string. - * - * Specifications of the fasta format: - * - * - The number of sequences is not limited. - * - * - Each sequence is preceded by a header limited to a single - * line and starting by a ">" character. - * - * - The header length is not limited and all characters are - * allowed but white spaces and special characters are - * discouraged. - * - * - Group indices are specified by \@0, \@1, \@2... strings - * appearing at the end of the header string (just before the - * carriage return). Note that group labels are ignored by - * default. - * - * - Group indices are ignored unless specifically specified in a - * parser's options. - * - * - The sequence itself continues on following lines until the - * next ">" character or the end of the file. - * - * - White spaces, tab and carriage returns are allowed at any - * position There is no limitation in length and different - * sequences can have different lengths. - * - * - Although the standard is lower case characters, Fasta - * assumes upper case characters and only supports lower case - * characters (and converts them to upper case characters). - * Information coded by change in case is lost. - * - */ - class Fasta { - - public: - - /** \brief Imports a fasta file - * - * Imports the content of the file as is. Calls the method - * pase(std::istream*, bool) by creating its own istream. - * - * \param fname the name of a fasta file. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return A Container object containing the sequences. - * - */ - static Container parsef(const char* fname, bool importGroupLabels=false); - - - /** \brief Imports a fasta file - * - * Imports the content of the file as is. Calls the method - * pase(std::istream*, bool) by creating its own istream. This - * method expects a reference to a Container to which the - * sequences will be appended. - * - * \param fname the name of a fasta file. - * - * \param container a Container instance, empty or not. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return Nothings: the new sequences are appended to the - * Container passed as argument. - * - */ - static void parsef(const char* fname, Container& container, bool importGroupLabels=false); - - - /** \brief Imports a fasta file - * - * Imports the content of the file as is. Calls the method - * pase(std::istream*, bool) by creating its own istream. - * - * \param str a string containing the data. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return A Container object containing the sequences. - * - */ - static Container parse(const std::string& str, bool importGroupLabels=false); - - - /** \brief Imports a fasta file - * - * Imports the content of the file as is. Calls the method - * pase(std::istream*, bool) by creating its own istream. This - * method expects a reference to a Container to which the - * sequences will be appended. - * - * \param str a string containing the data. - * - * \param container a Container instance, empty or not. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return Nothing: new sequences are appended to the Container - * passed as argument. - * - */ - static void parse(const std::string& str, Container& container, bool importGroupLabels=false); - - - /** \brief Imports a fasta file from an open stream - * - * Imports the content of the file as is. - * - * \param stream an open stream (file or string) containing the - * data. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return A Container object containing the sequences. - * - */ - static Container parse(std::istream& stream, bool importGroupLabels=false); - - - /** \brief Imports a fasta file from an open stream - * - * Imports the content of the file as is. This - * method expects a reference to a Container to which the - * sequences will be appended. - * - * \param stream an open stream (file or string) containing the - * data. - * - * \param container a Container instance, empty or not. - * - * \param importGroupLabels if set to true, scan automatically - * for groups. The format is @ followed by an integer, placed - * at the end of the header string(sequences without labels - * will be treated as \@0). - * - * \return Nothing: the new sequences are appended to the - * Container passed as argument. - * - */ - static void parse(std::istream& stream, Container& container, bool importGroupLabels=false); - - - /** \brief Export sequences as fasta - * - * \param fname the name of the file where to place the result. - * - * \param container Container object to export. - * - * \param exportGroupLabels if set to true, exports group - * indices as a \@x at the end of the sequence name, where x is - * the group index. Otherwise, this information is discarded. - * - * \param lineLength the number of characters to place on a - * single line. If zero, no newlines are inserted within - * sequences. - * - */ - static void formatf(const char* fname, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); - - - /** \brief Export sequences as fasta - * - * \param file an open stream. - * - * \param container Container object to export. - * - * \param exportGroupLabels if set to true, exports group - * indices as a \@x at the end of the sequence name, where x is - * the group index. Otherwise, this information is discarded. - * - * \param lineLength the number of characters to place on a - * single line. If zero, no newlines are inserted within - * sequences. - * - */ - static void format(std::ostream& file, const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); - - - /** \brief Export sequences as fasta - * - * This medod creates internally an ostringstream, calls the - * method format(ostream, container, bool) and returns the - * resulting string. - * - * \param container Container object to export. - * - * \param exportGroupLabels if set to true, exports group - * indices as a \@x at the end of the sequence name, where x is - * the group index. Otherwise, this information is discarded. - * - * \param lineLength the number of characters to place on a - * single line. If zero, no newlines are inserted within - * sequences. - * - * \return The formatted string. - * - */ - static std::string format(const Container& container, bool exportGroupLabels=false, unsigned int lineLength=50); - - - - protected: - - /// This class cannot be instantiated - Fasta() { } - - /// This class cannot be instantiated - Fasta(const Fasta& source) { } - - /// This class cannot be or copied - Fasta& operator=(const Fasta& source) { return *this; } - - /// This class cannot be instantiated - virtual ~Fasta() { } - - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/HFStatistics.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,227 +0,0 @@ -/* - Copyright 2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_HFSTATISTICS_HPP -#define EGGLIB_HFSTATISTICS_HPP - - - -namespace egglib { - - - /** \brief Computes Fst and Fit from haploid data - * - * The class requires loading data. Data are loaded by haploid - * (one genotype per individual). The analyses are cached: they are - * performed upon the first call to statistics accessors. The cache - * is emptied whenever a datum is loaded. - * - * The computations are performed after Weir and Cockerham. The - * statistic theta is generalized for multiple alleles. To allow - * computation of multi-locus statistics, variance components are - * also available. The two components of the variance are T1 and T2 - * and theta is T1/T2 (from Weir 1996 "Genetic Data Analysis II", - * Sinauer associates, Sunderland MA). - * - * \ingroup polymorphism - * - */ - class HFStatistics { - - public: - - /** \brief Constructor - * - */ - HFStatistics(); - - - /** \brief Destructor - * - */ - virtual ~HFStatistics(); - - - /** \brief Reserve sufficient memory for a given number of - * individuals. - * - * This method makes the load function faster by allocating - * all required memory at once. - * - * \param numberOfIndividuals a strictly positive integer. - * - */ - void reserve(unsigned int numberOfIndividuals); - - - /** \brief Loads the data for one individual - * - * \param genotype an integer giving the allele. - * \param populationLabel an integer indication belonging to - * a population. - * - * Genotypes and population labels are not required to be - * consecutive (both are labels, not indices). They are - * internally mapped to indices (the mapping can be obtained - * by accessors populationLabel and allele). - * - * All genotypes are considered to be valid (no missing data). - * If statistics were computed previous to call to this - * function, all data will be erased. - * - */ - void loadIndividual(unsigned int genotype, unsigned int populationLabel); - - - /** \brief Label of a population - * - * The index corresponds to the local mapping of populations - * regardless of the ranking of population labels. (No out - * of bound checking.) - * - */ - unsigned int populationLabel(unsigned int populationIndex); - - - /** \brief Value of an allele - * - * The index corresponds to the local mapping of alleles - * regardless of the ranking of allele values. (No out of - * bound checking.) - * - */ - unsigned int alleleValue(unsigned int alleleIndex); - - - /// Allele of a given individual (no checking) - unsigned int allele(unsigned int individualIndex) const; - - /// Population label of a given individual (no checking) - unsigned int individualLabel(unsigned int individualIndex) const; - - - /** \brief Number of alleles - * - */ - unsigned int numberOfAlleles(); - - - /** \brief Number of populations - * - */ - unsigned int numberOfPopulations(); - - - /** \brief Number of loaded genotypes - * - */ - unsigned int numberOfGenotypes() const; - - - /** \brief Absolute total allele frequency - * - */ - unsigned int alleleFrequencyTotal(unsigned int alleleIndex); - - - /** \brief Absolute allele frequency in a population - * - */ - unsigned int alleleFrequencyPerPopulation(unsigned int populationIndex, unsigned int alleleIndex); - - - /** \brief Sample size of a population - * - */ - unsigned int populationFrequency(unsigned int populationIndex); - - - /** \brief Weir-Cockerham theta-statistic - * - * Note: equivalent to Fst. - * - */ - double theta(); - - - /** \brief Between-population component of variance - * - */ - double T1(); - - - /** \brief Total variance - * - */ - double T2(); - - - protected: - - bool d_flag; - void d_init(); - void d_clear(); - unsigned int d_reserved; - unsigned int d_numberOfGenotypes; - unsigned int *d_genotypes; - unsigned int *d_populationLabels; - - bool s_flag; - void s_init(); - void s_clear(); - void s_compute(); - void processPopulations(); - void processAlleles(); - unsigned int