Mercurial > repos > miller-lab > snp_analysis_conversion
changeset 2:35c20b109be5
Retrying upload with "bare" tarball (i.e. one without a top containing directory).
| author | cathy |
|---|---|
| date | Tue, 28 May 2013 17:54:02 -0400 |
| parents | 1d8b23a21735 |
| children | edf12470a1a6 |
| files | dividePgSnpAlleles.pl dividePgSnpAlleles.xml gd_snp2vcf.pl gd_snp2vcf.xml master2gd_snp.pl master2gd_snp.xml master2pg.pl master2pg.xml pgSnp2gd_snp.pl pgSnp2gd_snp.xml test-data/dividePgSnp_input.pgSnp test-data/dividePgSnp_output.txt test-data/master2snp_output.txt test-data/masterVarTest.txt test-data/masterVar_output.txt test-data/pgSnp2snp_output.txt test-data/pgSnpTest.ref.txt test-data/sample.gd_snp test-data/snpsForSubmission.text test-data/snpsForSubmission.vcf test-data/vcf2pgSnp_input.vcf test-data/vcf2pgSnp_output.pgSnp vcf2pgSnp.pl vcf2pgSnp.xml vcf2pgSnpMult.pl |
| diffstat | 25 files changed, 27568 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dividePgSnpAlleles.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,44 @@ +#!/usr/bin/perl -w +use strict; + +#divide the alleles and their information into separate columns for pgSnp-like +#files. Keep any additional columns beyond the pgSnp ones. +#reads from stdin, writes to stdout +my $ref; +my $in; +if (@ARGV && $ARGV[0] =~ /-ref=(\d+)/) { + $ref = $1 -1; + if ($ref == -1) { undef $ref; } + shift @ARGV; +} +if (@ARGV) { + $in = shift @ARGV; +} + +open(FH, $in) or die "Couldn't open $in, $!\n"; +while (<FH>) { + chomp; + my @f = split(/\t/); + if ($f[0] =~ /^\d+$/ && $f[1] =~ /chr/) { #has bin column shift list + shift @f; #remove bin + } + my @a = split(/\//, $f[3]); + my @fr = split(/,/, $f[5]); + my @sc = split(/,/, $f[6]); + if ($f[4] == 1) { #homozygous add N, 0, 0 + if ($ref) { push(@a, $f[$ref]); } + else { push(@a, "N"); } + push(@fr, 0); + push(@sc, 0); + } + if ($f[4] > 2) { next; } #skip those with more than 2 alleles + print "$f[0]\t$f[1]\t$f[2]\t$a[0]\t$fr[0]\t$sc[0]\t$a[1]\t$fr[1]\t$sc[1]"; + if (scalar @f > 7) { + splice(@f, 0, 7); #remove first 7 + print "\t", join("\t", @f), "\n"; + }else { print "\n"; } +} +close FH; + +exit; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dividePgSnpAlleles.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,78 @@ +<tool id="dividePgSnp" name="Separate pgSnp Alleles" version="1.1.0" hidden="false"> + <description>: Split allele info into separate columns</description> + <command interpreter="perl"> + #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1 + #else #dividePgSnpAlleles.pl $input1 > $out_file1 + #end if + </command> + <inputs> + <param format="interval" name="input1" type="data" label="pgSnp dataset" /> + <conditional name="refcol"> + <param name="ref" type="select" label="Dataset has a column with the reference allele"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> + <when value="no"> <!-- do nothing --> + </when> + </conditional> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> + <tests> + <test> + <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' /> + <param name='refcol' value='no' /> + <output name="output" file="dividePgSnp_output.txt" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is of Galaxy datatype interval_, with the additional columns +required for pgSnp_ format. +Any further columns beyond those defined for pgSnp will be appended to the output. +The output dataset is in interval_ format. (`Dataset missing?`_) + +.. _interval: ./static/formatHelp.html#interval +.. _pgSnp: ./static/formatHelp.html#pgSnp +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This separates the alleles from a pgSnp dataset into separate columns, +and also the frequencies and scores that go with the alleles. It will skip +any positions with more than 2 alleles. If only a single allele is given then "N" +will be used for the second, with a frequency and score of zero. Or, if a +column with reference alleles is provided, +the value in that column will be used in place of the "N". + +----- + +**Example** + +- input pgSnp file:: + + chr1 256 257 A/C 2 3,4 10,20 + chr1 56100 56101 A 1 5 30 + chr1 77052 77053 A/G 2 6,7 40,50 + chr1 110904 110905 A 1 8 60 + etc. + +- output:: + + chr1 256 257 A 3 10 C 4 20 + chr1 56100 56101 A 5 30 N 0 0 + chr1 77052 77053 A 6 40 G 7 50 + chr1 110904 110905 A 8 60 N 0 0 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gd_snp2vcf.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,197 @@ +#!/usr/bin/perl -w +use strict; + +#convert from gd_snp file to vcf file (with dbSNP fields) + +#gd_snp table format: +#1. chr +#2. position (0 based) +#3. ref allele +#4. second allele +#5. overall quality +#foreach individual (6-9, 10-13, ...) +#a. count of allele in 3 +#b. count of allele in 4 +#c. genotype call (-1, or count of ref allele) +#d. quality of genotype call (quality of non-ref allele from masterVar) + +if (!@ARGV) { + print "usage: gd_snp2vcf.pl file.gd_snp[.gz|.bz2] -geno=8[,12:16,20...] -handle=HANDLE -batch=BATCHNAME -ref=REFERENCEID [-bioproj=XYZ -biosamp=ABC -pop=POPID[,POPID2...] -chrCol=9 -posCol=9 ] > snpsForSubmission.vcf\n"; + exit; +} + +my $in = shift @ARGV; +my $genoCols = ''; +my $handle; +my $batch; +my $bioproj; +my $biosamp; +my $ref; +my $pop; +my $cr = 0; #allow to use alternate reference? +my $cp = 1; +my $meta; +foreach (@ARGV) { + if (/-geno=([0-9,]+)/) { $genoCols .= "$1:"; } + elsif (/-handle=(.*)/) { $handle = $1; } + elsif (/-batch=(.*)/) { $batch = $1; } + elsif (/-bioproj=(.*)/) { $bioproj = $1; } + elsif (/-biosamp=(.*)/) { $biosamp = $1; } + elsif (/-ref=(.*)/) { $ref = $1; } + elsif (/-population=(\S+)/) { $pop = $1; } + elsif (/-chrCol=(\d+)/) { $cr = $1 - 1; } + elsif (/-posCol=(\d+)/) { $cp = $1 - 1; } + elsif (/-metaOut=(.*)/) { $meta = $1; } +} +if ($cr < 0 or $cp < 0) { die "ERROR the column numbers should be 1 based.\n"; } + +#remove trailing delimiters +$genoCols =~ s/,:/:/g; +$genoCols =~ s/[,:]$//; + +my @gnc = split(/,|:/, $genoCols); + +if ($in =~ /.gz$/) { + open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; +}elsif ($in =~ /.bz2$/) { + open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; +}else { + open(FH, $in) or die "Couldn't open $in, $!\n"; +} +my @head = prepHeader(); +if (@head) { + print join("\n", @head), "\n"; + #now column headers + print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"; + if (defined $pop) { + $pop =~ s/,$//; + my $t = $pop; + $t =~ s/,/\t/g; + print "\tFORMAT\t$t"; + } + print "\n"; +} +while (<FH>) { + chomp; + if (/^#/) { next; } + if (/^\s*$/) { next; } + my @f = split(/\t/); + #vcf columns: chrom pos id ref alt qual filter info + # info must have VRT=[0-9] 1==SNV 2=indel 6=NoVariation 8=MNV ... + my $vrt = 1; + if ($f[2] !~ /^[ACTG]$/ or $f[3] !~ /^[ACTG]$/) { + die "Sorry this can only do SNV's at this time\n"; + } + if (scalar @gnc == 1) { #single genotype column + if (!defined $f[4] or $f[4] == -1) { $f[4] = '.'; } + if ($f[$gnc[0]-1] == 2) { $vrt = 6; } #reference match + print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n"; + #TODO? put read counts in comment? + }elsif ($pop) { #do as population + my @cols; + foreach my $gp (split(/:/,$genoCols)) { #foreach population + my @g = split(/,/, $gp); + my $totChrom = 2*(scalar @g); + my $totRef = 0; + foreach my $i (@g) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; } + if ($totChrom == $totRef) { $vrt = 6; } + if ($totRef > $totChrom) { die "ERROR likely the wrong column was chosen for genotype\n"; } + my $altCnt = $totChrom - $totRef; + push(@cols, "$totChrom:$altCnt"); + } + print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\tNA:AC\t", join("\t", @cols), "\n"; + }else { #leave allele counts off + my $totChrom = 2*(scalar @gnc); + my $totRef = 0; + foreach my $i (@gnc) { if ($f[$i-1] == -1) { next; } $totRef += $f[$i-1]; } + if ($totChrom == $totRef) { $vrt = 6; } + print "$f[$cr]\t$f[$cp]\t$f[$cr];$f[$cp]\t$f[2]\t$f[3]\t$f[4]\t.\tVRT=$vrt\n"; + } +} +close FH or die "Couldn't close $in, $!\n"; + +if ($meta) { + open(FH, ">", $meta) or die "Couldn't open $meta, $!\n"; + print FH "TYPE: CONT\n", + "HANDLE: $handle\n", + "NAME: \n", + "FAX: \n", + "TEL: \n", + "EMAIL: \n", + "LAB: \n", + "INST: \n", + "ADDR: \n", + "||\n", + "TYPE: METHOD\n", + "HANDLE: $handle\n", + "ID: \n", + "METHOD_CLASS: Sequence\n", + "TEMPLATE_TYPE: \n", + "METHOD:\n", + "||\n"; + if ($pop) { + my @p = split(/,/, $pop); + foreach my $t (@p) { + print FH + "TYPE: POPULATION\n", + "HANDLE: $handle\n", + "ID: $t\n", + "POPULATION: \n", + "||\n"; + } + } + print FH "TYPE: SNPASSAY\n", + "HANDLE: $handle\n", + "BATCH: $batch\n", + "MOLTYPE: \n", + "METHOD: \n", + "ORGANISM: \n", + "||\n", + "TYPE: SNPPOPUSE | SNPINDUSE\n", + "HANDLE: $handle\n", + "BATCH: \n", + "METHOD: \n", + "||\n"; + + close FH or die "Couldn't close $meta, $!\n"; +} + +exit 0; + +#parse old header and add or create new +sub prepHeader { + my @h; + $h[0] = '##fileformat=VCFv4.1'; + my ($day, $mo, $yr) = (localtime)[3,4,5]; + $mo++; + $yr+=1900; + $h[1] = '##fileDate=' . "$yr$mo$day"; + $h[2] = "##handle=$handle"; + $h[3] = "##batch=$batch"; + my $i = 4; + if ($bioproj) { $h[$i] = "##bioproject_id=$bioproj"; $i++; } + if ($biosamp) { $h[$i] = "##biosample_id=$biosamp"; $i++; } + $h[$i] = "##reference=$ref"; ##reference=GCF_999999.99 + #$i++; + #$h[$i] = '##INFO=<ID=LID, Number=1,Type=string, Description="Unique local variation ID or name for display. The LID provided here combined with the handle must be unique for a particular submitter.">' + $i++; + $h[$i] = '##INFO=<ID=VRT,Number=1,Type=Integer,Description="Variation type,1 - SNV: single nucleotide variation,2 - DIV: deletion/insertion variation,3 - HETEROZYGOUS: variable, but undefined at nucleotide level,4 - STR: short tandem repeat (microsatellite) variation, 5 - NAMED: insertion/deletion variation of named repetitive element,6 - NO VARIATON: sequence scanned for variation, but none observed,7 - MIXED: cluster contains submissions from 2 or more allelic classes (not used) ,8 - MNV: multiple nucleotide variation with all eles of common length greater than 1,9 - Exception">'; + #sometimes have allele freqs? + if (defined $pop) { + $i++; + $h[$i] = "##FORMAT=<ID=NA,Number=1,Type=Integer,Description=\"Number of alleles for the population.\""; + $i++; + $h[$i] = '##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count for each alternate allele.">'; + my @p = split(/,/, $pop); + foreach my $t (@p) { + $i++; + $h[$i] = "##population_id=$t"; + } + } + #PMID? +##INFO=<ID=PMID,Number=.,Type=Integer,Description="PubMed ID linked to variation if available."> + + return @h; +} +####End +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gd_snp2vcf.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,141 @@ +<tool id="gd_snp2vcf" name="gd_snp to VCF" version="1.0.0" force_history_refresh="True"> + <description>: Convert from gd_snp to VCF format, for submission to dbSNP</description> + + <command interpreter="perl"> + gd_snp2vcf.pl "$input" -handle=$hand -batch=$batch -ref=$ref -metaOut=$output2 + #if $individuals.choice == '0' + #set $geno = '' + #for $individual_col in $input.dataset.metadata.individual_columns + ##need to check to number of cols per individual + #set $t = $individual_col + 2 + #set $geno += "%d," % ($t) + #end for + #if $individuals.pall_id != '' + -population=$individuals.pall_id + #end if + #else if $individuals.choice == '1' + #set $geno = '' + #set $pop = '' + #for $population in $individuals.populations + -geno=`perl -ane 'print \$F[0]+2, ",";' $population.p1_input` + #set $pop += "%s," % ($population.p1_id) + #end for + -population=$pop + #else if $individuals.choice == '2' + #set $geno = $individuals.geno + #end if + -geno=$geno + #if $bioproj.value != '' + -bioproj=$bioproj + #end if + #if $biosamp.value != '' + -biosamp=$biosamp + #end if + > $output + </command> + + <inputs> + <param name="input" type="data" format="gd_snp" label="SNP dataset" /> + <conditional name="individuals"> + <param name="choice" type="select" label="Generate dataset for"> + <option value="0" selected="true">All individuals</option> + <option value="1">Individuals in populations</option> + <option value="2">A single individual</option> + </param> + <when value="0"> + <param name="pall_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" /> + </when> + <when value="1"> + <repeat name="populations" title="Population" min="1"> + <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> + <param name="p1_id" type="text" size="20" label="ID for this population" help="Leaving this blank will omit allele counts from the output" /> + </repeat> + </when> + <when value="2"> + <param name="geno" type="data_column" data_ref="input" label="Column containing genotype" value="8" /> + </when> + </conditional> + <param name="hand" type="text" size="20" label="dbSNP handle" help="If you do not have a handle, request one at http://www.ncbi.nlm.nih.gov/projects/SNP/handle.html" /> + <param name="batch" type="text" size="20" label="Batch ID" help="ID used to tie dbSNP metadata to the VCF submission" /> + <param name="ref" type="text" size="20" label="Reference sequence ID" help="The RefSeq assembly accession.version on which the SNP positions are based (see http://www.ncbi.nlm.nih.gov/assembly/)" /> + <param name="bioproj" type="text" size="20" label="Optional: Registered BioProject ID" /> + <param name="biosamp" type="text" size="20" label="Optional: Comma-separated list of registered BioSample IDs" /> + </inputs> + + <outputs> + <data name="output" format="vcf" /> + <data name="output2" format="text" /> + </outputs> + + <tests> + <test> + <param name="input" value="sample.gd_snp" ftype="gd_snp" /> + <param name="choice" value="2" /> + <param name="geno" value="11" /> + <param name="hand" value="MyHandle" /> + <param name="batch" value="Test1" /> + <param name="ref" value="pb_000001.1" /> + <output name="output" file="snpsForSubmission.vcf" ftype="vcf" compare="diff" /> + <output name="output2" file="snpsForSubmission.text" ftype="text" compare="diff" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is in gd_snp_ format. +The output consists of two datasets needed for submitting SNPs: +a VCF_ file in the specific format required by dbSNP, and a partially +completed text_ file for the associated dbSNP metadata. +(`Dataset missing?`_) + +.. _gd_snp: ./static/formatHelp.html#gd_snp +.. _VCF: ./static/formatHelp.html#vcf +.. _text: ./static/formatHelp.html#text +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This tool converts a dataset in gd_snp format to a VCF file formatted +for submission to the dbSNP database at NCBI. It also creates a partially +filled-in template to assist you in preparing the required "metadata" file +describing the SNP submission. + +----- + +**Example** + +- input:: + + #{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist", + #"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"} + Contig161 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 + Contig48 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 + Contig20 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 + etc. + +- VCF output (for all individuals, and giving a population ID):: + + #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PB + Contig161 115 Contig161;115 C T 73.5 . VRT=6 NA:AC 8:0 + Contig48 11 Contig48;11 A G 94.3 . VRT=6 NA:AC 8:0 + Contig 66 Contig20;66 C T 54.0 . VRT=6 NA:AC 8:0 + etc. + +Note: This excerpt from the output does not show all of the headers. Also, +if the population ID had not been given, then the last two columns would not +appear in the output. + +----- + +**Reference** + +Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. +dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 +Jan 1;29(1):308-11. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/master2gd_snp.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,221 @@ +#!/usr/bin/perl -w +use strict; + +#convert from master variant file to snp table (Webb format?) +#new format for version 2.0, also different format for cancer normal pairs +#set columns for 2.0 version Cancer format +my $aCnt1 = 21; +my $aCnt2 = 22; + +#snp table format: +#1. chr +#2. position (0 based) +#3. ref allele +#4. second allele +#5. overall quality +#foreach individual (6-9, 10-13, ...) +#a. count of allele in 3 +#b. count of allele in 4 +#c. genotype call (-1, or count of ref allele) +#d. quality of genotype call (quality of non-ref allele from masterVar) + +if (!@ARGV) { + print "usage: master2gd_snp.pl masterVar.txt[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na ] > newSnpTable.txt\n"; + exit; +} + +my $in = shift @ARGV; +my $tab; +my $tabOnly; +my $build; +my $name; +foreach (@ARGV) { + if (/-tab=(.*)/) { $tab = $1; } + elsif (/-addColsOnly/) { $tabOnly = 1; } + elsif (/-build=(.*)/) { $build = $1; } + elsif (/-name=(.*)/) { $name = $1; } +} + +#WARNING loads snp table in memory, this could take > 1G ram +my %old; +my $colcnt = 0; +my @head; +if ($tab) { + open(FH, $tab) or die "Couldn't open $tab, $!\n"; + while (<FH>) { + chomp; + if (/^#/) { push(@head, $_); next; } + my @f = split(/\t/); + $old{"$f[0]:$f[1]"} = join("\t", @f); + $colcnt = scalar @f; + } + close FH or die "Couldn't close $tab, $!\n"; +} + +if ($in =~ /.gz$/) { + open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; +}elsif ($in =~ /.bz2$/) { + open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; +}else { + open(FH, $in) or die "Couldn't open $in, $!\n"; +} +prepHeader(); +if (@head) { #keep old header, add new? + print join("\n", @head), "\n"; +} +while (<FH>) { + chomp; + #FORMAT_VERSION 2.0 + if (/^#FORMAT_VERSION\s+1\./) { + $aCnt1 = 16; + $aCnt2 = 17; + } + if (/^#/) { next; } + if (/^>/) { next; } #headers + if (/^\s*$/) { next; } + my @f = split(/\t/); + if (!$f[6]) { next; } #WHAT? most likely still zipped? + if ($f[6] ne 'snp') { next; } #table only has substitutions + if ($f[5] eq 'het-alt') { next; } #skip heterozygous with no ref match + if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY? + my $a = $f[7]; #reference allele + my $a2; + my $freq; + my $freq2; + my $sc = -1; + my $alt; + my $g = 1; #genotype == ref allele count + if ($f[8] eq $f[9]) { #should be homozygous? + $a2 = $f[8]; + $g = 0; + if ($f[10] && $f[10] ne '') { $sc = $f[10]; }#is this the best one to use? or smallest? + }else { + if ($a ne $f[8]) { $a2 = $f[8]; $alt = 8; } + elsif ($a ne $f[9]) { $a2 = $f[9]; $alt = 9; } + } + if (defined $f[10] && defined $f[11] && $alt) { #VAF score in 2.0 format + if ($f[$alt+2] && $f[$alt+2] ne '') { $sc = $f[$alt+2]; } + } + #version 1.12 columns 16 & 17, version 2.0 Cancer columns 21 & 22 + if (defined $f[$aCnt1] && defined $f[$aCnt2] && $alt) { + if ($alt == 8) { + $freq = $f[$aCnt2]; + $freq2 = $f[$aCnt1]; + }elsif ($alt == 9) { + $freq = $f[$aCnt1]; + $freq2 = $f[$aCnt2]; + } + }elsif (defined $f[$aCnt1]) { + $freq = 0; + $freq2 = $f[$aCnt1]; + } + #if starting a new table or new SNP in old table + #add option to only build on current table? + if (!$tab) { + print "$f[2]\t$f[3]\t$a\t$a2\t-1"; + }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) { + print "$f[2]\t$f[3]\t$a\t$a2\t-1"; + }elsif (exists $old{"$f[2]:$f[3]"}) { + print $old{"$f[2]:$f[3]"}; + $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed + }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) { + next; #skip this one entirely + } + if ($colcnt && !exists $old{"$f[2]:$f[3]"}) { + #new SNP pad for missing individuals + my $i = 5; + while ($i < $colcnt) { + print "\t-1\t-1\t-1\t-1"; + $i += 4; + } + } + #add columns for individual + print "\t$freq\t$freq2\t$g\t$sc\n"; + }elsif ($f[5] eq 'hap') { + my $g = 0; + my $freq = 0; + my $freq2 = 0; + if (defined $f[10]) { $freq2 = $f[10]; } + my $sc = -1; + if (defined $f[$aCnt1] && $f[$aCnt1] ne '') { $sc = $f[$aCnt1]; } + if ($f[8]) { + if (!$tab) { + print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1"; + }elsif (!$tabOnly && !exists $old{"$f[2]:$f[3]"}) { + print "$f[2]\t$f[3]\t$f[7]\t$f[8]\t-1"; + }elsif (exists $old{"$f[2]:$f[3]"}) { + print $old{"$f[2]:$f[3]"}; + $old{"$f[2]:$f[3]"} = ''; #unset so we know it is printed + }elsif ($tabOnly && !exists $old{"$f[2]:$f[3]"}) { + next; #skip this one entirely + } + if ($colcnt && !exists $old{"$f[2]:$f[3]"}) { + #new SNP pad for missing individuals + my $i = 5; + while ($i < $colcnt) { + print "\t-1\t-1\t-1\t-1"; + $i += 4; + } + } + #add columns for individual + print "\t$freq\t$freq2\t$g\t$sc\n"; + } + } +} +close FH or die "Couldn't close $in, $!\n"; + +#if adding to a snp table, now we need to finish those not in the latest set +foreach my $k (keys %old) { + if ($old{$k} ne '') { #not printed yet + print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one + } +} + +exit; + +#parse old header and add or create new +sub prepHeader { + if (!$build) { $build = 'hg19'; } #set default + my @cnames; + my @ind; + my $n; + if (@head) { #parse previous header + my $h = join("", @head); #may split between lines + if ($h =~ /"column_names":\[(.*?)\]/) { + my @t = split(/,/, $1); + foreach (@t) { s/"//g; } + @cnames = @t; + $n = $cnames[$#cnames]; + $n =~ s/Q//; + $n++; + } + if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; } + if ($h =~ /"individuals":\[(.*)\]/) { + my $t = $1; + $t =~ s/\]\].*/]/; #remove if there is more categories + @ind = split(/,/, $t); + } + }else { #start new header + @cnames = ("chr", "pos", "A", "B", "Q"); + $n = 1; + } + #add current + if (!$name) { $name= 'na'; } + my $stcol = $colcnt + 1; + if ($stcol == 1) { $stcol = 6; } #move past initial columns + push(@ind, "[\"$name\",$stcol]"); + push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q"); + #reassign head + undef @head; + foreach (@cnames) { $_ = "\"$_\""; } #quote name + $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],"; + $head[1] = "#\"individuals\":[" . join(",", @ind) . "],"; + $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}"; +} +####End + +##example header +#{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","7A","7B","7G","7Q","8A","8B","8G", +#"8Q","9A","9B","9G","9Q","10A","10B","10G","10Q"],"dbkey":"hg19","individuals":[["Boh_15M",6],["Boh_19M",10],["Paya_27F",14],["Paya_2F",18],["Paya_32F",22],["Ruil_2M",26],["Ruil_36M",30],["Ruil_3M", +#34],["Ruil_40",38],["Ruil_47F",42]],"pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} +#chr1 10290 C T 46.4 0 2 0 7 1 2 0 4 3 2 1 22 0 0 -1 0 1 0 1 4 0 2 0 7 0 0 -1 0 2 3 1 14 0 1 0 4 1 1 1 6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/master2gd_snp.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,85 @@ +<tool id="master2gd_snp" name="MasterVar to gd_snp" version="1.1.0" hidden="false"> + <description>: Convert from MasterVar to gd_snp format</description> + <command interpreter="perl"> + #if $snptab.tab2 == "yes" + #if $snptab.colsOnly.value == "addColsOnly" #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly > $out_file1 + #else #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} > $out_file1 + #end if + #else #master2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} > $out_file1 + #end if + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Complete Genomics MasterVar dataset" /> + <conditional name="snptab"> + <param name="tab2" type="select" label="Append to gd_snp dataset in history"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> + <param name="colsOnly" type="select" label="Skip new SNPs"> + <option value="" selected="true">no</option> + <option value="addColsOnly">yes</option> + </param> + </when> + <when value="no"> <!-- do nothing --> + </when> + </conditional> + <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" /> + </inputs> + <outputs> + <data format="gd_snp" name="out_file1" /> + </outputs> + <tests> + <test> + <param name='input1' value='masterVarTest.txt' ftype='tab' /> + <param name='tab2' value='no' /> + <param name='indName' value='na' /> + <output name="output" file="master2snp_output.txt" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is in the MasterVar_ format provided by the Complete Genomics +analysis process (Galaxy considers this to be tabular_, but it must have the +columns specified for MasterVar). +The output dataset is in gd_snp_ format. (`Dataset missing?