getPopulationIndex(unsigned int) const; - unsigned int getAlleleIndex(unsigned int) const; - unsigned int s_numberOfAlleles; - unsigned int *s_alleleValueMapping; - unsigned int s_numberOfPopulations; - unsigned int *s_populationLabelMapping; - unsigned int *s_populationFrequencies; - unsigned int *s_alleleFrequenciesTotal; - unsigned int **s_alleleFrequenciesPerPopulation; - - bool w_flag; - void w_init(); - void w_clear(); - void w_compute(); - double w_T; - double *w_T1; - double *w_T2; - double w_nbar; - double w_nc; - double *w_pbar; - double *w_ssquare; - double w_sum_T1; - double w_sum_T2; - - - private: - - HFStatistics(const HFStatistics& source) { } - - HFStatistics& operator=(const HFStatistics& source) { - return *this; - } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/HaplotypeDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,176 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_HAPLOTYPEDIVERSITY_HPP -#define EGGLIB_HAPLOTYPEDIVERSITY_HPP - -#include "BaseDiversity.hpp" - -namespace egglib { - - - /** \brief Computes diversity based on haplotype analysis - * - * \ingroup polymorphism - * - * This class relies on detection of polymorphic sites, as does - * NucleotideDiversity, with the exception that sites with missing - * data cannot be processed (minimumExploitableData is enforced to - * 1.). - * - * Like NucleotideDiversity, the same object can be used to analyze - * different data sets. Only the call to load() is required before - * accessing the data. - * - * Hst, Gst and Kst are between population differenciation indices. - * They are respectively defined in equations 2, 5-6 and 9 of Hudson - * et al. 1992a (Molecular Biology and Evolution 9:138-151). Also, - * Fst is defined in equation 3 of Hudson et al. 1992b (Genetics - * 132:583-589). Finally, Snn is from Hudson 2000 Genetics. It is - * computed as the average of Xi for all sequences. Where Xi is the - * ratio of nearest neighbours from the same group to the number of - * nearest neighbours. Nearest neigbours are all the sequences with - * the lowest number of differences to the focal sequence. NOTE: - * Gst/Hst are quite similar, but Fst and Kst are more different. Snn - * is a different statistic. Gst and Hst are two ways to estimate the - * between-population fraction of haplotypic diversity. - * - */ - class HaplotypeDiversity : public BaseDiversity { - - public: - - /** \brief Constructor - * - */ - HaplotypeDiversity(); - - /** \brief Destructor - * - */ - virtual ~HaplotypeDiversity(); - - /** \brief Identifies polymorphic sites and computes basis - * statistics - * - * \param data an alignment object (subclass of CharMatrix). - * The presence of outgroup or of different populations will - * be detected based on the populationLabel members of the - * passed object. The populationLabel 999 will be interpreted - * as outgroups. If several outgroups are passed, sites were - * the outgroups are not consistent will be treated as "non- - * orientable". - * - * \param allowMultipleMutations if true, sites with more - * than two alleles will not be ignored. The sum of the - * frequencies of all alleles not matching the outgroup will - * treated as the derived allele frequency (for orientable - * sites). - * - * \param ignoreFrequency removes sites that are polymorph - * because of an allele at absolute frequency smaller than or - * equal to this value. If ignoreFrequency=1, no sites are - * removed, if ignoreFrequency=1, singleton sites are - * ignored. Such sites are completely removed from the - * analysis (not counted in lseff). Note that if more than - * one mutation is allowed, the site is removed only if all - * the alleles but one are smaller than or equal to this - * value. For example, an alignment column AAAAAAGAAT is - * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is - * conserved (including the third allele T which is a - * singleton). - * - * \param characterMapping a string giving the list of - * characters that should be considered as valid data. If a - * space is present in the string, the characters left of the - * space will be treated as valid data and the characters - * right of the space will be treated as missing data, that - * is tolerated but ignored. All characters not in the string - * will cause an EggInvalidCharacterError to be raised. - * - */ - void load(CharMatrix& data, - bool allowMultipleMutations=false, - unsigned int ignoreFrequency=0, - std::string characterMapping=dnaMapping - ); - - /// Number of distinct haplotypes - unsigned int K() const; - - /// Haplotype diversity (unbiased) - double He() const; - - /** \brief Returns the allele number of a given sequence - * - * The passed index must be given ignoring any outgroup - * sequence. - * - */ - unsigned int haplotypeIndex(unsigned int) const; - - /// Population differenciation, based on nucleotides (Hudson 1992a) - double Kst() const; - - /// Population differenciation, based on nucleotides (Hudson 1992b) - double Fst() const; - - /// Population differenciation, based on haplotypes (Nei version) - double Gst() const; - - /// Population differenciation, based on haplotypes (Hudson et al. version) - double Hst() const; - - /// Hudson's Snn (nearest neighbor statistics) - double Snn() const; - - - protected: - - void init(); - void clear(); - - inline unsigned int diff(CharMatrix& data, unsigned int ind1, unsigned int ind2) const; - - bool m_loaded; - unsigned int m_K; - double m_He; - double m_Kst; - double m_Fst; - double m_Gst; - double m_Hst; - double m_Snn; - unsigned int *m_haplotypeIndex; - - - private: - - HaplotypeDiversity(const HaplotypeDiversity& source) { - - } - - HaplotypeDiversity& operator=(const HaplotypeDiversity& source) { - return *this; - } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/LinkageDisequilibrium.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,233 +0,0 @@ -/* - Copyright 2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_LINKAGEDISEQUILIBRUM_HPP -#define EGGLIB_LINKAGEDISEQUILIBRUM_HPP - - -#include "BaseDiversity.hpp" -#include "EggException.hpp" - - -namespace egglib { - - /** \brief Analyzes linkage disequilibrium per pair of polymorphic sites - * - * \ingroup polymorphism - * - * The class considers an alignment and detects polymorphic sites - * using the BaseDiversity functionality (shared with other classes - * of the module). Only sites with exactly two alleles are - * considered. Statistics of pairwise linkage disequilibrium can - * be accessed by pair index (note that out-of-range errors are not - * checked). Population labels are ignored (but outgroups are - * excluded from the analysis). - * - */ - class LinkageDisequilibrium : public BaseDiversity { - - public: - - /// Default constructor - LinkageDisequilibrium(); - - /// Destructor - virtual ~LinkageDisequilibrium(); - - /** \brief Analyzes polymorphic sites of an alignment - * - * \param data an alignment object (subclass of CharMatrix). - * The presence of outgroup or of different populations will - * be detected based on the populationLabel members of the - * passed object. The populationLabel 999 will be interpreted - * as outgroups. If several outgroups are passed, sites were - * the outgroups are not consistent will be treated as "non- - * orientable". - * - * \param minimumExploitableData site where the non-missing - * data (as defined by characterMapping) are at a frequency - * larger than this value will be removed from the analysis. - * Use 1. to take only 'complete' sites into account and 0. - * to use all sites. - * - * \param ignoreFrequency removes sites that are polymorphic - * because of an allele at absolute frequency smaller than or - * equal to this value. If ignoreFrequency=1, no sites are - * removed, if ignoreFrequency=1, singleton sites are - * ignored. Such sites are completely removed from the - * analysis (not counted in lseff). Note that if more than - * one mutation is allowed, the site is removed only if all - * the alleles but one are smaller than or equal to this - * value. For example, an alignment column AAAAAAGAAT is - * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is - * conserved (including the third allele T which is a - * singleton). - * - * \param characterMapping a string giving the list of - * characters that should be considered as valid data. If a - * space is present in the string, the characters left of the - * space will be treated as valid data and the characters - * right of the space will be treated as missing data, that - * is tolerated but ignored. All characters not in the string - * will cause an EggInvalidCharacterError to be raised. - */ - void load(CharMatrix& data, - double minimumExploitableData=1., - unsigned int ignoreFrequency=0, - std::string characterMapping=dnaMapping); - - - /// Number of pairs contained in the instance - unsigned int numberOfPairs() const; - - /// Alignment distance between a given pair - int d(unsigned int pair_index); - - /// D statistic for a given pair - double D(unsigned int pair_index); - - /// D' statistic for a given pair - double Dp(unsigned int pair_index); - - /// r statistic for a given pair - double r(unsigned int pair_index); - - /// r2 statistic for a given pair - double r2(unsigned int pair_index); - - /// position of the first site for a given pair - unsigned int site1(unsigned int pair_index); - - /// position of the second site for a given pair - unsigned int site2(unsigned int pair_index); - - /// correlation coefficient between r2 and distance - double correl() const; - - /** \brief Computes the minimal number of recombination events - * - * The computation is performed as described in Hudson, RR and - * NL Kaplan. 1985. Statistical properties of the number of - * recombination events in the history of a sample of DNA - * sequences. Genetics 111: 147-164. The returned parameter is - * the minimal number of recombination events, given by the - * number of non-overlapping pairs of segregating sites violating - * the rule of the four gamete. Only sites with two alleles are - * considered. Note that homoplasy (multiple mutations) mimicks - * recombination. The result of this function is not stored - * in this instance, and re-computed at each call. - * - * \param data the same CharMatrix instance as passed to the load - * method. The instance must not have been modified. - * - */ - unsigned int Rmin(CharMatrix& data) const; - - - - protected: - - // adds a pair of polymorphic sites - // assume position2>position1, - // sites are polymorphic with exactly 2 alleles - void add(CharMatrix& data, unsigned int position1, unsigned int position2); - - // Constructor help - void init(); - - // Destructor helper - void clear(); - - // Resizes arrays - void reset(); - - // Small helper - inline double min(double a, double b) { return (a>b)?a:b;} - - // Small helper - inline double max(double a, double b) { return (a>b)?b:a;} - - // Small helper - inline void check(unsigned int pos) { if (pos>=_n) throw EggRuntimeError("tried to access an invalid index"); } - - /* Performs correlation - * - * This function works independently from the rest of the class. - * - * \param n length of data arrays. - * \param x first data vector. - * \param y second data vector. - * \param r variable to receive the correlation coefficient. - * \param a variable to receive the regression slope. - */ - static void _correl(unsigned int n, const int* x, const double* y, double& r, double& a); - - // Distance between pairs - int* _d; - - // D (classical) measure of LD - double *_D; - - // D' - double *_Dp; - - // r, correlation coefficient - double *_r; - - // square r - double *_r2; - - // Data array (not managed by the instance) - unsigned int *_site1; - - // Data array (not managed by the instance) - unsigned int *_site2; - - // Number of pairs - unsigned int _n; - - private: - - /// Copy constructor not available - LinkageDisequilibrium(const LinkageDisequilibrium&) { } - - /// Assignment operator not available - LinkageDisequilibrium& operator=(const LinkageDisequilibrium&) { - return *this; - } - - - class Interval { - public: - Interval(unsigned int, unsigned int); - unsigned int a() const; - unsigned int b() const; - bool good() const; - void set_false(); - private: - unsigned int _a; - unsigned int _b; - unsigned int _good; - }; - - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/MicrosatelliteDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,120 +0,0 @@ -/* - Copyright 2008-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_MICROSATELLITEDIVERSITY_HPP -#define EGGLIB_MICROSATELLITEDIVERSITY_HPP - -#include "DataMatrix.hpp" -#include <cstdlib> - -namespace egglib { - - /** \brief Analyzes microsatellite data - * - * \ingroup polymorphism - * - * Use the load() method to analyze data. All sites will be analyzed - * and accessors allow to access the value of a given statistics for - * a given site. There is no out-of-bound checking implemented in - * accessors. - * - */ - class MicrosatelliteDiversity { - - public: - - /** \brief Creates an object - * - */ - MicrosatelliteDiversity(); - - - /** \brief Destroys an object - * - */ - virtual ~MicrosatelliteDiversity(); - - - /** \brief Performs the analysis - * - * \param dataMatrix the object to analyze. - * - * \param missingData the integer identifying missing data. - * - * \param noMissingData if true, no allele will be - * excluded (including the one identified by the argument - * missingData). - * - */ - void load(const DataMatrix& dataMatrix, - int missingData=999, bool noMissingData=false); - - - /// Number of sites (or markers) - unsigned int numberOfSites() const; - - /// Heterozygosity - double He(unsigned int siteIndex) const; - - /// Number of alleles - unsigned int numberOfAlleles(unsigned int siteIndex) const; - - /// Variance of allele size - double sizeVariance(unsigned int siteIndex) const; - - /// IAM-based estimator of theta - double thetaAssumingIAM(unsigned int siteIndex) const; - - /// SMM-based estimator of theta, calculated from He - double thetaAssumingSMMfromHe(unsigned int siteIndex) const; - - /// SMM-based estimator of theta, calculated from VarSize - double thetaAssumingSMMfromSizeVariance(unsigned int siteIndex) const; - - - protected: - - unsigned int v_numberOfSites; - double *v_He; - unsigned int *v_numberOfAlleles; - double *v_sizeVariance; - double *v_thetaAssumingIAM; - double *v_thetaAssumingSMMfromHe; - double *v_thetaAssumingSMMfromSizeVariance; - - void init(); - void clear(); - - - private: - - - /// No copy allowed - MicrosatelliteDiversity(const MicrosatelliteDiversity& source) { - } - - /// No copy allowed - MicrosatelliteDiversity& operator=(const MicrosatelliteDiversity& source) { - return *this; - } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Ms.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,199 +0,0 @@ -/* - Copyright 2008,2009,2011 Stéphane De Mita and Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_GMS_HPP -#define EGGLIB_GMS_HPP - -#include "DataMatrix.hpp" -#include <string> -#include <istream> - -namespace egglib { - - /** \brief ms-like sequence format parser - * - * The class provides parsing (input) and formatting (output) - * operations in ms format, that is the format used by Richard - * Hudson's program ms for outputting genotypes and by the - * associated program samplestat for reading them. Both types of - * operations are available through static methods using either - * a string or a stream (which can be a stream to or from a file - * or a string). In either case, types from the STL are used. - * Although ms deals only with data coded with 0 and 1, the class Ms - * offers the possibility of both importing and exporting data coded - * with by integer. All methods have an option named "separated". If - * this option is true, the parser or formatter introduces a slight - * modification of the format: genotypes individual data are - * separated by a white space ("1 0 1 1" instead of "1011", allowing - * genotype values larger than 9: "1 0 11 1"). - * - * \ingroup core - * - */ - class Ms { - - public: - - /** \brief Imports a sequence alignment - * - * Creates a istringstream from the string and calls the - * overloaded method. - * - * \param str the string to parse. - * \param ns the expected number of sequences. - * \param separated true if a white space separator is placed - * between genotype at each site. - * - * \return A sequence alignment as a data matrix. - */ - static DataMatrix get(std::string, unsigned int ns, bool separated=false); - - - /** \brief Imports a sequence alignment - * - * Attemps to generate a DataMatrix object from the stream. - * Reads only one simulation and throws a SeqlibFormatError - * exception in case of format error. - * - * Allows any number of white lines before the //, but no other - * data. Supports \r at the end of lines (before the \n). - * Accepted symbols are all integers (0-9). - * - * \param stream the stream to parse. - * \param ns the expected number of sequences. - * \param separated true if a white space separator is placed - * between genotype at each site. - * - * \return A sequence alignment as a data matrix. - */ - static DataMatrix get(std::istream& stream, unsigned int ns, bool separated=false); - - - /** \brief Exports a sequence alignment - * - * Internally creates a stringstream, calls the overloaded method - * and returns the outcome. - * - * \param dataMatrix the alignment object to write. - * \param separated true if a white space separator must be placed - * between the genotype at each site. - * - */ - static std::string format(DataMatrix& dataMatrix, bool separated=false); - - - /** \brief Exports a sequence alignment - * - * Writes the formatted string to the stream 'on the fly'. The - * formatted string is guaranteed to starts with a // line and - * ends with an empty line. The client is expected to take care - * of writing any header and add an additional white line between - * simulations if needed. The method throws a SeqlibRuntimeError - * if the stream is not writable. The data matrix should contain - * only data within range 0-9 if separated is false (default) and - * any positive (>=0) integer if separated is true. Note that - * output generated with separated=true is never compatible with - * the original ms format, and that output generated with - * separator=false is compatible with the original ms format only - * if all alleles are 0 or 1 (which is not checked by this - * formatted). - * - * \param stream the stream (file or string stream) where to - * write the output. - * \param dataMatrix the alignment object to write. - * \param separated true if a white space separator must be placed - * between the genotype at each site. - * - */ - static void format(std::ostream& stream, DataMatrix& dataMatrix, bool separated=false); - - - /** \brief Returns the last tMRCA read by any Ms instance - * - * If a tMRCA value was present in the last simulation read by - * any Ms instance, it will be returned by this method. A value - * of -1. is returned if no simulation was read, or if the last - * simulation didn't contain a tMRCA value or if the last - * simulation provoked an exception before reaching the tMRCA - * line. - * - */ - static double tMRCA(); - - - /** \brief Returns the last "prob" read by any Ms instance - * - * "prob" is returned by ms when a fixed number of segregating - * sites is used in conjunction with a theta value. If a "prob" - * value was present in the last simulation read by any Ms - * instance, it will be returned by this method. A value of -1 - * is returned if no simulation was read, or if the last - * simulation didn't contain a "prob" value or if the last - * simulation provoked an exception before reaching the "prob" - * line. - * - */ - static double prob(); - - - /** \brief Returns the tree string found in the last simulation read by any Ms instance - * - * If one or more trees were present in the last simulation read - * by any Ms instance, they will be returned as a unique string - * by this method. An empty string is returned if no simulation - * was read, or if the last simulation, or if the last simulation - * didn't contain any tree value or if the last simulation - * provoked an exception before reaching the tree line. - * - * Note: the trees are returned as a single line. - * - */ - static std::string trees(); - - - private: - // Line parser (the last \n is extracted and discarded - no error upon EOF) - std::string next_line(std::istream& stream); - - /// tMRCA (-1 if not found in ms output) - static double _tMRCA; - - /// probability (-1 if not found in ms output) - static double _prob; - - /// tree string (maybe contain several trees) (empty string if not found in ms output) - static std::string _trees; - - - /// No instantiation allowed - Ms() { } - - /// A fortiori no destruction allowed - ~Ms() { } - - /// No copy allowed - Ms(const Ms&) { } - - /// No copy allowed - Ms& operator=(const Ms&) { return *this; } - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Mutation.