`_) + +.. _MasterVar: ./static/formatHelp.html#mastervar +.. _tabular: ./static/formatHelp.html#tab +.. _gd_snp: ./static/formatHelp.html#gd_snp +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This converts a Complete Genomics MasterVar file to gd_snp format, +so it can be used with the Genome Diversity tools. It can either +start a new dataset or append to an old one. When appending, if any new SNPs +appear only in the MasterVar file they can either be skipped or backfilled with +"-1" (unknown) for previous individuals/groups in the gd_snp dataset. +Positions homozygous for the reference allele are skipped. + +----- + +**Example** + +- input MasterVar file:: + + 934 2 chr1 41980 41981 hom snp A G G 76 97 dbsnp.86:rs806721 425 1 1 1 2 -170 ERVL-E-int:ERVL:47.4 2 1.17 N + 935 2 chr1 41981 42198 hom ref = = = -170 1.17 N + 1102 2 chr1 53205 53206 het-ref snp G C G 93 127 dbsnp.100:rs2854676 477 7 30 0 37 -127 2 1.17 N + etc. + +- output:: + + chr1 41980 A G -1 0 1 0 76 + chr1 53205 G C -1 30 7 1 93 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/master2pg.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,157 @@ +#!/usr/bin/perl -w +use strict; + +#convert from master variant file to pgSnp +my $snpsOnly = 1; #flag for if doing SNPs or indels +my $addRef = 0; #flag whether to append ref allele +if (@ARGV && $ARGV[0] eq 'indel') { shift @ARGV; $snpsOnly = 0; } +if (@ARGV && $ARGV[0] eq 'addRef') { shift @ARGV; $addRef = 1; } +if (!@ARGV) { + print STDERR "usage: master2pg.pl [indel addRef] infile.masterVar > outfile.pgSnp\n"; + exit; +} +my $in = shift @ARGV; +open(FH, $in) or die "Couldn't open input file $in, $!\n"; + +while (<FH>) { + chomp; + if (/^#/) { next; } + if (/^>/) { next; } #headers + if (/^\s*$/) { next; } + my @f = split(/\t/); + if (!$f[5]) { next; } #WHAT? most likely still zipped? + if ($f[5] =~ /(hom|het)/) { #zygosity #haploid chrX and chrY? + #only get snps for now + if ($snpsOnly && $f[6] eq 'snp') { #varType + my $a; + my $c = 2; + my $freq = 0; #set defaults + my $sc = 0; + if ($f[8] eq $f[9]) { #should be homozygous? + $a = $f[8]; + $c = 1; + }else { + $a = "$f[8]/$f[9]"; + $sc = "0,0"; #set defaults in case not included + $freq = '0,0'; + } + if (defined $f[10] && $f[10] eq '') { $f[10] = 0; } + if (defined $f[11] && $f[11] eq '') { $f[11] = 0; } + if (defined $f[10] && $c == 1) { + $sc = $f[10]; + }elsif (defined $f[10] && defined $f[11] && $c == 2) { + $sc = "$f[10],$f[11]"; + } + if (defined $f[16] && $f[16] eq '') { $f[16] = 0; } + if (defined $f[17] && $f[17] eq '') { $f[17] = 0; } + if (defined $f[16] && $c == 1) { + $freq = $f[16]; + }elsif (defined $f[16] && defined $f[17] && $c == 2) { + $freq = "$f[16],$f[17]"; + } + print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc"; + if ($addRef) { print "\t$f[7]\n"; } + else { print "\n"; } + }elsif (!$snpsOnly) { + if ($f[8] =~ /^\s*$/) { undef $f[8]; } + if ($f[9] =~ /^\s*$/) { undef $f[9]; } + my $a; + my $c = 2; + #do indels + if ($f[6] eq "ins") { + if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) { $a = $f[8]; $c = 1; } + elsif (defined $f[8] && defined $f[9] && $f[8] ne '?' && $f[9] ne '?') { + $a = "$f[8]/$f[9]"; + }elsif (!defined $f[8] && defined $f[9]) { + $a = "$f[9]/-"; + }elsif (defined $f[8] && !defined $f[9]) { + $a = "$f[8]/-"; + } + }elsif ($f[6] eq "del") { + if (!defined $f[8] && !defined $f[9]) { + $a = '-'; #homozygous deletion + $c = 1; + }elsif (!defined $f[8] && defined $f[9]) { + $a = "$f[9]/-"; + }elsif (defined $f[8] && !defined $f[9]) { + $a = "$f[8]/-"; + } + }elsif ($f[6] eq "sub") { #multiple nt substitutions + if ($f[8] eq $f[9]) { + $a = $f[8]; + $c = 1; + }else { + $a = "$f[8]/$f[9]"; + } + }elsif ($f[6] eq "complex") { #treat same as multi-nt sub + if ($f[5] =~ /het-alt/ && !defined $f[8]) { $f[8] = '-'; } + if ($f[5] =~ /het-alt/ && !defined $f[9]) { $f[9] = '-'; } + if (defined $f[8] && defined $f[9] && $f[8] eq $f[9]) { + $c = 1; + $a = $f[8]; + }elsif (defined $f[8] && defined $f[9]) { + $a = "$f[8]/$f[9]"; + } + } + my $sc = '0'; + my $freq = '0'; + if ($c == 2) { $sc = '0,0'; $freq = '0,0'; } + if (defined $f[10] && $f[10] eq '') { $f[10] = 0; } + if (defined $f[11] && $f[11] eq '') { $f[11] = 0; } + if (defined $f[10] && $c == 1) { + $sc = $f[10]; + }elsif (defined $f[10] && defined $f[11] && $c == 2) { + $sc = "$f[10],$f[11]"; + } + if (defined $f[16] && $f[16] eq '') { $f[16] = 0; } + if (defined $f[17] && $f[17] eq '') { $f[17] = 0; } + if (defined $f[16] && $c == 1) { + if ($f[16] eq '') { $f[16] = 0; } + $freq = $f[16]; + }elsif (defined $f[16] && defined $f[17] && $c == 2) { + $freq = "$f[16],$f[17]"; + } + if ($a) { + print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc"; + if ($addRef) { print "\t$f[7]\n"; } + else { print "\n"; } + } + } + }elsif ($f[5] eq 'hap' && $f[6] eq 'snp' && $snpsOnly) { + my $c = 1; + my $freq = '0'; + if (defined $f[10] && $f[10] ne '') { $freq = $f[10]; } + my $sc = '0'; + if (defined $f[16] && $f[16] ne '') { $sc = $f[16]; } + if ($f[8]) { + print "$f[2]\t$f[3]\t$f[4]\t$f[8]\t$c\t$freq\t$sc"; + if ($addRef) { print "\t$f[7]\n"; } + else { print "\n"; } + } + }elsif ($f[5] eq 'hap' && !$snpsOnly && $f[6] =~ /(del|ins|sub)/) { + if ($f[8] =~ /^\s*$/) { undef $f[8]; } + my $a; + my $c = 1; + #do indels + if ($f[6] eq "ins") { + $a = $f[8]; + }elsif ($f[6] eq "del") { + $a = '-'; #deletion + }elsif ($f[6] eq "sub") { #multiple nt substitutions + $a = $f[8]; + } + my $sc = '0'; + my $freq = '0'; + if (defined $f[10] && $f[10] ne '') { $sc = $f[10]; } + if (defined $f[16] && $f[16] ne '') { $freq = $f[16]; } + if ($a) { + print "$f[2]\t$f[3]\t$f[4]\t$a\t$c\t$freq\t$sc"; + if ($addRef) { print "\t$f[7]\n"; } + else { print "\n"; } + } + } +} + +close FH or die "Couldn't close $in, $!\n"; + +exit;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/master2pg.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,74 @@ +<tool id="master2pgSnp" name="MasterVar to pgSnp" version="1.1.0" hidden="false"> + <description>: Convert from MasterVar to pgSnp format</description> + <command interpreter="perl"> + master2pg.pl $indel $addRef $input1 > $out_file1 + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Complete Genomics MasterVar dataset" /> + <param name="indel" type="select" label="Convert indels"> + <option value="" selected="true">no</option> + <option value="indel">yes</option> + </param> + <param name="addRef" type="select" label="Add column with reference nt"> + <option value="" selected="true">no</option> + <option value="addRef">yes</option> + </param> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> + <tests> + <test> + <param name='input1' value='masterVarTest.txt' ftype='tab' /> + <param name='indel' value="" /> + <output name="output" file="masterVar_output.txt" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is in the MasterVar_ format provided by the Complete Genomics +analysis process (Galaxy considers this to be tabular_, but it must have the +columns specified for MasterVar). +The output dataset is in pgSnp_ format. (`Dataset missing?`_) + +.. _MasterVar: ./static/formatHelp.html#mastervar +.. _tabular: ./static/formatHelp.html#tab +.. _pgSnp: ./static/formatHelp.html#pgSnp +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This converts a Complete Genomics MasterVar file to pgSnp format, +so it can be viewed in genome browsers or used with the Phenotype Association +and Operate on Genomic Intervals tools. +Positions homozygous for the reference allele are skipped. +You can optionally add the reference nt as an extra column at the end. This +will make the file not work in genome browsers (the extra column could be +removed later) but will work with other Galaxy tools. + +----- + +**Example** + +- input MasterVar file:: + + 934 2 chr1 41980 41981 hom snp A G G 76 97 dbsnp.86:rs806721 425 1 1 1 2 -170 ERVL-E-int:ERVL:47.4 2 1.17 N + 935 2 chr1 41981 42198 hom ref = = = -170 1.17 N + 1102 2 chr1 53205 53206 het-ref snp G C G 93 127 dbsnp.100:rs2854676 477 7 30 0 37 -127 2 1.17 N + etc. + +- output:: + + chr1 41980 41981 G 1 1 76 + chr1 51672 51673 C 1 1 53 + chr1 52237 52238 G 1 7 63 + chr1 53205 53206 C/G 2 7,30 93,127 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pgSnp2gd_snp.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,208 @@ +#!/usr/bin/perl -w +use strict; + +#convert from pgSnp file to snp table (Webb format?) + +#snp table format: +#1. chr +#2. position (0 based) +#3. ref allele +#4. second allele +#5. overall quality +#foreach individual (6-9, 10-13, ...) +#a. count of allele in 3 +#b. count of allele in 4 +#c. genotype call (-1, or count of ref allele) +#d. quality of genotype call (quality of non-ref allele from masterVar) + +if (!@ARGV) { + print "usage: pgSnp2gd_snp.pl file.pgSnp[.gz|.bz2] [-tab=snpTable.txt -addColsOnly -build=hg19 -name=na -ref=#1based -chr=#1based ] > newSnpTable.txt\n"; + exit; +} + +my $in = shift @ARGV; +my $tab; +my $tabOnly; +my $build; +my $name; +my $ref; +my $binChr = 1; #position of chrom column, indicates if bin is added +foreach (@ARGV) { + if (/-tab=(.*)/) { $tab = $1; } + elsif (/-addColsOnly/) { $tabOnly = 1; } + elsif (/-build=(.*)/) { $build = $1; } + elsif (/-name=(.*)/) { $name = $1; } + elsif (/-ref=(\d+)/) { $ref = $1 - 1; } #go to index + elsif (/-chr=(\d+)/) { $binChr = $1; } +} + +if ($binChr == 2 && $ref) { $ref--; } #shift over by 1, we will delete bin +if ((!$tab or !$tabOnly) && !$ref) { + print "Error the reference allele must be in a column in the file if not just adding to a previous SNP table.\n"; + exit; +} + +#WARNING loads snp table in memory, this could take > 1G ram +my %old; +my $colcnt = 0; +my @head; +if ($tab) { + open(FH, $tab) or die "Couldn't open $tab, $!\n"; + while (<FH>) { + chomp; + if (/^#/) { push(@head, $_); next; } + my @f = split(/\t/); + $old{"$f[0]:$f[1]"} = join("\t", @f); + $colcnt = scalar @f; + } + close FH or die "Couldn't close $tab, $!\n"; +} + +if ($in =~ /.gz$/) { + open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; +}elsif ($in =~ /.bz2$/) { + open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; +}else { + open(FH, $in) or die "Couldn't open $in, $!\n"; +} +prepHeader(); +if (@head) { #keep old header, add new? + print join("\n", @head), "\n"; +} +while (<FH>) { + chomp; + if (/^#/) { next; } + if (/^\s*$/) { next; } + my @f = split(/\t/); + if ($binChr == 2) { #must have a bin column prepended on the beginning + shift @f; #delete it + } + if (!$f[3]) { next; } #WHAT? most likely still zipped? + if ($f[4] > 2) { next; } #can only do cases of 2 alleles + if ($f[2] == $f[1] or $f[2] - $f[1] != 1) { next; } #no indels + if ($f[3] =~ /-/) { next; } #no indels + #if creating a new table need the reference allele in a column + if (%old && $old{"$f[0]:$f[1]"}) { + my @o = split(/\t/, $old{"$f[0]:$f[1]"}); + my $freq = 0; + my $freq2 = 0; + my $sc; + my $g = 1; #genotype == ref allele count + if ($f[4] == 1) { #should be homozygous + if ($f[3] eq $o[2]) { $g = 2; $freq = $f[5]; } + elsif ($f[3] eq $o[3]) { $g = 0; $freq2 = $f[5]; } + else { next; } #doesn't match either allele, skip + $sc = $f[6]; + }else { + my $a = 0; #index of a alleles, freq, scores + my $b = 1; #same for b + my @all = split(/\//, $f[3]); + if ($o[2] ne $all[0] && $o[2] ne $all[1]) { next; } #must match one + if ($o[3] ne $all[0] && $o[3] ne $all[1]) { next; } + if ($o[2] eq $all[1]) { #switch indexes + $a = 1; + $b = 0; + } + my @fr = split(/,/, $f[5]); + $freq = $fr[$a]; + $freq2 = $fr[$b]; + my @s = split(/,/, $f[6]); + $sc = $s[$b]; + } + #print old + print $old{"$f[0]:$f[1]"}; + #add new columns + print "\t$freq\t$freq2\t$g\t$sc\n"; + $old{"$f[0]:$f[1]"} = ''; + }elsif (!$tabOnly) { #new table, or don't have this SNP + #need reference allele + if ($f[3] !~ /$f[$ref]/ && $f[4] == 2) { next; } #no reference allele + my $freq = 0; + my $freq2 = 0; + my $sc; + my $g = 1; #genotype == ref allele count + my $alt; + if ($f[4] == 1) { #should be homozygous + if ($f[3] eq $f[$ref]) { $g = 2; $freq = $f[5]; $alt = 'N'; } + else { $g = 0; $freq2 = $f[5]; $alt = $f[3]; } #matches alternate + $sc = $f[6]; + }else { + my $a = 0; #index of a alleles, freq, scores + my $b = 1; #same for b + my @all = split(/\//, $f[3]); + if ($f[$ref] ne $all[0] && $f[$ref] ne $all[1]) { next; } #must match one + if ($f[$ref] eq $all[1]) { #switch indexes + $a = 1; + $b = 0; + } + my @fr = split(/,/, $f[5]); + $freq = $fr[$a]; + $freq2 = $fr[$b]; + my @s = split(/,/, $f[6]); + $sc = $s[$b]; + $alt = $all[$b]; + } + #print initial columns + print "$f[0]\t$f[1]\t$f[$ref]\t$alt\t-1"; + #pad for other individuals if needed + my $i = 5; + while ($i < $colcnt) { + print "\t-1\t-1\t-1\t-1"; + $i += 4; + } + #add new columns + print "\t$freq\t$freq2\t$g\t$sc\n"; + } +} +close FH or die "Couldn't close $in, $!\n"; + +#if adding to a snp table, now we need to finish those not in the latest set +foreach my $k (keys %old) { + if ($old{$k} ne '') { #not printed yet + print $old{$k}, "\t-1\t-1\t-1\t-1\n"; #plus blank for this one + } +} + +exit; + +#parse old header and add or create new +sub prepHeader { + if (!$build) { $build = 'hg19'; } #set default + my @cnames; + my @ind; + my $n; + if (@head) { #parse previous header + my $h = join("", @head); #may split between lines + if ($h =~ /"column_names":\[(.*?)\]/) { + my @t = split(/,/, $1); + foreach (@t) { s/"//g; } + @cnames = @t; + $n = $cnames[$#cnames]; + $n =~ s/Q//; + $n++; + } + if ($h =~ /"dbkey":"(.*?)"/) { $build = $1; } + if ($h =~ /"individuals":\[(.*)\]/) { + my $t = $1; + $t =~ s/\]\].*/]/; #remove if there is more categories + @ind = split(/,/, $t); + } + }else { #start new header + @cnames = ("chr", "pos", "A", "B", "Q"); + $n = 1; + } + #add current + if (!$name) { $name= 'na'; } + my $stcol = $colcnt + 1; + if ($stcol == 1) { $stcol = 6; } #move past initial columns + push(@ind, "[\"$name\",$stcol]"); + push(@cnames, "${n}A", "${n}B", "${n}G", "${n}Q"); + #reassign head + undef @head; + foreach (@cnames) { $_ = "\"$_\""; } #quote name + $head[0] = "#{\"column_names\":[" . join(",", @cnames) . "],"; + $head[1] = "#\"individuals\":[" . join(",", @ind) . "],"; + $head[2] = "#\"dbkey\":\"$build\",\"pos\":2,\"rPos\":2,\"ref\":1,\"scaffold\":1,\"species\":\"$build\"}"; +} +####End +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pgSnp2gd_snp.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,97 @@ +<tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" version="1.1.0" hidden="false"> + <description>: Convert from pgSnp to gd_snp format</description> + <command interpreter="perl"> + #if $snptab.tab2 == "yes" + #if $snptab.needRef.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1 + #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.needRef.ref} -chr=${input1.metadata.chromCol} > $out_file1 + #end if + #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.ref} -chr=${input1.metadata.chromCol} > $out_file1 + #end if + </command> + <inputs> + <param format="interval" name="input1" type="data" label="pgSnp dataset" /> + <conditional name="snptab"> + <param name="tab2" type="select" label="Append to gd_snp dataset in history"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> + <conditional name="needRef"> + <param name="colsOnly" type="select" label="Skip new SNPs"> + <option value="no" selected="true">no</option> + <option value="addColsOnly">yes</option> + </param> + <when value="no"> + <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> + <when value="addColsOnly"> <!-- do nothing --> + </when> + </conditional> + </when> + <when value="no"> + <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> + </conditional> + <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" /> + </inputs> + <outputs> + <data format="gd_snp" name="out_file1" /> + </outputs> + <tests> + <test> + <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' /> + <param name='tab2' value='no' /> + <param name='ref' value='8' /> + <param name='indName' value='na' /> + <output name="output" file="pgSnp2snp_output.txt" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is of Galaxy datatype interval_, with the additional columns +required for pgSnp_ format. +Any further columns beyond those defined for pgSnp will be ignored. +The output dataset is in gd_snp_ format. (`Dataset missing?`_) + +.. _interval: ./static/formatHelp.html#interval +.. _pgSnp: ./static/formatHelp.html#pgSnp +.. _gd_snp: ./static/formatHelp.html#gd_snp +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This tool converts a pgSnp dataset to gd_snp format, either starting a new +dataset or appending to an old one. When appending, +if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or +backfilled with "-1" (meaning "unknown") for previous individuals/groups in the +input gd_snp dataset. +If any new SNPs are being added (either by creating a new dataset or by backfilling), +then an extra column with the reference allele must be supplied in the pgSnp dataset, +as shown in the example below. + +----- + +**Example** + +- input pgSnp file, with reference allele added:: + + chr1 1888681 1888682 C/T 2 4,3 0.8893,0.8453 T + chr1 3118325 3118326 T 1 8 0.8796 C + chr1 3211457 3211458 A/C 2 17,10 0.8610,0.8576 A + etc. + +- gd_snp output:: + + chr1 1888681 T C -1 3 4 1 0.8893 + chr1 3118325 C T -1 0 8 0 0.8796 + chr1 3211457 A C -1 17 10 1 0.8576 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dividePgSnp_input.pgSnp Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,10 @@ +chr1 256 257 A/C 2 4,5 0,0 +chr1 56100 56101 A 1 8 0 +chr1 77052 77053 A/G 2 3,5 0,0 +chr1 110904 110905 A 1 5 0 +chr1 160592 160593 G 1 3 0 +chr1 640353 640354 G 1 1 0 +chr1 695314 695315 A 1 7 0 +chr1 713681 713682 A 1 8 0 +chr1 713965 713966 A/G 2 3,2 0,0 +chr1 714056 714057 A/G 2 1,5 0,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dividePgSnp_output.txt Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,10 @@ +chr1 256 257 A 4 0 C 5 0 +chr1 56100 56101 A 8 0 N 0 0 +chr1 77052 77053 A 3 0 G 5 0 +chr1 110904 110905 A 5 0 N 0 0 +chr1 160592 160593 G 3 0 N 0 0 +chr1 640353 640354 G 1 0 N 0 0 +chr1 695314 695315 A 7 0 N 0 0 +chr1 713681 713682 A 8 0 N 0 0 +chr1 713965 713966 A 3 0 G 2 0 +chr1 714056 714057 A 1 0 G 5 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/master2snp_output.txt Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,30 @@ +#{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q"], +#"individuals":[["na",6]], +#"dbkey":"hg19","pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} +chr1 41980 A G -1 0 1 0 76 +chr1 51672 T C -1 0 1 0 53 +chr1 52237 T G -1 0 7 0 63 +chr1 53205 G C -1 30 7 1 93 +chr1 54042 C T -1 10 3 1 66 +chr1 54585 T C -1 19 9 1 94 +chr1 55163 C A -1 0 9 0 76 +chr1 55301 C T -1 19 15 1 87 +chr1 55321 C T -1 12 12 1 95 +chr1 55325 T C -1 11 12 1 95 +chr1 55925 T C -1 0 12 0 66 +chr1 57951 A C -1 0 2 0 72 +chr1 58210 A G -1 0 11 0 98 +chr1 59050 A G -1 21 6 1 66 +chr1 59343 C T -1 23 25 1 57 +chr1 59497 T C -1 15 12 1 74 +chr1 60828 C T -1 11 1 1 60 +chr1 61441 A G -1 0 8 0 23 +chr1 68305 C T -1 20 27 1 44 +chr1 68315 T C -1 20 27 1 44 +chr1 69452 G A -1 37 6 1 61 +chr1 69510 A G -1 0 3 0 123 +chr1 69551 G C -1 27 4 1 98 +chr1 69568 T C -1 29 3 1 98 +chr1 77461 G A -1 0 4 0 26 +chr1 82733 T C -1 17 18 1 42 +chr1 233472 C G -1 42 21 1 118
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masterVarTest.txt Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,5000 @@ +#ASSEMBLY_ID GS19026-1100-37-ASM +#CNV_WINDOW_WIDTH 2000 +#COSMIC COSMIC v48 +#DBSNP_BUILD dbSNP build 131 +#DGV_VERSION 9 +#FORMAT_VERSION 1.5 +#GENERATED_AT 2011-Feb-18 17:35:36.151072 +#GENERATED_BY cgatools +#GENE_ANNOTATIONS NCBI build 37.1 +#GENOME_REFERENCE NCBI build 37 +#MIRBASE_VERSION miRBase version 15 +#PFAM_DATE August 13, 2010 +#REPMASK_GENERATED_AT 2010-Dec-03 14:38 +#SAMPLE GS00392-DNA_F04 +#SEGDUP_GENERATED_AT 2010-Dec-01 13:40 +#SOFTWARE_VERSION 1.3.0 +#SRC_SOFTWARE_VERSION 1.10.0.26 +#TYPE VAR-OLPL + +>locus ploidy chromosome begin end zygosity varType reference allele1Seq allele2Seq allele1Score allele2Score allele1HapLink allele2HapLink xRef evidenceIntervalId allele1ReadCount allele2ReadCount neitherAlleleReadCount totalReadCount minReferenceScore allele1Gene allele2Gene miRBaseId repeatMasker segDupOverlap relativeCoverage calledPloidy +1 2 chr1 0 10000 no-call complex = ? ? -16 +2 2 chr1 10000 11093 no-call complex = ? ? -172 1.17 N +3 2 chr1 11093 11108 hom ref = = = 15 1.17 N +4 2 chr1 11108 11135 no-call complex = ? ? -15 1.17 N +5 2 chr1 11135 11145 hom ref = = = 13 1.17 N +6 2 chr1 11145 11170 no-call complex = ? ? -15 1.17 N +7 2 chr1 11170 11177 hom ref = = = 12 1.17 N +8 2 chr1 11177 11204 no-call complex = ? ? -111 1.17 N +9 2 chr1 11204 11214 hom ref = = = 17 1.17 N +10 2 chr1 11214 11236 no-call complex = ? ? -10 1.17 N +11 2 chr1 11236 11269 hom ref = = = 10 1.17 N +12 2 chr1 11269 11276 no-call complex = ? ? -82 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +13 2 chr1 11276 11287 hom ref = = = 16 1.17 N +14 2 chr1 11287 11321 no-call complex = ? ? -53 1.17 N +15 2 chr1 11321 11339 hom ref = = = 10 1.17 N +16 2 chr1 11339 11350 no-call complex = ? ? -22 1.17 N +17 2 chr1 11350 11364 hom ref = = = 17 1.17 N +18 2 chr1 11364 11395 no-call complex = ? ? -186 1.17 N +19 2 chr1 11395 11405 hom ref = = = 23 1.17 N +20 2 chr1 11405 11436 no-call complex = ? ? -93 1.17 N +21 2 chr1 11436 11453 hom ref = = = 49 1.17 N +22 2 chr1 11453 11481 no-call complex = ? ? -329 1.17 N +23 2 chr1 11481 11504 hom ref = = = 60 1.17 N +24 2 chr1 11504 11511 no-call complex = ? ? -215 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +25 2 chr1 11511 11527 hom ref = = = 88 1.17 N +26 2 chr1 11527 11579 no-call complex = ? ? -1562 1.17 N +27 2 chr1 11579 11637 hom ref = = = 86 1.17 N +28 2 chr1 11637 11677 no-call complex = ? ? -427 1.17 N +29 2 chr1 11677 11706 hom ref = = = 41 1.17 N +30 2 chr1 11706 11713 no-call complex = ? ? -44 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +31 2 chr1 11713 11777 hom ref = = = 21 1.17 N +32 2 chr1 11777 11816 no-call complex = ? ? -272 1.17 N +33 2 chr1 11816 11859 hom ref = = = 18 1.17 N +34 2 chr1 11859 11866 no-call complex = ? ? -288 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +35 2 chr1 11866 11903 hom ref = = = 76 1.17 N +36 2 chr1 11903 11925 no-call complex = ? ? -490 1.17 N +37 2 chr1 11925 11956 hom ref = = = 53 1.17 N +38 2 chr1 11956 11973 no-call complex = ? ? -166 1.17 N +39 2 chr1 11973 12006 hom ref = = = 41 1.17 N +40 2 chr1 12006 12052 no-call complex = ? ? -257 1.17 N +41 2 chr1 12052 12117 hom ref = = = -3 1.17 N +42 2 chr1 12117 12124 no-call complex = ? ? -165 100287102:XM_002342010.1:LOC100287102::::UTR5:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR5:UNKNOWN-INC 1.17 N +43 2 chr1 12124 12133 hom ref = = = 38 1.17 N +44 2 chr1 12133 12172 no-call complex = ? ? -212 1.17 N +45 2 chr1 12172 12186 hom ref = = = 87 1.17 N +46 2 chr1 12186 12217 no-call complex = ? ? -1410 1.17 N +47 2 chr1 12217 12237 hom ref = = = 64 1.17 N +48 2 chr1 12237 12244 no-call complex = ? ? -426 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 1.17 N +49 2 chr1 12244 12262 hom ref = = = 54 1.17 N +50 2 chr1 12262 12300 no-call complex = ? ? -185 1.17 N +51 2 chr1 12300 12313 hom ref = = = 11 1.17 N +52 2 chr1 12313 12359 no-call complex = ? ? -131 1.17 N +53 2 chr1 12359 12375 hom ref = = = 25 1.17 N +54 2 chr1 12375 12387 no-call complex = ? ? -206 1.17 N +55 2 chr1 12387 12395 hom ref = = = 37 1.17 N +56 2 chr1 12395 12426 no-call complex = ? ? -189 1.17 N +57 2 chr1 12426 12655 hom ref = = = 12 1.17 N +58 2 chr1 12655 12676 no-call complex = ? ? -135 1.17 N +59 2 chr1 12676 12746 hom ref = = = -2 1.17 N +60 2 chr1 12746 12758 no-call complex = ? ? -94 1.17 N +61 2 chr1 12758 12768 hom ref = = = 25 1.17 N +62 2 chr1 12768 12810 no-call complex = ? ? -446 1.17 N +63 2 chr1 12810 12850 hom ref = = = 42 1.17 N +64 2 chr1 12850 12858 no-call complex = ? ? -152 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 1.17 N +65 2 chr1 12858 12920 hom ref = = = 11 1.17 N +66 2 chr1 12920 12951 no-call complex = ? ? -31 1.17 N +67 2 chr1 12951 12978 hom ref = = = 75 1.17 N +68 2 chr1 12978 12998 no-call complex = ? ? -32 1.17 N +69 2 chr1 12998 13075 hom ref = = = 33 1.17 N +70 2 chr1 13075 13124 no-call complex = ? ? -109 1.17 N +71 2 chr1 13124 13172 hom ref = = = 25 1.17 N +72 2 chr1 13172 13182 no-call complex = ? ? -338 1.17 N +73 2 chr1 13182 13280 hom ref = = = 35 1.17 N +74 2 chr1 13280 13287 no-call complex = ? ? -104 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::INTRON:UNKNOWN-INC 1.17 N +75 2 chr1 13287 13297 hom ref = = = 41 1.17 N +76 2 chr1 13297 13338 no-call complex = ? ? -325 1.17 N +77 2 chr1 13338 13355 hom ref = = = 19 1.17 N +78 2 chr1 13355 13371 no-call complex = ? ? -287 1.17 N +79 2 chr1 13371 13414 hom ref = = = 23 1.17 N +80 2 chr1 13414 13432 no-call complex = ? ? -464 1.17 N +81 2 chr1 13432 13476 hom ref = = = 50 1.17 N +82 2 chr1 13476 13507 no-call complex = ? ? -83 1.17 N +83 2 chr1 13507 13609 hom ref = = = 14 1.17 N +84 2 chr1 13609 13616 no-call complex = ? ? -84 100287102:XM_002342010.1:LOC100287102::::CDS:UNKNOWN-VNC 100287102:XM_002342010.1:LOC100287102::::CDS:UNKNOWN-VNC 1.17 N +85 2 chr1 13616 13653 hom ref = = = 28 1.17 N +86 2 chr1 13653 13687 no-call complex = ? ? -379 1.17 N +87 2 chr1 13687 13773 hom ref = = = 22 1.17 N +88 2 chr1 13773 13802 no-call complex = ? ? -5 1.17 N +89 2 chr1 13802 13809 hom ref = = = 66 1.17 N +90 2 chr1 13809 13841 no-call complex = ? ? -274 1.17 N +91 2 chr1 13841 13858 hom ref = = = 48 1.17 N +92 2 chr1 13858 13865 no-call complex = ? ? -59 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 1.17 N +93 2 chr1 13865 13942 hom ref = = = 14 1.17 N +94 2 chr1 13942 13986 no-call complex = ? ? -711 1.17 N +95 2 chr1 13986 14111 hom ref = = = 9 1.17 N +96 2 chr1 14111 14118 no-call complex = ? ? -281 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 1.17 N +97 2 chr1 14118 14161 hom ref = = = 60 1.17 N +98 2 chr1 14161 14168 no-call complex = ? ? -5 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 1.17 N +99 2 chr1 14168 14193 hom ref = = = 58 1.17 N +100 2 chr1 14193 14218 no-call complex = ? ? -127 1.17 N +101 2 chr1 14218 14244 hom ref = = = 30 1.17 N +102 2 chr1 14244 14251 no-call complex = ? ? -115 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC 1.17 N +103 2 chr1 14251 14320 hom ref = = = 14 1.17 N +104 2 chr1 14320 14357 no-call complex = ? ? -349 1.17 N +105 2 chr1 14357 14394 hom ref = = = 53 1.17 N +106 2 chr1 14394 14403 no-call complex = ? ? 