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_MUTATION_HPP -#define EGGLIB_MUTATION_HPP - -#include <vector> -#include "Edge.hpp" - -namespace egglib { - - /** \brief Very simple container of some information relative to a mutation - * - * \ingroup coalesce - * - */ - class Mutation { - - public: - - /// Default constructor - Mutation(); - - /// Age - //double age; - - /// Mutation index (for finding in Edge) - unsigned int actualSiteIndex; - - /// Position - double position; - - /// Segment index - unsigned int segmentIndex; - - /// Pointer to edge - //const Edge* edge; - - private: - - void init(); - - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Mutator.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,397 +0,0 @@ -/* - Copyright 2009, 2010, 2012 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_MUTATOR_HPP -#define EGGLIB_MUTATOR_HPP - - -#include "DataMatrix.hpp" -#include "Random.hpp" -#include "Arg.hpp" -#include "Mutation.hpp" - - -namespace egglib { - - - /** \brief Implements mutation models - * - * \ingroup coalesce - * - * Works with a previously built Ancestral Reconbination Graph. The - * user must sets options using the setter-based interface. After - * that he or she can call the method mute() that will generates - * a DataMatrix object. - * - * Genotype data are represented by integer numbers. Regardless of - * the mutation model, the ancestral state is always 0. The user can - * set the rate of mutation (or, alternatively, fix the number of - * mutations that occurred - which is the number of segregating sites - * only with an infinite site model). - * - * Other options fall into two separate groups: the positions of the - * mutated sites and the process of mutation (how new alleles are - * generated). - * - * Concerning allele generation, several mutation models are available - * (coded by single letters): - * - F: fixed number of alleles. Among other markers, this model is - * appropriate for simulating nucleotides. The user is able - * to choose the number of alleles (where 2 is the standard - * for an infinite site model and 4 for a finite site model). - * Mutator allows assigning independent weights between all - * different transition types and can draw randomly the - * ancestral states, providing a way to emulate evolution of - * nucleotides with multiple mutations at the same site and - * reversion. - * - I: infinite number of alleles. At a given site, each mutation - * raises a new allele. The value of the alleles is therefore - * irrelevant (it only denotes its order of appearance). This - * model does not permit homoplasy. - * - S: stepwise mutation model. In this model the value of the - * alleles are interpreted as a size (typically for simulating - * a microsatellite marker). Each mutation either increases - * or decreases the allele size by an increment of one. - * - T: two-phase mutation model. This model is a generalization - * of the stepwise mutation model (S). For a mutation, the - * increment (either increase or decrease) is 1 with the - * probability given by the parameter (1-TPMproba). With - * probability TPMproba, the increment is drawn from a - * geometric distribution of parameter given by the other - * parameter (TPMparam). - * - * By default, the program will assume an infinite site model (ISM). - * Each mutation will occur to a new position drawn from the interval - * [0,1]. It is possible to set any mutation model with an ISM - * (including microsatellite-like models I, S and T). Alternatively, - * the user can specify a finite number of sites available for - * mutation. For a microsatellite marker, the user will want to - * specify a single site. It is possible to set a finite number of - * sites for all mutation models. In all cases, the mutations will - * be forced to target these sites. It is possible to apply weights - * independently to all sites. The higher the weight value - * (comparatively to the other sites), the higher the probability - * that this site mutes. The weights needs not to be relative. In - * addition, the user can set the positions of the different sites. - * Nothings forces him or her to place them in order. Note that this - * does not affect the mutation process, but on the amount of - * recombination that will be allowed between sites. - * - */ - class Mutator { - - public: - - /** \brief Initializes with default values - * - * List of default values: - * - theta = 0 - * - fixedNumberOfMutations = 0 - * - model = F (fixed number of alleles) - * - fixed number of alleles = 2 - * - infinite site model - * - TPM parameters are both preset to 0.5 - * - */ - Mutator(); - - - /** \brief Destroys the object - * - */ - ~Mutator(); - - - /** \brief Copy constructor - * - */ - Mutator(const Mutator&); - - - /** \brief Assignement operator - * - */ - Mutator& operator=(const Mutator&); - - - /** \brief Restores default values of all parameters - * - */ - void reset(); - - - /** \brief Gets the fixed number of mutations - * - */ - unsigned int fixedNumberOfMutations() const; - - - /** \brief Sets the fixed number of mutations - * - * The value can be 0. It is not allowed to set both the - * fixed number of mutations and the mutation rate at - * non-zero value - * - */ - void fixedNumberOfMutations(unsigned int); - - - /** \brief Gets the mutation rate - * - */ - double mutationRate() const; - - - /** \brief Sets the mutation rate - * - * The value cannot be negative. The value can be 0. It is - * not allowed to set both the fixed number of mutations and - * the mutation rate at non-zero value - * - */ - void mutationRate(double); - - - /** \brief Gets the mutation model - * - * See the class documentation for the signification of the - * different one-letter codes. - * - */ - char mutationModel() const; - - - /** \brief Sets the mutation model - * - * The passed character must be one of F, I, S and T. See the - * class documentation for their signification. - * - */ - void mutationModel(char); - - - /** \brief Gets the fixed number of possible alleles - * - */ - unsigned int numberOfAlleles() const; - - - /** \brief Sets the fixed number of possible alleles - * - * The value must be larger than 1. This parameter is - * meaningful only for the fixed number allele model of - * mutation, and ignored otherwise. - * - */ - void numberOfAlleles(unsigned int); - - - /** \brief Sets a transition weight - * - * \param i row (previous allele index). - * \param j column (next allele index). - * \param value weight to apply. - * - * Indices i and j must be different. Weights can be any - * strictly positive value. - * - */ - void transitionWeight(unsigned int i, unsigned int j, double value); - - - /** \brief Gets a transition weight - * - * \param i row (previous allele index). - * \param j column (next allele index). - * - * Indices i and j must be different. - * - */ - double transitionWeight(unsigned int i, unsigned int j); - - - /** \brief Set to true to draw ancestral alleles randomly - * - * By default, the ancestral allele is always 0. If this - * variable is set to true, the ancestral allele will be - * randomly drawn from the defined number of alleles. This - * option is always ignored unless in combination with the - * Fixed Allele Number model. - * - */ - void randomAncestralAllele(bool flag); - - - /** \brief true if ancestral alleles must be drawn randomly - * - */ - bool randomAncestralAllele() const; - - - /** \brief Gets the TPM probability parameter - * - */ - double TPMproba() const; - - - /** \brief Sets the TPM probability parameter - * - * This parameter is considered only if the mutation model - * is T (two-phase mutation model). It gives the probability - * that a mutation step is not fixed to be 1. If TPMproba is - * 0, the mutation model is SMM. - * - * The value must be >=0. and <=1. - * - */ - void TPMproba(double value); - - - /** \brief Gets the TPM distribution parameter - * - */ - double TPMparam() const; - - - /** \brief Sets the TPM distribution parameter - * - * This parameter is considered only if the mutation model - * is T (two-phase mutation model). It gives the parameter - * of the geometric distribution which is used to generate - * the mutation step (if it is not one). - * - * The value must be >=0. and <=1. - * - */ - void TPMparam(double value); - - - /** \brief Gets the number of mutable sites - * - * A value a zero must be interpreted as the infinite site - * model. Note that after all calls all data from the tables - * sitePositions and siteWeights will be reset. - * - */ - unsigned int numberOfSites() const; - - - /** \brief Sets the number of mutable sites - * - * The value of zero is accepted and imposed the infinite - * site model. - * - */ - void numberOfSites(unsigned int); - - - /** \brief Gets the position of a given site - * - */ - double sitePosition(unsigned int siteIndex) const; - - - /** \brief Set the position of a given site - * - * The position must be >=0 and <=1 - * - */ - void sitePosition(unsigned int siteIndex, double position); - - - /** \brief Gets the mutation weight of a given site - * - */ - double siteWeight(unsigned int siteIndex) const; - - - /** \brief Set the site weight of a given site - * - * The weight must be strictly positive. - * - */ - void siteWeight(unsigned int siteIndex, double weight); - - - /** \brief Performs mutation - * - * \param arg Ancestral recombination graph instance. If the - * ARG is partially built or not a all, or improperly so, - * the behaviour of this method is not defined. - * - * \param random The address of a Random instance to be - * used for generating random numbers. - * - * \return A DataMatrix instance containing simulated data. - * - */ - DataMatrix mute(Arg* arg, Random* random); - - - /** \brief Gets the last number of mutations - * - * Returns the number of mutations of the last call of mute( ). - * By default, this method returns 0. - * - */ - unsigned int numberOfMutations() const; - - - private: - - void clear(); - void init(); - void copy(const Mutator&); - - //int nextAllele(int allele, Random* random); - int TPMstep(double inTPMproba, Random* random); - void apply_mutation(unsigned int matrixIndex, - unsigned int actualSite, DataMatrix& data, - const Edge* edge, int allele, - unsigned int segment, Random* random); - - - char _model; - double _mutationRate; - unsigned int _fixedNumberOfMutations; - unsigned int _numberOfAlleles; - double** _transitionWeights; - bool _randomAncestralAllele; - unsigned int _numberOfSites; - double* _sitePositions; - double* _siteWeights; - double _TPMproba; - double _TPMparam; - int maxAllele; - unsigned int _numberOfMutations; - std::vector<Mutation> _cache_mutations; - unsigned int _cache_mutations_reserved; - - }; - - - bool compare(Mutation mutation1, Mutation mutation2); // returns True if mutation1 is older - -} - - - - -#endif -
--- a/egglib/egglib-2.1.5/include/egglib-cpp/NucleotideDiversity.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,377 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_NUCLEOTIDEDIVERSITY_HPP -#define EGGLIB_NUCLEOTIDEDIVERSITY_HPP - - -#include "BaseDiversity.hpp" -#include <string> -#include <vector> - - - -namespace egglib { - - - /** \brief Performs analyzes of population genetics - * - * \ingroup polymorphism - * - * This class computes several summary statistics based on - * nucleotide analysis. Note that it is possible to use the same - * object to analyze different data set. Calling the load() method - * erases all data preivously computed (if any). Calling the load() - * method is absolutely required to compute any statistics. Some - * statistics are not computed by default, but are if the - * corresponding accessor is used (only load() is required). - * - * Note that "unsecure" accessors don't perform out-of-bound checks. - * - * S is the number of varying sites (only in sites that were not - * rejected). - * - * eta is the minimum number of mutations, that is the sum of the - * number of alleles minus 1 for each varying site. eta = S if all - * sites have no variant or 2 alleles. eta is computed independently - * of the option multiple and IS NOT computed over lseff sites. - * - * Pi is the average number of pairwise differences between sequences - * (expressed here per site) or (as computed here) the mean per site - * (unbiased) heterozygosity. Pi is zero if no polymorphic sites. - * - * D is the Tajima's test of neutrality - * Ref. Tajima F.: Statistical method for testing the neutral - * mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595. - * It is arbitrary set to 0 if no polymorphic sites. - * - * tW: thetaW: estimator of theta based on polymorphic sites (ref. - * e.g. Watterson 1975 Theor. Pop. Biol.). - * Both D and thetaW are computed assuming that rounded nseff samples - * have been sampled. - * The variance of D is computed using rounded nseff instead of ns. - * - * H is the Fay and Wu's test of neutrality. - * Z is the standardized version and E a similar test. - * Ref. Fay J. C., Wu C.-I.: Hitchhiking under positive Darwinian - * selection. Genetics 2000, 155:1405-1413. and Zeng K., Fu Y. X., - * Shi S., Wu C.-I.: Statistical tests for detecting positive - * selection by utilizing high-frequency variants. Genetics 2006, - * 174:1431-9. Both are arbitrary set to 0 if no polymorphic or - * orientable sites. - * - * tH and tL: theta H: estimators of theta based on derived - * polymorphic sites (ref in Fay and Wu and Zeng al.). The variance - * of H/Z are computed assuming that rounded nseff samples have - * been sampled. - * - */ - class NucleotideDiversity : public BaseDiversity { - - public: - - /** \brief Builds an object - * - */ - NucleotideDiversity(); - - - /** \brief Destroys an object - * - */ - virtual ~NucleotideDiversity(); - - - /** \brief Identifies polymorphic sites and computes basis - * statistics - * - * \param data an alignment object (subclass of CharMatrix). - * The presence of outgroup or of different populations will - * be detected based on the populationLabel members of the - * passed object. The populationLabel 999 will be interpreted - * as outgroups. If several outgroups are passed, sites were - * the outgroups are not consistent will be treated as "non- - * orientable". - * - * \param allowMultipleMutations if true, sites with more - * than two alleles will not be ignored. The sum of the - * frequencies of all alleles not matching the outgroup will - * treated as the derived allele frequency (for orientable - * sites). - * - * \param minimumExploitableData sites where the non-missing - * data (as defined by characterMapping) are at a frequency - * larger than this value will be removed from the analysis. - * Use 1. to take only 'complete' sites into account and 0. - * to use all sites. (The outgroup is not considered in this - * computation.) - * - * \param ignoreFrequency removes sites that are polymorph - * because of an allele at absolute frequency smaller than or - * equal to this value. If ignoreFrequency=1, no sites are - * removed, if ignoreFrequency=0, singleton sites are - * ignored. Such sites are completely removed from the - * analysis (not counted in lseff). Note that if more than - * one mutation is allowed, the site is removed only if all - * the alleles but one are smaller than or equal to this - * value. For example, an alignment column AAAAAAGAAT is - * ignored with an ignoreFrequency of 1, but AAAAAAGGAT is - * conserved (including the third allele T which is a - * singleton). - * - * \param characterMapping a string giving the list of - * characters that should be considered as valid data. If a - * space is present in the string, the characters left of the - * space will be treated as valid data and the characters - * right of the space will be treated as missing data, that - * is tolerated but ignored. All characters not in the string - * will cause an EggInvalidCharacterError to be raised. - * - * \param useZeroAsAncestral if true, all outgroups (if - * present) will be ignored and the character "0" will be - * considered as ancestral for all sites, whatever the - * character mapping. - * - */ - virtual void load( - CharMatrix& data, - bool allowMultipleMutations=false, - double minimumExploitableData=1., - unsigned int ignoreFrequency=0, - std::string characterMapping=dnaMapping, - bool useZeroAsAncestral=false - ); - - - // accessors for the "site analysis" section - - /// Number of polymorphic sites - unsigned int S() const; - - /// Number of polymorphic orientable sites - unsigned int So() const; - - /// Minimum number of mutations - unsigned int eta() const; - - /// Average of per-site number of sequences effectively used - double nseff() const; - - /// Number of sites effectively used - unsigned int lseff() const; - - /// Average of number of sequences effectively used at orientable sites - double nseffo() const; - - /// Number of orientable sites - unsigned int lseffo() const; - - /// Number of detected populations - unsigned int npop() const; - - /// Label of the population with given index (unsecure) - unsigned int popLabel(unsigned int popIndex) const; // no check! - - - // accessors for the "diversity" section - - /// Nucleotide diversity - double Pi(); - - /// Watterson estimator of theta - double thetaW(); - - /// Average of Pi over populations - double average_Pi(); - - /// Pi of a given population (unsecure) - double pop_Pi(unsigned int popIndex); // no check! - - /// Tajima's D - double D(); - - // accessors for the "outgroup diversity" section - - /// Fay and Wu estimator of theta - double thetaH(); - - /// Zeng et al. estimator of theta - double thetaL(); - - /// Fay and Wu's H - double H(); - - /// Standardized H - double Z(); - - /// Zeng et al.'s E - double E(); - - // accessors for the "differentiation" section - - /// Number of sites with at least one fixed difference - unsigned int FixedDifferences(); - - /// Number of sites with at least one allele shared among at least two populations - unsigned int CommonAlleles(); - - /// Number of sites with at least one non-fixed allele shared among at least two populations - unsigned int SharedAlleles(); - - /// Number of sites with at least one allele specific to one population - unsigned int SpecificAlleles(); - - /// Number of sites with at least one derived allele specific to one population - unsigned int SpecificDerivedAlleles(); - - /// Number of polymorphisms in a given population (unsecure) - unsigned int Polymorphisms(unsigned int pop); - - /// Number of specific alleles for a given population (unsecure) - unsigned int SpecificAlleles(unsigned int pop); - - /// Number of specific derived allele for a given population (unsecure) - unsigned int SpecificDerivedAlleles(unsigned int pop); - - /// Number of fixed differences between a given pair of populations (unsecure; pop2 must be larger than pop1) - unsigned int FixedDifferences(unsigned int pop1, unsigned int pop2); - - /// Number of common alleles between a given pair of populations (unsecure; pop2 must be larger than pop1) - unsigned int CommonAlleles(unsigned int pop1, unsigned int pop2); - - /// Number of shared non-fixed alleles between a given pair of populations (unsecure; pop2 must be larger than pop1) - unsigned int SharedAlleles(unsigned int pop1, unsigned int pop2); - - - // accessor for the "triConfigurations" section - - /** \brief Number falling into one of the possible site configurations - * - * The statistics are limited to three populations. - * Assuming an unrooted A/G polymorphism (A and G can be - * substitued), the site configurations are: - * - 0: A&G A A specific 1 - * - 1: A&G A G specific 1 + fixed 2-3 - * - 2: A A&G A specific 2 - * - 3: A A&G G specific 2 + fixed 1-3 - * - 4: A A A&G specific 3 - * - 5: A G A&G specific 3 + fixed 1-2 - * - 6: A&G A&G A shared 1-2 - * - 7: A&G A A&G shared 1-3 - * - 8: A A&G A&G shared 2-3 - * - 9: A&G A&G A&G shared 1-2-3 - * - 10: A G G fixed 1 - * - 11: A G A fixed 2 - * - 12: A A G fixed 3 - * - * \param index must be an index from 0 to 12. - * - */ - unsigned int triConfiguration(unsigned int index); - - - /// Builds and returns the vector of positions of all polymorphic sites - std::vector<unsigned int> polymorphic_positions() const; - - - /** \brief Builds and returns the vector of positions of all singleton sites - * - * A site singleton when it is polymorphic according to - * parameter of the diversity analysis, when it has exactly two - * alleles and one of them is at absolute frequency 1 (one - * copy) disregarding the outgroup. - * - */ - std::vector<unsigned int> singleton_positions() const; - - - protected: - - /** \brief This class cannot be copied - * - */ - NucleotideDiversity(const NucleotideDiversity& source) { } - - - /** \brief This class cannot be copied - * - */ - NucleotideDiversity& operator=(const NucleotideDiversity& source) { return *this; } - - - void init(); // initializes values - void clear(); // free memory but doesn't initializes - - // diversity (without outgroup) - void diversity(); - - // diversity with outgroup - void outgroupDiversity(); - - // site patterns - void differentiation(); - - // triconfigurations - void triConfigurations(); - - - // holders for statistics, with booleans flagging groups of stats - - bool b_analysisSites; - - bool b_diversity; - - double v_Pi; // nucleotide diversity - double v_thetaW; // theta (Watterson estimator) - double v_average_Pi; // average diversity across populations - double *v_pop_Pi; // diversity per population - double v_D; // Tajima's D - - bool b_outgroupDiversity; - - double v_thetaH; // theta (Fay and Wu estimator) - double v_thetaL; // theta (Zeng