22 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC;653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 100287102:XM_002342010.1:LOC100287102::::UTR3:UNKNOWN-INC;653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +107 2 chr1 14403 14431 hom ref = = = 64 1.17 N +108 2 chr1 14431 14461 no-call complex = ? ? -250 1.17 N +109 2 chr1 14461 14509 hom ref = = = 14 1.17 N +110 2 chr1 14509 14553 no-call complex = ? ? -284 1.17 N +111 2 chr1 14553 14573 hom ref = = = -44 1.17 N +112 2 chr1 14573 14574 half ref A A N 121 121 -44 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 7 1.17 N +113 2 chr1 14574 14600 hom ref = = = -44 1.17 N +114 2 chr1 14600 14629 no-call complex = ? ? -81 1.17 N +115 2 chr1 14629 14649 hom ref = = = 38 1.17 N +116 2 chr1 14649 14676 no-call complex = ? ? -261 1.17 N +117 2 chr1 14676 14695 hom ref = = = 19 1.17 N +118 2 chr1 14695 14702 no-call complex = ? ? -76 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +119 2 chr1 14702 14811 hom ref = = = 23 1.17 N +120 2 chr1 14811 14857 no-call complex = ? ? -193 1.17 N +121 2 chr1 14857 14888 hom ref = = = 26 1.17 N +122 2 chr1 14888 14910 no-call complex = ? ? -354 1.17 N +123 2 chr1 14910 14926 hom ref = = = 107 1.17 N +124 2 chr1 14926 14940 no-call complex = ? ? -297 1.17 N +125 2 chr1 14940 15009 hom ref = = = 28 1.17 N +126 2 chr1 15009 15032 no-call complex = ? ? -256 1.17 N +127 2 chr1 15032 15041 hom ref = = = 56 1.17 N +128 2 chr1 15041 15056 no-call complex = ? ? -221 1.17 N +129 2 chr1 15056 15114 hom ref = = = 22 1.17 N +130 2 chr1 15114 15121 no-call complex = ? ? -402 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +131 2 chr1 15121 15185 hom ref = = = 49 1.17 N +132 2 chr1 15185 15214 no-call complex = ? ? -631 1.17 N +133 2 chr1 15214 15236 hom ref = = = 58 1.17 N +134 2 chr1 15236 15278 no-call complex = ? ? -543 1.17 N +135 2 chr1 15278 15326 hom ref = = = 18 1.17 N +136 2 chr1 15326 15355 no-call complex = ? ? -20 1.17 N +137 2 chr1 15355 15370 hom ref = = = 43 1.17 N +138 2 chr1 15370 15377 no-call complex = ? ? -4 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +139 2 chr1 15377 15421 hom ref = = = 44 1.17 N +140 2 chr1 15421 15454 no-call complex = ? ? -136 1.17 N +141 2 chr1 15454 15515 hom ref = = = 20 1.17 N +142 2 chr1 15515 15548 no-call complex = ? ? -113 1.17 N +143 2 chr1 15548 15588 hom ref = = = 21 1.17 N +144 2 chr1 15588 15598 no-call complex = ? ? -29 1.17 N +145 2 chr1 15598 15684 hom ref = = = 24 1.17 N +146 2 chr1 15684 15721 no-call complex = ? ? -173 1.17 N +147 2 chr1 15721 15765 hom ref = = = 12 1.17 N +148 2 chr1 15765 15780 no-call complex = ? ? -70 1.17 N +149 2 chr1 15780 15813 hom ref = = = 23 1.17 N +150 2 chr1 15813 15847 no-call complex = ? ? -163 1.17 N +151 2 chr1 15847 15865 hom ref = = = 17 1.17 N +152 2 chr1 15865 15873 no-call complex = ? ? 3 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +153 2 chr1 15873 15899 hom ref = = = 14 1.17 N +154 2 chr1 15899 15926 no-call complex = ? ? -101 1.17 N +155 2 chr1 15926 15952 hom ref = = = 20 1.17 N +156 2 chr1 15952 15959 no-call complex = ? ? -95 653635:NR_024540.1:WASH5P::::ACCEPTOR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::ACCEPTOR:UNKNOWN-INC 1.17 N +157 2 chr1 15959 15987 hom ref = = = 33 1.17 N +158 2 chr1 15987 16017 no-call complex = ? ? -374 1.17 N +159 2 chr1 16017 16054 hom ref = = = 34 1.17 N +160 2 chr1 16054 16071 no-call complex = ? ? -245 1.17 N +161 2 chr1 16071 16092 hom ref = = = 29 1.17 N +162 2 chr1 16092 16112 no-call complex = ? ? -665 1.17 N +163 2 chr1 16112 16137 hom ref = = = 30 1.17 N +164 2 chr1 16137 16144 no-call complex = ? ? -199 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +165 2 chr1 16144 16202 hom ref = = = 31 1.17 N +166 2 chr1 16202 16232 no-call complex = ? ? -434 1.17 N +167 2 chr1 16232 16283 hom ref = = = 35 1.17 N +168 2 chr1 16283 16316 no-call complex = ? ? -279 1.17 N +169 2 chr1 16316 16344 hom ref = = = 37 1.17 N +170 2 chr1 16344 16382 no-call complex = ? ? -1045 1.17 N +171 2 chr1 16382 16491 hom ref = = = 40 1.17 N +172 2 chr1 16491 16537 no-call complex = ? ? -687 1.17 N +173 2 chr1 16537 16567 hom ref = = = 21 1.17 N +174 2 chr1 16567 16597 no-call complex = ? ? -270 1.17 N +175 2 chr1 16597 16615 hom ref = = = 32 1.17 N +176 2 chr1 16615 16622 no-call complex = ? ? 5 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +177 2 chr1 16622 16666 hom ref = = = 14 1.17 N +178 2 chr1 16666 16707 no-call complex = ? ? -146 1.17 N +179 2 chr1 16707 16715 hom ref = = = 16 1.17 N +180 2 chr1 16715 16747 no-call complex = ? ? -200 1.17 N +181 2 chr1 16747 16797 hom ref = = = 45 1.17 N +182 2 chr1 16797 16826 no-call complex = ? ? -85 1.17 N +183 2 chr1 16826 16852 hom ref = = = 35 1.17 N +184 2 chr1 16852 16859 no-call complex = ? ? -13 653635:NR_024540.1:WASH5P::::SPAN3:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::SPAN3:UNKNOWN-INC 1.17 N +185 2 chr1 16859 16896 hom ref = = = 14 1.17 N +186 2 chr1 16896 16903 no-call complex = ? ? -41 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +187 2 chr1 16903 16959 hom ref = = = 25 1.17 N +188 2 chr1 16959 16981 no-call complex = ? ? -382 1.17 N +189 2 chr1 16981 16992 hom ref = = = 44 1.17 N +190 2 chr1 16992 17023 no-call complex = ? ? -200 1.17 N +191 2 chr1 17023 17217 hom ref = = = 27 1.17 N +192 2 chr1 17217 17225 no-call complex = ? ? -355 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +193 2 chr1 17225 17371 hom ref = = = -4 1.17 N +194 2 chr1 17371 17409 no-call complex = ? ? -256 1.17 N +195 2 chr1 17409 17447 hom ref = = = 42 1.17 N +196 2 chr1 17447 17454 no-call complex = ? ? -64 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +197 2 chr1 17454 17498 hom ref = = = 19 1.17 N +198 2 chr1 17498 17505 no-call complex = ? ? -158 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +199 2 chr1 17505 17534 hom ref = = = 69 1.17 N +200 2 chr1 17534 17566 no-call complex = ? ? -116 1.17 N +201 2 chr1 17566 17590 hom ref = = = 22 1.17 N +202 2 chr1 17590 17597 no-call complex = ? ? -26 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +203 2 chr1 17597 17657 hom ref = = = 33 1.17 N +204 2 chr1 17657 17698 no-call complex = ? ? -30 1.17 N +205 2 chr1 17698 17712 hom ref = = = 21 1.17 N +206 2 chr1 17712 17756 no-call complex = ? ? -171 1.17 N +207 2 chr1 17756 17761 hom ref = = = 41 1.17 N +208 2 chr1 17761 17768 no-call complex = ? ? -69 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +209 2 chr1 17768 17801 hom ref = = = 66 1.17 N +210 2 chr1 17801 17808 no-call complex = ? ? -64 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +211 2 chr1 17808 17839 hom ref = = = 39 1.17 N +212 2 chr1 17839 17846 no-call complex = ? ? 3 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +213 2 chr1 17846 17923 hom ref = = = -6 1.17 N +214 2 chr1 17923 17924 half ref C C N 85 85 109 110 -6 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 7 1.17 N +215 2 chr1 17924 17929 hom ref = = = -6 1.17 N +216 2 chr1 17929 17930 half ref G G N 85 85 109 110 8 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 7 1.17 N +217 2 chr1 17930 17934 hom ref = = = -15 1.17 N +218 2 chr1 17934 17934 half ref ? 25 0 109 110 -15 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 7 1.17 N +219 2 chr1 17934 17959 hom ref = = = -101 1.17 N +220 2 chr1 17959 17972 no-call complex = ? ? -184 1.17 N +221 2 chr1 17972 17995 hom ref = = = 26 1.17 N +222 2 chr1 17995 18033 no-call complex = ? ? -115 1.17 N +223 2 chr1 18033 18087 hom ref = = = 28 1.17 N +224 2 chr1 18087 18097 no-call complex = ? ? -264 1.17 N +225 2 chr1 18097 18139 hom ref = = = 46 1.17 N +226 2 chr1 18139 18167 no-call complex = ? ? -204 1.17 N +227 2 chr1 18167 18182 hom ref = = = 48 1.17 N +228 2 chr1 18182 18204 no-call complex = ? ? -444 1.17 N +229 2 chr1 18204 18220 hom ref = = = 22 1.17 N +230 2 chr1 18220 18259 no-call complex = ? ? -322 1.17 N +231 2 chr1 18259 18339 hom ref = = = 2 1.17 N +232 2 chr1 18339 18375 no-call complex = ? ? -244 1.17 N +233 2 chr1 18375 18414 hom ref = = = 53 1.17 N +234 2 chr1 18414 18425 no-call complex = ? ? -82 1.17 N +235 2 chr1 18425 18437 hom ref = = = 19 1.17 N +236 2 chr1 18437 18477 no-call complex = ? ? -53 1.17 N +237 2 chr1 18477 18495 hom ref = = = 11 1.17 N +238 2 chr1 18495 18502 no-call complex = ? ? -82 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +239 2 chr1 18502 18561 hom ref = = = 20 1.17 N +240 2 chr1 18561 18592 no-call complex = ? ? -264 1.17 N +241 2 chr1 18592 18627 hom ref = = = 37 1.17 N +242 2 chr1 18627 18665 no-call complex = ? ? -351 1.17 N +243 2 chr1 18665 18707 hom ref = = = 13 1.17 N +244 2 chr1 18707 18714 no-call complex = ? ? -243 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +245 2 chr1 18714 18729 hom ref = = = 15 1.17 N +246 2 chr1 18729 18765 no-call complex = ? ? -262 1.17 N +247 2 chr1 18765 18823 hom ref = = = 0 1.17 N +248 2 chr1 18823 18830 no-call complex = ? ? -84 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +249 2 chr1 18830 18842 hom ref = = = 15 1.17 N +250 2 chr1 18842 18884 no-call complex = ? ? -168 1.17 N +251 2 chr1 18884 18930 hom ref = = = 4 1.17 N +252 2 chr1 18930 18958 no-call complex = ? ? -146 1.17 N +253 2 chr1 18958 19000 hom ref = = = 23 1.17 N +254 2 chr1 19000 19008 no-call complex = ? ? -501 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +255 2 chr1 19008 19047 hom ref = = = 37 1.17 N +256 2 chr1 19047 19054 no-call complex = ? ? -85 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +257 2 chr1 19054 19129 hom ref = = = 20 1.17 N +258 2 chr1 19129 19136 no-call complex = ? ? -188 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +259 2 chr1 19136 19156 hom ref = = = 49 1.17 N +260 2 chr1 19156 19198 no-call complex = ? ? -33 1.17 N +261 2 chr1 19198 19213 hom ref = = = 15 1.17 N +262 2 chr1 19213 19220 no-call complex = ? ? -83 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +263 2 chr1 19220 19244 hom ref = = = 14 1.17 N +264 2 chr1 19244 19291 no-call complex = ? ? -95 1.17 N +265 2 chr1 19291 19302 hom ref = = = 27 1.17 N +266 2 chr1 19302 19352 no-call complex = ? ? -126 1.17 N +267 2 chr1 19352 19387 hom ref = = = 21 1.17 N +268 2 chr1 19387 19435 no-call complex = ? ? -297 1.17 N +269 2 chr1 19435 19579 hom ref = = = -22 1.17 N +270 2 chr1 19579 19604 no-call complex = ? ? -244 1.17 N +271 2 chr1 19604 19636 hom ref = = = 23 1.17 N +272 2 chr1 19636 19643 no-call complex = ? ? -118 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +273 2 chr1 19643 19768 hom ref = = = 12 1.17 N +274 2 chr1 19768 19791 no-call complex = ? ? -91 1.17 N +275 2 chr1 19791 19854 hom ref = = = 26 1.17 N +276 2 chr1 19854 19875 no-call complex = ? ? -569 1.17 N +277 2 chr1 19875 19914 hom ref = = = 30 1.17 N +278 2 chr1 19914 19928 no-call complex = ? ? -145 1.17 N +279 2 chr1 19928 20003 hom ref = = = 34 1.17 N +280 2 chr1 20003 20027 no-call complex = ? ? -84 1.17 N +281 2 chr1 20027 20040 hom ref = = = 62 1.17 N +282 2 chr1 20040 20053 no-call complex = ? ? -139 1.17 N +283 2 chr1 20053 20154 hom ref = = = 18 1.17 N +284 2 chr1 20154 20169 no-call complex = ? ? -375 1.17 N +285 2 chr1 20169 20187 hom ref = = = 19 1.17 N +286 2 chr1 20187 20230 no-call complex = ? ? -236 1.17 N +287 2 chr1 20230 20241 hom ref = = = 77 1.17 N +288 2 chr1 20241 20265 no-call complex = ? ? -224 1.17 N +289 2 chr1 20265 20300 hom ref = = = 22 1.17 N +290 2 chr1 20300 20325 no-call complex = ? ? -1402 1.17 N +291 2 chr1 20325 20463 hom ref = = = -39 1.17 N +292 2 chr1 20463 20470 no-call complex = ? ? -757 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +293 2 chr1 20470 20494 hom ref = = = 83 1.17 N +294 2 chr1 20494 20515 no-call complex = ? ? -545 1.17 N +295 2 chr1 20515 20543 hom ref = = = 75 1.17 N +296 2 chr1 20543 20555 no-call complex = ? ? -153 1.17 N +297 2 chr1 20555 20594 hom ref = = = -31 1.17 N +298 2 chr1 20594 20595 half ref A A N 32 120 -31 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC Plat_L3:CR1:36.5 5 1.17 N +299 2 chr1 20595 20707 hom ref = = = -33 1.17 N +300 2 chr1 20707 20732 no-call complex = ? ? -535 1.17 N +301 2 chr1 20732 20800 hom ref = = = 18 1.17 N +302 2 chr1 20800 20816 no-call complex = ? ? -227 1.17 N +303 2 chr1 20816 20858 hom ref = = = 16 1.17 N +304 2 chr1 20858 20869 no-call complex = ? ? -209 1.17 N +305 2 chr1 20869 20910 hom ref = = = 10 1.17 N +306 2 chr1 20910 20938 no-call complex = ? ? -442 1.17 N +307 2 chr1 20938 20956 hom ref = = = 48 1.17 N +308 2 chr1 20956 20963 no-call complex = ? ? -310 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +309 2 chr1 20963 21006 hom ref = = = 15 1.17 N +310 2 chr1 21006 21039 no-call complex = ? ? -182 1.17 N +311 2 chr1 21039 21045 hom ref = = = 29 1.17 N +312 2 chr1 21045 21052 no-call complex = ? ? -26 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +313 2 chr1 21052 21089 hom ref = = = 19 1.17 N +314 2 chr1 21089 21124 no-call complex = ? ? -321 1.17 N +315 2 chr1 21124 21148 hom ref = = = 17 1.17 N +316 2 chr1 21148 21183 no-call complex = ? ? -113 1.17 N +317 2 chr1 21183 21220 hom ref = = = 29 1.17 N +318 2 chr1 21220 21227 no-call complex = ? ? -209 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +319 2 chr1 21227 21302 hom ref = = = 19 1.17 N +320 2 chr1 21302 21355 no-call complex = ? ? -312 1.17 N +321 2 chr1 21355 21382 hom ref = = = 36 1.17 N +322 2 chr1 21382 21434 no-call complex = ? ? -109 1.17 N +323 2 chr1 21434 21460 hom ref = = = 38 1.17 N +324 2 chr1 21460 21483 no-call complex = ? ? -271 1.17 N +325 2 chr1 21483 21499 hom ref = = = 43 1.17 N +326 2 chr1 21499 21518 no-call complex = ? ? -386 1.17 N +327 2 chr1 21518 21558 hom ref = = = 53 1.17 N +328 2 chr1 21558 21586 no-call complex = ? ? -91 1.17 N +329 2 chr1 21586 21711 hom ref = = = 14 1.17 N +330 2 chr1 21711 21718 no-call complex = ? ? -72 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +331 2 chr1 21718 21759 hom ref = = = 21 1.17 N +332 2 chr1 21759 21799 no-call complex = ? ? -452 1.17 N +333 2 chr1 21799 21836 hom ref = = = 26 1.17 N +334 2 chr1 21836 21877 no-call complex = ? ? -451 1.17 N +335 2 chr1 21877 21987 hom ref = = = 26 1.17 N +336 2 chr1 21987 22028 no-call complex = ? ? -588 1.17 N +337 2 chr1 22028 22065 hom ref = = = 37 1.17 N +338 2 chr1 22065 22073 no-call complex = ? ? -385 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +339 2 chr1 22073 22085 hom ref = = = 47 1.17 N +340 2 chr1 22085 22117 no-call complex = ? ? -460 1.17 N +341 2 chr1 22117 22153 hom ref = = = 14 1.17 N +342 2 chr1 22153 22181 no-call complex = ? ? -75 1.17 N +343 2 chr1 22181 22191 hom ref = = = 12 1.17 N +344 2 chr1 22191 22198 no-call complex = ? ? -134 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +345 2 chr1 22198 22214 hom ref = = = 23 1.17 N +346 2 chr1 22214 22252 no-call complex = ? ? -92 1.17 N +347 2 chr1 22252 22295 hom ref = = = 11 1.17 N +348 2 chr1 22295 22312 no-call complex = ? ? -215 1.17 N +349 2 chr1 22312 22346 hom ref = = = 56 1.17 N +350 2 chr1 22346 22353 no-call complex = ? ? -34 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +351 2 chr1 22353 22371 hom ref = = = 47 1.17 N +352 2 chr1 22371 22414 no-call complex = ? ? -88 1.17 N +353 2 chr1 22414 22463 hom ref = = = 34 1.17 N +354 2 chr1 22463 22497 no-call complex = ? ? -226 1.17 N +355 2 chr1 22497 22525 hom ref = = = 32 1.17 N +356 2 chr1 22525 22536 no-call complex = ? ? -274 1.17 N +357 2 chr1 22536 22650 hom ref = = = 15 1.17 N +358 2 chr1 22650 22690 no-call complex = ? ? -246 1.17 N +359 2 chr1 22690 22741 hom ref = = = 34 1.17 N +360 2 chr1 22741 22761 no-call complex = ? ? -103 1.17 N +361 2 chr1 22761 22768 hom ref = = = 38 1.17 N +362 2 chr1 22768 22775 no-call complex = ? ? -31 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +363 2 chr1 22775 22821 hom ref = = = 25 1.17 N +364 2 chr1 22821 22877 no-call complex = ? ? -470 1.17 N +365 2 chr1 22877 22894 hom ref = = = 38 1.17 N +366 2 chr1 22894 22902 no-call complex = ? ? -411 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +367 2 chr1 22902 22944 hom ref = = = 24 1.17 N +368 2 chr1 22944 22983 no-call complex = ? ? -552 1.17 N +369 2 chr1 22983 22991 hom ref = = = 16 1.17 N +370 2 chr1 22991 23033 no-call complex = ? ? -244 1.17 N +371 2 chr1 23033 23043 hom ref = = = 54 1.17 N +372 2 chr1 23043 23076 no-call complex = ? ? -559 1.17 N +373 2 chr1 23076 23093 hom ref = = = 36 1.17 N +374 2 chr1 23093 23129 no-call complex = ? ? -275 1.17 N +375 2 chr1 23129 23170 hom ref = = = 50 1.17 N +376 2 chr1 23170 23206 no-call complex = ? ? -162 1.17 N +377 2 chr1 23206 23238 hom ref = = = 29 1.17 N +378 2 chr1 23238 23281 no-call complex = ? ? -498 1.17 N +379 2 chr1 23281 23287 hom ref = = = 51 1.17 N +380 2 chr1 23287 23295 no-call complex = ? ? -478 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +381 2 chr1 23295 23338 hom ref = = = 37 1.17 N +382 2 chr1 23338 23382 no-call complex = ? ? -328 1.17 N +383 2 chr1 23382 23389 hom ref = = = 12 1.17 N +384 2 chr1 23389 23422 no-call complex = ? ? -42 1.17 N +385 2 chr1 23422 23469 hom ref = = = -22 1.17 N +386 2 chr1 23469 23470 half ref A A N 80 121 -22 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 5 1.17 N +387 2 chr1 23470 23502 hom ref = = = -22 1.17 N +388 2 chr1 23502 23541 no-call complex = ? ? -394 1.17 N +389 2 chr1 23541 23555 hom ref = = = 29 1.17 N +390 2 chr1 23555 23587 no-call complex = ? ? -297 1.17 N +391 2 chr1 23587 23642 hom ref = = = 31 1.17 N +392 2 chr1 23642 23672 no-call complex = ? ? -823 1.17 N +393 2 chr1 23672 23692 hom ref = = = 34 1.17 N +394 2 chr1 23692 23740 no-call complex = ? ? -141 1.17 N +395 2 chr1 23740 23775 hom ref = = = 32 1.17 N +396 2 chr1 23775 23814 no-call complex = ? ? -126 1.17 N +397 2 chr1 23814 23843 hom ref = = = 27 1.17 N +398 2 chr1 23843 23874 no-call complex = ? ? -176 1.17 N +399 2 chr1 23874 23926 hom ref = = = 14 1.17 N +400 2 chr1 23926 23933 no-call complex = ? ? -51 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +401 2 chr1 23933 23971 hom ref = = = 27 1.17 N +402 2 chr1 23971 23979 no-call complex = ? ? -89 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +403 2 chr1 23979 24030 hom ref = = = 23 1.17 N +404 2 chr1 24030 24077 no-call complex = ? ? -212 1.17 N +405 2 chr1 24077 24094 hom ref = = = 65 1.17 N +406 2 chr1 24094 24117 no-call complex = ? ? -404 1.17 N +407 2 chr1 24117 24124 hom ref = = = 22 1.17 N +408 2 chr1 24124 24169 no-call complex = ? ? -119 1.17 N +409 2 chr1 24169 24189 hom ref = = = 27 1.17 N +410 2 chr1 24189 24200 no-call complex = ? ? -348 1.17 N +411 2 chr1 24200 24214 hom ref = = = 44 1.17 N +412 2 chr1 24214 24248 no-call complex = ? ? -83 1.17 N +413 2 chr1 24248 24257 hom ref = = = 42 1.17 N +414 2 chr1 24257 24283 no-call complex = ? ? -277 1.17 N +415 2 chr1 24283 24298 hom ref = = = 36 1.17 N +416 2 chr1 24298 24315 no-call complex = ? ? -813 1.17 N +417 2 chr1 24315 24343 hom ref = = = 51 1.17 N +418 2 chr1 24343 24365 no-call complex = ? ? -279 1.17 N +419 2 chr1 24365 24415 hom ref = = = 22 1.17 N +420 2 chr1 24415 24454 no-call complex = ? ? -749 1.17 N +421 2 chr1 24454 24483 hom ref = = = 12 1.17 N +422 2 chr1 24483 24490 no-call complex = ? ? -373 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +423 2 chr1 24490 24507 hom ref = = = 11 1.17 N +424 2 chr1 24507 24539 no-call complex = ? ? -270 1.17 N +425 2 chr1 24539 24605 hom ref = = = 22 1.17 N +426 2 chr1 24605 24620 no-call complex = ? ? -101 1.17 N +427 2 chr1 24620 24634 hom ref = = = 10 1.17 N +428 2 chr1 24634 24659 no-call complex = ? ? -302 1.17 N +429 2 chr1 24659 24681 hom ref = = = 6 1.17 N +430 2 chr1 24681 24682 half ref A A N 52 116 6 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 5 1.17 N +431 2 chr1 24682 24719 hom ref = = = 6 1.17 N +432 2 chr1 24719 24742 no-call complex = ? ? -75 1.17 N +433 2 chr1 24742 24750 hom ref = = = 15 1.17 N +434 2 chr1 24750 24757 no-call complex = ? ? -215 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::UTR:UNKNOWN-INC 1.17 N +435 2 chr1 24757 24773 hom ref = = = 11 1.17 N +436 2 chr1 24773 24801 no-call complex = ? ? -144 1.17 N +437 2 chr1 24801 24807 hom ref = = = 16 1.17 N +438 2 chr1 24807 24835 no-call complex = ? ? -99 1.17 N +439 2 chr1 24835 24896 hom ref = = = 12 1.17 N +440 2 chr1 24896 24945 no-call complex = ? ? -141 1.17 N +441 2 chr1 24945 25060 hom ref = = = 8 1.17 N +442 2 chr1 25060 25085 no-call complex = ? ? -240 1.17 N +443 2 chr1 25085 25103 hom ref = = = 16 1.17 N +444 2 chr1 25103 25119 no-call complex = ? ? -272 1.17 N +445 2 chr1 25119 25149 hom ref = = = 11 1.17 N +446 2 chr1 25149 25156 no-call complex = ? ? -475 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +447 2 chr1 25156 25214 hom ref = = = 47 1.17 N +448 2 chr1 25214 25231 no-call complex = ? ? -295 1.17 N +449 2 chr1 25231 25268 hom ref = = = 36 1.17 N +450 2 chr1 25268 25282 no-call complex = ? ? -11 1.17 N +451 2 chr1 25282 25309 hom ref = = = 36 1.17 N +452 2 chr1 25309 25321 no-call complex = ? ? -507 1.17 N +453 2 chr1 25321 25342 hom ref = = = 44 1.17 N +454 2 chr1 25342 25368 no-call complex = ? ? -514 1.17 N +455 2 chr1 25368 25392 hom ref = = = 39 1.17 N +456 2 chr1 25392 25421 no-call complex = ? ? -63 1.17 N +457 2 chr1 25421 25495 hom ref = = = 22 1.17 N +458 2 chr1 25495 25536 no-call complex = ? ? -145 1.17 N +459 2 chr1 25536 25556 hom ref = = = 61 1.17 N +460 2 chr1 25556 25571 no-call complex = ? ? -472 1.17 N +461 2 chr1 25571 25697 hom ref = = = 4 1.17 N +462 2 chr1 25697 25736 no-call complex = ? ? -47 1.17 N +463 2 chr1 25736 25770 hom ref = = = 16 1.17 N +464 2 chr1 25770 25780 no-call complex = ? ? -87 1.17 N +465 2 chr1 25780 25872 hom ref = = = 16 1.17 N +466 2 chr1 25872 25879 no-call complex = ? ? -136 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +467 2 chr1 25879 25930 hom ref = = = 37 1.17 N +468 2 chr1 25930 25937 no-call complex = ? ? -645 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +469 2 chr1 25937 25956 hom ref = = = 11 1.17 N +470 2 chr1 25956 25999 no-call complex = ? ? -107 1.17 N +471 2 chr1 25999 26006 hom ref = = = 18 1.17 N +472 2 chr1 26006 26018 no-call complex = ? ? -483 1.17 N +473 2 chr1 26018 26032 hom ref = = = 24 1.17 N +474 2 chr1 26032 26065 no-call complex = ? ? -176 1.17 N +475 2 chr1 26065 26157 hom ref = = = 25 1.17 N +476 2 chr1 26157 26164 no-call complex = ? ? -124 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +477 2 chr1 26164 26212 hom ref = = = 32 1.17 N +478 2 chr1 26212 26228 no-call complex = ? ? -139 1.17 N +479 2 chr1 26228 26247 hom ref = = = 37 1.17 N +480 2 chr1 26247 26289 no-call complex = ? ? -231 1.17 N +481 2 chr1 26289 26338 hom ref = = = 13 1.17 N +482 2 chr1 26338 26361 no-call complex = ? ? -415 1.17 N +483 2 chr1 26361 26420 hom ref = = = 11 1.17 N +484 2 chr1 26420 26465 no-call complex = ? ? -293 1.17 N +485 2 chr1 26465 26500 hom ref = = = 11 1.17 N +486 2 chr1 26500 26525 no-call complex = ? ? -450 1.17 N +487 2 chr1 26525 26560 hom ref = = = 43 1.17 N +488 2 chr1 26560 26567 no-call complex = ? ? -397 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +489 2 chr1 26567 26594 hom ref = = = 32 1.17 N +490 2 chr1 26594 26617 no-call complex = ? ? -329 1.17 N +491 2 chr1 26617 26696 hom ref = = = 26 1.17 N +492 2 chr1 26696 26715 no-call complex = ? ? -129 1.17 N +493 2 chr1 26715 26735 hom ref = = = 32 1.17 N +494 2 chr1 26735 26769 no-call complex = ? ? -368 1.17 N +495 2 chr1 26769 26790 hom ref = = = 40 1.17 N +496 2 chr1 26790 26806 no-call complex = ? ? -343 1.17 N +497 2 chr1 26806 26834 hom ref = = = 18 1.17 N +498 2 chr1 26834 26854 no-call complex = ? ? -343 1.17 N +499 2 chr1 26854 26866 hom ref = = = 45 1.17 N +500 2 chr1 26866 26893 no-call complex = ? ? -469 1.17 N +501 2 chr1 26893 26925 hom ref = = = 40 1.17 N +502 2 chr1 26925 26971 no-call complex = ? ? -690 1.17 N +503 2 chr1 26971 26978 hom ref = = = 29 1.17 N +504 2 chr1 26978 27062 no-call complex = ? ? -137 1.17 N +505 2 chr1 27062 27102 hom ref = = = 40 1.17 N +506 2 chr1 27102 27109 no-call complex = ? ? -397 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +507 2 chr1 27109 27134 hom ref = = = 53 1.17 N +508 2 chr1 27134 27157 no-call complex = ? ? -491 1.17 N +509 2 chr1 27157 27172 hom ref = = = 57 1.17 N +510 2 chr1 27172 27199 no-call complex = ? ? -534 1.17 N +511 2 chr1 27199 27217 hom ref = = = 46 1.17 N +512 2 chr1 27217 27243 no-call complex = ? ? -70 1.17 N +513 2 chr1 27243 27312 hom ref = = = 26 1.17 N +514 2 chr1 27312 27334 no-call complex = ? ? -211 1.17 N +515 2 chr1 27334 27360 hom ref = = = 37 1.17 N +516 2 chr1 27360 27410 no-call complex = ? ? -206 1.17 N +517 2 chr1 27410 27416 hom ref = = = 23 1.17 N +518 2 chr1 27416 27445 no-call complex = ? ? -114 1.17 N +519 2 chr1 27445 27485 hom ref = = = 18 1.17 N +520 2 chr1 27485 27492 no-call complex = ? ? -209 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +521 2 chr1 27492 27524 hom ref = = = 18 1.17 N +522 2 chr1 27524 27543 no-call complex = ? ? -169 1.17 N +523 2 chr1 27543 27550 hom ref = = = 68 1.17 N +524 2 chr1 27550 27577 no-call complex = ? ? -569 1.17 N +525 2 chr1 27577 27592 hom ref = = = 14 1.17 N +526 2 chr1 27592 27636 no-call complex = ? ? -243 1.17 N +527 2 chr1 27636 27652 hom ref = = = 22 1.17 N +528 2 chr1 27652 27672 no-call complex = ? ? -216 1.17 N +529 2 chr1 27672 27719 hom ref = = = 25 1.17 N +530 2 chr1 27719 27729 no-call complex = ? ? -418 1.17 N +531 2 chr1 27729 27776 hom ref = = = 18 1.17 N +532 2 chr1 27776 27826 no-call complex = ? ? -290 1.17 N +533 2 chr1 27826 27839 hom ref = = = 56 1.17 N +534 2 chr1 27839 27888 no-call complex = ? ? -236 1.17 N +535 2 chr1 27888 27903 hom ref = = = 22 1.17 N +536 2 chr1 27903 27931 no-call complex = ? ? -395 1.17 N +537 2 chr1 27931 27956 hom ref = = = 15 1.17 N +538 2 chr1 27956 27972 no-call complex = ? ? -126 1.17 N +539 2 chr1 27972 27986 hom ref = = = 19 1.17 N +540 2 chr1 27986 28023 no-call complex = ? ? -506 1.17 N +541 2 chr1 28023 28049 hom ref = = = 69 1.17 N +542 2 chr1 28049 28088 no-call complex = ? ? -804 1.17 N +543 2 chr1 28088 28109 hom ref = = = 63 1.17 N +544 2 chr1 28109 28140 no-call complex = ? ? -250 1.17 N +545 2 chr1 28140 28172 hom ref = = = 27 1.17 N +546 2 chr1 28172 28217 no-call complex = ? ? -303 1.17 N +547 2 chr1 28217 28242 hom ref = = = 26 1.17 N +548 2 chr1 28242 28259 no-call complex = ? ? -213 1.17 N +549 2 chr1 28259 28323 hom ref = = = 4 1.17 N +550 2 chr1 28323 28357 no-call complex = ? ? -639 1.17 N +551 2 chr1 28357 28372 hom ref = = = 13 1.17 N +552 2 chr1 28372 28379 no-call complex = ? ? -577 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 1.17 N +553 2 chr1 28379 28402 hom ref = = = 46 1.17 N +554 2 chr1 28402 28444 no-call complex = ? ? -198 1.17 N +555 2 chr1 28444 28469 hom ref = = = 15 1.17 N +556 2 chr1 28469 28514 no-call complex = ? ? -834 1.17 N +557 2 chr1 28514 28534 hom ref = = = 60 1.17 N +558 2 chr1 28534 28545 no-call complex = ? ? -387 1.17 N +559 2 chr1 28545 28554 hom ref = = = 50 1.17 N +560 2 chr1 28554 28625 no-call complex = ? ? -490 1.17 N +561 2 chr1 28625 28659 hom ref = = = 17 1.17 N +562 2 chr1 28659 28697 no-call complex = ? ? -286 1.17 N +563 2 chr1 28697 28747 hom ref = = = 32 1.17 N +564 2 chr1 28747 28773 no-call complex = ? ? -349 1.17 N +565 2 chr1 28773 28801 hom ref = = = 57 1.17 N +566 2 chr1 28801 28840 no-call complex = ? ? -189 1.17 N +567 2 chr1 28840 28859 hom ref = = = 20 1.17 N +568 2 chr1 28859 28878 no-call complex = ? ? -240 1.17 N +569 2 chr1 28878 28922 hom ref = = = 4 1.17 N +570 2 chr1 28922 28923 half ref T T N 38 119 4 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 5 1.17 N +571 2 chr1 28923 28941 hom ref = = = 4 1.17 N +572 2 chr1 28941 28991 no-call complex = ? ? -34 1.17 N +573 2 chr1 28991 29013 hom ref = = = -39 1.17 N +574 2 chr1 29013 29014 half ref G G N 120 120 -39 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::INTRON:UNKNOWN-INC 5 1.17 N +575 2 chr1 29014 29059 hom ref = = = -39 1.17 N +576 2 chr1 29059 29094 no-call complex = ? ? -151 1.17 N +577 2 chr1 29094 29121 hom ref = = = 13 1.17 N +578 2 chr1 29121 29193 no-call complex = ? ? -173 1.17 N +579 2 chr1 29193 29252 hom ref = = = 4 1.17 N +580 2 chr1 29252 29289 no-call complex = ? ? -167 1.17 N +581 2 chr1 29289 29312 hom ref = = = 17 1.17 N +582 2 chr1 29312 29328 no-call complex = ? ? -79 1.17 N +583 2 chr1 29328 29341 hom ref = = = 26 1.17 N +584 2 chr1 29341 29373 no-call complex = ? ? -21 1.17 N +585 2 chr1 29373 29389 hom ref = = = 27 1.17 N +586 2 chr1 29389 29415 no-call complex = ? ? -93 1.17 N +587 2 chr1 29415 29420 hom ref = = = 15 1.17 N +588 2 chr1 29420 29466 no-call complex = ? ? -91 1.17 N +589 2 chr1 29466 29477 hom ref = = = 17 1.17 N +590 2 chr1 29477 29514 no-call complex = ? ? -77 1.17 N +591 2 chr1 29514 29567 hom ref = = = 15 1.17 N +592 2 chr1 29567 29591 no-call complex = ? ? -335 1.17 N +593 2 chr1 29591 29629 hom ref = = = 15 1.17 N +594 2 chr1 29629 29636 no-call complex = ? ? -106 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +595 2 chr1 29636 29691 hom ref = = = 16 1.17 N +596 2 chr1 29691 29705 no-call complex = ? ? -164 1.17 N +597 2 chr1 29705 29716 hom ref = = = 16 1.17 N +598 2 chr1 29716 29762 no-call complex = ? ? -252 1.17 N +599 2 chr1 29762 29786 hom ref = = = 31 1.17 N +600 2 chr1 29786 29823 no-call complex = ? ? -885 1.17 N +601 2 chr1 29823 29845 hom ref = = = 62 1.17 N +602 2 chr1 29845 29852 no-call complex = ? ? -417 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +603 2 chr1 29852 29877 hom ref = = = 47 1.17 N +604 2 chr1 29877 29897 no-call complex = ? ? -224 1.17 N +605 2 chr1 29897 29935 hom ref = = = 19 1.17 N +606 2 chr1 29935 29971 no-call complex = ? ? -191 1.17 N +607 2 chr1 29971 30017 hom ref = = = 25 1.17 N +608 2 chr1 30017 30040 no-call complex = ? ? -505 1.17 N +609 2 chr1 30040 30075 hom ref = = = 33 1.17 N +610 2 chr1 30075 30107 no-call complex = ? ? -178 1.17 N +611 2 chr1 30107 30184 hom ref = = = 8 1.17 N +612 2 chr1 30184 30202 no-call complex = ? ? -116 1.17 N +613 2 chr1 30202 30235 hom ref = = = 43 1.17 N +614 2 chr1 30235 30256 no-call complex = ? ? -250 1.17 N +615 2 chr1 30256 30272 hom ref = = = 14 1.17 N +616 2 chr1 30272 30292 no-call complex = ? ? -272 1.17 N +617 2 chr1 30292 30311 hom ref = = = 37 1.17 N +618 2 chr1 30311 30323 no-call complex = ? ? -466 1.17 N +619 2 chr1 30323 30358 hom ref = = = 12 1.17 N +620 2 chr1 30358 30379 no-call complex = ? ? -684 hsa-mir-1302-2:MI0006363 1.17 N +621 2 chr1 30379 30407 hom ref = = = 29 1.17 N +622 2 chr1 30407 30427 no-call complex = ? ? -385 hsa-mir-1302-2:MI0006363 1.17 N +623 2 chr1 30427 30485 hom ref = = = 15 1.17 N +624 2 chr1 30485 30492 no-call complex = ? ? -174 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC hsa-mir-1302-2:MI0006363 1.17 N +625 2 chr1 30492 30524 hom ref = = = 32 1.17 N +626 2 chr1 30524 30548 no-call complex = ? ? -197 1.17 N +627 2 chr1 30548 30566 hom ref = = = 26 1.17 N +628 2 chr1 30566 30589 no-call complex = ? ? -226 1.17 N +629 2 chr1 30589 30632 hom ref = = = 47 1.17 N +630 2 chr1 30632 30652 no-call complex = ? ? -157 1.17 N +631 2 chr1 30652 30659 hom ref = = = 20 1.17 N +632 2 chr1 30659 30675 no-call complex = ? ? -195 1.17 N +633 2 chr1 30675 30727 hom ref = = = 6 1.17 N +634 2 chr1 30727 30728 half ref G G N 70 120 6 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC MLT1A:ERVL-MaLR:23.2 5 1.17 N +635 2 chr1 30728 30775 hom ref = = = 6 1.17 N +636 2 chr1 30775 30797 no-call complex = ? ? -240 1.17 N +637 2 chr1 30797 30803 hom ref = = = 52 1.17 N +638 2 chr1 30803 30822 no-call complex = ? ? -141 1.17 N +639 2 chr1 30822 30851 hom ref = = = 15 1.17 N +640 2 chr1 30851 30899 no-call complex = ? ? -117 1.17 N +641 2 chr1 30899 30906 hom ref = = = 10 1.17 N +642 2 chr1 30906 30974 no-call complex = ? ? -323 1.17 N +643 2 chr1 30974 30981 hom ref = = = 38 1.17 N +644 2 chr1 30981 31000 no-call complex = ? ? -286 1.17 N +645 2 chr1 31000 31025 hom ref = = = 41 1.17 N +646 2 chr1 31025 31040 no-call complex = ? ? -144 1.17 N +647 2 chr1 31040 31162 hom ref = = = 27 1.17 N +648 2 chr1 31162 31169 no-call complex = ? ? -199 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +649 2 chr1 31169 31281 hom ref = = = 26 1.17 N +650 2 chr1 31281 31298 no-call complex = ? ? -365 1.17 N +651 2 chr1 31298 31391 hom ref = = = 21 1.17 N +652 2 chr1 31391 31399 no-call complex = ? ? -104 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +653 2 chr1 31399 31440 hom ref = = = 39 1.17 N +654 2 chr1 31440 31470 no-call complex = ? ? -224 1.17 N +655 2 chr1 31470 31483 hom ref = = = 18 1.17 N +656 2 chr1 31483 31530 no-call complex = ? ? -323 1.17 N +657 2 chr1 31530 31546 hom ref = = = 44 1.17 N +658 2 chr1 31546 31575 no-call complex = ? ? -1093 1.17 N +659 2 chr1 31575 31619 hom ref = = = 23 1.17 N +660 2 chr1 31619 31653 no-call complex = ? ? -37 1.17 N +661 2 chr1 31653 31668 hom ref = = = 34 1.17 N +662 2 chr1 31668 31700 no-call complex = ? ? -475 1.17 N +663 2 chr1 31700 31715 hom ref = = = 29 1.17 N +664 2 chr1 31715 31743 no-call complex = ? ? -129 1.17 N +665 2 chr1 31743 31758 hom ref = = = 25 1.17 N +666 2 chr1 31758 31775 no-call complex = ? ? -43 1.17 N +667 2 chr1 31775 31789 hom ref = = = 34 1.17 N +668 2 chr1 31789 31821 no-call complex = ? ? -239 1.17 N +669 2 chr1 31821 31855 hom ref = = = 63 1.17 N +670 2 chr1 31855 31878 no-call complex = ? ? -507 1.17 N +671 2 chr1 31878 31930 hom ref = = = 33 1.17 N +672 2 chr1 31930 31980 no-call complex = ? ? -532 1.17 N +673 2 chr1 31980 32000 hom ref = = = 28 1.17 N +674 2 chr1 32000 32007 no-call complex = ? ? -92 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +675 2 chr1 32007 32037 hom ref = = = 37 1.17 N +676 2 chr1 32037 32076 no-call complex = ? ? -134 1.17 N +677 2 chr1 32076 32101 hom ref = = = 12 1.17 N +678 2 chr1 32101 32126 no-call complex = ? ? -87 1.17 N +679 2 chr1 32126 32146 hom ref = = = 26 1.17 N +680 2 chr1 32146 32180 no-call complex = ? ? -379 1.17 N +681 2 chr1 32180 32237 hom ref = = = 59 1.17 N +682 2 chr1 32237 32273 no-call complex = ? ? -191 1.17 N +683 2 chr1 32273 32321 hom ref = = = 48 1.17 N +684 2 chr1 32321 32364 no-call complex = ? ? -298 1.17 N +685 2 chr1 32364 32376 hom ref = = = 23 1.17 N +686 2 chr1 32376 32413 no-call complex = ? ? -286 1.17 N +687 2 chr1 32413 32435 hom ref = = = 10 1.17 N +688 2 chr1 32435 32442 no-call complex = ? ? -130 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +689 2 chr1 32442 32463 hom ref = = = 35 1.17 N +690 2 chr1 32463 32492 no-call complex = ? ? -631 1.17 N +691 2 chr1 32492 32584 hom ref = = = 32 1.17 N +692 2 chr1 32584 32591 no-call complex = ? ? -952 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +693 2 chr1 32591 32645 hom ref = = = 49 1.17 N +694 2 chr1 32645 32677 no-call complex = ? ? -318 1.17 N +695 2 chr1 32677 32732 hom ref = = = 14 1.17 N +696 2 chr1 32732 32759 no-call complex = ? ? -152 1.17 N +697 2 chr1 32759 32814 hom ref = = = 18 1.17 N +698 2 chr1 32814 32837 no-call complex = ? ? -457 1.17 N +699 2 chr1 32837 32890 hom ref = = = 40 1.17 N +700 2 chr1 32890 32897 no-call complex = ? ? -591 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +701 2 chr1 32897 32962 hom ref = = = 39 1.17 N +702 2 chr1 32962 32992 no-call complex = ? ? -196 1.17 N +703 2 chr1 32992 33040 hom ref = = = 26 1.17 N +704 2 chr1 33040 33061 no-call complex = ? ? -154 1.17 N +705 2 chr1 33061 33132 hom ref = = = 38 1.17 N +706 2 chr1 33132 33153 no-call complex = ? ? -208 1.17 N +707 2 chr1 33153 33163 hom ref = = = 18 1.17 N +708 2 chr1 33163 33182 no-call complex = ? ? -356 1.17 N +709 2 chr1 33182 33257 hom ref = = = 47 1.17 N +710 2 chr1 33257 33264 no-call complex = ? ? -50 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +711 2 chr1 33264 33328 hom ref = = = 33 1.17 N +712 2 chr1 33328 33360 no-call complex = ? ? -1120 1.17 N +713 2 chr1 33360 33376 hom ref = = = 41 1.17 N +714 2 chr1 33376 33383 no-call complex = ? ? -163 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +715 2 chr1 33383 33397 hom ref = = = 23 1.17 N +716 2 chr1 33397 33476 no-call complex = ? ? -230 1.17 N +717 2 chr1 33476 33491 hom ref = = = 39 1.17 N +718 2 chr1 33491 33498 no-call complex = ? ? -168 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +719 2 chr1 33498 33503 hom ref = = = 85 1.17 N +720 2 chr1 33503 33545 no-call complex = ? ? -335 1.17 N +721 2 chr1 33545 33551 hom ref = = = 38 1.17 N +722 2 chr1 33551 33558 no-call complex = ? ? -47 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +723 2 chr1 33558 33627 hom ref = = = 40 1.17 N +724 2 chr1 33627 33634 no-call complex = ? ? -193 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +725 2 chr1 33634 33652 hom ref = = = 35 1.17 N +726 2 chr1 33652 33689 no-call complex = ? ? -429 1.17 N +727 2 chr1 33689 33702 hom ref = = = 20 1.17 N +728 2 chr1 33702 33750 no-call complex = ? ? -259 1.17 N +729 2 chr1 33750 33877 hom ref = = = -12 1.17 N +730 2 chr1 33877 33878 half ref A A N 64 120 -12 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC L1PA6:L1:7.4 5 1.17 N +731 2 chr1 33878 33903 hom ref = = = -14 1.17 N +732 2 chr1 33903 33937 no-call complex = ? ? -156 1.17 N +733 2 chr1 33937 33967 hom ref = = = 18 1.17 N +734 2 chr1 33967 33974 no-call complex = ? ? -179 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +735 2 chr1 33974 34025 hom ref = = = 22 1.17 N +736 2 chr1 34025 34052 no-call complex = ? ? -251 1.17 N +737 2 chr1 34052 34076 hom ref = = = 48 1.17 N +738 2 chr1 34076 34084 no-call complex = ? ? -93 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +739 2 chr1 34084 34120 hom ref = = = 46 1.17 N +740 2 chr1 34120 34127 no-call complex = ? ? -149 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +741 2 chr1 34127 34241 hom ref = = = 24 1.17 N +742 2 chr1 34241 34248 no-call complex = ? ? -13 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 653635:NR_024540.1:WASH5P::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +743 2 chr1 34248 34290 hom ref = = = 35 1.17 N +744 2 chr1 34290 34331 no-call complex = ? ? -209 1.17 N +745 2 chr1 34331 34370 hom ref = = = 11 1.17 N +746 2 chr1 34370 34388 no-call complex = ? ? 16 1.17 N +747 2 chr1 34388 34407 hom ref = = = 15 1.17 N +748 2 chr1 34407 34437 no-call complex = ? ? -17 1.17 N +749 2 chr1 34437 34452 hom ref = = = 40 1.17 N +750 2 chr1 34452 34474 no-call complex = ? ? -406 1.17 N +751 2 chr1 34474 34512 hom ref = = = 24 1.17 N +752 2 chr1 34512 34553 no-call complex = ? ? -391 1.17 N +753 2 chr1 34553 34580 hom ref = = = 12 1.17 N +754 2 chr1 34580 34606 no-call complex = ? ? -153 1.17 N +755 2 chr1 34606 34630 hom ref = = = 65 1.17 N +756 2 chr1 34630 34640 no-call complex = ? ? -762 1.17 N +757 2 chr1 34640 34703 hom ref = = = 44 1.17 N +758 2 chr1 34703 34717 no-call complex = ? ? -63 1.17 N +759 2 chr1 34717 34739 hom ref = = = 38 1.17 N +760 2 chr1 34739 34766 no-call complex = ? ? -94 1.17 N +761 2 chr1 34766 34775 hom ref = = = 39 1.17 N +762 2 chr1 34775 34813 no-call complex = ? ? -231 1.17 N +763 2 chr1 34813 34912 hom ref = = = 1 1.17 N +764 2 chr1 34912 34913 half ref G G N 49 120 1 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC MLT1J2:ERVL-MaLR:40.8 6 1.17 N +765 2 chr1 34913 34967 hom ref = = = -20 1.17 N +766 2 chr1 34967 34990 no-call complex = ? ? -230 1.17 N +767 2 chr1 34990 35006 hom ref = = = 49 1.17 N +768 2 chr1 35006 35038 no-call complex = ? ? -217 1.17 N +769 2 chr1 35038 35075 hom ref = = = 36 1.17 N +770 2 chr1 35075 35098 no-call complex = ? ? -239 1.17 N +771 2 chr1 35098 35118 hom ref = = = -4 1.17 N +772 2 chr1 35118 35119 half ref G G ? 149 0 -4 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 6 1.17 N +773 2 chr1 35119 35168 hom ref = = = -4 1.17 N +774 2 chr1 35168 35189 no-call complex = ? ? -171 1.17 N +775 2 chr1 35189 35202 hom ref = = = 54 1.17 N +776 2 chr1 35202 35211 no-call complex = ? ? 33 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 1.17 N +777 2 chr1 35211 35228 hom ref = = = 64 1.17 N +778 2 chr1 35228 35254 no-call complex = ? ? -153 1.17 N +779 2 chr1 35254 35282 hom ref = = = 36 1.17 N +780 2 chr1 35282 35319 no-call complex = ? ? -84 1.17 N +781 2 chr1 35319 35393 hom ref = = = 16 1.17 N +782 2 chr1 35393 35419 no-call complex = ? ? -145 1.17 N +783 2 chr1 35419 35469 hom ref = = = 28 1.17 N +784 2 chr1 35469 35514 no-call complex = ? ? -83 1.17 N +785 2 chr1 35514 35554 hom ref = = = 35 1.17 N +786 2 chr1 35554 35582 no-call complex = ? ? -112 1.17 N +787 2 chr1 35582 35656 hom ref = = = 14 1.17 N +788 2 chr1 35656 35663 no-call complex = ? ? -369 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 1.17 N +789 2 chr1 35663 35699 hom ref = = = -22 1.17 N +790 2 chr1 35699 35700 half ref C C N 74 123 -22 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::INTRON:UNKNOWN-INC 6 1.17 N +791 2 chr1 35700 35754 hom ref = = = -22 1.17 N +792 2 chr1 35754 35762 no-call complex = ? ? -67 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 1.17 N +793 2 chr1 35762 35812 hom ref = = = 24 1.17 N +794 2 chr1 35812 35853 no-call complex = ? ? -3 1.17 N +795 2 chr1 35853 35932 hom ref = = = 16 1.17 N +796 2 chr1 35932 35939 no-call complex = ? ? -106 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::UTR:UNKNOWN-INC 1.17 N +797 2 chr1 35939 35998 hom ref = = = 27 1.17 N +798 2 chr1 35998 36029 no-call complex = ? ? -127 1.17 N +799 2 chr1 36029 36128 hom ref = = = -8 1.17 N +800 2 chr1 36128 36128 half ref ? 28 0 423 424 -8 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 6 1.17 N +801 2 chr1 36128 36136 hom ref = = = -8 1.17 N +802 2 chr1 36136 36136 half ref ? 22 0 423 424 53 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 6 1.17 N +803 2 chr1 36136 36149 hom ref = = = -8 1.17 N +804 2 chr1 36149 36150 half ref A A N 120 120 423 424 -8 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 6 1.17 N +805 2 chr1 36150 36178 hom ref = = = -8 1.17 N +806 2 chr1 36178 36200 no-call complex = ? ? -13 1.17 N +807 2 chr1 36200 36213 hom ref = = = 20 1.17 N +808 2 chr1 36213 36242 no-call complex = ? ? -13 1.17 N +809 2 chr1 36242 36283 hom ref = = = 4 1.17 N +810 2 chr1 36283 36284 half ref G G N 121 121 4 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 6 1.17 N +811 2 chr1 36284 36337 hom ref = = = 4 1.17 N +812 2 chr1 36337 36368 no-call complex = ? ? -116 1.17 N +813 2 chr1 36368 36385 hom ref = = = 16 1.17 N +814 2 chr1 36385 36435 no-call complex = ? ? -179 1.17 N +815 2 chr1 36435 36482 hom ref = = = 25 1.17 N +816 2 chr1 36482 36511 no-call complex = ? ? -425 1.17 N +817 2 chr1 36511 36524 hom ref = = = 13 1.17 N +818 2 chr1 36524 36531 no-call complex = ? ? -296 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +819 2 chr1 36531 36714 hom ref = = = 17 1.17 N +820 2 chr1 36714 36753 no-call complex = ? ? -240 1.17 N +821 2 chr1 36753 36788 hom ref = = = -16 1.17 N +822 2 chr1 36788 36789 half ref C C N 62 120 -16 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 6 1.17 N +823 2 chr1 36789 36847 hom ref = = = -16 1.17 N +824 2 chr1 36847 36855 no-call complex = ? ? -49 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +825 2 chr1 36855 36887 hom ref = = = 25 1.17 N +826 2 chr1 36887 36926 no-call complex = ? ? -85 1.17 N +827 2 chr1 36926 37050 hom ref = = = -2 1.17 N +828 2 chr1 37050 37058 no-call complex = ? ? -74 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +829 2 chr1 37058 37142 hom ref = = = -23 1.17 N +830 2 chr1 37142 37143 half ref G G N 94 130 -23 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC Charlie5:hAT-Charlie:25.8 6 1.17 N +831 2 chr1 37143 37235 hom ref = = = -23 1.17 N +832 2 chr1 37235 37254 no-call complex = ? ? -240 1.17 N +833 2 chr1 37254 37317 hom ref = = = 11 1.17 N +834 2 chr1 37317 37340 no-call complex = ? ? -50 1.17 N +835 2 chr1 37340 37361 hom ref = = = 15 1.17 N +836 2 chr1 37361 37387 no-call complex = ? ? -278 1.17 N +837 2 chr1 37387 37505 hom ref = = = 7 1.17 N +838 2 chr1 37505 37536 no-call complex = ? ? -65 1.17 N +839 2 chr1 37536 37578 hom ref = = = 20 1.17 N +840 2 chr1 37578 37592 no-call complex = ? ? -172 1.17 N +841 2 chr1 37592 37649 hom ref = = = 14 1.17 N +842 2 chr1 37649 37679 no-call complex = ? ? -103 1.17 N +843 2 chr1 37679 37723 hom ref = = = 26 1.17 N +844 2 chr1 37723 37730 no-call complex = ? ? -42 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +845 2 chr1 37730 37768 hom ref = = = 56 1.17 N +846 2 chr1 37768 37775 no-call complex = ? ? -501 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +847 2 chr1 37775 37810 hom ref = = = 42 1.17 N +848 2 chr1 37810 37840 no-call complex = ? ? -38 1.17 N +849 2 chr1 37840 38005 hom ref = = = -45 1.17 N +850 2 chr1 38005 38031 no-call complex = ? ? -529 1.17 N +851 2 chr1 38031 38049 hom ref = = = 29 1.17 N +852 2 chr1 38049 38056 no-call complex = ? ? -60 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +853 2 chr1 38056 38139 hom ref = = = 14 1.17 N +854 2 chr1 38139 38187 no-call complex = ? ? -64 1.17 N +855 2 chr1 38187 38216 hom ref = = = 24 1.17 N +856 2 chr1 38216 38237 no-call complex = ? ? -92 1.17 N +857 2 chr1 38237 38281 hom ref = = = 22 1.17 N +858 2 chr1 38281 38301 no-call complex = ? ? -78 1.17 N +859 2 chr1 38301 38394 hom ref = = = 22 1.17 N +860 2 chr1 38394 38406 no-call complex = ? ? 29 1.17 N +861 2 chr1 38406 38448 hom ref = = = 36 1.17 N +862 2 chr1 38448 38455 no-call complex = ? ? -215 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +863 2 chr1 38455 38498 hom ref = = = 29 1.17 N +864 2 chr1 38498 38536 no-call complex = ? ? -43 1.17 N +865 2 chr1 38536 38599 hom ref = = = 20 1.17 N +866 2 chr1 38599 38609 no-call complex = ? ? -212 1.17 N +867 2 chr1 38609 38738 hom ref = = = 31 1.17 N +868 2 chr1 38738 38745 no-call complex = ? ? -192 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +869 2 chr1 38745 38771 hom ref = = = 29 1.17 N +870 2 chr1 38771 38789 no-call complex = ? ? -121 1.17 N +871 2 chr1 38789 38807 hom ref = = = 44 1.17 N +872 2 chr1 38807 38828 no-call complex = ? ? -179 1.17 N +873 2 chr1 38828 38869 hom ref = = = 20 1.17 N +874 2 chr1 38869 38911 no-call complex = ? ? -86 1.17 N +875 2 chr1 38911 39011 hom ref = = = 30 1.17 N +876 2 chr1 39011 39018 no-call complex = ? ? 3 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +877 2 chr1 39018 39176 hom ref = = = 35 1.17 N +878 2 chr1 39176 39191 no-call complex = ? ? -166 1.17 N +879 2 chr1 39191 39216 hom ref = = = 35 1.17 N +880 2 chr1 39216 39265 no-call complex = ? ? -664 1.17 N +881 2 chr1 39265 39402 hom ref = = = -2 1.17 N +882 2 chr1 39402 39426 no-call complex = ? ? -329 1.17 N +883 2 chr1 39426 39436 hom ref = = = 57 1.17 N +884 2 chr1 39436 39443 no-call complex = ? ? -20 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +885 2 chr1 39443 39483 hom ref = = = 37 1.17 N +886 2 chr1 39483 39500 no-call complex = ? ? -585 1.17 N +887 2 chr1 39500 39574 hom ref = = = 15 1.17 N +888 2 chr1 39574 39607 no-call complex = ? ? -258 1.17 N +889 2 chr1 39607 39627 hom ref = = = 55 1.17 N +890 2 chr1 39627 39645 no-call complex = ? ? -69 1.17 N +891 2 chr1 39645 39656 hom ref = = = 15 1.17 N +892 2 chr1 39656 39681 no-call complex = ? ? -88 1.17 N +893 2 chr1 39681 39718 hom ref = = = 31 1.17 N +894 2 chr1 39718 39752 no-call complex = ? ? -61 1.17 N +895 2 chr1 39752 39775 hom ref = = = 35 1.17 N +896 2 chr1 39775 39782 no-call complex = ? ? -104 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +897 2 chr1 39782 39870 hom ref = = = 34 1.17 N +898 2 chr1 39870 39882 no-call complex = ? ? -126 1.17 N +899 2 chr1 39882 39951 hom ref = = = -31 1.17 N +900 2 chr1 39951 39958 no-call complex = ? ? -57 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +901 2 chr1 39958 40028 hom ref = = = -7 1.17 N +902 2 chr1 40028 40032 half ref GCTA GCTA NCNN 37 93 3 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC MLT1E1A:ERVL-MaLR:44.5 6 1.17 N +903 2 chr1 40032 40156 hom ref = = = 21 1.17 N +904 2 chr1 40156 40163 no-call complex = ? ? -550 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +905 2 chr1 40163 40238 hom ref = = = 13 1.17 N +906 2 chr1 40238 40264 no-call complex = ? ? -311 1.17 N +907 2 chr1 40264 40294 hom ref = = = 39 1.17 N +908 2 chr1 40294 40301 no-call complex = ? ? -369 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +909 2 chr1 40301 40341 hom ref = = = 30 1.17 N +910 2 chr1 40341 40348 no-call complex = ? ? -100 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +911 2 chr1 40348 40383 hom ref = = = 38 1.17 N +912 2 chr1 40383 40412 no-call complex = ? ? -58 1.17 N +913 2 chr1 40412 40623 hom ref = = = 0 1.17 N +914 2 chr1 40623 40662 no-call complex = ? ? -142 1.17 N +915 2 chr1 40662 40889 hom ref = = = 51 1.17 N +916 2 chr1 40889 40912 no-call complex = ? ? -1389 1.17 N +917 2 chr1 40912 41049 hom ref = = = 59 1.17 N +918 2 chr1 41049 41056 no-call complex = ? ? -222 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 645520:NR_026818.1:FAM138A::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +919 2 chr1 41056 41214 hom ref = = = 52 1.17 N +920 2 chr1 41214 41259 no-call complex = ? ? -264 1.17 N +921 2 chr1 41259 41384 hom ref = = = 17 1.17 N +922 2 chr1 41384 41414 no-call complex = ? ? -124 1.17 N +923 2 chr1 41414 41506 hom ref = = = 60 1.17 N +924 2 chr1 41506 41514 no-call complex = ? ? -408 1.17 N +925 2 chr1 41514 41590 hom ref = = = 38 1.17 N +926 2 chr1 41590 41591 half ref C C ? 