estimator) - double v_H; // Fay and Wu's H - double v_Z; // normalized Fay and Wu's H - double v_E; // Zeng et al.'s E - - bool b_differentiation; - - unsigned int *v_pairwiseFixedDifferences; - unsigned int *v_pairwiseCommonAlleles; - unsigned int *v_pairwiseSharedAlleles; - unsigned int *v_popPolymorphic; - unsigned int *v_popSpecific; - unsigned int *v_popSpecificDerived; - unsigned int v_countFixedDifferences; - unsigned int v_countCommonAlleles; - unsigned int v_countSharedAlleles; - unsigned int v_countSpecificAlleles; - unsigned int v_countSpecificDerivedAlleles; - - - bool b_triConfigurations; - - unsigned int *v_triConfigurations; - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,279 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_PARAMSET_HPP -#define EGGLIB_PARAMSET_HPP - - -#include "DataMatrix.hpp" - - -namespace egglib { - - class Change; - class Controller; - - - /** \brief Set of parameters - * - * \ingroup coalesce - * - */ - class ParamSet { - - public: - - /** \brief Default constructor - * - * Initializes all parameters to reasonnable values (except - * that the sample size is null: 1 population, 0 samples, - * selfing rate of 0, recombination rate of 0, growth rate of - * 0, population size of 1 and no changes. - * - */ - ParamSet(); - - /** \brief Destructor - * - */ - ~ParamSet(); - - /** \brief Copy constructor - * - */ - ParamSet(const ParamSet&); - - /** \brief Assignment operator - * - */ - ParamSet& operator=(const ParamSet&); - - /** \brief Restores default value of all parameters - * - */ - void reset(); - - /** \brief Gets the number of populations - * - */ - unsigned int numberOfPopulations() const; - - /** \brief Gets a pairwise migration rate - * - * It is allowed to access a diagonal value. Diagonal - * values contain the sum of values of the corresponding - * line (diagonal cell excepted, of course). - * - */ - double pairwiseMigrationRate(unsigned int source, unsigned int dest) const; - - /** \brief Sets a pairwise migration rate - * - * It is not allowed to set a value on the diagonal (this - * would raise an exception). The method takes care of - * modifying the diagonal accordingly (still this is not - * relevant for the client); - * - */ - void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value); - - /** \brief Sets the migration rate for all matrix - * - */ - void migrationRate(double value); - - /** \brief Gets a population size - * - */ - double populationSize(unsigned int populationIndex) const; - - /** \brief Sets a population size - * - * The size must be strictly positive. - * - */ - void populationSize(unsigned int populationIndex, double value); - - /** \brief Gets a growth rate - * - */ - double growthRate(unsigned int populationIndex) const; - - /** \brief Sets a growth rate - * - */ - void growthRate(unsigned int populationIndex, double value); - - /** \brief Gets the recombination rate - * - */ - double recombinationRate() const; - - /** \brief Sets the recombination rate - * - */ - void recombinationRate(double value); - - /** \brief Gets the number of recombining segments - * - */ - unsigned int numberOfSegments() const; - - /** \brief Sets the number of recombining segments - * - */ - void numberOfSegments(unsigned int value); - - /** \brief Gets the selfing rate - * - */ - double selfingRate() const; - - /** \brief Sets the selfing rate - * - */ - void selfingRate(double value); - - /** \brief Adds a population to the model - * - * \param migr pairwise migration rate between other - * population and the new one. - * - * The parameters for the new population are equivalent to - * the default parameters. - * - */ - void addPopulation(double migr); - - /** \brief Adds a change - * - * The change can be of any type derived from Change. A - * const Change* must be passed, so ParamSet will neither - * modify or delete the object itself. All passed Change - * object must be kept available for use by ParamSet. - * - */ - void addChange(const Change* change); - - /** \brief Gets the date of the next change - * - * Returns -1 if no change is planned. - * - */ - double nextChangeDate() const; - - /** \brief Applies the next change event - * - * \param controller the Change event might need to have - * access to simulation controller (to trigger coalescent - * events, for example). - * - */ - void nextChangeDo(Controller* controller); - - /** \brief Gets the number of single sample from a population - * - */ - unsigned int singles(unsigned int populationIndex) const; - - /** \brief Sets the number of single sample from a population - * - */ - void singles(unsigned int populationIndex, unsigned int value); - - /** \brief Gets the number of double sample from a population - * - */ - unsigned int doubles(unsigned int populationIndex) const; - - /** \brief Sets the number of double sample from a population - * - */ - void doubles(unsigned int populationIndex, unsigned int value); - - /** \brief Computes the total number of samples - * - */ - unsigned int numberOfSamples() const; - - /** \brief Gives the date of the last size change - * - * \param populationIndex the index of the population. - * \return The date where the last change occurred, or 0. if - * no change occurred during the simulation. - * - */ - double dateOfLastChange(unsigned int populationIndex) const; - - - /** \brief Sets the date of the last size change - * - * \param populationIndex the index of the population. - * \param date the date where the last change occurred, or 0. - * if no change occurred during the simulation. - * - */ - void dateOfLastChange(unsigned int populationIndex, double date) const; - - - /** \brief Set groups labels - * - * Sets the group labels of the DataMatrix, according to the - * current state of population structure, and assuming that - * the DataMatrix was generated by the class Arg. - * - * \param dataMatrix the DataMatrix object to modify. The - * number of sequences must match the total number of samples - * defined by the ParamSet object this method is called on. - * - * \param labelIndividuals by default, labels the different - * samples depending on the population they come from (0 - * being the label of the first population). If this flag is - * set to true, then the samples are labelled depending on - * the individual they come from, regardless of populations. - * In that case there can be only one or two genes for a - * given group label. - * - */ - void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false); - - private: - - void clear(); - void init(); - void copy(const ParamSet&); - - double _selfingRate; - double _recombinationRate; - unsigned int _numberOfSegments; - unsigned int _numberOfPopulations; - unsigned int* _singles; - unsigned int* _doubles; - double* _growthRates; - double* _populationSize; - double* _dateOfLastChange; - double** migrationMatrix; - unsigned int _numberOfChanges; - unsigned int nextChangeIndex; - Change const** changes; - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Population.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,143 +0,0 @@ -/* - Copyright 2009-2010 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_POPULATION_HPP -#define EGGLIB_POPULATION_HPP - - -#include "Edge.hpp" - -namespace egglib { - - class Random; - - /** \brief Handles a single population - * - * \ingroup coalesce - * - */ - class Population { - - public: - - /** \brief Default constructor - * - * Generates an empty population. - * - */ - Population(); - - /** \brief Copy constructor - * - */ - Population(const Population& source); - - /** \brief Assignment operator - * - */ - Population& operator=(const Population& source); - - /** \brief Destructor - * - * The object only cleans Edge objects currently stored in it. - * - */ - ~Population(); - - /** \brief Standard constructor - * - * The Edge instances will be handled by address and they - * MUST be passed using the method set(). - * - * \param numberOfSegments number of recombining segments. - * - * \param numberOfLineages the number of lineages contained - * in this population. - * - * \param firstIndex the absolute index (or ID) of the first - * lineage (the other will have consecutive incremented - * ID's). - * - */ - Population(unsigned int numberOfSegments, - unsigned int numberOfLineages, unsigned firstIndex); - - /** \brief Gets the number of lineages - * - */ - unsigned int numberOfLineages() const; - - /** \brief Gets the efficient number of lineages - * - * The number of lineages is multiplied by the number of - * covered segments of each lineages. - * - */ - unsigned int efficientNumberOfLineages() const; - - /** \brief Sets the Edge of a lineage - * - * \param index the index of the lineage within the - * population. - * \param edge the address of the Edge instance representing - * the lineage. - * - */ - void set(unsigned int index, Edge* edge); - - /** \brief Removes and returns a random lineage. - * - * \param random pointer to simulator's random generator - * instance. - * - */ - Edge* extractRandomly(Random* random); - - /** \brief Removes and returns a given lineage. - * - * \param index the relative index of the lineage. - * - */ - Edge* extractByIndex(unsigned int index); - - /** \brief Appends a lineage to the object - * - */ - void push(Edge* edge); - - /** \brief Gets coverage - * - */ - unsigned int coverage(unsigned int edgeIndex) const; - - - private: - - void copy(const Population& source); - void clear(); - Edge* pick(unsigned int index); - void init(); - unsigned int _numberOfLineages; - unsigned int _efficientNumberOfLineages; - Edge** lineages; - }; - -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Random.