121 0 481 482 63 ERVL-E-int:ERVL:47.4 2 1.17 N +927 2 chr1 41591 41615 hom ref = = = -34 1.17 N +928 2 chr1 41615 41616 half ref T T N 38 121 481 482 7 ERVL-E-int:ERVL:47.4 2 1.17 N +929 2 chr1 41616 41757 hom ref = = = 7 1.17 N +930 2 chr1 41757 41764 no-call complex = ? ? -157 1.17 N +931 2 chr1 41764 41838 hom ref = = = 22 1.17 N +932 2 chr1 41838 41845 no-call complex = ? ? -187 1.17 N +933 2 chr1 41845 41980 hom ref = = = -170 1.17 N +934 2 chr1 41980 41981 hom snp A G G 76 97 dbsnp.86:rs806721 425 1 1 1 2 -170 ERVL-E-int:ERVL:47.4 2 1.17 N +935 2 chr1 41981 42198 hom ref = = = -170 1.17 N +936 2 chr1 42198 42205 no-call complex = ? ? -516 1.17 N +937 2 chr1 42205 42389 hom ref = = = 68 1.17 N +938 2 chr1 42389 42396 no-call complex = ? ? -307 1.17 N +939 2 chr1 42396 42499 hom ref = = = 65 1.17 N +940 2 chr1 42499 42528 no-call complex = ? ? -123 1.17 N +941 2 chr1 42528 42573 hom ref = = = 30 1.17 N +942 2 chr1 42573 42582 no-call complex = ? ? -119 1.17 N +943 2 chr1 42582 42684 hom ref = = = 45 1.17 N +944 2 chr1 42684 42692 no-call complex = ? ? -700 1.17 N +945 2 chr1 42692 42745 hom ref = = = 65 1.17 N +946 2 chr1 42745 42789 no-call complex = ? ? -179 1.17 N +947 2 chr1 42789 42800 hom ref = = = 28 1.17 N +948 2 chr1 42800 42827 no-call complex = ? ? -312 1.17 N +949 2 chr1 42827 42871 hom ref = = = 15 1.17 N +950 2 chr1 42871 42888 no-call complex = ? ? -1 1.17 N +951 2 chr1 42888 43038 hom ref = = = 12 1.17 N +952 2 chr1 43038 43045 no-call complex = ? ? -248 1.17 N +953 2 chr1 43045 43091 hom ref = = = 8 1.17 N +954 2 chr1 43091 43092 half ref T T N 71 71 487 488 8 2 1.17 N +955 2 chr1 43092 43101 hom ref = = = 8 1.17 N +956 2 chr1 43101 43105 half ref ATTT ATTT ? 20 0 487 488 6 2 1.17 N +957 2 chr1 43105 43175 hom ref = = = 6 1.17 N +958 2 chr1 43175 43222 no-call complex = ? ? -77 1.17 N +959 2 chr1 43222 43370 hom ref = = = 11 1.17 N +960 2 chr1 43370 43402 no-call complex = ? ? -223 1.17 N +961 2 chr1 43402 43582 hom ref = = = 13 1.17 N +962 2 chr1 43582 43608 no-call complex = ? ? -148 1.17 N +963 2 chr1 43608 43647 hom ref = = = 45 1.17 N +964 2 chr1 43647 43686 no-call complex = ? ? -102 1.17 N +965 2 chr1 43686 43792 hom ref = = = 13 1.17 N +966 2 chr1 43792 43816 no-call complex = ? ? -23 1.17 N +967 2 chr1 43816 44073 hom ref = = = 16 1.17 N +968 2 chr1 44073 44081 no-call complex = ? ? -297 1.17 N +969 2 chr1 44081 44161 hom ref = = = 22 1.17 N +970 2 chr1 44161 44187 no-call complex = ? ? -481 1.17 N +971 2 chr1 44187 44328 hom ref = = = 18 1.17 N +972 2 chr1 44328 44339 no-call complex = ? ? -162 1.17 N +973 2 chr1 44339 44458 hom ref = = = 30 1.17 N +974 2 chr1 44458 44479 no-call complex = ? ? -10 1.17 N +975 2 chr1 44479 44657 hom ref = = = 10 1.17 N +976 2 chr1 44657 44719 no-call complex = ? ? -400 1.17 N +977 2 chr1 44719 44783 hom ref = = = 10 1.17 N +978 2 chr1 44783 44790 no-call complex = ? ? -180 1.17 N +979 2 chr1 44790 44831 hom ref = = = 30 1.17 N +980 2 chr1 44831 44882 no-call complex = ? ? -46 1.17 N +981 2 chr1 44882 45022 hom ref = = = 11 1.17 N +982 2 chr1 45022 45043 no-call complex = ? ? -124 1.17 N +983 2 chr1 45043 45087 hom ref = = = 13 1.17 N +984 2 chr1 45087 45116 no-call complex = ? ? -78 1.17 N +985 2 chr1 45116 45312 hom ref = = = 0 1.17 N +986 2 chr1 45312 45312 half ref ? 27 0 1 L1MA8:L1:28.0 2 1.17 N +987 2 chr1 45312 45517 hom ref = = = 1 1.17 N +988 2 chr1 45517 45533 no-call complex = ? ? -108 1.17 N +989 2 chr1 45533 45622 hom ref = = = 2 1.17 N +990 2 chr1 45622 45630 no-call complex = ? ? -28 1.17 N +991 2 chr1 45630 45725 hom ref = = = -21 1.17 N +992 2 chr1 45725 45744 no-call complex TATATAATTTTTGTCAATT TATATANTTTTTGTCAATT ? 32 0 499 500 4 L1MA8:L1:28.0 2 1.17 N +993 2 chr1 45744 45749 hom ref = = = 16 1.17 N +994 2 chr1 45749 45760 no-call complex ATAATTTTTAA ATAATT?TTAA ? 0 0 499 500 4 L1MA8:L1:28.0 2 1.17 N +995 2 chr1 45760 45783 hom ref = = = -3 1.17 N +996 2 chr1 45783 45783 half ref ? 22 0 501 502 -3 2 1.17 N +997 2 chr1 45783 45794 hom ref = = = -8 1.17 N +998 2 chr1 45794 45794 half ref ? 21 0 501 502 -8 2 1.17 N +999 2 chr1 45794 45856 hom ref = = = -12 1.17 N +1000 2 chr1 45856 45894 no-call complex = ? ? -55 1.17 N +1001 2 chr1 45894 45973 hom ref = = = 10 1.17 N +1002 2 chr1 45973 46017 no-call complex = ? ? -18 1.17 N +1003 2 chr1 46017 46091 hom ref = = = 19 1.17 N +1004 2 chr1 46091 46098 no-call complex = ? ? -24 1.17 N +1005 2 chr1 46098 46147 hom ref = = = 10 1.17 N +1006 2 chr1 46147 46148 half ref A A N 25 70 507 508 12 L1MA9:L1:24.3 2 1.17 N +1007 2 chr1 46148 46150 hom ref = = = 6 1.17 N +1008 2 chr1 46150 46151 half ref T T N 70 70 507 508 6 L1MA9:L1:24.3 2 1.17 N +1009 2 chr1 46151 46212 hom ref = = = 6 1.17 N +1010 2 chr1 46212 46245 no-call complex = ? ? -53 1.17 N +1011 2 chr1 46245 46263 hom ref = = = 8 1.17 N +1012 2 chr1 46263 46264 half ref A A N 32 121 8 2 1.17 N +1013 2 chr1 46264 46398 hom ref = = = 8 1.17 N +1014 2 chr1 46398 46420 no-call complex = ? ? -509 1.17 N +1015 2 chr1 46420 46488 hom ref = = = 17 1.17 N +1016 2 chr1 46488 46496 no-call complex = ? ? -320 1.17 N +1017 2 chr1 46496 46666 hom ref = = = 22 1.17 N +1018 2 chr1 46666 46673 no-call complex = ? ? -11 1.17 N +1019 2 chr1 46673 47104 hom ref = = = 15 1.17 N +1020 2 chr1 47104 47111 no-call complex = ? ? -46 1.17 N +1021 2 chr1 47111 47286 hom ref = = = 29 1.17 N +1022 2 chr1 47286 47332 no-call complex = ? ? -142 1.17 N +1023 2 chr1 47332 47657 hom ref = = = 30 1.17 N +1024 2 chr1 47657 47664 no-call complex = ? ? -44 1.17 N +1025 2 chr1 47664 47757 hom ref = = = 15 1.17 N +1026 2 chr1 47757 47764 no-call complex = ? ? -23 1.17 N +1027 2 chr1 47764 47929 hom ref = = = 8 1.17 N +1028 2 chr1 47929 47930 half ref T T N 84 120 8 2 1.17 N +1029 2 chr1 47930 48142 hom ref = = = 5 1.17 N +1030 2 chr1 48142 48186 no-call complex = ? ? -47 1.17 N +1031 2 chr1 48186 48933 hom ref = = = -14 1.17 N +1032 2 chr1 48933 48940 no-call complex = ? ? -91 1.17 N +1033 2 chr1 48940 48972 hom ref = = = 63 1.17 N +1034 2 chr1 48972 49007 no-call complex = ? ? -29 1.17 N +1035 2 chr1 49007 49084 hom ref = = = 12 1.17 N +1036 2 chr1 49084 49091 no-call complex = ? ? -496 1.17 N +1037 2 chr1 49091 49182 hom ref = = = -45 1.17 N +1038 2 chr1 49182 49182 half ref ? 36 0 -45 L1PA14:L1:12.3 2 1.17 N +1039 2 chr1 49182 49239 hom ref = = = -45 1.17 N +1040 2 chr1 49239 49246 no-call complex = ? ? -63 1.17 N +1041 2 chr1 49246 49268 hom ref = = = 43 1.17 N +1042 2 chr1 49268 49294 no-call complex = ? ? -59 1.17 N +1043 2 chr1 49294 49423 hom ref = = = 33 1.17 N +1044 2 chr1 49423 49430 no-call complex = ? ? -26 1.17 N +1045 2 chr1 49430 49478 hom ref = = = 91 1.17 N +1046 2 chr1 49478 49518 no-call complex = ? ? -175 1.17 N +1047 2 chr1 49518 49849 hom ref = = = -36 1.17 N +1048 2 chr1 49849 49853 half ref CAAA CAAA ? 115 0 -36 2 1.17 N +1049 2 chr1 49853 50136 hom ref = = = -36 1.17 N +1050 2 chr1 50136 50144 half ref ATTTAATA ATTTAATA ? 36 0 517 518 -3 AT_rich:Low_complexity:0.0 2 1.17 N +1051 2 chr1 50144 50149 hom ref = = = -3 1.17 N +1052 2 chr1 50149 50151 half ref AT AT ? 26 0 517 518 4 AT_rich:Low_complexity:0.0 2 1.17 N +1053 2 chr1 50151 50477 hom ref = = = 9 1.17 N +1054 2 chr1 50477 50517 no-call complex = ? ? -21 1.17 N +1055 2 chr1 50517 51354 hom ref = = = -21 1.17 N +1056 2 chr1 51354 51389 no-call complex = ? ? -72 1.17 N +1057 2 chr1 51389 51399 hom ref = = = 30 1.17 N +1058 2 chr1 51399 51406 no-call complex = ? ? -12 1.17 N +1059 2 chr1 51406 51455 hom ref = = = 34 1.17 N +1060 2 chr1 51455 51502 no-call complex = ? ? -54 1.17 N +1061 2 chr1 51502 51600 hom ref = = = 16 1.17 N +1062 2 chr1 51600 51643 no-call complex = ? ? -510 1.17 N +1063 2 chr1 51643 51672 hom ref = = = -74 1.17 N +1064 2 chr1 51672 51673 hom snp T C C 53 53 dbsnp.100:rs2531251 469 1 1 0 1 -74 AluY:Alu:7.7 2 1.17 N +1065 2 chr1 51673 51679 hom ref = = = -74 1.17 N +1066 2 chr1 51679 51679 no-call complex ? ? 0 0 525 526 469 17 AluY:Alu:7.7 2 1.17 N +1067 2 chr1 51679 51682 hom ref = = = -13 1.17 N +1068 2 chr1 51682 51682 no-call complex ? ? 0 0 525 526 469 -13 AluY:Alu:7.7 2 1.17 N +1069 2 chr1 51682 51689 hom ref = = = -13 1.17 N +1070 2 chr1 51689 51692 half ref CCC CCC NNN 53 36 525 526 469 -2 AluY:Alu:7.7 2 1.17 N +1071 2 chr1 51692 51712 hom ref = = = -2 1.17 N +1072 2 chr1 51712 51750 no-call complex = ? ? -1 1.17 N +1073 2 chr1 51750 51867 hom ref = = = 7 1.17 N +1074 2 chr1 51867 51867 half ref ? 22 0 529 530 7 AluY:Alu:7.7 2 1.17 N +1075 2 chr1 51867 51874 hom ref = = = 7 1.17 N +1076 2 chr1 51874 51876 half ref AA AA ? 81 0 529 530 7 AluY:Alu:7.7 2 1.17 N +1077 2 chr1 51876 51894 hom ref = = = 7 1.17 N +1078 2 chr1 51894 51912 no-call complex = ? ? -16 1.17 N +1079 2 chr1 51912 51924 hom ref = = = 33 1.17 N +1080 2 chr1 51924 51954 no-call complex = ? ? -19 1.17 N +1081 2 chr1 51954 52021 hom ref = = = 12 1.17 N +1082 2 chr1 52021 52045 no-call complex ACTGCACGATGCGCATGGTAAAGA ACTGC?ACGATGCGCATGGTAAAGA ? 0 0 -1 2 1.17 N +1083 2 chr1 52045 52054 hom ref = = = 22 1.17 N +1084 2 chr1 52054 52066 no-call complex = ? ? -8 1.17 N +1085 2 chr1 52066 52101 hom ref = = = 26 1.17 N +1086 2 chr1 52101 52108 no-call complex = ? ? -21 1.17 N +1087 2 chr1 52108 52147 hom ref = = = 10 1.17 N +1088 2 chr1 52147 52177 no-call complex = ? ? -7 1.17 N +1089 2 chr1 52177 52183 hom ref = = = 12 1.17 N +1090 2 chr1 52183 52220 half ref ATTAATAATAACTTATCATCACATGATTTATTAATAA ATTAATAATAACTTATCATCACATGATTTATTAATAA ? 39 0 473 -30 AT_rich:Low_complexity:3.1 2 1.17 N +1091 2 chr1 52220 52237 hom ref = = = -92 1.17 N +1092 2 chr1 52237 52238 hom snp T G G 63 115 dbsnp.100:rs2691277 473 7 7 0 7 -92 AT_rich:Low_complexity:3.1 2 1.17 N +1093 2 chr1 52238 52373 hom ref = = = -92 1.17 N +1094 2 chr1 52373 52380 no-call complex = ? ? -411 1.17 N +1095 2 chr1 52380 52723 hom ref = = = 20 1.17 N +1096 2 chr1 52723 52730 no-call complex = ? ? -8 1.17 N +1097 2 chr1 52730 52859 hom ref = = = 74 1.17 N +1098 2 chr1 52859 52866 no-call complex = ? ? -22 1.17 N +1099 2 chr1 52866 53005 hom ref = = = -26 1.17 N +1100 2 chr1 53005 53012 no-call complex = ? ? -81 1.17 N +1101 2 chr1 53012 53205 hom ref = = = -127 1.17 N +1102 2 chr1 53205 53206 het-ref snp G C G 93 127 dbsnp.100:rs2854676 477 7 30 0 37 -127 2 1.17 N +1103 2 chr1 53206 53413 hom ref = = = -127 1.17 N +1104 2 chr1 53413 53431 no-call complex = ? ? -498 1.17 N +1105 2 chr1 53431 53687 hom ref = = = 19 1.17 N +1106 2 chr1 53687 53694 no-call complex = ? ? -5 1.17 N +1107 2 chr1 53694 53755 hom ref = = = 15 1.17 N +1108 2 chr1 53755 53792 no-call complex = ? ? -26 1.17 N +1109 2 chr1 53792 53811 hom ref = = = 34 1.17 N +1110 2 chr1 53811 53824 no-call complex = ? ? -27 1.17 N +1111 2 chr1 53824 54042 hom ref = = = -80 1.17 N +1112 2 chr1 54042 54043 het-ref snp C T C 66 84 dbsnp.100:rs2531228 481 3 10 0 13 -80 2 1.17 N +1113 2 chr1 54043 54174 hom ref = = = -80 1.17 N +1114 2 chr1 54174 54181 no-call complex = ? ? -27 1.17 N +1115 2 chr1 54181 54218 hom ref = = = 54 1.17 N +1116 2 chr1 54218 54225 no-call complex = ? ? -35 1.17 N +1117 2 chr1 54225 54285 hom ref = = = 36 1.17 N +1118 2 chr1 54285 54293 no-call complex = ? ? -704 1.17 N +1119 2 chr1 54293 54376 hom ref = = = 61 1.17 N +1120 2 chr1 54376 54398 no-call complex = ? ? -59 1.17 N +1121 2 chr1 54398 54475 hom ref = = = 19 1.17 N +1122 2 chr1 54475 54482 no-call complex = ? ? -50 1.17 N +1123 2 chr1 54482 54585 hom ref = = = -161 1.17 N +1124 2 chr1 54585 54586 het-ref snp T C T 94 94 dbsnp.131:rs79600414 486 9 19 0 28 -161 L2:L2:49.7 2 1.17 N +1125 2 chr1 54586 54708 hom ref = = = -161 1.17 N +1126 2 chr1 54708 54778 no-call complex = ? ? -154 1.17 N +1127 2 chr1 54778 55034 hom ref = = = 40 1.17 N +1128 2 chr1 55034 55041 no-call complex = ? ? -121 1.17 N +1129 2 chr1 55041 55125 hom ref = = = 17 1.17 N +1130 2 chr1 55125 55126 half ref C C N 92 92 543 544 488 0 L2:L2:49.7 2 1.17 N +1131 2 chr1 55126 55130 hom ref = = = -20 1.17 N +1132 2 chr1 55130 55131 half ref A A ? 46 0 543 544 488 -20 L2:L2:49.7 2 1.17 N +1133 2 chr1 55131 55163 hom ref = = = -239 1.17 N +1134 2 chr1 55163 55164 hom snp C A A 76 92 dbsnp.103:rs3091274 488 9 9 1 10 -239 L2:L2:49.7 2 1.17 N +1135 2 chr1 55164 55301 hom ref = = = -239 1.17 N +1136 2 chr1 55301 55302 het-ref snp C T C 87 95 546 545 dbsnp.103:rs3091273 489 15 19 0 34 -13 L2:L2:49.7 2 1.17 N +1137 2 chr1 55302 55321 hom ref = = = -13 1.17 N +1138 2 chr1 55321 55322 het-ref snp C T C 95 95 546 545 dbsnp.103:rs3107974 489 12 12 0 24 30 L2:L2:49.7 2 1.17 N +1139 2 chr1 55322 55325 hom ref = = = -9 1.17 N +1140 2 chr1 55325 55326 het-ref snp T C T 95 95 546 545 dbsnp.103:rs3107975 489 12 11 0 23 -9 L2:L2:49.7 2 1.17 N +1141 2 chr1 55326 55377 hom ref = = = -9 1.17 N +1142 2 chr1 55377 55397 no-call complex = ? ? -32 1.17 N +1143 2 chr1 55397 55424 hom ref = = = 59 1.17 N +1144 2 chr1 55424 55468 no-call complex = ? ? -340 1.17 N +1145 2 chr1 55468 55541 hom ref = = = 46 1.17 N +1146 2 chr1 55541 55553 no-call complex = ? ? 20 1.17 N +1147 2 chr1 55553 55597 hom ref = = = 60 1.17 N +1148 2 chr1 55597 55605 no-call complex = ? ? 54 1.17 N +1149 2 chr1 55605 55812 hom ref = = = 43 1.17 N +1150 2 chr1 55812 55853 no-call complex = ? ? -59 1.17 N +1151 2 chr1 55853 55925 hom ref = = = -300 1.17 N +1152 2 chr1 55925 55926 hom snp T C C 66 97 dbsnp.101:rs3020698;dbsnp.121:rs13343114 495 12 12 0 12 -300 2 1.17 N +1153 2 chr1 55926 55972 hom ref = = = -300 1.17 N +1154 2 chr1 55972 55979 no-call complex = ? ? -92 1.17 N +1155 2 chr1 55979 56273 hom ref = = = 41 1.17 N +1156 2 chr1 56273 56301 no-call complex = ? ? -76 1.17 N +1157 2 chr1 56301 56377 hom ref = = = 72 1.17 N +1158 2 chr1 56377 56384 no-call complex = ? ? -492 1.17 N +1159 2 chr1 56384 56481 hom ref = = = 36 1.17 N +1160 2 chr1 56481 56501 no-call complex = ? ? -93 1.17 N +1161 2 chr1 56501 56616 hom ref = = = 1 1.17 N +1162 2 chr1 56616 56618 half ref TT TT ? 109 0 557 558 -6 2 1.17 N +1163 2 chr1 56618 56637 hom ref = = = -6 1.17 N +1164 2 chr1 56637 56638 half ref C C N 41 120 557 558 -1 2 1.17 N +1165 2 chr1 56638 56793 hom ref = = = -1 1.17 N +1166 2 chr1 56793 56814 no-call complex = ? ? -67 1.17 N +1167 2 chr1 56814 56943 hom ref = = = 29 1.17 N +1168 2 chr1 56943 56950 no-call complex = ? ? -303 1.17 N +1169 2 chr1 56950 56995 hom ref = = = -5 1.17 N +1170 2 chr1 56995 56995 half ref ? 26 0 2 2 1.17 N +1171 2 chr1 56995 57029 hom ref = = = 2 1.17 N +1172 2 chr1 57029 57072 no-call complex = ? ? -10 1.17 N +1173 2 chr1 57072 57242 hom ref = = = 28 1.17 N +1174 2 chr1 57242 57249 no-call complex = ? ? 0 1.17 N +1175 2 chr1 57249 57372 hom ref = = = 24 1.17 N +1176 2 chr1 57372 57379 no-call complex = ? ? -49 1.17 N +1177 2 chr1 57379 57432 hom ref = = = -23 1.17 N +1178 2 chr1 57432 57432 half ref ? 35 0 74 2 1.17 N +1179 2 chr1 57432 57524 hom ref = = = -6 1.17 N +1180 2 chr1 57524 57525 half ref A A N 121 121 -6 2 1.17 N +1181 2 chr1 57525 57618 hom ref = = = -6 1.17 N +1182 2 chr1 57618 57644 no-call complex = ? ? -22 1.17 N +1183 2 chr1 57644 57678 hom ref = = = 19 1.17 N +1184 2 chr1 57678 57685 no-call complex = ? ? -11 1.17 N +1185 2 chr1 57685 57814 hom ref = = = 43 1.17 N +1186 2 chr1 57814 57858 no-call complex = ? ? -67 1.17 N +1187 2 chr1 57858 57951 hom ref = = = -148 1.17 N +1188 2 chr1 57951 57952 hom snp A C C 72 157 dbsnp.100:rs2691334 505 2 2 0 2 -148 2 1.17 N +1189 2 chr1 57952 57995 hom ref = = = -148 1.17 N +1190 2 chr1 57995 58002 no-call complex = ? ? -27 1.17 N +1191 2 chr1 58002 58210 hom ref = = = -327 1.17 N +1192 2 chr1 58210 58211 hom snp A G G 98 114 dbsnp.100:rs2691335 507 11 11 0 11 -327 2 1.17 N +1193 2 chr1 58211 58405 hom ref = = = -327 1.17 N +1194 2 chr1 58405 58451 no-call complex = ? ? -89 1.17 N +1195 2 chr1 58451 58483 hom ref = = = 5 1.17 N +1196 2 chr1 58483 58484 half ref G G N 88 120 5 2 1.17 N +1197 2 chr1 58484 58777 hom ref = = = 5 1.17 N +1198 2 chr1 58777 58815 no-call complex = ? ? -105 1.17 N +1199 2 chr1 58815 59050 hom ref = = = -118 1.17 N +1200 2 chr1 59050 59051 het-ref snp A G A 66 91 dbsnp.100:rs2691352 510 6 21 0 27 -118 2 1.17 N +1201 2 chr1 59051 59168 hom ref = = = -118 1.17 N +1202 2 chr1 59168 59169 half ref A A ? 121 0 -4 L2a:L2:37.1 2 1.17 N +1203 2 chr1 59169 59254 hom ref = = = -4 1.17 N +1204 2 chr1 59254 59279 no-call complex = ? ? -3 1.17 N +1205 2 chr1 59279 59343 hom ref = = = -47 1.17 N +1206 2 chr1 59343 59344 het-ref snp C T C 57 120 dbsnp.100:rs2854667 511 25 23 0 48 -47 2 1.17 N +1207 2 chr1 59344 59497 hom ref = = = -98 1.17 N +1208 2 chr1 59497 59498 het-ref snp T C T 74 120 dbsnp.100:rs2854666;dbsnp.131:rs76479716 512 12 15 0 27 -98 2 1.17 N +1209 2 chr1 59498 59584 hom ref = = = -98 1.17 N +1210 2 chr1 59584 59598 no-call complex = ? ? -18 1.17 N +1211 2 chr1 59598 60268 hom ref = = = -17 1.17 N +1212 2 chr1 60268 60282 no-call complex = ? ? -155 1.17 N +1213 2 chr1 60282 60404 hom ref = = = 19 1.17 N +1214 2 chr1 60404 60436 no-call complex = ? ? -96 1.17 N +1215 2 chr1 60436 60559 hom ref = = = 7 1.17 N +1216 2 chr1 60559 60560 half ref T T ? 27 0 7 MER47A:TcMar-Tigger:35.4 2 1.17 N +1217 2 chr1 60560 60691 hom ref = = = 7 1.17 N +1218 2 chr1 60691 60729 no-call complex = ? ? -64 1.17 N +1219 2 chr1 60729 60784 hom ref = = = 14 1.17 N +1220 2 chr1 60784 60797 no-call complex AAAAATACATGCA AAAAATNCATGCA ? 46 0 516 -72 2 1.17 N +1221 2 chr1 60797 60808 hom ref = = = 17 1.17 N +1222 2 chr1 60808 60813 half ref TAGAA TAGAA NANAN 41 97 516 16 2 1.17 N +1223 2 chr1 60813 60828 hom ref = = = -64 1.17 N +1224 2 chr1 60828 60829 het-ref snp C T C 60 97 dbsnp.100:rs2691284 516 1 11 0 12 -64 2 1.17 N +1225 2 chr1 60829 60905 hom ref = = = -64 1.17 N +1226 2 chr1 60905 60912 no-call complex = ? ? -94 1.17 N +1227 2 chr1 60912 61090 hom ref = = = 6 1.17 N +1228 2 chr1 61090 61093 half ref TCA TCA ? 64 0 6 2 1.17 N +1229 2 chr1 61093 61285 hom ref = = = 12 1.17 N +1230 2 chr1 61285 61293 no-call complex = ? ? -45 1.17 N +1231 2 chr1 61293 61353 hom ref = = = 7 1.17 N +1232 2 chr1 61353 61353 half ref ? 35 0 581 582 7 2 1.17 N +1233 2 chr1 61353 61359 hom ref = = = 7 1.17 N +1234 2 chr1 61359 61364 half ref AATAT AATAT ? 45 0 581 582 7 2 1.17 N +1235 2 chr1 61364 61416 hom ref = = = 1 1.17 N +1236 2 chr1 61416 61417 half ref T T N 79 79 583 584 518 1 2 1.17 N +1237 2 chr1 61417 61428 hom ref = = = 1 1.17 N +1238 2 chr1 61428 61429 half ref T T N 24 79 583 584 518 -11 2 1.17 N +1239 2 chr1 61429 61441 hom ref = = = -134 1.17 N +1240 2 chr1 61441 61442 hom snp A G G 23 79 dbsnp.100:rs2531261;dbsnp.129:rs62637818;dbsnp.131:rs74970982 518 8 8 0 8 -134 2 1.17 N +1241 2 chr1 61442 61452 hom ref = = = -134 1.17 N +1242 2 chr1 61452 61457 half ref TAATT TAATT NANTN 24 132 7 2 1.17 N +1243 2 chr1 61457 61476 hom ref = = = 17 1.17 N +1244 2 chr1 61476 61511 no-call complex = ? ? -2 1.17 N +1245 2 chr1 61511 61537 hom ref = = = -8 1.17 N +1246 2 chr1 61537 61538 half ref G G N 120 120 587 588 -8 2 1.17 N +1247 2 chr1 61538 61556 hom ref = = = -8 1.17 N +1248 2 chr1 61556 61561 half ref TTAAT TTAAT ? 53 0 587 588 6 2 1.17 N +1249 2 chr1 61561 61677 hom ref = = = 15 1.17 N +1250 2 chr1 61677 61709 no-call complex = ? ? 2 1.17 N +1251 2 chr1 61709 61847 hom ref = = = 13 1.17 N +1252 2 chr1 61847 61886 no-call complex = ? ? -27 1.17 N +1253 2 chr1 61886 61986 hom ref = = = -2 1.17 N +1254 2 chr1 61986 61987 half ref A A ? 36 0 593 594 -2 AluSc:Alu:8.4 2 1.17 N +1255 2 chr1 61987 61996 hom ref = = = -2 1.17 N +1256 2 chr1 61996 62009 half ref GACTACAGGCATG GACTACAGGCATG ? 45 0 593 594 9 AluSc:Alu:8.4 2 1.17 N +1257 2 chr1 62009 62136 hom ref = = = 18 1.17 N +1258 2 chr1 62136 62143 no-call complex = ? ? -49 1.17 N +1259 2 chr1 62143 62176 hom ref = = = 52 1.17 N +1260 2 chr1 62176 62206 no-call complex = ? ? -25 1.17 N +1261 2 chr1 62206 62235 hom ref = = = 18 1.17 N +1262 2 chr1 62235 62250 no-call complex = ? ? -60 1.17 N +1263 2 chr1 62250 62422 hom ref = = = 15 1.17 N +1264 2 chr1 62422 62429 no-call complex = ? ? -37 1.17 N +1265 2 chr1 62429 62574 hom ref = = = 29 1.17 N +1266 2 chr1 62574 62581 no-call complex = ? ? -15 1.17 N +1267 2 chr1 62581 62624 hom ref = = = 45 1.17 N +1268 2 chr1 62624 62647 no-call complex = ? ? -92 1.17 N +1269 2 chr1 62647 62703 hom ref = = = 23 1.17 N +1270 2 chr1 62703 62710 no-call complex = ? ? -25 1.17 N +1271 2 chr1 62710 62918 hom ref = = = 12 1.17 N +1272 2 chr1 62918 62928 no-call complex = ? ? -16 1.17 N +1273 2 chr1 62928 63029 hom ref = = = 41 1.17 N +1274 2 chr1 63029 63077 no-call complex = ? ? -49 1.17 N +1275 2 chr1 63077 63235 hom ref = = = 27 1.17 N +1276 2 chr1 63235 63271 no-call complex = ? ? -59 1.17 N +1277 2 chr1 63271 63300 hom ref = = = 14 1.17 N +1278 2 chr1 63300 63335 no-call complex = ? ? -4 1.17 N +1279 2 chr1 63335 63420 hom ref = = = 26 1.17 N +1280 2 chr1 63420 63438 no-call complex = ? ? -238 1.17 N +1281 2 chr1 63438 63523 hom ref = = = 29 1.17 N +1282 2 chr1 63523 63530 no-call complex = ? ? -14 1.17 N +1283 2 chr1 63530 63666 hom ref = = = 37 1.17 N +1284 2 chr1 63666 63673 no-call complex = ? ? -18 1.17 N +1285 2 chr1 63673 63788 hom ref = = = 32 1.17 N +1286 2 chr1 63788 63795 no-call complex = ? ? -26 1.17 N +1287 2 chr1 63795 63876 hom ref = = = 31 1.17 N +1288 2 chr1 63876 63914 no-call complex = ? ? -174 1.17 N +1289 2 chr1 63914 64121 hom ref = = = 15 1.17 N +1290 2 chr1 64121 64160 no-call complex = ? ? -37 1.17 N +1291 2 chr1 64160 64235 hom ref = = = 8 1.17 N +1292 2 chr1 64235 64236 half ref T T N 123 123 8 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1293 2 chr1 64236 64287 hom ref = = = 8 1.17 N +1294 2 chr1 64287 64337 no-call complex = ? ? 4 1.17 N +1295 2 chr1 64337 64581 hom ref = = = 10 1.17 N +1296 2 chr1 64581 64599 no-call complex = ? ? 6 1.17 N +1297 2 chr1 64599 64609 hom ref = = = 18 1.17 N +1298 2 chr1 64609 64632 no-call complex = ? ? -44 1.17 N +1299 2 chr1 64632 64711 hom ref = = = 9 1.17 N +1300 2 chr1 64711 64712 half ref T T ? 120 0 9 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1301 2 chr1 64712 64831 hom ref = = = -14 1.17 N +1302 2 chr1 64831 64832 half ref C C N 120 156 -14 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1303 2 chr1 64832 64923 hom ref = = = -14 1.17 N +1304 2 chr1 64923 64930 no-call complex = ? ? -17 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1305 2 chr1 64930 64972 hom ref = = = 39 1.17 N +1306 2 chr1 64972 64989 no-call complex = ? ? -121 1.17 N +1307 2 chr1 64989 65249 hom ref = = = 5 1.17 N +1308 2 chr1 65249 65256 no-call complex = ? ? -89 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1309 2 chr1 65256 65924 hom ref = = = -2 1.17 N +1310 2 chr1 65924 65927 half ref TTA TTA ? 36 0 3 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1311 2 chr1 65927 66002 hom ref = = = -31 1.17 N +1312 2 chr1 66002 66033 half ref TTTTACAGCTTTTGAAAGAATAAACTCATTT TTTTACAGCTTTTGAAAGAATAAACTCATTT ?TTT?GCTT?TGAA?GAA? 40 80 535 -35 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC MIR3:MIR:38.5 2 1.17 N +1313 2 chr1 66033 66077 hom ref = = = 14 1.17 N +1314 2 chr1 66077 66098 no-call complex = ? ? 1 1.17 N +1315 2 chr1 66098 66130 hom ref = = = 3 1.17 N +1316 2 chr1 66130 66131 half ref C C N 36 196 3 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC MIR3:MIR:38.5 2 1.17 N +1317 2 chr1 66131 66156 hom ref = = = 3 1.17 N +1318 2 chr1 66156 66636 no-call complex = ? ? -7 1.17 N +1319 2 chr1 66636 66647 hom ref = = = 14 1.17 N +1320 2 chr1 66647 66654 no-call complex = ? ? 