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -/* - Copyright 2008,2009,2012 Stéphane De Mita, Mathieu Siol - Adapted from MStrat, developed by Charles-Edouard Coste, - Thomas M. Bataillon, Mathieu Cotisson, Guy Decoux, Chistophe Rozale, - Daniel J. Schoen and Jacques L. David. - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_RANDOM_HPP -#define EGGLIB_RANDOM_HPP - -namespace egglib { - - /** \brief Pseudo-random number generator - * - * \ingroup core - * - * Random is a pseudo-random number generator, adapted from a part of MStrat, - * developed by Charles-Edouard Coste, Thomas M. Bataillon, Mathieu Cotisson, - * Guy Decoux, Chistophe Rozale, Daniel J. Schoen and Jacques L. David. - * - * It uses two different seeds. By default, they are initialized to available - * arbitrary values. However, a given sequence can be repeated by passing the - * same two seeds. - * - */ - class Random { - public: - /** \brief Initializes using default seeds - * - * Uses the current system time and the memory address of the object as an attempt to generate unique sequences. - */ - Random(); - - /** \brief Initializes using given seeds - * - * This constructor can be used to reproduce a given sequence. - */ - Random(double seed1, double seed2); - - /** \brief Draws a number from an exponential distribution - * - * \param expectation the distribution mean (also 1/lambda - * where lambda is the rate parameter). - * - */ - double erand(double expectation); - - /** \brief Draws an integer from a uniform distribution bound by 0 and max (max is not included) - * - * max is not included. - * - */ - unsigned int irand(unsigned int max); - - /** \brief Draws an integer from a Poisson distribution with parameter p - * - * The Poisson transformation algorithm was taken from (in French) - * http://www.u-picardie.fr/~cochard/IEM/demos/C107/C107_3.htm. - */ - unsigned int prand(double p); - - /** \brief Draws a number from a normal distribution of expectation 0 and variance 1 - * - * The algorithm used is the polar form of the Box-Muller - * algorithm. \todo use the Ziggurat algorithm for the - * nrand() method of Random. - * - */ - double nrand(); - - /** \brief Draws a number from a geometric law - * - * \param param the parameter of the law - * - */ - unsigned int grand(double); - - /** \brief Draws a number from a uniform distribution between 0 and 1 - * - */ - double uniform(); - - /** \brief Gets the current value of the first seed - * - */ - double seed1() const; - - /** \brief Gets the current value of the second seed - * - */ - double seed2() const; - - /** \brief Sets the current value of the first seed - * - */ - void seed1(double); - - /** \brief Sets the current value of the second seed - * - */ - void seed2(double); - - private: - // First seed - double _seed1; - - // Second seed - double _seed2; - - /* since the normal random generator draws two numbers at - * a time, one is cached and returned at any subsequent call - */ - bool b_ncached; - double v_ncached; - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/SitePolymorphism.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,207 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of the EggLib library. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - - -#ifndef EGGLIB_SITEPOLYMORPHISM_HPP -#define EGGLIB_SITEPOLYMORPHISM_HPP - - - -namespace egglib { - - - /** \brief Implements diversity analysis at the site level - * - * \ingroup polymorphism - * - * Data are loaded along with a population index. It is necessary to - * set the number of populations prior to use. - * - * Outgroup sequence must be loaded separetedly. There can be any - * number of outgroups, but they must be all consistent otherwise the - * site will be considered as not orientable. - * - */ - class SitePolymorphism { - - public: - - /** \brief Builds an object - * - */ - SitePolymorphism(); - - - /** \brief Builds an object - * - * \param npop number of populations - * - */ - SitePolymorphism(unsigned int npop); - - - /** \brief Destroys an object - * - */ - virtual ~SitePolymorphism(); - - - /** \brief Copy constructor - * - */ - SitePolymorphism(const SitePolymorphism& source); - - - /** \brief Assignment operator - * - */ - SitePolymorphism& operator=(const SitePolymorphism& source); - - - /** \brief Sets the number of populations - * - * NOTE THAT all previous data is lost. - * - */ - void numberOfPopulations(unsigned int npop); - - - /** \brief Adds a character - * - * \param populationIndex the index of the population from - * which is sampled this character (do not use "population - * label"). - * - * \param character the character value (it is assumed it - * represents a valid character. - * - */ - void load(unsigned int populationIndex, char character); - - - /** \brief Loads outgroup state - * - * There can be any number of outgroup states. Only - * characters that are considered as valid (whatever the list - * is) should be loaded. - * - */ - void outgroup(char state); - - - /** \brief Number of different alleles - * - */ - unsigned int numberOfAlleles() const; - - - /** \brief Gets an allele (unsecure) - * - * Assumes that the index provided lies in the valid range - * - */ - char allele(unsigned int index) const; - - - /** \brief Gets a frequency (unsecure) - * - * The sum of of frequencies of the allele over populations - * is computed. Not out-of-bounds check is performed. - * - */ - unsigned int alleleFrequency(unsigned int alleleIndex) const; - - - /** \brief Gets the frequency of an allele in one pop (unsecure) - * - * The frequency of the allele in the given population is - * returned. Not out-of-bounds check is performed. - * - */ - unsigned int alleleFrequency(unsigned int popIndex, unsigned int alleleIndex) const; - - - /** \brief Sums the frequency of derived allele(s) - * - * This method assumes that the site is orientable. It will - * use as outgroup the first outgroup character entered, - * assuming at least one was entered and that all (if more - * than one) were identical. - * - */ - unsigned int derivedAlleleFrequency() const; - - - /** \brief Number of sequences that were analyzed - * - */ - unsigned int ns() const; - - - /** \brief Gets the number of analyzed sequences for a population - * - * No out-of-bound check is performed - * - */ - unsigned int ns(unsigned int popIndex) const; - - - /** \brief Checks if the site can be oriented - * - * Returns true if at least one outgroup datum has been - * loaded, if all outgroup data are identical (regardless of - * their value) and if the outgroup allele is one of the - * allele in the sample. - * - */ - bool isOrientable() const; - - bool isPolymorphic(unsigned int popIndex) const; - bool hasSpecificAllele(unsigned int popIndex, bool restrictToDerived) const; - bool haveFixedDifference(unsigned int pop1, unsigned int pop2) const; - bool haveCommonAllele(unsigned int pop1, unsigned int pop2) const; - bool haveSharedAllele(unsigned int pop1, unsigned int pop2) const; - - - - - protected: - - // helpers - void init(); - void clear(); - void copy(const SitePolymorphism& site); - - - // data - unsigned int m_numberOfPopulations; - unsigned int m_numberOfStates; - char * m_states; - unsigned int ** m_frequencies; - unsigned int m_numberOfOutgroups; - char * m_outgroups; - unsigned int m_ns; - unsigned int * m_pop_ns; - - bool m_cache_orientable; - - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -/* - Copyright 2008-2009 Stéphane De Mita, Mathieu Siol - - This file is part of EggLib. - - EggLib is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - EggLib is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with EggLib. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef EGGLIB_STADEN_HPP -#define EGGLIB_STADEN_HPP - -#include <string> -#include <istream> -#include "Align.hpp" - -namespace egglib { - - /** \brief Parser of Staden output format - * - * \ingroup core - * - * The parser is available as a static method. It takes either a - * stream or a string containing data formatted by the program GAP4 - * of the Staden package (command 'dump contig to file'). - * - */ - class Staden { - - public: - - - /** \brief Parses a string - * - * \param string a string containing an alignment formatted - * by the program GAP4 of the Staden package. - * - * \param deleteConsensus if true, the sequence named - * "CONSENSUS" is deleted from the file (if it is present). - * - * \return An Align instance containing the data found in - * the Staden while, after recoding the character following - * the standard codes. - * - * This method opens a stream to the string and calls the - * overloaded method. - * - * The character replacement rules assume Staden default - * convention, as follows: - * - "-" codes for an unknown base and is replaced by "N". - * - "*" codes for an alignment gap and is replaced by "-". - * - A white space represents missing data and is replaced - * by "?". - * - */ - static Align parse(const std::string& string, bool deleteConsensus=true); - - - /** \brief Parses an open stream - * - * \param stream the open containing an alignment formatted - * by the program GAP4 of the Staden package. - * - * \param deleteConsensus if true, the sequence named - * "CONSENSUS" is deleted from the file (if it is present). - * - * \return An Align instance containing the data found in - * the Staden while, after recoding the character following - * the standard codes. - * - * The character replacement rules assume Staden default - * convention, as follows: - * - "-" codes for an unknown base and is replaced by "N". - * - "*" codes for an alignment gap and is replaced by "-". - * - A white space represents missing data and is replaced - * by "?". - * - */ - static Align parse(std::istream& stream, bool deleteConsensus=true); - - - private: - - /// Not allowed to instantiate this class - Staden() { } - - /// Not allowed to instantiate this class - Staden(const Staden& source) { } - - /// Not allowed to instantiate this class - ~Staden() { } - - - /* Gets the start position of sequences - * - * The functions gives total number of characters before the start of sequences - * and reads through until the next backspace (ignores the first line). - */ - static void getShift(); - - // Translates according to the Staden format - static char transforme(char); - - // Imports one sequence - static bool readOneSequence(); - - // Imports and concatenates one sequence - static bool readAppendOneSequence(); - - // Replaces dots by the matching character from CONSENSUS - static void undot(bool delete_consensus=true); - - // The number of characters before the start of sequences - static int shift; - - // The dynamically filled container (will result in an aligment) - static Container container; - - // The current position - static int currpos; - - // The reading stream - static std::istream* stream; - - // Stores unique 8 characters discriminating readings - static std::vector<std::string> ID; - }; -} - -#endif