2 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1321 2 chr1 66654 66714 hom ref = = = 16 1.17 N +1322 2 chr1 66714 66743 no-call complex = ? ? -22 1.17 N +1323 2 chr1 66743 66762 hom ref = = = 10 1.17 N +1324 2 chr1 66762 66817 no-call complex = ? ? -14 1.17 N +1325 2 chr1 66817 66926 hom ref = = = 10 1.17 N +1326 2 chr1 66926 66933 no-call complex = ? ? -162 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1327 2 chr1 66933 67173 hom ref = = = 23 1.17 N +1328 2 chr1 67173 67188 no-call complex = ? ? -59 1.17 N +1329 2 chr1 67188 67219 hom ref = = = 17 1.17 N +1330 2 chr1 67219 67245 no-call complex = ? ? -80 1.17 N +1331 2 chr1 67245 67325 hom ref = = = 29 1.17 N +1332 2 chr1 67325 67354 no-call complex = ? ? -87 1.17 N +1333 2 chr1 67354 67601 hom ref = = = 41 1.17 N +1334 2 chr1 67601 67645 no-call complex = ? ? -51 1.17 N +1335 2 chr1 67645 68305 hom ref = = = 17 1.17 N +1336 2 chr1 68305 68306 het-ref snp C T C 44 44 618 617 dbsnp.101:rs3020702 543 27 20 0 47 17 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1337 2 chr1 68306 68315 hom ref = = = 6 1.17 N +1338 2 chr1 68315 68316 het-ref snp T C T 44 44 618 617 dbsnp.101:rs2907081 543 27 20 0 47 6 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1339 2 chr1 68316 68612 hom ref = = = 6 1.17 N +1340 2 chr1 68612 68628 no-call complex = ? ? -107 1.17 N +1341 2 chr1 68628 68704 hom ref = = = 8 1.17 N +1342 2 chr1 68704 68705 half ref T T N 69 133 8 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 2 1.17 N +1343 2 chr1 68705 68845 hom ref = = = 8 1.17 N +1344 2 chr1 68845 68852 no-call complex = ? ? -11 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 79501:NM_001005484.1:OR4F5::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1345 2 chr1 68852 68885 hom ref = = = 47 1.17 N +1346 2 chr1 68885 68902 no-call complex = ? ? -212 1.17 N +1347 2 chr1 68902 69452 hom ref = = = -57 1.17 N +1348 2 chr1 69452 69453 het-ref snp G A G 61 121 dbsnp.100:rs2854682 546 6 37 0 43 -57 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:COMPATIBLE 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:NO-CHANGE 2 1.17 N +1349 2 chr1 69453 69510 hom ref = = = -307 1.17 N +1350 2 chr1 69510 69511 hom snp A G G 123 123 dbsnp.100:rs2691305;dbsnp.131:rs75062661 547 3 3 0 3 -307 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:MISSENSE 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:MISSENSE 2 1.17 N +1351 2 chr1 69511 69551 hom ref = = = -307 1.17 N +1352 2 chr1 69551 69552 het-ref snp G C G 98 98 623 624 dbsnp.100:rs2531266;dbsnp.129:rs55874132 548 4 27 0 31 -1 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:COMPATIBLE 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:NO-CHANGE 2 1.17 N +1353 2 chr1 69552 69568 hom ref = = = -52 1.17 N +1354 2 chr1 69568 69569 het-ref snp T C T 98 98 623 624 dbsnp.100:rs2531267 548 3 29 0 32 -52 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:MISSENSE 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:NO-CHANGE 2 1.17 N +1355 2 chr1 69569 69750 hom ref = = = -52 1.17 N +1356 2 chr1 69750 69751 half ref C C N 118 121 9 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:NO-CHANGE 79501:NM_001005484.1:OR4F5:PFAM:PF00001:7tm_1:CDS:UNKNOWN-VNC 2 1.17 N +1357 2 chr1 69751 69964 hom ref = = = 9 1.17 N +1358 2 chr1 69964 69971 no-call complex = ? ? 5 79501:NM_001005484.1:OR4F5::::CDS:UNKNOWN-VNC 79501:NM_001005484.1:OR4F5::::CDS:UNKNOWN-VNC 1.17 N +1359 2 chr1 69971 70241 hom ref = = = 25 1.17 N +1360 2 chr1 70241 70249 no-call complex = ? ? 36 1.17 N +1361 2 chr1 70249 70296 hom ref = = = 20 1.17 N +1362 2 chr1 70296 70320 no-call complex = ? ? -325 1.17 N +1363 2 chr1 70320 70348 hom ref = = = 20 1.17 N +1364 2 chr1 70348 70348 half ref ? 29 0 627 628 20 AT_rich:Low_complexity:0.0 3 1.17 N +1365 2 chr1 70348 70350 hom ref = = = -5 1.17 N +1366 2 chr1 70350 70351 half ref T T ? 30 0 627 628 -5 AT_rich:Low_complexity:0.0 3 1.17 N +1367 2 chr1 70351 70357 hom ref = = = -5 1.17 N +1368 2 chr1 70357 70361 half ref AAAT AAAT ? 24 0 627 628 -17 AT_rich:Low_complexity:0.0 3 1.17 N +1369 2 chr1 70361 70384 hom ref = = = -17 1.17 N +1370 2 chr1 70384 70425 no-call complex = ? ? -37 1.17 N +1371 2 chr1 70425 70600 hom ref = = = 26 1.17 N +1372 2 chr1 70600 70631 no-call complex = ? ? -94 1.17 N +1373 2 chr1 70631 70660 hom ref = = = 43 1.17 N +1374 2 chr1 70660 70669 no-call complex = ? ? -36 1.17 N +1375 2 chr1 70669 71574 hom ref = = = 7 1.17 N +1376 2 chr1 71574 71580 half ref TTCAAA TTCAAA ? 30 0 6 L1MC4a:L1:44.9 3 1.17 N +1377 2 chr1 71580 71674 hom ref = = = -20 1.17 N +1378 2 chr1 71674 71676 half ref AA AA ? 24 0 631 632 6 3 1.17 N +1379 2 chr1 71676 71681 hom ref = = = 12 1.17 N +1380 2 chr1 71681 71681 half ref ? 27 0 631 632 24 3 1.17 N +1381 2 chr1 71681 71688 hom ref = = = 23 1.17 N +1382 2 chr1 71688 71695 half ref CTATGAG CTATGAG ? 26 0 631 632 18 3 1.17 N +1383 2 chr1 71695 71709 hom ref = = = -37 1.17 N +1384 2 chr1 71709 71710 half ref A A N 47 47 -37 3 1.17 N +1385 2 chr1 71710 71744 hom ref = = = -37 1.17 N +1386 2 chr1 71744 71745 half ref T T N 120 120 6 L1MC4a:L1:38.2 3 1.17 N +1387 2 chr1 71745 71799 hom ref = = = -8 1.17 N +1388 2 chr1 71799 71799 half ref ? 25 0 -8 L1MC4a:L1:38.2 3 1.17 N +1389 2 chr1 71799 71842 hom ref = = = -8 1.17 N +1390 2 chr1 71842 71879 no-call complex = ? ? -27 1.17 N +1391 2 chr1 71879 71887 hom ref = = = 10 1.17 N +1392 2 chr1 71887 71905 no-call complex = ? ? -14 1.17 N +1393 2 chr1 71905 72001 hom ref = = = 11 1.17 N +1394 2 chr1 72001 72004 half ref ATT ATT NNN 20 120 8 3 1.17 N +1395 2 chr1 72004 72082 hom ref = = = 14 1.17 N +1396 2 chr1 72082 72167 no-call complex = ? ? -39 1.17 N +1397 2 chr1 72167 72183 hom ref = = = 26 1.17 N +1398 2 chr1 72183 72200 no-call complex = ? ? -5 1.17 N +1399 2 chr1 72200 72247 hom ref = = = 19 1.17 N +1400 2 chr1 72247 72254 no-call complex = ? ? -23 1.17 N +1401 2 chr1 72254 72399 hom ref = = = -13 1.17 N +1402 2 chr1 72399 72422 no-call complex = ? ? -35 1.17 N +1403 2 chr1 72422 72452 hom ref = = = 23 1.17 N +1404 2 chr1 72452 72459 no-call complex = ? ? -199 1.17 N +1405 2 chr1 72459 72486 hom ref = = = 16 1.17 N +1406 2 chr1 72486 72526 no-call complex = ? ? -639 1.17 N +1407 2 chr1 72526 72582 hom ref = = = -1 1.17 N +1408 2 chr1 72582 72583 half ref C C N 120 120 639 640 -1 L1PA7:L1:7.3 3 1.17 N +1409 2 chr1 72583 72586 hom ref = = = -1 1.17 N +1410 2 chr1 72586 72586 half ref ? 28 0 639 640 3 L1PA7:L1:7.3 3 1.17 N +1411 2 chr1 72586 72648 hom ref = = = 3 1.17 N +1412 2 chr1 72648 72655 no-call complex = ? ? -85 1.17 N +1413 2 chr1 72655 72693 hom ref = = = 53 1.17 N +1414 2 chr1 72693 72708 no-call complex = ? ? -59 1.17 N +1415 2 chr1 72708 72781 hom ref = = = 23 1.17 N +1416 2 chr1 72781 72791 no-call complex = ? ? -195 1.17 N +1417 2 chr1 72791 72858 hom ref = = = 13 1.17 N +1418 2 chr1 72858 72865 no-call complex = ? ? -489 1.17 N +1419 2 chr1 72865 73084 hom ref = = = 17 1.17 N +1420 2 chr1 73084 73091 no-call complex = ? ? -147 1.17 N +1421 2 chr1 73091 73196 hom ref = = = 1 1.17 N +1422 2 chr1 73196 73206 no-call complex = ? ? -39 1.17 N +1423 2 chr1 73206 73245 hom ref = = = 16 1.17 N +1424 2 chr1 73245 73252 no-call complex = ? ? -10 1.17 N +1425 2 chr1 73252 73634 hom ref = = = 0 1.17 N +1426 2 chr1 73634 73635 half ref T T N 111 111 643 644 3 L1PA16:L1:18.4 3 1.17 N +1427 2 chr1 73635 73655 hom ref = = = 3 1.17 N +1428 2 chr1 73655 73656 half ref C C N 111 111 643 644 9 L1PA16:L1:18.4 3 1.17 N +1429 2 chr1 73656 73658 hom ref = = = 9 1.17 N +1430 2 chr1 73658 73659 half ref T T N 22 54 643 644 17 L1PA16:L1:18.4 3 1.17 N +1431 2 chr1 73659 73688 hom ref = = = 10 1.17 N +1432 2 chr1 73688 73709 no-call complex = ? ? -69 1.17 N +1433 2 chr1 73709 73739 hom ref = = = 2 1.17 N +1434 2 chr1 73739 73740 half ref T T N 36 122 2 L1MC4a:L1:31.9 3 1.17 N +1435 2 chr1 73740 73770 hom ref = = = 2 1.17 N +1436 2 chr1 73770 73804 half ref ATAAAATATCAAATATCTGACCTCAATATTTGAT ATAAAATATCAAATATCTGACCTCAATATTTGAT ? 21 0 -4 L1MC4a:L1:31.9 3 1.17 N +1437 2 chr1 73804 73817 hom ref = = = 10 1.17 N +1438 2 chr1 73817 73893 no-call complex = ? ? -44 1.17 N +1439 2 chr1 73893 73898 hom ref = = = 14 1.17 N +1440 2 chr1 73898 73926 no-call complex = ? ? -34 1.17 N +1441 2 chr1 73926 73973 hom ref = = = 13 1.17 N +1442 2 chr1 73973 73981 no-call complex = ? ? 6 1.17 N +1443 2 chr1 73981 73986 hom ref = = = 11 1.17 N +1444 2 chr1 73986 74040 no-call complex = ? ? -60 1.17 N +1445 2 chr1 74040 74062 hom ref = = = 13 1.17 N +1446 2 chr1 74062 74326 no-call complex = ? ? -49 1.17 N +1447 2 chr1 74326 74335 hom ref = = = 12 1.17 N +1448 2 chr1 74335 74370 no-call complex = ? ? -13 1.17 N +1449 2 chr1 74370 74395 hom ref = = = 11 1.17 N +1450 2 chr1 74395 74419 no-call complex = ? ? -37 1.17 N +1451 2 chr1 74419 74424 hom ref = = = 10 1.17 N +1452 2 chr1 74424 74459 no-call complex = ? ? -7 1.17 N +1453 2 chr1 74459 74464 hom ref = = = 16 1.17 N +1454 2 chr1 74464 74536 no-call complex = ? ? -16 1.17 N +1455 2 chr1 74536 74551 hom ref = = = 10 1.17 N +1456 2 chr1 74551 74594 no-call complex = ? ? -9 1.17 N +1457 2 chr1 74594 74632 hom ref = = = 10 1.17 N +1458 2 chr1 74632 74730 no-call complex = ? ? -175 1.17 N +1459 2 chr1 74730 74736 hom ref = = = 23 1.17 N +1460 2 chr1 74736 74747 half ref TGGATATTAGC TGGATATTAGC ? 36 0 7 L1PA2:L1:1.6 3 1.17 N +1461 2 chr1 74747 74758 hom ref = = = 13 1.17 N +1462 2 chr1 74758 74759 no-call complex T N N 36 36 659 660 13 L1PA2:L1:1.6 3 1.17 N +1463 2 chr1 74759 74763 hom ref = = = 13 1.17 N +1464 2 chr1 74763 74782 no-call complex AGGTTGCAAAAATTTTCTC AGGTTGC?AAAAATTTTCTC ? 0 0 659 660 2 L1PA2:L1:1.6 3 1.17 N +1465 2 chr1 74782 74803 hom ref = = = 1 1.17 N +1466 2 chr1 74803 74804 half ref C C N 121 121 661 662 1 L1PA2:L1:1.6 3 1.17 N +1467 2 chr1 74804 74814 hom ref = = = -5 1.17 N +1468 2 chr1 74814 74815 half ref T T N 101 121 661 662 -5 L1PA2:L1:1.6 3 1.17 N +1469 2 chr1 74815 74824 hom ref = = = -5 1.17 N +1470 2 chr1 74824 74886 no-call complex = ? ? -12 1.17 N +1471 2 chr1 74886 74926 hom ref = = = 13 1.17 N +1472 2 chr1 74926 74983 no-call complex = ? ? -5 1.17 N +1473 2 chr1 74983 74991 hom ref = = = 22 1.17 N +1474 2 chr1 74991 75019 no-call complex = ? ? -77 1.17 N +1475 2 chr1 75019 75086 hom ref = = = 18 1.17 N +1476 2 chr1 75086 75281 no-call complex = ? ? -47 1.17 N +1477 2 chr1 75281 75294 hom ref = = = 19 1.17 N +1478 2 chr1 75294 75318 no-call complex = ? ? -52 1.17 N +1479 2 chr1 75318 75323 hom ref = = = 13 1.17 N +1480 2 chr1 75323 75353 no-call complex = ? ? -47 1.17 N +1481 2 chr1 75353 75359 hom ref = = = 11 1.17 N +1482 2 chr1 75359 75389 no-call complex = ? ? -54 1.17 N +1483 2 chr1 75389 75396 hom ref = = = 10 1.17 N +1484 2 chr1 75396 76267 no-call complex = ? ? -47 1.17 N +1485 2 chr1 76267 76274 hom ref = = = 11 1.17 N +1486 2 chr1 76274 76312 no-call complex = ? ? -25 1.17 N +1487 2 chr1 76312 76337 hom ref = = = 14 1.17 N +1488 2 chr1 76337 76348 no-call complex = ? ? -56 1.17 N +1489 2 chr1 76348 76512 hom ref = = = -49 1.17 N +1490 2 chr1 76512 76514 half ref CT CT ? 49 0 -49 L1PA2:L1:2.1 3 1.17 N +1491 2 chr1 76514 76587 hom ref = = = 14 1.17 N +1492 2 chr1 76587 76603 no-call complex = ? ? -20 1.17 N +1493 2 chr1 76603 76623 hom ref = = = 19 1.17 N +1494 2 chr1 76623 76656 no-call complex = ? ? -55 1.17 N +1495 2 chr1 76656 76928 hom ref = = = 15 1.17 N +1496 2 chr1 76928 76943 no-call complex = ? ? -16 1.17 N +1497 2 chr1 76943 77027 hom ref = = = 15 1.17 N +1498 2 chr1 77027 77038 no-call complex = ? ? 27 1.17 N +1499 2 chr1 77038 77170 hom ref = = = 14 1.17 N +1500 2 chr1 77170 77207 no-call complex = ? ? -34 1.17 N +1501 2 chr1 77207 77335 hom ref = = = 17 1.17 N +1502 2 chr1 77335 77371 no-call complex = ? ? -188 1.17 N +1503 2 chr1 77371 77413 hom ref = = = 10 1.17 N +1504 2 chr1 77413 77435 no-call complex = ? ? -8 1.17 N +1505 2 chr1 77435 77461 hom ref = = = -86 1.17 N +1506 2 chr1 77461 77462 hom snp G A A 26 28 dbsnp.100:rs2462497 590 4 4 0 4 -86 3 1.17 N +1507 2 chr1 77462 77466 hom ref = = = -86 1.17 N +1508 2 chr1 77466 77469 half ref ACA ACA NCN 30 91 590 4 3 1.17 N +1509 2 chr1 77469 77546 hom ref = = = 4 1.17 N +1510 2 chr1 77546 77621 no-call complex = ? ? -101 1.17 N +1511 2 chr1 77621 77784 hom ref = = = 6 1.17 N +1512 2 chr1 77784 77789 half ref TCAGA TCAGA NCNGN 21 78 675 676 6 3 1.17 N +1513 2 chr1 77789 77796 hom ref = = = 12 1.17 N +1514 2 chr1 77796 77797 half ref A A N 120 120 675 676 20 3 1.17 N +1515 2 chr1 77797 77801 hom ref = = = 19 1.17 N +1516 2 chr1 77801 77802 half ref T T N 60 120 675 676 2 3 1.17 N +1517 2 chr1 77802 77806 hom ref = = = 2 1.17 N +1518 2 chr1 77806 77807 half ref T T ? 120 0 675 676 2 3 1.17 N +1519 2 chr1 77807 77873 hom ref = = = -7 1.17 N +1520 2 chr1 77873 77873 half ref ? 29 0 46 3 1.17 N +1521 2 chr1 77873 77915 hom ref = = = 21 1.17 N +1522 2 chr1 77915 77922 no-call complex = ? ? -18 1.17 N +1523 2 chr1 77922 77953 hom ref = = = 12 1.17 N +1524 2 chr1 77953 77964 no-call complex = ? ? -30 1.17 N +1525 2 chr1 77964 78034 hom ref = = = 8 1.17 N +1526 2 chr1 78034 78035 half ref G G N 30 205 8 L1MC4a:L1:35.4 3 1.17 N +1527 2 chr1 78035 78085 hom ref = = = 8 1.17 N +1528 2 chr1 78085 78129 no-call complex = ? ? -16 1.17 N +1529 2 chr1 78129 78180 hom ref = = = 13 1.17 N +1530 2 chr1 78180 78229 no-call complex = ? ? -82 1.17 N +1531 2 chr1 78229 78387 hom ref = = = 12 1.17 N +1532 2 chr1 78387 78404 no-call complex = ? ? 2 1.17 N +1533 2 chr1 78404 78431 hom ref = = = 10 1.17 N +1534 2 chr1 78431 78479 no-call complex = ? ? -15 1.17 N +1535 2 chr1 78479 78506 hom ref = = = 50 1.17 N +1536 2 chr1 78506 78513 no-call complex = ? ? -47 1.17 N +1537 2 chr1 78513 78629 hom ref = = = 17 1.17 N +1538 2 chr1 78629 78662 no-call complex = ? ? -11 1.17 N +1539 2 chr1 78662 78732 hom ref = = = 26 1.17 N +1540 2 chr1 78732 78746 no-call complex = ? ? -4 1.17 N +1541 2 chr1 78746 78918 hom ref = = = 2 1.17 N +1542 2 chr1 78918 78928 no-call complex = ? ? -137 1.17 N +1543 2 chr1 78928 78964 hom ref = = = 19 1.17 N +1544 2 chr1 78964 78971 no-call complex = ? ? -15 1.17 N +1545 2 chr1 78971 79021 hom ref = = = 11 1.17 N +1546 2 chr1 79021 79053 no-call complex = ? ? -291 1.17 N +1547 2 chr1 79053 79147 hom ref = = = 24 1.17 N +1548 2 chr1 79147 79158 no-call complex = ? ? -27 1.17 N +1549 2 chr1 79158 79176 hom ref = = = 31 1.17 N +1550 2 chr1 79176 79205 no-call complex = ? ? -24 1.17 N +1551 2 chr1 79205 79244 hom ref = = = 20 1.17 N +1552 2 chr1 79244 79251 no-call complex = ? ? -359 1.17 N +1553 2 chr1 79251 79350 hom ref = = = 11 1.17 N +1554 2 chr1 79350 79382 no-call complex = ? ? -48 1.17 N +1555 2 chr1 79382 79417 hom ref = = = 1 1.17 N +1556 2 chr1 79417 79418 half ref G G N 43 189 1 L1PREC2:L1:19.7 3 1.17 N +1557 2 chr1 79418 79537 hom ref = = = -12 1.17 N +1558 2 chr1 79537 79538 half ref C C N 48 120 -12 L1PREC2:L1:19.7 3 1.17 N +1559 2 chr1 79538 79607 hom ref = = = -12 1.17 N +1560 2 chr1 79607 79610 half ref GCC GCC ? 66 0 -13 L1PREC2:L1:19.7 3 1.17 N +1561 2 chr1 79610 79659 hom ref = = = -13 1.17 N +1562 2 chr1 79659 79681 no-call complex = ? ? 3 1.17 N +1563 2 chr1 79681 79805 hom ref = = = 2 1.17 N +1564 2 chr1 79805 79806 half ref C C N 64 288 2 L1PREC2:L1:19.7 3 1.17 N +1565 2 chr1 79806 79849 hom ref = = = 2 1.17 N +1566 2 chr1 79849 79856 no-call complex = ? ? -29 1.17 N +1567 2 chr1 79856 79893 hom ref = = = 49 1.17 N +1568 2 chr1 79893 79900 no-call complex = ? ? -343 1.17 N +1569 2 chr1 79900 79997 hom ref = = = 14 1.17 N +1570 2 chr1 79997 80004 no-call complex = ? ? -4 1.17 N +1571 2 chr1 80004 80137 hom ref = = = -18 1.17 N +1572 2 chr1 80137 80144 no-call complex = ? ? -9 1.17 N +1573 2 chr1 80144 80191 hom ref = = = -29 1.17 N +1574 2 chr1 80191 80191 half ref ? 27 0 -29 L1PB:L1:9.0 3 1.17 N +1575 2 chr1 80191 80382 hom ref = = = -29 1.17 N +1576 2 chr1 80382 80389 no-call complex = ? ? -3 1.17 N +1577 2 chr1 80389 80515 hom ref = = = -3 1.17 N +1578 2 chr1 80515 80561 no-call complex = ? ? -18 1.17 N +1579 2 chr1 80561 80845 hom ref = = = 17 1.17 N +1580 2 chr1 80845 80852 no-call complex = ? ? -143 1.17 N +1581 2 chr1 80852 80948 hom ref = = = 24 1.17 N +1582 2 chr1 80948 80977 no-call complex = ? ? -336 1.17 N +1583 2 chr1 80977 81035 hom ref = = = 6 1.17 N +1584 2 chr1 81035 81036 half ref T T N 120 120 6 AluSc5:Alu:7.5 3 1.17 N +1585 2 chr1 81036 81096 hom ref = = = 6 1.17 N +1586 2 chr1 81096 81103 no-call complex = ? ? -16 1.17 N +1587 2 chr1 81103 81200 hom ref = = = 45 1.17 N +1588 2 chr1 81200 81207 no-call complex = ? ? 5 1.17 N +1589 2 chr1 81207 81370 hom ref = = = 37 1.17 N +1590 2 chr1 81370 81377 no-call complex = ? ? -22 1.17 N +1591 2 chr1 81377 81433 hom ref = = = 23 1.17 N +1592 2 chr1 81433 81440 no-call complex = ? ? -20 1.17 N +1593 2 chr1 81440 81476 hom ref = = = 9 1.17 N +1594 2 chr1 81476 81477 half ref A A ? 35 0 689 690 9 Tigger5:TcMar-Tigger:24.7 3 1.17 N +1595 2 chr1 81477 81480 hom ref = = = 9 1.17 N +1596 2 chr1 81480 81480 half ref ? 25 0 689 690 12 Tigger5:TcMar-Tigger:24.7 3 1.17 N +1597 2 chr1 81480 81543 hom ref = = = 12 1.17 N +1598 2 chr1 81543 81550 no-call complex = ? ? -72 1.17 N +1599 2 chr1 81550 81750 hom ref = = = -4 1.17 N +1600 2 chr1 81750 81791 no-call complex = ? ? -59 1.17 N +1601 2 chr1 81791 81801 hom ref = = = 41 1.17 N +1602 2 chr1 81801 81840 no-call complex = ? ? -189 1.17 N +1603 2 chr1 81840 81928 hom ref = = = 5 1.17 N +1604 2 chr1 81928 81929 half ref G G ? 121 0 5 L1M5:L1:43.5 3 1.17 N +1605 2 chr1 81929 81946 hom ref = = = 5 1.17 N +1606 2 chr1 81946 81989 no-call complex = ? ? -60 1.17 N +1607 2 chr1 81989 82071 hom ref = = = -16 1.17 N +1608 2 chr1 82071 82071 half ref ? 22 0 -16 L1M5:L1:43.5 3 1.17 N +1609 2 chr1 82071 82110 hom ref = = = -16 1.17 N +1610 2 chr1 82110 82111 half ref T T N 36 89 -4 L1M5:L1:43.5 3 1.17 N +1611 2 chr1 82111 82129 hom ref = = = -4 1.17 N +1612 2 chr1 82129 82165 no-call complex = ? ? -5 1.17 N +1613 2 chr1 82165 82245 hom ref = = = 15 1.17 N +1614 2 chr1 82245 82252 no-call complex = ? ? 6 1.17 N +1615 2 chr1 82252 82278 hom ref = = = 33 1.17 N +1616 2 chr1 82278 82319 no-call complex = ? ? -19 1.17 N +1617 2 chr1 82319 82435 hom ref = = = -3 1.17 N +1618 2 chr1 82435 82435 half ref ? 25 0 -3 L1M4c:L1:45.3 3 1.17 N +1619 2 chr1 82435 82529 hom ref = = = -3 1.17 N +1620 2 chr1 82529 82573 no-call complex = ? ? -91 1.17 N +1621 2 chr1 82573 82619 hom ref = = = 18 1.17 N +1622 2 chr1 82619 82648 no-call complex = ? ? -61 1.17 N +1623 2 chr1 82648 82733 hom ref = = = -45 1.17 N +1624 2 chr1 82733 82734 het-ref snp T C T 42 118 705 706 dbsnp.108:rs4030331 620 18 17 0 35 -45 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1625 2 chr1 82734 82739 hom ref = = = -45 1.17 N +1626 2 chr1 82739 82739 half ref ? 118 0 706 705 620 33 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1627 2 chr1 82739 82796 hom ref = = = 14 1.17 N +1628 2 chr1 82796 82803 no-call complex = ? ? -15 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1629 2 chr1 82803 82831 hom ref = = = 14 1.17 N +1630 2 chr1 82831 82862 no-call complex = ? ? -52 1.17 N +1631 2 chr1 82862 82880 hom ref = = = 23 1.17 N +1632 2 chr1 82880 82896 no-call complex = ? ? -45 1.17 N +1633 2 chr1 82896 82947 hom ref = = = 17 1.17 N +1634 2 chr1 82947 82991 no-call complex = ? ? -41 1.17 N +1635 2 chr1 82991 83051 hom ref = = = 14 1.17 N +1636 2 chr1 83051 83091 no-call complex = ? ? -100 1.17 N +1637 2 chr1 83091 83107 hom ref = = = 10 1.17 N +1638 2 chr1 83107 83133 no-call complex = ? ? -35 1.17 N +1639 2 chr1 83133 83204 hom ref = = = -1 1.17 N +1640 2 chr1 83204 83209 half ref ATGAA ATGAA ? 42 0 709 710 -1 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1641 2 chr1 83209 83220 hom ref = = = -1 1.17 N +1642 2 chr1 83220 83221 half ref T T N 121 121 709 710 8 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1643 2 chr1 83221 83256 hom ref = = = -24 1.17 N +1644 2 chr1 83256 83256 half ref ? 36 0 -24 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1645 2 chr1 83256 83337 hom ref = = = -24 1.17 N +1646 2 chr1 83337 83338 half ref T T N 27 120 711 712 -6 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1647 2 chr1 83338 83340 hom ref = = = -6 1.17 N +1648 2 chr1 83340 83341 half ref T T N 30 120 711 712 20 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1649 2 chr1 83341 83378 hom ref = = = 20 1.17 N +1650 2 chr1 83378 83382 half ref AAAA AAAA ? 22 0 5 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1651 2 chr1 83382 83425 hom ref = = = 5 1.17 N +1652 2 chr1 83425 83427 half ref AT AT ? 121 0 5 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1653 2 chr1 83427 83475 hom ref = = = 2 1.17 N +1654 2 chr1 83475 83479 half ref GGCA GGCA ? 75 0 2 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:45.3 3 1.17 N +1655 2 chr1 83479 83511 hom ref = = = 17 1.17 N +1656 2 chr1 83511 83549 no-call complex = ? ? -80 1.17 N +1657 2 chr1 83549 83605 hom ref = = = 10 1.17 N +1658 2 chr1 83605 83735 no-call complex = ? ? -14 1.17 N +1659 2 chr1 83735 83782 hom ref = = = 15 1.17 N +1660 2 chr1 83782 84045 no-call complex = ? ? -93 1.17 N +1661 2 chr1 84045 84085 hom ref = = = 21 1.17 N +1662 2 chr1 84085 84109 no-call complex = ? ? -87 1.17 N +1663 2 chr1 84109 84121 hom ref = = = 11 1.17 N +1664 2 chr1 84121 84125 half ref AACT AACT NNCN 22 63 715 716 -6 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:32.1 3 1.17 N +1665 2 chr1 84125 84146 hom ref = = = -6 1.17 N +1666 2 chr1 84146 84147 half ref C C ? 63 0 715 716 8 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:32.1 3 1.17 N +1667 2 chr1 84147 84209 hom ref = = = 8 1.17 N +1668 2 chr1 84209 84271 no-call complex = ? ? -56 1.17 N +1669 2 chr1 84271 84302 hom ref = = = 22 1.17 N +1670 2 chr1 84302 84312 no-call complex = ? ? -12 1.17 N +1671 2 chr1 84312 84383 hom ref = = = 11 1.17 N +1672 2 chr1 84383 84408 no-call complex = ? ? -83 1.17 N +1673 2 chr1 84408 84434 hom ref = = = 27 1.17 N +1674 2 chr1 84434 84442 no-call complex = ? ? -31 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1675 2 chr1 84442 84488 hom ref = = = 30 1.17 N +1676 2 chr1 84488 84495 no-call complex = ? ? -32 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1677 2 chr1 84495 84613 hom ref = = = 8 1.17 N +1678 2 chr1 84613 84647 no-call complex = ? ? -234 1.17 N +1679 2 chr1 84647 84679 hom ref = = = 14 1.17 N +1680 2 chr1 84679 84707 no-call complex = ? ? -45 1.17 N +1681 2 chr1 84707 84839 hom ref = = = 11 1.17 N +1682 2 chr1 84839 84847 no-call complex = ? ? -25 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1683 2 chr1 84847 84903 hom ref = = = 32 1.17 N +1684 2 chr1 84903 84911 no-call complex = ? ? -4 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1685 2 chr1 84911 84972 hom ref = = = 14 1.17 N +1686 2 chr1 84972 85015 no-call complex = ? ? -182 1.17 N +1687 2 chr1 85015 85026 hom ref = = = 13 1.17 N +1688 2 chr1 85026 85066 no-call complex = ? ? -33 1.17 N +1689 2 chr1 85066 85146 hom ref = = = 2 1.17 N +1690 2 chr1 85146 85153 no-call complex = ? ? -74 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1691 2 chr1 85153 85196 hom ref = = = 35 1.17 N +1692 2 chr1 85196 85203 no-call complex = ? ? -101 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1693 2 chr1 85203 85261 hom ref = = = 19 1.17 N +1694 2 chr1 85261 85301 no-call complex = ? ? -43 1.17 N +1695 2 chr1 85301 85360 hom ref = = = -18 1.17 N +1696 2 chr1 85360 85361 half ref G G N 52 120 -18 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:32.1 4 1.17 N +1697 2 chr1 85361 85402 hom ref = = = -18 1.17 N +1698 2 chr1 85402 85423 no-call complex = ? ? -51 1.17 N +1699 2 chr1 85423 85576 hom ref = = = -26 1.17 N +1700 2 chr1 85576 85577 half ref G G N 56 143 -26 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1M4c:L1:32.1 4 1.17 N +1701 2 chr1 85577 85634 hom ref = = = -26 1.17 N +1702 2 chr1 85634 85663 no-call complex = ? ? -25 1.17 N +1703 2 chr1 85663 85721 hom ref = = = 10 1.17 N +1704 2 chr1 85721 85766 no-call complex = ? ? -40 1.17 N +1705 2 chr1 85766 85787 hom ref = = = 26 1.17 N +1706 2 chr1 85787 85816 no-call complex = ? ? -91 1.17 N +1707 2 chr1 85816 85872 hom ref = = = 32 1.17 N +1708 2 chr1 85872 85910 no-call complex = ? ? -73 1.17 N +1709 2 chr1 85910 85933 hom ref = = = 12 1.17 N +1710 2 chr1 85933 85945 no-call complex = ? ? -1 1.17 N +1711 2 chr1 85945 86007 hom ref = = = 12 1.17 N +1712 2 chr1 86007 86022 half ref CTGAAAACATCTATT CTGAAAACATCTATT ? 22 0 -2 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 4 1.17 N +1713 2 chr1 86022 86050 hom ref = = = 14 1.17 N +1714 2 chr1 86050 86078 no-call complex = ? ? -13 1.17 N +1715 2 chr1 86078 86110 hom ref = = = -7 1.17 N +1716 2 chr1 86110 86110 half ref ? 22 0 737 738 -7 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1717 2 chr1 86110 86113 hom ref = = = -7 1.17 N +1718 2 chr1 86113 86118 half ref TTAAT TTAAT ? 