--- a/egglib/egglib-2.1.5/include/egglib-cpp/config.h Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -/* config.h. Generated from config.h.in by configure. */ -/* config.h.in. Generated from configure.ac by autoheader. */ - -/* Define to 1 if you have the <inttypes.h> header file. */ -#define HAVE_INTTYPES_H 1 - -/* Define to 1 if you have the `bpp-core' library (-lbpp-core). */ -/* #undef HAVE_LIBBPP_CORE */ - -/* Define to 1 if you have the `bpp-seq' library (-lbpp-seq). */ -/* #undef HAVE_LIBBPP_SEQ */ - -/* Define to 1 if you have the <memory.h> header file. */ -#define HAVE_MEMORY_H 1 - -/* Define to 1 if you have the `sqrt' function. */ -/* #undef HAVE_SQRT */ - -/* Define to 1 if stdbool.h conforms to C99. */ -#define HAVE_STDBOOL_H 1 - -/* Define to 1 if you have the <stdint.h> header file. */ -#define HAVE_STDINT_H 1 - -/* Define to 1 if you have the <stdlib.h> header file. */ -#define HAVE_STDLIB_H 1 - -/* Define to 1 if you have the <strings.h> header file. */ -#define HAVE_STRINGS_H 1 - -/* Define to 1 if you have the <string.h> header file. */ -#define HAVE_STRING_H 1 - -/* Define to 1 if you have the <sys/stat.h> header file. */ -#define HAVE_SYS_STAT_H 1 - -/* Define to 1 if you have the <sys/types.h> header file. */ -#define HAVE_SYS_TYPES_H 1 - -/* Define to 1 if you have the <unistd.h> header file. */ -#define HAVE_UNISTD_H 1 - -/* Define to 1 if the system has the type `_Bool'. */ -#define HAVE__BOOL 1 - -/* Name of package */ -#define PACKAGE "egglib-cpp" - -/* Define to the address where bug reports for this package should be sent. */ -#define PACKAGE_BUGREPORT "demita@gmail.com" - -/* Define to the full name of this package. */ -#define PACKAGE_NAME "EggLib C++ library" - -/* Define to the full name and version of this package. */ -#define PACKAGE_STRING "EggLib C++ library 2.1.5" - -/* Define to the one symbol short name of this package. */ -#define PACKAGE_TARNAME "egglib-cpp" - -/* Define to the home page for this package. */ -#define PACKAGE_URL "" - -/* Define to the version of this package. */ -#define PACKAGE_VERSION "2.1.5" - -/* Define to 1 if you have the ANSI C header files. */ -#define STDC_HEADERS 1 - -/* Version number of package */ -#define VERSION "2.1.5" - -/* Define to `__inline__' or `__inline' if that's what the C compiler - calls it, or to nothing if 'inline' is not supported under any name. */ -#ifndef __cplusplus -/* #undef inline */ -#endif - -/* Define to `unsigned int' if <sys/types.h> does not define. */ -/* #undef size_t */
--- a/hapmap2mlmm/HapmapToMLMMFiles.pl Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -h, --hapmap <Hapmap input file> - -m, --map <Map output file> - -g, --geno <Genotype output file> - -p, --path <Path for transpose executable> -~; -$usage .= "\n"; - -my ($hapmap,$map,$geno,$path); - - -GetOptions( - "geno=s" => \$geno, - "map=s" => \$map, - "hapmap=s" => \$hapmap, - "path=s" => \$path, -); - - -die $usage - if ( !$geno || !$map || !$hapmap || !$path); - -my $TRANSPOSE_EXE = "$path/transpose.awk"; - -my @snps; -my %chrom_pos; -my $num_line = 0; -open(my $O,">geno_transposed"); -open(my $H,$hapmap); -while(<$H>) -{ - $num_line++; - my $line = $_; - chomp($line); - $line =~s/\r//g; - $line =~s/\n//g; - my @infos = split(/\t/,$line); - if ($num_line == 1) - { - print $O "Ind_id"; - for (my $i = 11; $i <= $#infos; $i++) - { - my $individual = $infos[$i]; - print $O " " . $individual; - } - print $O "\n"; - } - elsif ($num_line > 1) - { - my $snp = $infos[0]; - my $variation = $infos[1]; - my %scores; - if ($variation =~/(\w)\/(\w)/) - { - my $allele1 = $1; - my $allele2 = $2; - $scores{$allele1} = 0; - $scores{$allele2} = 1; - } - my $chrom = $infos[2]; - my $pos = $infos[3]; - $chrom_pos{$snp}{"chrom"} = $chrom; - $chrom_pos{$snp}{"pos"} = $pos; - push(@snps,$snp); - print $O "$snp"; - for (my $i = 11; $i <= $#infos; $i++) - { - my $genotype = $infos[$i]; - my @alleles = split("",$genotype); - if ($genotype ne "NN") - { - my $score = $scores{$alleles[0]} + $scores{$alleles[1]}; - print $O " $score"; - } - else - { - print $O " NA"; - } - } - print $O "\n"; - } -} -close($H); -close($O); - -open(my $M,">$map"); -print $M "SNP Chr Pos\n"; -foreach my $snp(@snps) -{ - print $M "$snp " . $chrom_pos{$snp}{"chrom"} . " ". $chrom_pos{$snp}{"pos"} . "\n"; -} -close($M); - -system("$TRANSPOSE_EXE geno_transposed >geno_transposed2"); - -open(my $F,">$geno"); -open(my $G,"geno_transposed2"); -while(<$G>) -{ - my $line = $_; - $line =~s/ /\t/g; - print $F $line; -} -close($G); -close($F); - -unlink("geno_transposed"); -unlink("geno_transposed2"); - -
--- a/hapmap2mlmm/HapmapToMLMMFiles.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -#!/bin/bash -hapmap=$1 -map=$2 -geno=$3 - -directory=`dirname $0` - -perl $directory/HapmapToMLMMFiles.pl -h $hapmap -g $geno -m $map -p $directory - - -
--- a/hapmap2mlmm/HapmapToMLMMFiles.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,158 +0,0 @@ -<tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> - <description>converts a hapmap file into MLMM input files</description> - <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot - </command> - <inputs> - <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> - </inputs> - <outputs> - <data format="txt" name="snp_info" label="SNP Info file"/> - <data format="txt" name="genot" label="Genotyping file for MLMM"/> - </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - <help> - - - - -.. class:: infomark - -**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform - - | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - -.. class:: infomark - -**Galaxy integration** South Green. - ---------------------------------------------------- - - -================= -HapmapToMLMMFiles -================= - ------------ -Description ------------ - - | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ====================== =========== -Name output file(s) format -=============== ====================== =========== -VCF to Hapmap Fasta alignment fasta -=============== ====================== =========== - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -MLMM -=========== ========================== ======= - - - ----------- -Input file ----------- - -Hapmap file - Allelic file in Hapmap format - - - ------------- -Output files ------------- - -SNP Info file - -Genotyping file for MLMM - - - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -Hapmap file ------------ - -:: - - rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 - SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA - SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA - - -Output files -============ - -SNP Info file -------------- - -:: - - SNP Chr Pos - SNP1 1 3102 - SNP2 1 4648 - SNP3 1 7601 - - -Genotyping file for MLMM ------------------------- - -:: - - Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14 - Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0 - Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- a/hapmap2mlmm/transpose.awk Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#!/usr/bin/gawk -f - -BEGIN { - max_x =0; - max_y =0; -} - -{ - max_y++; - for( i=1; i<=NF; i++ ) - { - if (i>max_x) max_x=i; - A[i,max_y] = $i; - } -} - -END { - for ( x=1; x<=max_x; x++ ) - { - for ( y=1; y<=max_y; y++ ) - { - if ( (x,y) in A ) printf "%s",A[x,y]; - if ( y!=max_y ) printf " "; - } - printf "\n"; - } -}
--- a/ped2bed/ped2bed.sh Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -#!/bin/bash -ped=$1 -map=$2 -bed=$3 -fam=$4 -bim=$5 -logs=$6 - -directory=`dirname $0` -mkdir tmpdir$$ -cp -rf $ped tmpdir$$/input.ped -cp -rf $map tmpdir$$/input.map - -plink --file tmpdir$$/input --out tmpdir$$/out --make-bed --noweb >>$logs 2>&1 - -mv tmpdir$$/out.bed $bed -mv tmpdir$$/out.fam $fam -mv tmpdir$$/out.bim $bim - -
--- a/ped2bed/ped2bed.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ -<tool id="ped2bed" name="plink: ped2bed" version="1.24"> - <description>Convert ped to bed</description> - <requirements> - <requirement type="package" version="1.07">plink</requirement> - </requirements> - <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs - </command> - <inputs> - <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/> - <param format="txt" name="map" type="data" label="Map file" help="Map file"/> - </inputs> - <outputs> - <data format="txt" name="bed" label="Bed file"/> - <data format="txt" name="fam" label="Fam file"/> - <data format="txt" name="bim" label="Bim file"/> - <data format="txt" name="logs" label="All Logs"/> - </outputs> - <!-- [STRONGLY RECOMMANDED] Exit code rules --> - <stdio> - <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> - <exit_code range="1:" level="fatal" /> - </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - <help> - - -.. class:: infomark - -**Authors** plink_ - -.. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ - - | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007. - -.. class:: infomark - -**Galaxy integration** South Green. - -.. class:: infomark - -**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). - - ---------------------------------------------------- - - - -======= -Ped2Bed -======= - ------------ -Description ------------ - - | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. - | For further informations, please visite the plink website_. - -.. _website: http://pngu.mgh.harvard.edu/purcell/plink/ - - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== =========== -Name output file(s) format -=============== ========================== =========== -VCFtools filter PED and map files ped and map -=============== ========================== =========== - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Admixture Bed, fam and bim file txt -=========== ========================== ======= - - ----------- -Input file ----------- - -PED file - Allelic file in PED format - -MAP file - - - ------------- -Output files ------------- - -Bed file - -Fam file - -Bim file - -All logs - Log file - - ------------- -Dependencies ------------- -plink - version 1.07 - ---------------------------------------------------- - ---------------- -Working example ---------------- - -Input files -=========== - -PED file --------- - -:: - - AZUCENA AZUCENA 0 0 0 0 G G A A C C T T T - BULUPANDAK BULUPANDAK 0 0 0 0 G G A A A A T - -MAP file --------- - -:: - - 0 Chr1:4299 0 4299 - 0 Chr1:26710 0 26710 - 0 Chr1:56184 0 56184 - 0 Chr1:93272 0 93272 - - -Output files -============ - -Bed file --------- - -:: - - binary file - -Fam file --------- - -:: - - AZUCENA AZUCENA 0 0 0 -9 - BULUPANDAK BULUPANDAK 0 0 0 -9 - -Bim file --------- - -:: - - 0 Chr1:4299 0 4299 A G - 0 Chr8:18058 0 18058 C T - - - </help> - <citations> - <!-- [HELP] As DOI or BibTex entry --> - <citation type="bibtex">@article{Dereeper03062015, -author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, -title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, -year = {2015}, -doi = {10.1093/nar/gkv351}, -abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, -URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, -eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, -journal = {Nucleic Acids Research} -} - - </citation> - - </citations> -</tool>
--- a/tool_dependencies.xml Fri Jul 10 04:39:30 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="plink" version="1.07"> - <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>