29 0 737 738 -5 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1719 2 chr1 86118 86132 hom ref = = = 7 1.17 N +1720 2 chr1 86132 86133 half ref A A N 20 46 737 738 7 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1721 2 chr1 86133 86163 hom ref = = = 7 1.17 N +1722 2 chr1 86163 86170 no-call complex = ? ? -173 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +1723 2 chr1 86170 86218 hom ref = = = 13 1.17 N +1724 2 chr1 86218 86219 half ref A A N 21 98 -5 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1725 2 chr1 86219 86266 hom ref = = = -5 1.17 N +1726 2 chr1 86266 86269 half ref AAT AAT NNN 38 21 739 740 6 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1727 2 chr1 86269 86272 hom ref = = = 14 1.17 N +1728 2 chr1 86272 86272 half ref ? 22 0 739 740 29 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1729 2 chr1 86272 86281 hom ref = = = 22 1.17 N +1730 2 chr1 86281 86287 half ref TAATTT TAATTT NANNNN 24 74 739 740 2 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1731 2 chr1 86287 86298 hom ref = = = -8 1.17 N +1732 2 chr1 86298 86306 half ref TTTAGTTC TTTAGTTC NTNNNNNN 21 74 739 740 -4 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1733 2 chr1 86306 86345 hom ref = = = 13 1.17 N +1734 2 chr1 86345 86426 no-call complex = ? ? -50 1.17 N +1735 2 chr1 86426 86467 hom ref = = = 11 1.17 N +1736 2 chr1 86467 86490 no-call complex = ? ? -24 1.17 N +1737 2 chr1 86490 86535 hom ref = = = 11 1.17 N +1738 2 chr1 86535 86538 half ref TAT TAT ? 51 0 8 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:45.3 4 1.17 N +1739 2 chr1 86538 86630 hom ref = = = 8 1.17 N +1740 2 chr1 86630 86697 no-call complex = ? ? -5 1.17 N +1741 2 chr1 86697 86703 hom ref = = = 25 1.17 N +1742 2 chr1 86703 86713 no-call complex = ? ? 18 1.17 N +1743 2 chr1 86713 86760 hom ref = = = 6 1.17 N +1744 2 chr1 86760 86762 half ref AT AT ? 72 0 649 3 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 4 1.17 N +1745 2 chr1 86762 86787 hom ref = = = -392 1.17 N +1746 2 chr1 86787 86788 no-call complex G ? ? 0 0 649 -392 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 4 1.17 N +1747 2 chr1 86788 86833 hom ref = = = -392 1.17 N +1748 2 chr1 86833 86833 half ref ? 33 0 -28 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:37.7 4 1.17 N +1749 2 chr1 86833 86907 hom ref = = = -28 1.17 N +1750 2 chr1 86907 86912 half ref ATTTG ATTTG ? 95 0 -11 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:37.7 4 1.17 N +1751 2 chr1 86912 87038 hom ref = = = -53 1.17 N +1752 2 chr1 87038 87038 half ref ? 28 0 -53 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC L1MC5:L1:37.7 4 1.17 N +1753 2 chr1 87038 87371 hom ref = = = -53 1.17 N +1754 2 chr1 87371 87372 half ref T T N 33 115 7 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::TSS-UPSTREAM:UNKNOWN-INC AluJo:Alu:16.3 3 1.17 N +1755 2 chr1 87372 87544 hom ref = = = 7 1.17 N +1756 2 chr1 87544 87566 no-call complex = ? ? -39 1.17 N +1757 2 chr1 87566 87682 hom ref = = = 24 1.17 N +1758 2 chr1 87682 87685 half ref TTC TTC NTN 127 34 745 746 24 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 3 1.17 N +1759 2 chr1 87685 87701 hom ref = = = -10 1.17 N +1760 2 chr1 87701 87702 half ref G G N 44 127 745 746 -10 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 3 1.17 N +1761 2 chr1 87702 87725 hom ref = = = -10 1.17 N +1762 2 chr1 87725 87725 half ref ? 25 0 745 746 -4 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 3 1.17 N +1763 2 chr1 87725 87751 hom ref = = = -4 1.17 N +1764 2 chr1 87751 87758 no-call complex = ? ? -197 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR5:UNKNOWN-INC 1.17 N +1765 2 chr1 87758 87792 hom ref = = = 27 1.17 N +1766 2 chr1 87792 87841 no-call complex = ? ? -43 1.17 N +1767 2 chr1 87841 88165 hom ref = = = 18 1.17 N +1768 2 chr1 88165 88175 no-call complex = ? ? 37 1.17 N +1769 2 chr1 88175 88212 hom ref = = = 22 1.17 N +1770 2 chr1 88212 88245 no-call complex = ? ? -422 1.17 N +1771 2 chr1 88245 88274 hom ref = = = 27 1.17 N +1772 2 chr1 88274 88298 no-call complex = ? ? -81 1.17 N +1773 2 chr1 88298 88328 hom ref = = = 21 1.17 N +1774 2 chr1 88328 88335 no-call complex = ? ? -10 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 1.17 N +1775 2 chr1 88335 88383 hom ref = = = 48 1.17 N +1776 2 chr1 88383 88390 no-call complex = ? ? -66 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 1.17 N +1777 2 chr1 88390 88459 hom ref = = = 29 1.17 N +1778 2 chr1 88459 88466 no-call complex = ? ? -84 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 1.17 N +1779 2 chr1 88466 88568 hom ref = = = 13 1.17 N +1780 2 chr1 88568 88576 no-call complex = ? ? -334 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 100132632:XM_001724183.2:LOC100132632::::CDS:UNKNOWN-VNC 1.17 N +1781 2 chr1 88576 88667 hom ref = = = 25 1.17 N +1782 2 chr1 88667 88709 no-call complex = ? ? -10 1.17 N +1783 2 chr1 88709 88781 hom ref = = = -40 1.17 N +1784 2 chr1 88781 88815 no-call complex = ? ? -111 1.17 N +1785 2 chr1 88815 88905 hom ref = = = 12 1.17 N +1786 2 chr1 88905 88932 no-call complex = ? ? -172 1.17 N +1787 2 chr1 88932 89148 hom ref = = = 8 1.17 N +1788 2 chr1 89148 89149 half ref A A N 39 122 8 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC L2a:L2:26.5 7 1.17 N +1789 2 chr1 89149 89243 hom ref = = = -52 1.17 N +1790 2 chr1 89243 89243 half ref ? 46 0 -52 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 7 1.17 N +1791 2 chr1 89243 89279 hom ref = = = -52 1.17 N +1792 2 chr1 89279 89286 no-call complex = ? ? -246 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 1.17 N +1793 2 chr1 89286 89414 hom ref = = = -32 1.17 N +1794 2 chr1 89414 89415 half ref C C N 71 120 -32 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 7 1.17 N +1795 2 chr1 89415 89484 hom ref = = = -32 1.17 N +1796 2 chr1 89484 89522 no-call complex = ? ? -140 1.17 N +1797 2 chr1 89522 89627 hom ref = = = -14 1.17 N +1798 2 chr1 89627 89642 no-call complex = ? ? -26 1.17 N +1799 2 chr1 89642 89714 hom ref = = = 21 1.17 N +1800 2 chr1 89714 89728 no-call complex = ? ? -104 1.17 N +1801 2 chr1 89728 89803 hom ref = = = 25 1.17 N +1802 2 chr1 89803 89816 no-call complex = ? ? -50 1.17 N +1803 2 chr1 89816 89833 hom ref = = = 25 1.17 N +1804 2 chr1 89833 89865 no-call complex = ? ? -52 1.17 N +1805 2 chr1 89865 89876 hom ref = = = -12 1.17 N +1806 2 chr1 89876 89884 no-call complex GAGGAGAT GAGGNGAT NANGNGAN 24 31 765 766 -12 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC MLT1H2:ERVL-MaLR:36.8 7 1.17 N +1807 2 chr1 89884 89887 hom ref = = = 6 1.17 N +1808 2 chr1 89887 89888 half ref C C N 24 121 765 766 6 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC MLT1H2:ERVL-MaLR:36.8 7 1.17 N +1809 2 chr1 89888 89918 hom ref = = = 6 1.17 N +1810 2 chr1 89918 89926 no-call complex = ? ? -31 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 1.17 N +1811 2 chr1 89926 89971 hom ref = = = 11 1.17 N +1812 2 chr1 89971 89992 no-call complex = ? ? -43 1.17 N +1813 2 chr1 89992 90010 hom ref = = = 26 1.17 N +1814 2 chr1 90010 90019 no-call complex = ? ? -3 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 100132632:XM_001724183.2:LOC100132632::::UTR3:UNKNOWN-INC 1.17 N +1815 2 chr1 90019 90058 hom ref = = = 11 1.17 N +1816 2 chr1 90058 90416 no-call complex = ? ? -322 1.17 N +1817 2 chr1 90416 90433 hom ref = = = 18 1.17 N +1818 2 chr1 90433 90468 no-call complex = ? ? -60 1.17 N +1819 2 chr1 90468 90496 hom ref = = = 14 1.17 N +1820 2 chr1 90496 90544 no-call complex = ? ? -94 1.17 N +1821 2 chr1 90544 90593 hom ref = = = 1 1.17 N +1822 2 chr1 90593 90594 half ref T T N 22 120 1 7 1.17 N +1823 2 chr1 90594 90637 hom ref = = = -2 1.17 N +1824 2 chr1 90637 90644 no-call complex = ? ? -1 1.17 N +1825 2 chr1 90644 90706 hom ref = = = 10 1.17 N +1826 2 chr1 90706 90719 no-call complex = ? ? -19 1.17 N +1827 2 chr1 90719 90746 hom ref = = = 14 1.17 N +1828 2 chr1 90746 90784 no-call complex = ? ? -25 1.17 N +1829 2 chr1 90784 90818 hom ref = = = 12 1.17 N +1830 2 chr1 90818 90859 no-call complex = ? ? -1 1.17 N +1831 2 chr1 90859 90894 hom ref = = = -26 1.17 N +1832 2 chr1 90894 90895 half ref C C N 115 120 -26 7 1.17 N +1833 2 chr1 90895 90970 hom ref = = = -26 1.17 N +1834 2 chr1 90970 91010 no-call complex = ? ? -47 1.17 N +1835 2 chr1 91010 91060 hom ref = = = 17 1.17 N +1836 2 chr1 91060 91067 no-call complex = ? ? -34 1.17 N +1837 2 chr1 91067 91091 hom ref = = = 18 1.17 N +1838 2 chr1 91091 91111 no-call complex = ? ? -57 1.17 N +1839 2 chr1 91111 91140 hom ref = = = 8 1.17 N +1840 2 chr1 91140 91141 half ref G G N 122 122 8 AluY:Alu:9.9 7 1.17 N +1841 2 chr1 91141 91171 hom ref = = = 8 1.17 N +1842 2 chr1 91171 91217 no-call complex = ? ? -54 1.17 N +1843 2 chr1 91217 91332 hom ref = = = 24 1.17 N +1844 2 chr1 91332 91339 no-call complex = ? ? -62 1.17 N +1845 2 chr1 91339 91415 hom ref = = = 16 1.17 N +1846 2 chr1 91415 91431 no-call complex = ? ? -58 1.17 N +1847 2 chr1 91431 91461 hom ref = = = 11 1.17 N +1848 2 chr1 91461 91493 no-call complex = ? ? -23 1.17 N +1849 2 chr1 91493 91511 hom ref = = = 19 1.17 N +1850 2 chr1 91511 91539 no-call complex = ? ? -29 1.17 N +1851 2 chr1 91539 91571 hom ref = = = 14 1.17 N +1852 2 chr1 91571 91584 no-call complex = ? ? -49 1.17 N +1853 2 chr1 91584 91612 hom ref = = = 16 1.17 N +1854 2 chr1 91612 91646 no-call complex = ? ? -77 1.17 N +1855 2 chr1 91646 91659 hom ref = = = 31 1.17 N +1856 2 chr1 91659 91688 no-call complex = ? ? -16 1.17 N +1857 2 chr1 91688 91841 hom ref = = = 2 1.17 N +1858 2 chr1 91841 91842 half ref C C N 60 123 2 MER4A:ERV1:31.2 9 1.17 N +1859 2 chr1 91842 91936 hom ref = = = 2 1.17 N +1860 2 chr1 91936 91964 no-call complex = ? ? -13 1.17 N +1861 2 chr1 91964 91981 hom ref = = = 12 1.17 N +1862 2 chr1 91981 91995 no-call complex = ? ? -13 1.17 N +1863 2 chr1 91995 92111 hom ref = = = 16 1.17 N +1864 2 chr1 92111 92118 no-call complex = ? ? -98 1.17 N +1865 2 chr1 92118 92226 hom ref = = = 8 1.17 N +1866 2 chr1 92226 92260 no-call complex = ? ? -145 1.17 N +1867 2 chr1 92260 92477 hom ref = = = -3 1.17 N +1868 2 chr1 92477 92484 no-call complex = ? ? -83 1.17 N +1869 2 chr1 92484 92634 hom ref = = = 10 1.17 N +1870 2 chr1 92634 92692 no-call complex = ? ? -23 1.17 N +1871 2 chr1 92692 92790 hom ref = = = 26 1.17 N +1872 2 chr1 92790 92797 no-call complex = ? ? -60 1.17 N +1873 2 chr1 92797 92866 hom ref = = = 16 1.17 N +1874 2 chr1 92866 92873 no-call complex = ? ? -44 1.17 N +1875 2 chr1 92873 92908 hom ref = = = 10 1.17 N +1876 2 chr1 92908 92915 no-call complex = ? ? -100 1.17 N +1877 2 chr1 92915 93010 hom ref = = = -9 1.17 N +1878 2 chr1 93010 93011 half ref G G N 94 120 6 14 1.17 N +1879 2 chr1 93011 93178 hom ref = = = -25 1.17 N +1880 2 chr1 93178 93210 no-call complex = ? ? -233 1.17 N +1881 2 chr1 93210 93275 hom ref = = = 11 1.17 N +1882 2 chr1 93275 93309 no-call complex = ? ? -42 1.17 N +1883 2 chr1 93309 93568 hom ref = = = -24 1.17 N +1884 2 chr1 93568 93608 no-call complex = ? ? -67 1.17 N +1885 2 chr1 93608 93872 hom ref = = = -19 1.17 N +1886 2 chr1 93872 93874 half ref AT AT NN 83 120 17 AluSc:Alu:14.5 14 1.17 N +1887 2 chr1 93874 93904 hom ref = = = 17 1.17 N +1888 2 chr1 93904 93917 no-call complex = ? ? -61 1.17 N +1889 2 chr1 93917 93982 hom ref = = = 20 1.17 N +1890 2 chr1 93982 94022 no-call complex = ? ? -5 1.17 N +1891 2 chr1 94022 94060 hom ref = = = -24 1.17 N +1892 2 chr1 94060 94061 half ref C C N 52 120 -24 14 1.17 N +1893 2 chr1 94061 94117 hom ref = = = -24 1.17 N +1894 2 chr1 94117 94129 no-call complex = ? ? -13 1.17 N +1895 2 chr1 94129 94238 hom ref = = = 7 1.17 N +1896 2 chr1 94238 94276 no-call complex = ? ? -129 1.17 N +1897 2 chr1 94276 94366 hom ref = = = -2 1.17 N +1898 2 chr1 94366 94373 no-call complex = ? ? -5 1.17 N +1899 2 chr1 94373 94402 hom ref = = = 22 1.17 N +1900 2 chr1 94402 94438 no-call complex = ? ? -163 1.17 N +1901 2 chr1 94438 94456 hom ref = = = 13 1.17 N +1902 2 chr1 94456 94494 no-call complex = ? ? -38 1.17 N +1903 2 chr1 94494 94521 hom ref = = = 10 1.17 N +1904 2 chr1 94521 94550 no-call complex = ? ? -88 1.17 N +1905 2 chr1 94550 94556 hom ref = = = 12 1.17 N +1906 2 chr1 94556 94573 no-call complex = ? ? -71 1.17 N +1907 2 chr1 94573 94648 hom ref = = = -8 1.17 N +1908 2 chr1 94648 94649 half ref T T N 123 123 -8 MLT1H:ERVL-MaLR:43.2 14 1.17 N +1909 2 chr1 94649 94694 hom ref = = = -8 1.17 N +1910 2 chr1 94694 94728 no-call complex = ? ? -81 1.17 N +1911 2 chr1 94728 94804 hom ref = = = 11 1.17 N +1912 2 chr1 94804 94852 no-call complex = ? ? -69 1.17 N +1913 2 chr1 94852 94857 hom ref = = = 10 1.17 N +1914 2 chr1 94857 94874 no-call complex = ? ? -98 1.17 N +1915 2 chr1 94874 94885 hom ref = = = 14 1.17 N +1916 2 chr1 94885 94922 no-call complex = ? ? -59 1.17 N +1917 2 chr1 94922 94974 hom ref = = = 11 1.17 N +1918 2 chr1 94974 95024 no-call complex = ? ? -50 1.17 N +1919 2 chr1 95024 95088 hom ref = = = 23 1.17 N +1920 2 chr1 95088 95095 no-call complex = ? ? -39 1.17 N +1921 2 chr1 95095 95188 hom ref = = = 12 1.17 N +1922 2 chr1 95188 95195 no-call complex = ? ? -61 1.17 N +1923 2 chr1 95195 95595 hom ref = = = -14 1.17 N +1924 2 chr1 95595 95625 no-call complex = ? ? -32 1.17 N +1925 2 chr1 95625 95697 hom ref = = = -23 1.17 N +1926 2 chr1 95697 95698 half ref C C N 67 120 8 14 1.17 N +1927 2 chr1 95698 95929 hom ref = = = -19 1.17 N +1928 2 chr1 95929 95936 no-call complex = ? ? -152 1.17 N +1929 2 chr1 95936 95967 hom ref = = = 18 1.17 N +1930 2 chr1 95967 96003 no-call complex = ? ? -67 1.17 N +1931 2 chr1 96003 96144 hom ref = = = -28 1.17 N +1932 2 chr1 96144 96147 half ref TCT TCT NNN 30 114 4 14 1.17 N +1933 2 chr1 96147 96166 hom ref = = = 4 1.17 N +1934 2 chr1 96166 96213 no-call complex = ? ? -62 1.17 N +1935 2 chr1 96213 96228 hom ref = = = 22 1.17 N +1936 2 chr1 96228 96270 no-call complex = ? ? -77 1.17 N +1937 2 chr1 96270 96371 hom ref = = = 20 1.17 N +1938 2 chr1 96371 96408 no-call complex = ? ? -157 1.17 N +1939 2 chr1 96408 96462 hom ref = = = 15 1.17 N +1940 2 chr1 96462 96469 no-call complex = ? ? -3 1.17 N +1941 2 chr1 96469 96584 hom ref = = = 12 1.17 N +1942 2 chr1 96584 96620 no-call complex = ? ? -87 1.17 N +1943 2 chr1 96620 96735 hom ref = = = -14 1.17 N +1944 2 chr1 96735 96742 no-call complex = ? ? -10 1.17 N +1945 2 chr1 96742 96814 hom ref = = = 13 1.17 N +1946 2 chr1 96814 96836 no-call complex = ? ? -132 1.17 N +1947 2 chr1 96836 97017 hom ref = = = -52 1.17 N +1948 2 chr1 97017 97064 no-call complex = ? ? -55 1.17 N +1949 2 chr1 97064 97081 hom ref = = = 22 1.17 N +1950 2 chr1 97081 97093 no-call complex = ? ? -47 1.17 N +1951 2 chr1 97093 97168 hom ref = = = -44 1.17 N +1952 2 chr1 97168 97169 half ref G G N 121 121 -44 14 1.17 N +1953 2 chr1 97169 97320 hom ref = = = -44 1.17 N +1954 2 chr1 97320 97368 no-call complex = ? ? -15 1.17 N +1955 2 chr1 97368 97392 hom ref = = = 14 1.17 N +1956 2 chr1 97392 97434 no-call complex = ? ? -15 1.17 N +1957 2 chr1 97434 97464 hom ref = = = 14 1.17 N +1958 2 chr1 97464 97471 no-call complex = ? ? -65 1.17 N +1959 2 chr1 97471 97542 hom ref = = = 19 1.17 N +1960 2 chr1 97542 97570 no-call complex = ? ? -58 1.17 N +1961 2 chr1 97570 97820 hom ref = = = -45 1.17 N +1962 2 chr1 97820 97821 half ref C C N 86 121 -4 MLT1I:ERVL-MaLR:56.8 14 1.17 N +1963 2 chr1 97821 97866 hom ref = = = -4 1.17 N +1964 2 chr1 97866 97900 no-call complex = ? ? -151 1.17 N +1965 2 chr1 97900 97949 hom ref = = = 31 1.17 N +1966 2 chr1 97949 97956 no-call complex = ? ? -37 1.17 N +1967 2 chr1 97956 97987 hom ref = = = 33 1.17 N +1968 2 chr1 97987 98026 no-call complex = ? ? -19 1.17 N +1969 2 chr1 98026 98219 hom ref = = = -13 1.17 N +1970 2 chr1 98219 98248 no-call complex = ? ? -99 1.17 N +1971 2 chr1 98248 98353 hom ref = = = 10 1.17 N +1972 2 chr1 98353 98407 no-call complex = ? ? -59 1.17 N +1973 2 chr1 98407 98453 hom ref = = = 3 1.17 N +1974 2 chr1 98453 98460 no-call complex = ? ? -20 1.17 N +1975 2 chr1 98460 98477 hom ref = = = 21 1.17 N +1976 2 chr1 98477 98517 no-call complex = ? ? -25 1.17 N +1977 2 chr1 98517 98582 hom ref = = = 11 1.17 N +1978 2 chr1 98582 98601 no-call complex = ? ? -47 1.17 N +1979 2 chr1 98601 98614 hom ref = = = 10 1.17 N +1980 2 chr1 98614 98641 no-call complex = ? ? -138 1.17 N +1981 2 chr1 98641 98655 hom ref = = = -1 1.17 N +1982 2 chr1 98655 98656 half ref T T N 121 121 -1 14 1.17 N +1983 2 chr1 98656 98676 hom ref = = = -1 1.17 N +1984 2 chr1 98676 98709 no-call complex = ? ? -108 1.17 N +1985 2 chr1 98709 98797 hom ref = = = 8 1.17 N +1986 2 chr1 98797 98808 no-call complex = ? ? -262 1.17 N +1987 2 chr1 98808 98863 hom ref = = = 12 1.17 N +1988 2 chr1 98863 98910 no-call complex = ? ? -103 1.17 N +1989 2 chr1 98910 98922 hom ref = = = 11 1.17 N +1990 2 chr1 98922 98950 no-call complex = ? ? -45 1.17 N +1991 2 chr1 98950 98989 hom ref = = = 10 1.17 N +1992 2 chr1 98989 99058 no-call complex = ? ? -279 1.17 N +1993 2 chr1 99058 99068 hom ref = = = 10 1.17 N +1994 2 chr1 99068 99120 no-call complex = ? ? -202 1.17 N +1995 2 chr1 99120 99306 hom ref = = = -7 1.17 N +1996 2 chr1 99306 99329 no-call complex = ? ? -90 1.17 N +1997 2 chr1 99329 99343 hom ref = = = 13 1.17 N +1998 2 chr1 99343 99346 half ref CAC CAC NAN 25 107 829 830 2 AluSg4:Alu:12.0 14 1.17 N +1999 2 chr1 99346 99357 hom ref = = = 2 1.17 N +2000 2 chr1 99357 99358 half ref A A N 20 107 829 830 14 AluSg4:Alu:12.0 14 1.17 N +2001 2 chr1 99358 99361 hom ref = = = 5 1.17 N +2002 2 chr1 99361 99362 half ref T T N 23 107 829 830 5 AluSg4:Alu:12.0 14 1.17 N +2003 2 chr1 99362 99373 hom ref = = = 5 1.17 N +2004 2 chr1 99373 99376 half ref AGG AGG NNN 22 107 829 830 7 AluSg4:Alu:12.0 14 1.17 N +2005 2 chr1 99376 99382 hom ref = = = -7 1.17 N +2006 2 chr1 99382 99383 half ref C C N 34 107 829 830 -7 AluSg4:Alu:12.0 14 1.17 N +2007 2 chr1 99383 99539 hom ref = = = -7 1.17 N +2008 2 chr1 99539 99570 no-call complex = ? ? -40 1.17 N +2009 2 chr1 99570 99597 hom ref = = = 20 1.17 N +2010 2 chr1 99597 99638 no-call complex = ? ? -69 1.17 N +2011 2 chr1 99638 99706 hom ref = = = 5 1.17 N +2012 2 chr1 99706 99761 no-call complex = ? ? -127 1.17 N +2013 2 chr1 99761 99766 hom ref = = = 34 1.17 N +2014 2 chr1 99766 99797 no-call complex = ? ? -255 1.17 N +2015 2 chr1 99797 99828 hom ref = = = 18 1.17 N +2016 2 chr1 99828 99878 no-call complex = ? ? -96 1.17 N +2017 2 chr1 99878 99908 hom ref = = = 25 1.17 N +2018 2 chr1 99908 99921 no-call complex = ? ? -4 1.17 N +2019 2 chr1 99921 100098 hom ref = = = 14 1.17 N +2020 2 chr1 100098 100118 no-call complex = ? ? -41 1.17 N +2021 2 chr1 100118 100242 hom ref = = = -14 1.17 N +2022 2 chr1 100242 100272 no-call complex = ? ? -8 1.17 N +2023 2 chr1 100272 100328 hom ref = = = 11 1.17 N +2024 2 chr1 100328 100353 no-call complex = ? ? -41 1.17 N +2025 2 chr1 100353 100487 hom ref = = = 23 1.17 N +2026 2 chr1 100487 100504 no-call complex = ? ? -259 1.17 N +2027 2 chr1 100504 100642 hom ref = = = 7 1.17 N +2028 2 chr1 100642 100684 no-call complex = ? ? -48 1.17 N +2029 2 chr1 100684 100854 hom ref = = = 6 1.17 N +2030 2 chr1 100854 100879 no-call complex = ? ? -140 1.17 N +2031 2 chr1 100879 100894 hom ref = = = -15 1.17 N +2032 2 chr1 100894 100895 half ref A A N 120 120 -15 14 1.17 N +2033 2 chr1 100895 100980 hom ref = = = -24 1.17 N +2034 2 chr1 100980 100981 half ref A A N 41 104 -24 14 1.17 N +2035 2 chr1 100981 101026 hom ref = = = -24 1.17 N +2036 2 chr1 101026 101074 no-call complex = ? ? -23 1.17 N +2037 2 chr1 101074 101098 hom ref = = = 1 1.17 N +2038 2 chr1 101098 101098 half ref ? 32 0 843 844 1 AluSz:Alu:13.5 14 1.17 N +2039 2 chr1 101098 101100 hom ref = = = 1 1.17 N +2040 2 chr1 101100 101101 half ref G G N 75 120 843 844 25 AluSz:Alu:13.5 14 1.17 N +2041 2 chr1 101101 101110 hom ref = = = -10 1.17 N +2042 2 chr1 101110 101111 half ref G G N 71 120 -10 AluSz:Alu:13.5 14 1.17 N +2043 2 chr1 101111 101152 hom ref = = = -10 1.17 N +2044 2 chr1 101152 101184 no-call complex = ? ? -62 1.17 N +2045 2 chr1 101184 101221 hom ref = = = 11 1.17 N +2046 2 chr1 101221 101249 no-call complex = ? ? -41 1.17 N +2047 2 chr1 101249 101264 hom ref = = = 21 1.17 N +2048 2 chr1 101264 101294 no-call complex = ? ? -40 1.17 N +2049 2 chr1 101294 101331 hom ref = = = 2 1.17 N +2050 2 chr1 101331 101370 no-call complex = ? ? -21 1.17 N +2051 2 chr1 101370 101398 hom ref = = = -13 1.17 N +2052 2 chr1 101398 101398 half ref ? 22 0 847 848 -12 14 1.17 N +2053 2 chr1 101398 101401 hom ref = = = -12 1.17 N +2054 2 chr1 101401 101402 half ref T T N 103 103 847 848 -4 14 1.17 N +2055 2 chr1 101402 101490 hom ref = = = -4 1.17 N +2056 2 chr1 101490 101531 no-call complex = ? ? -49 1.17 N +2057 2 chr1 101531 101544 hom ref = = = 25 1.17 N +2058 2 chr1 101544 101574 no-call complex = ? ? -108 1.17 N +2059 2 chr1 101574 101610 hom ref = = = 6 1.17 N +2060 2 chr1 101610 101611 half ref G G ? 122 0 851 852 6 AluJr:Alu:23.7 14 1.17 N +2061 2 chr1 101611 101619 hom ref = = = 6 1.17 N +2062 2 chr1 101619 101620 half ref A A N 122 122 851 852 3 AluJr:Alu:23.7 14 1.17 N +2063 2 chr1 101620 101626 hom ref = = = 3 1.17 N +2064 2 chr1 101626 101630 half ref ATCA ATCA ? 122 0 851 852 23 AluJr:Alu:23.7 14 1.17 N +2065 2 chr1 101630 101670 hom ref = = = 8 1.17 N +2066 2 chr1 101670 101694 no-call complex = ? ? -38 1.17 N +2067 2 chr1 101694 101712 hom ref = = = 18 1.17 N +2068 2 chr1 101712 101739 no-call complex = ? ? -12 1.17 N +2069 2 chr1 101739 101792 hom ref = = = 14 1.17 N +2070 2 chr1 101792 101839 no-call complex = ? ? -47 1.17 N +2071 2 chr1 101839 101864 hom ref = = = 2 1.17 N +2072 2 chr1 101864 101865 half ref A A N 23 125 853 854 2 AluSx:Alu:14.3 14 1.17 N +2073 2 chr1 101865 101868 hom ref = = = 2 1.17 N +2074 2 chr1 101868 101871 half ref TGA TGA NGN 25 125 853 854 9 AluSx:Alu:14.3 14 1.17 N +2075 2 chr1 101871 101881 hom ref = = = -24 1.17 N +2076 2 chr1 101881 101882 half ref T T ? 125 0 853 854 -24 AluSx:Alu:14.3 14 1.17 N +2077 2 chr1 101882 101899 hom ref = = = -24 1.17 N +2078 2 chr1 101899 101918 no-call complex = ? ? -314 1.17 N +2079 2 chr1 101918 101984 hom ref = = = -85 1.17 N +2080 2 chr1 101984 101991 no-call complex = ? ? -41 1.17 N +2081 2 chr1 101991 102108 hom ref = = = 12 1.17 N +2082 2 chr1 102108 102148 no-call complex = ? ? -54 1.17 N +2083 2 chr1 102148 102167 hom ref = = = 10 1.17 N +2084 2 chr1 102167 102174 no-call complex = ? ? -28 1.17 N +2085 2 chr1 102174 102209 hom ref = = = -7 1.17 N +2086 2 chr1 102209 102210 half ref A A N 120 120 857 858 -7 14 1.17 N +2087 2 chr1 102210 102236 hom ref = = = -7 1.17 N +2088 2 chr1 102236 102237 half ref G G N 120 120 857 858 7 14 1.17 N +2089 2 chr1 102237 102441 hom ref = = = 1 1.17 N +2090 2 chr1 102441 102442 half ref C C N 101 101 1 14 1.17 N +2091 2 chr1 102442 102493 hom ref = = = -3 1.17 N +2092 2 chr1 102493 102509 no-call complex = ? ? -4 1.17 N +2093 2 chr1 102509 102589 hom ref = = = 13 1.17 N +2094 2 chr1 102589 102599 no-call complex = ? ? -183 1.17 N +2095 2 chr1 102599 102660 hom ref = = = 15 1.17 N +2096 2 chr1 102660 102667 no-call complex = ? ? -61 1.17 N +2097 2 chr1 102667 102693 hom ref = = = 45 1.17 N +2098 2 chr1 102693 102711 no-call complex = ? ? 1 1.17 N +2099 2 chr1 102711 102756 hom ref = = = 25 1.17 N +2100 2 chr1 102756 102772 no-call complex = ? ? -223 1.17 N +2101 2 chr1 102772 102779 hom ref = = = 22 1.17 N +2102 2 chr1 102779 102818 no-call complex = ? ? -102 1.17 N +2103 2 chr1 102818 102853 hom ref = = = -8 1.17 N +2104 2 chr1 102853 102854 half ref G G N 22 78 859 860 -8 L3:CR1:44.0 14 1.17 N +2105 2 chr1 102854 102863 hom ref = = = -8 1.17 N +2106 2 chr1 102863 102863 half ref ? 52 0 859 860 2 L3:CR1:44.0 14 1.17 N +2107 2 chr1 102863 102865 hom ref = = = -13 1.17 N +2108 2 chr1 102865 102866 half ref A A ? 35 0 859 860 -13 L3:CR1:44.0 14 1.17 N +2109 2 chr1 102866 102930 hom ref = = = -13 1.17 N +2110 2 chr1 102930 102972 no-call complex = ? ? -238 1.17 N +2111 2 chr1 102972 102983 hom ref = = = 21 1.17 N +2112 2 chr1 102983 103010 no-call complex = ? ? -164 1.17 N +2113 2 chr1 103010 103029 hom ref = = = 11 1.17 N +2114 2 chr1 103029 103069 no-call complex = ? ? 3 1.17 N +2115 2 chr1 103069 103076 hom ref = = = 16 1.17 N +2116 2 chr1 103076 103119 no-call complex = ? ? -40 1.17 N +2117 2 chr1 103119 103169 hom ref = = = 10 1.17 N +2118 2 chr1 103169 103211 no-call complex = ? ? -51 1.17 N +2119 2 chr1 103211 103222 hom ref = = = 14 1.17 N +2120 2 chr1 103222 103244 no-call complex = ? ? -45 1.17 N +2121 2 chr1 103244 103296 hom ref = = = -20 1.17 N +2122 2 chr1 103296 103297 half ref A A N 40 98 1 L3:CR1:44.0 14 1.17 N +2123 2 chr1 103297 103314 hom ref = = = 1 1.17 N +2124 2 chr1 103314 103344 no-call complex = ? ? -22 1.17 N +2125 2 chr1 103344 103373 hom ref = = = 10 1.17 N +2126 2 chr1 103373 103416 no-call complex = ? ? -51 1.17 N +2127 2 chr1 103416 103440 hom ref = = = 21 1.17 N +2128 2 chr1 103440 103478 no-call complex = ? ? -114 1.17 N +2129 2 chr1 103478 103512 hom ref = = = 10 1.17 N +2130 2 chr1 103512 103548 no-call complex = ? ? -55 1.17 N +2131 2 chr1 103548 103565 hom ref = = = 15 1.17 N +2132 2 chr1 103565 103587 no-call complex = ? ? -15 1.17 N +2133 2 chr1 103587 103605 hom ref = = = 20 1.17 N +2134 2 chr1 103605 103628 no-call complex = ? ? -107 1.17 N +2135 2 chr1 103628 103740 hom ref = = = 7 1.17 N +2136 2 chr1 103740 103762 no-call complex = ? ? -327 1.17 N +2137 2 chr1 103762 103832 hom ref = = = -39 1.17 N +2138 2 chr1 103832 103833 half ref T T N 111 111 0 AluSq:Alu:10.9 15 1.17 N +2139 2 chr1 103833 103843 hom ref = = = 0 1.17 N +2140 2 chr1 103843 103924 no-call complex = ? ? -89 1.17 N +2141 2 chr1 103924 103961 hom ref = = = 28 1.17 N +2142 2 chr1 103961 103986 no-call complex = ? ? -11 1.17 N +2143 2 chr1 103986 104013 hom ref = = = 48 1.17 N +2144 2 chr1 104013 104036 no-call complex = ? ? -663 1.17 N +2145 2 chr1 104036 104068 hom ref = = = 39 1.17 N +2146 2 chr1 104068 104075 no-call complex = ? ? -88 1.17 N +2147 2 chr1 104075 104103 hom ref = = = 27 1.17 N +2148 2 chr1 104103 104141 no-call complex = ? ? -698 1.17 N +2149 2 chr1 104141 104155 hom ref = = = 10 1.17 N +2150 2 chr1 104155 104203 no-call complex = ? ? -64 1.17 N +2151 2 chr1 104203 104209 hom ref = = = 24 1.17 N +2152 2 chr1 104209 104246 no-call complex = ? ? -84 1.17 N +2153 2 chr1 104246 104304 hom ref = = = 19 1.17 N +2154 2 chr1 104304 104352 no-call complex = ? ? -566 1.17 N +2155 2 chr1 104352 104407 hom ref = = = 18 1.17 N +2156 2 chr1 104407 104414 no-call complex = ? ? -919 1.17 N +2157 2 chr1 104414 104548 hom ref = = = 14 1.17 N +2158 2 chr1 104548 104556 no-call complex = ? ? -472 1.17 N +2159 2 chr1 104556 104610 hom ref = = = 26 1.17 N +2160 2 chr1 104610 104635 no-call complex = ? ? -72 1.17 N +2161 2 chr1 104635 104693 hom ref = = = 18 1.17 N +2162 2 chr1 104693 104723 no-call complex = ? ? -99 1.17 N +2163 2 chr1 104723 104818 hom ref = = = 36 1.17 N +2164 2 chr1 104818 104864 no-call complex = ? ? -180 1.17 N +2165 2 chr1 104864 104937 hom ref = = = 17 1.17 N +2166 2 chr1 104937 104977 no-call complex = ? ? -102 1.17 N +2167 2 chr1 104977 105119 hom ref = = = -4 1.17 N +2168 2 chr1 105119 105126 no-call complex = ? ? -1058 1.17 N +2169 2 chr1 105126 105177 hom ref = = = 24 1.17 N +2170 2 chr1 105177 105198 no-call complex = ? ? -323 1.17 N +2171 2 chr1 105198 105209 hom ref = = = 47 1.17 N +2172 2 chr1 105209 105224 no-call complex = ? ? -92 1.17 N +2173 2 chr1 105224 105275 hom ref = = = 23 1.17 N +2174 2 chr1 105275 105313 no-call complex = ? ? -850 1.17 N +2175 2 chr1 105313 105329 hom ref = = = 13 1.17 N +2176 2 chr1 105329 105353 no-call complex = ? ? -74 1.17 N +2177 2 chr1 105353 105432 hom ref = = = 15 1.17 N +2178 2 chr1 105432 105448 no-call complex = ? ? -107 1.17 N +2179 2 chr1 105448 105475 hom ref = = = 37 1.17 N +2180 2 chr1 105475 105492 no-call complex = ? ? -1260 1.17 N +2181 2 chr1 105492 105604 hom ref = = = 6 1.17 N +2182 2 chr1 105604 105637 no-call complex = ? ? -217 1.17 N +2183 2 chr1 105637 105696 hom ref = = = 10 1.17 N +2184 2 chr1 105696 105719 no-call complex = ? ? -488 1.17 N +2185 2 chr1 105719 105728 hom ref = = = 15 1.17 N +2186 2 chr1 105728 105742 no-call complex = ? ? -157 1.17 N +2187 2 chr1 105742 105770 hom ref = = = 13 1.17 N +2188 2 chr1 105770 105794 no-call complex = ? ? -346 1.17 N +2189 2 chr1 105794 105828 hom ref = = = 25 1.17 N +2190 2 chr1 105828 105835 no-call complex = ? ? -33 1.17 N +2191 2 chr1 105835 105863 hom ref = = = 20 1.17 N +2192 2 chr1 105863 105893 no-call complex = ? ? -197 1.17 N +2193 2 chr1 105893 105982 hom ref = = = -16 1.17 N +2194 2 chr1 105982 106059 no-call complex = ? ? -337 1.17 N +2195 2 chr1 106059 106107 hom ref = = = -21 1.17 N +2196 2 chr1 106107 106167 no-call complex = ? ? -173 1.17 N +2197 2 chr1 106167 106238 hom ref = = = -3 1.17 N +2198 2 chr1 106238 106245 no-call complex = ? ? -19 1.17 N +2199 2 chr1 106245 106320 hom ref = = = 10 1.17 N +2200 2 chr1 106320 106347 no-call complex = ? ? -206 1.17 N +2201 2 chr1 106347 106363 hom ref = = = 8 1.17 N +2202 2 chr1 106363 106364 half ref C C N 61 121 8 10 1.17 N +2203 2 chr1 106364 106406 hom ref = = = 8 1.17 N +2204 2 chr1 106406 106437 no-call complex = ? ? -128 1.17 N +2205 2 chr1 106437 106452 hom ref = = = 14 1.17 N +2206 2 chr1 106452 106492 no-call complex = ? ? -85 1.17 N +2207 2 chr1 106492 106504 hom ref = = = 11 1.17 N +2208 2 chr1 106504 106508 half ref AATA AATA ? 46 0 3 MER5B:hAT-Charlie:39.2 10 1.17 N +2209 2 chr1 106508 106516 hom ref = = = 3 1.17 N +2210 2 chr1 106516 106567 no-call complex = ? ? -117 1.17 N +2211 2 chr1 106567 106589 hom ref = = = 27 1.17 N +2212 2 chr1 106589 106628 no-call complex = ? ? -78 1.17 N +2213 2 chr1 106628 106637 hom ref = = = 10 1.17 N +2214 2 chr1 106637 106676 no-call complex = ? ? -321 1.17 N +2215 2 chr1 106676 106813 hom ref = = = -15 1.17 N +2216 2 chr1 106813 106814 half ref C C N 121 121 -15 10 1.17 N +2217 2 chr1 106814 106852 hom ref = = = -15 1.17 N +2218 2 chr1 106852 106888 no-call complex = ? ? -60 1.17 N +2219 2 chr1 106888 106909 hom ref = = = 35 1.17 N +2220 2 chr1 106909 106955 no-call complex = ? ? -814 1.17 N +2221 2 chr1 106955 106966 hom ref = = = 38 1.17 N +2222 2 chr1 106966 106973 no-call complex = ? ? -36 1.17 N +2223 2 chr1 106973 107155 hom ref = = = -55 1.17 N +2224 2 chr1 107155 107156 half ref C C N 74 120 29 10 1.17 N +2225 2 chr1 107156 107231 hom ref = = = 29 1.17 N +2226 2 chr1 107231 107275 no-call complex = ? ? -234 1.17 N +2227 2 chr1 107275 107324 hom ref = = = 27 1.17 N +2228 2 chr1 107324 107355 no-call complex = ? ? -165 1.17 N +2229 2 chr1 107355 107460 hom ref = = = 20 1.17 N +2230 2 chr1 107460 107467 no-call complex = ? ? -169 1.17 N +2231 2 chr1 107467 107504 hom ref = = = 15 1.17 N +2232 2 chr1 107504 107545 no-call complex = ? ? -173 1.17 N +2233 2 chr1 107545 107890 hom ref = = = -34 1.17 N +2234 2 chr1 107890 107897 no-call complex = ? ? -8 1.17 N +2235 2 chr1 107897 107966 hom ref = = = 15 1.17 N +2236 2 chr1 107966 107973 no-call complex = ? ? -634 1.17 N +2237 2 chr1 107973 108281 hom ref = = = -40 1.17 N +2238 2 chr1 108281 108313 no-call complex = ? ? -163 1.17 N +2239 2 chr1 108313 108361 hom ref = = = 10 1.17 N +2240 2 chr1 108361 108368 no-call complex = ? ? -92 1.17 N +2241 2 chr1 108368 108400 hom ref = = = 25 1.17 N +2242 2 chr1 108400 108420 no-call complex = ? ? -133 1.17 N +2243 2 chr1 108420 108536 hom ref = = = -14 1.17 N +2244 2 chr1 108536 108569 no-call complex = ? ? -198 1.17 N +2245 2 chr1 108569 108596 hom ref = = = 71 1.17 N +2246 2 chr1 108596 108632 no-call complex = ? ? -97 1.17 N +2247 2 chr1 108632 108771 hom ref = = = -16 1.17 N +2248 2 chr1 108771 108788 no-call complex = ? ? -187 1.17 N +2249 2 chr1 108788 108823 hom ref = = = 26 1.17 N +2250 2 chr1 108823 108850 no-call complex = ? ? -69 1.17 N +2251 2 chr1 108850 108867 hom ref = = = 13 1.17 N +2252 2 chr1 108867 108901 no-call complex = ? ? -254 1.17 N +2253 2 chr1 108901 108997 hom ref = = = 17 1.17 N +2254 2 chr1 108997 109004 no-call complex = ? ? -65 1.17 N +2255 2 chr1 109004 109166 hom ref = = = 1 1.17 N +2256 2 chr1 109166 109224 no-call complex = ? ? -92 1.17 N +2257 2 chr1 109224 109255 hom ref = = = 12 1.17 N +2258 2 chr1 109255 109275 no-call complex = ? ? -24 1.17 N +2259 2 chr1 109275 109324 hom ref = = = 4 1.17 N +2260 2 chr1 109324 109325 half ref T T N 21 21 4 11 1.17 N +2261 2 chr1 109325 109453 hom ref = = = -20 1.17 N +2262 2 chr1 109453 109491 no-call complex = ? ? -476 1.17 N +2263 2 chr1 109491 109571 hom ref = = = -19 1.17 N +2264 2 chr1 109571 109651 no-call complex = ? ? -80 1.17 N +2265 2 chr1 109651 109706 hom ref = = = -6 1.17 N +2266 2 chr1 109706 109735 no-call complex = ? ? -83 1.17 N +2267 2 chr1 109735 109777 hom ref = = = 30 1.17 N +2268 2 chr1 109777 109853 no-call complex = ? ? -109 1.17 N +2269 2 chr1 109853 109873 hom ref = = = 29 1.17 N +2270 2 chr1 109873 109880 no-call complex = ? ? -59 1.17 N +2271 2 chr1 109880 109963 hom ref = = = 18 1.17 N +2272 2 chr1 109963 109970 no-call complex = ? ? -51 1.17 N +2273 2 chr1 109970 110003 hom ref = = = 26 1.17 N +2274 2 chr1 110003 110010 no-call complex = ? ? -2 1.17 N +2275 2 chr1 110010 110150 hom ref = = = 15 1.17 N +2276 2 chr1 110150 110157 no-call complex = ? ? -27 1.17 N +2277 2 chr1 110157 110376 hom ref = = = -4 1.17 N +2278 2 chr1 110376 110422 no-call complex = ? ? -100 1.17 N +2279 2 chr1 110422 110438 hom ref = = = 26 1.17 N +2280 2 chr1 110438 110470 no-call complex = ? ? -58 1.17 N +2281 2 chr1 110470 110541 hom ref = = = 31 1.17 N +2282 2 chr1 110541 110548 no-call complex = ? ? -51 1.17 N +2283 2 chr1 110548 110602 hom ref = = = 31 1.17 N +2284 2 chr1 110602 110610 no-call complex = ? ? -123 1.17 N +2285 2 chr1 110610 110699 hom ref = = = 19 1.17 N +2286 2 chr1 110699 110706 no-call complex = ? ? -77 1.17 N +2287 2 chr1 110706 110742 hom ref = = = 15 1.17 N +2288 2 chr1 110742 110786 no-call complex = ? ? -221 1.17 N +2289 2 chr1 110786 110840 hom ref = = = 17 1.17 N +2290 2 chr1 110840 110848 no-call complex = ? ? 4 1.17 N +2291 2 chr1 110848 110944 hom ref = = = -14 1.17 N +2292 2 chr1 110944 110945 no-call complex = ? ? -14 1.17 N +2293 2 chr1 110945 111045 hom ref = = = -14 1.17 N +2294 2 chr1 111045 111052 no-call complex = ? ? -28 1.17 N +2295 2 chr1 111052 111073 hom ref = = = 44 1.17 N +2296 2 chr1 111073 111115 no-call complex = ? ? -39 1.17 N +2297 2 chr1 111115 111157 hom ref = = = -5 1.17 N +2298 2 chr1 111157 111158 half ref T T N 121 121 -6 AluSq2:Alu:11.7 20 1.17 N +2299 2 chr1 111158 111228 hom ref = = = -10 1.17 N +2300 2 chr1 111228 111241 no-call complex = ? ? -114 1.17 N +2301 2 chr1 111241 111358 hom ref = = = -18 1.17 N +2302 2 chr1 111358 111403 no-call complex = ? ? -175 1.17 N +2303 2 chr1 111403 111471 hom ref = = = -6 1.17 N +2304 2 chr1 111471 111529 no-call complex = ? ? -120 1.17 N +2305 2 chr1 111529 111560 hom ref = = = 20 1.17 N +2306 2 chr1 111560 111631 no-call complex = ? ? -139 1.17 N +2307 2 chr1 111631 111703 hom ref = = = 2 1.17 N +2308 2 chr1 111703 111718 no-call complex = ? ? -186 1.17 N +2309 2 chr1 111718 111753 hom ref = = = -15 1.17 N +2310 2 chr1 111753 111753 half ref ? 30 0 951 952 17 20 1.17 N +2311 2 chr1 111753 111763 hom ref = = = 17 1.17 N +2312 2 chr1 111763 111763 half ref ? 30 0 951 952 21 20 1.17 N +2313 2 chr1 111763 111779 hom ref = = = 1 1.17 N +2314 2 chr1 111779 111780 half ref A A N 52 52 9 20 1.17 N +2315 2 chr1 111780 111785 hom ref = = = 9 1.17 N +2316 2 chr1 111785 111786 half ref C C N 52 52 15 20 1.17 N +2317 2 chr1 111786 111790 hom ref = = = 11 1.17 N +2318 2 chr1 111790 111790 half ref ? 22 0 27 20 1.17 N +2319 2 chr1 111790 111796 hom ref = = = -6 1.17 N +2320 2 chr1 111796 111800 half ref TTTC TTTC ? 52 0 953 954 -6 20 1.17 N +2321 2 chr1 111800 111805 hom ref = = = 21 1.17 N +2322 2 chr1 111805 111806 half ref A A N 52 52 953 954 14 20 1.17 N +2323 2 chr1 111806 111810 hom ref = = = 3 1.17 N +2324 2 chr1 111810 111811 half ref T T N 52 52 953 954 3 20 1.17 N +2325 2 chr1 111811 111854 hom ref = = = -23 1.17 N +2326 2 chr1 111854 111901 no-call complex = ? ? -22 1.17 N +2327 2 chr1 111901 111924 hom ref = = = 13 1.17 N +2328 2 chr1 111924 111931 no-call complex = ? ? -5 1.17 N +2329 2 chr1 111931 111951 hom ref = = = -10 1.17 N +2330 2 chr1 111951 111952 half ref A A N 34 105 957 958 -10 20 1.17 N +2331 2 chr1 111952 111984 hom ref = = = -10 1.17 N +2332 2 chr1 111984 111985 half ref G G N 49 102 957 958 9 20 1.17 N +2333 2 chr1 111985 112004 hom ref = = = 9 1.17 N +2334 2 chr1 112004 112043 no-call complex = ? ? -26 1.17 N +2335 2 chr1 112043 112056 hom ref = = = 14 1.17 N +2336 2 chr1 112056 112087 no-call complex = ? ? -95 1.17 N +2337 2 chr1 112087 112101 hom ref = = = 22 1.17 N +2338 2 chr1 112101 112155 no-call complex = ? ? -64 1.17 N +2339 2 chr1 112155 112160 hom ref = = = 14 1.17 N +2340 2 chr1 112160 112181 no-call complex = ? ? -30 1.17 N +2341 2 chr1 112181 112215 hom ref = = = 7 1.17 N +2342 2 chr1 112215 112216 half ref C C N 120 120 7 L2b:L2:47.3 20 1.17 N +2343 2 chr1 112216 112239 hom ref = = = 6 1.17 N +2344 2 chr1 112239 112254 no-call complex = ? ? -104 1.17 N +2345 2 chr1 112254 112336 hom ref = = = -37 1.17 N +2346 2 chr1 112336 112383 no-call complex = ? ? -51 1.17 N +2347 2 chr1 112383 112388 hom ref = = = 10 1.17 N +2348 2 chr1 112388 112461 no-call complex = ? ? -52 1.17 N +2349 2 chr1 112461 112482 hom ref = = = 15 1.17 N +2350 2 chr1 112482 112489 no-call complex = ? ? -152 1.17 N +2351 2 chr1 112489 112523 hom ref = = = 11 1.17 N +2352 2 chr1 112523 112537 no-call complex = ? ? -79 1.17 N +2353 2 chr1 112537 112607 hom ref = = = 0 1.17 N +2354 2 chr1 112607 112608 half ref A A ? 41 0 0 20 1.17 N +2355 2 chr1 112608 112649 hom ref = = = 0 1.17 N +2356 2 chr1 112649 112656 no-call complex = ? ? -18 1.17 N +2357 2 chr1 112656 112678 hom ref = = = 10 1.17 N +2358 2 chr1 112678 112708 no-call complex = ? ? -43 1.17 N +2359 2 chr1 112708 112732 hom ref = = = 13 1.17 N +2360 2 chr1 112732 112800 no-call complex = ? ? -219 1.17 N +2361 2 chr1 112800 112812 hom ref = = = 10 1.17 N +2362 2 chr1 112812 112861 no-call complex = ? ? -190 1.17 N +2363 2 chr1 112861 112879 hom ref = = = 20 1.17 N +2364 2 chr1 112879 112897 no-call complex = ? ? -2 1.17 N +2365 2 chr1 112897 112924 hom ref = = = 12 1.17 N +2366 2 chr1 112924 112971 no-call complex = ? ? -80 1.17 N +2367 2 chr1 112971 112999 hom ref = = = 12 1.17 N +2368 2 chr1 112999 113015 no-call complex = ? ? -41 1.17 N +2369 2 chr1 113015 113071 hom ref = = = 12 1.17 N +2370 2 chr1 113071 113152 no-call complex = ? ? -188 1.17 N +2371 2 chr1 113152 113198 hom ref = = = -23 1.17 N +2372 2 chr1 113198 113198 half ref ? 22 0 2 20 1.17 N +2373 2 chr1 113198 113252 hom ref = = = 2 1.17 N +2374 2 chr1 113252 113275 no-call complex = ? ? -6 1.17 N +2375 2 chr1 113275 113315 hom ref = = = 1 1.17 N +2376 2 chr1 113315 113360 no-call complex = ? ? -42 1.17 N +2377 2 chr1 113360 113369 hom ref = = = 24 1.17 N +2378 2 chr1 113369 113384 no-call complex = ? ? -87 1.17 N +2379 2 chr1 113384 113489 hom ref = = = 12 1.17 N +2380 2 chr1 113489 113531 no-call complex = ? ? 3 1.17 N +2381 2 chr1 113531 113544 hom ref = = = 26 1.17 N +2382 2 chr1 113544 113576 no-call complex = ? ? -70 1.17 N +2383 2 chr1 113576 113600 hom ref = = = 11 1.17 N +2384 2 chr1 113600 113627 no-call complex = ? ? -96 1.17 N +2385 2 chr1 113627 113792 hom ref = = = -4 1.17 N +2386 2 chr1 113792 113825 no-call complex = ? ? -36 1.17 N +2387 2 chr1 113825 113936 hom ref = = = 2 1.17 N +2388 2 chr1 113936 113973 no-call complex = ? ? -154 1.17 N +2389 2 chr1 113973 113997 hom ref = = = 12 1.17 N +2390 2 chr1 113997 114045 no-call complex = ? ? -17 1.17 N +2391 2 chr1 114045 114094 hom ref = = = -13 1.17 N +2392 2 chr1 114094 114143 no-call complex = ? ? -95 1.17 N +2393 2 chr1 114143 114196 hom ref = = = -30 1.17 N +2394 2 chr1 114196 114210 no-call complex = ? ? -44 1.17 N +2395 2 chr1 114210 114227 hom ref = = = 14 1.17 N +2396 2 chr1 114227 114299 no-call complex = ? ? -40 1.17 N +2397 2 chr1 114299 114313 hom ref = = = 11 1.17 N +2398 2 chr1 114313 114349 no-call complex = ? ? -40 1.17 N +2399 2 chr1 114349 114370 hom ref = = = 10 1.17 N +2400 2 chr1 114370 114424 no-call complex = ? ? -28 1.17 N +2401 2 chr1 114424 114464 hom ref = = = 11 1.17 N +2402 2 chr1 114464 114509 no-call complex = ? ? -256 1.17 N +2403 2 chr1 114509 114542 hom ref = = = 18 1.17 N +2404 2 chr1 114542 114565 no-call complex = ? ? 4 1.17 N +2405 2 chr1 114565 114651 hom ref = = = 0 1.17 N +2406 2 chr1 114651 114705 no-call complex = ? ? -81 1.17 N +2407 2 chr1 114705 114712 hom ref = = = 14 1.17 N +2408 2 chr1 114712 114741 no-call complex = ? ? -16 1.17 N +2409 2 chr1 114741 114761 hom ref = = = 15 1.17 N +2410 2 chr1 114761 114790 no-call complex = ? ? -31 1.17 N +2411 2 chr1 114790 114869 hom ref = = = -92 1.17 N +2412 2 chr1 114869 114902 no-call complex = ? ? -9 1.17 N +2413 2 chr1 114902 114960 hom ref = = = 11 1.17 N +2414 2 chr1 114960 115002 no-call complex = ? ? -5 1.17 N +2415 2 chr1 115002 115008 hom ref = = = 10 1.17 N +2416 2 chr1 115008 115050 no-call complex = ? ? -42 1.17 N +2417 2 chr1 115050 115121 hom ref = = = -10 1.17 N +2418 2 chr1 115121 115171 no-call complex = ? ? -18 1.17 N +2419 2 chr1 115171 115195 hom ref = = = 16 1.17 N +2420 2 chr1 115195 115210 no-call complex = ? ? -19 1.17 N +2421 2 chr1 115210 115221 hom ref = = = 11 1.17 N +2422 2 chr1 115221 115277 no-call complex = ? ? -3 1.17 N +2423 2 chr1 115277 115282 hom ref = = = 16 1.17 N +2424 2 chr1 115282 115289 no-call complex = ? ? -182 1.17 N +2425 2 chr1 115289 115309 hom ref = = = 12 1.17 N +2426 2 chr1 115309 115336 no-call complex = ? ? -92 1.17 N +2427 2 chr1 115336 115387 hom ref = = = 8 1.17 N +2428 2 chr1 115387 115387 half ref ? 36 0 11 L2:L2:43.7 20 1.17 N +2429 2 chr1 115387 115430 hom ref = = = 9 1.17 N +2430 2 chr1 115430 115457 no-call complex = ? ? -160 1.17 N +2431 2 chr1 115457 115470 hom ref = = = 11 1.17 N +2432 2 chr1 115470 115508 no-call complex = ? ? -31 1.17 N +2433 2 chr1 115508 115519 hom ref = = = 24 1.17 N +2434 2 chr1 115519 115560 no-call complex = ? ? -20 1.17 N +2435 2 chr1 115560 115583 hom ref = = = 31 1.17 N +2436 2 chr1 115583 115608 no-call complex = ? ? -265 1.17 N +2437 2 chr1 115608 115661 hom ref = = = -49 1.17 N +2438 2 chr1 115661 115668 no-call complex = ? ? -20 1.17 N +2439 2 chr1 115668 115694 hom ref = = = 15 1.17 N +2440 2 chr1 115694 115752 no-call complex = ? ? -35 1.17 N +2441 2 chr1 115752 115759 hom ref = = = 12 1.17 N +2442 2 chr1 115759 115805 no-call complex = ? ? -23 1.17 N +2443 2 chr1 115805 115819 hom ref = = = 12 1.17 N +2444 2 chr1 115819 115853 no-call complex = ? ? -67 1.17 N +2445 2 chr1 115853 115870 hom ref = = = 10 1.17 N +2446 2 chr1 115870 115918 no-call complex = ? ? -27 1.17 N +2447 2 chr1 115918 116015 hom ref = = = -13 1.17 N +2448 2 chr1 116015 116057 no-call complex = ? ? -11 1.17 N +2449 2 chr1 116057 116081 hom ref = = = 12 1.17 N +2450 2 chr1 116081 116111 no-call complex = ? ? -67 1.17 N +2451 2 chr1 116111 116121 hom ref = = = 21 1.17 N +2452 2 chr1 116121 116170 no-call complex = ? ? -44 1.17 N +2453 2 chr1 116170 116246 hom ref = = = -32 1.17 N +2454 2 chr1 116246 116249 half ref GAT GAT ? 40 0 -8 20 1.17 N +2455 2 chr1 116249 116263 hom ref = = = -8 1.17 N +2456 2 chr1 116263 116309 no-call complex = ? ? -120 1.17 N +2457 2 chr1 116309 116467 hom ref = = = -7 1.17 N +2458 2 chr1 116467 116468 half ref A A N 63 109 1043 1044 -7 L2a:L2:36.4 20 1.17 N +2459 2 chr1 116468 116471 hom ref = = = -7 1.17 N +2460 2 chr1 116471 116471 half ref ? 28 0 1043 1044 10 L2a:L2:36.4 20 1.17 N +2461 2 chr1 116471 116482 hom ref = = = 4 1.17 N +2462 2 chr1 116482 116501 no-call complex = ? ? -12 1.17 N +2463 2 chr1 116501 116508 hom ref = = = 12 1.17 N +2464 2 chr1 116508 116568 no-call complex = ? ? -43 1.17 N +2465 2 chr1 116568 116583 hom ref = = = -71 1.17 N +2466 2 chr1 116583 116584 half ref G G N 120 120 -71 L2a:L2:36.4 20 1.17 N +2467 2 chr1 116584 116632 hom ref = = = -71 1.17 N +2468 2 chr1 116632 116632 half ref ? 39 0 1047 1048 8 L2a:L2:36.4 20 1.17 N +2469 2 chr1 116632 116645 hom ref = = = 4 1.17 N +2470 2 chr1 116645 116646 half ref C C N 121 121 1047 1048 4 L2a:L2:36.4 20 1.17 N +2471 2 chr1 116646 116682 hom ref = = = 4 1.17 N +2472 2 chr1 116682 116689 no-call complex = ? ? -25 1.17 N +2473 2 chr1 116689 116732 hom ref = = = -28 1.17 N +2474 2 chr1 116732 116732 half ref ? 25 0 32 L2a:L2:36.4 20 1.17 N +2475 2 chr1 116732 116781 hom ref = = = -39 1.17 N +2476 2 chr1 116781 116782 half ref T T N 36 99 -39 L2a:L2:36.4 20 1.17 N +2477 2 chr1 116782 116805 hom ref = = = -39 1.17 N +2478 2 chr1 116805 116821 no-call complex = ? ? -1 1.17 N +2479 2 chr1 116821 116864 hom ref = = = -11 1.17 N +2480 2 chr1 116864 116864 half ref ? 24 0 6 L2a:L2:36.4 20 1.17 N +2481 2 chr1 116864 116886 hom ref = = = 6 1.17 N +2482 2 chr1 116886 116933 no-call complex = ? ? -174 1.17 N +2483 2 chr1 116933 116988 hom ref = = = 11 1.17 N +2484 2 chr1 116988 117002 no-call complex = ? ? -176 1.17 N +2485 2 chr1 117002 117021 hom ref = = = 10 1.17 N +2486 2 chr1 117021 117059 no-call complex = ? ? -83 1.17 N +2487 2 chr1 117059 117099 hom ref = = = -1 1.17 N +2488 2 chr1 117099 117100 no-call complex A N N 59 59 -1 L1ME3E:L1:29.0 20 1.17 N +2489 2 chr1 117100 117106 hom ref = = = -6 1.17 N +2490 2 chr1 117106 117107 half ref T T N 37 59 6 L1ME3E:L1:29.0 20 1.17 N +2491 2 chr1 117107 117113 hom ref = = = 0 1.17 N +2492 2 chr1 117113 117114 half ref T T N 59 59 0 L1ME3E:L1:29.0 20 1.17 N +2493 2 chr1 117114 117123 hom ref = = = 0 1.17 N +2494 2 chr1 117123 117124 half ref T T N 59 59 10 L1ME3E:L1:29.0 20 1.17 N +2495 2 chr1 117124 117136 hom ref = = = -14 1.17 N +2496 2 chr1 117136 117137 half ref C C ? 59 0 -14 L1ME3E:L1:29.0 20 1.17 N +2497 2 chr1 117137 117147 hom ref = = = -21 1.17 N +2498 2 chr1 117147 117148 half ref T T N 59 33 1055 1056 -21 L1ME3E:L1:29.0 20 1.17 N +2499 2 chr1 117148 117156 hom ref = = = -21 1.17 N +2500 2 chr1 117156 117157 half ref C C N 24 59 1055 1056 -3 L1ME3E:L1:29.0 20 1.17 N +2501 2 chr1 117157 117201 hom ref = = = -43 1.17 N +2502 2 chr1 117201 117201 half ref ? 27 0 20 L1ME3E:L1:29.0 20 1.17 N +2503 2 chr1 117201 117231 hom ref = = = 18 1.17 N +2504 2 chr1 117231 117259 no-call complex = ? ? -26 1.17 N +2505 2 chr1 117259 117275 hom ref = = = 14 1.17 N +2506 2 chr1 117275 117288 no-call complex = ? ? -11 1.17 N +2507 2 chr1 117288 117293 hom ref = = = 24 1.17 N +2508 2 chr1 117293 117354 no-call complex = ? ? -25 1.17 N +2509 2 chr1 117354 117364 hom ref = = = 13 1.17 N +2510 2 chr1 117364 117410 no-call complex = ? ? -37 1.17 N +2511 2 chr1 117410 117453 hom ref = = = -21 1.17 N +2512 2 chr1 117453 117491 no-call complex = ? ? -23 1.17 N +2513 2 chr1 117491 117545 hom ref = = = -97 1.17 N +2514 2 chr1 117545 117552 no-call complex = ? ? -209 1.17 N +2515 2 chr1 117552 117606 hom ref = = = 14 1.17 N +2516 2 chr1 117606 117637 no-call complex = ? ? -31 1.17 N +2517 2 chr1 117637 117751 hom ref = = = 7 1.17 N +2518 2 chr1 117751 117787 no-call complex = ? ? -129 1.17 N +2519 2 chr1 117787 117800 hom ref = = = -3 1.17 N +2520 2 chr1 117800 117803 half ref TTA TTA NTN 31 79 1071 1072 -17 MLT1D:ERVL-MaLR:29.2 20 1.17 N +2521 2 chr1 117803 117808 hom ref = = = -17 1.17 N +2522 2 chr1 117808 117809 half ref G G N 79 79 1071 1072 12 MLT1D:ERVL-MaLR:29.2 20 1.17 N +2523 2 chr1 117809 117812 hom ref = = = -4 1.17 N +2524 2 chr1 117812 117812 half ref ? 31 0 1071 1072 -4 MLT1D:ERVL-MaLR:29.2 20 1.17 N +2525 2 chr1 117812 117854 hom ref = = = -4 1.17 N +2526 2 chr1 117854 117901 no-call complex = ? ? -31 1.17 N +2527 2 chr1 117901 117912 hom ref = = = 12 1.17 N +2528 2 chr1 117912 117919 no-call complex = ? ? -81 1.17 N +2529 2 chr1 117919 118070 hom ref = = = -2 1.17 N +2530 2 chr1 118070 118102 no-call complex = ? ? -8 1.17 N +2531 2 chr1 118102 118111 hom ref = = = 12 1.17 N +2532 2 chr1 118111 118201 no-call complex = ? ? -169 1.17 N +2533 2 chr1 118201 118243 hom ref = = = 11 1.17 N +2534 2 chr1 118243 118243 half ref ? 20 0 25 L1ME3E:L1:40.5 20 1.17 N +2535 2 chr1 118243 118265 hom ref = = = -23 1.17 N +2536 2 chr1 118265 118271 half ref GGAAAA GGAAAA ? 90 0 -27 L1ME3E:L1:40.5 20 1.17 N +2537 2 chr1 118271 118346 hom ref = = = -6 1.17 N +2538 2 chr1 118346 118434 no-call complex = ? ? -28 1.17 N +2539 2 chr1 118434 118446 hom ref = = = 18 1.17 N +2540 2 chr1 118446 118477 no-call complex = ? ? -362 1.17 N +2541 2 chr1 118477 118486 hom ref = = = 19 1.17 N +2542 2 chr1 118486 118519 no-call complex = ? ? -13 1.17 N +2543 2 chr1 118519 118525 hom ref = = = 13 1.17 N +2544 2 chr1 118525 118555 no-call complex = ? ? -20 1.17 N +2545 2 chr1 118555 118612 hom ref = = = 12 1.17 N +2546 2 chr1 118612 118640 no-call complex = ? ? -250 1.17 N +2547 2 chr1 118640 118661 hom ref = = = 11 1.17 N +2548 2 chr1 118661 118687 no-call complex = ? ? -98 1.17 N +2549 2 chr1 118687 118714 hom ref = = = 20 1.17 N +2550 2 chr1 118714 118728 no-call complex = ? ? 0 1.17 N +2551 2 chr1 118728 118803 hom ref = = = 15 1.17 N +2552 2 chr1 118803 118828 no-call complex = ? ? -37 1.17 N +2553 2 chr1 118828 118842 hom ref = = = 0 1.17 N +2554 2 chr1 118842 118843 half ref A A ? 23 0 1085 1086 0 L1ME3E:L1:40.5 20 1.17 N +2555 2 chr1 118843 118860 hom ref = = = -1 1.17 N +2556 2 chr1 118860 118861 half ref T T N 59 46 1085 1086 8 L1ME3E:L1:40.5 20 1.17 N +2557 2 chr1 118861 118874 hom ref = = = 8 1.17 N +2558 2 chr1 118874 118906 no-call complex = ? ? 5 1.17 N +2559 2 chr1 118906 118938 hom ref = = = -18 1.17 N +2560 2 chr1 118938 118940 half ref AA AA NN 26 120 -18 L1ME3E:L1:40.5 20 1.17 N +2561 2 chr1 118940 118952 hom ref = = = -18 1.17 N +2562 2 chr1 118952 118953 half ref A A N 39 44 2 L1ME3E:L1:40.5 20 1.17 N +2563 2 chr1 118953 118961 hom ref = = = 2 1.17 N +2564 2 chr1 118961 118962 half ref A A N 44 44 8 L1ME3E:L1:40.5 20 1.17 N +2565 2 chr1 118962 118968 hom ref = = = -11 1.17 N +2566 2 chr1 118968 118980 half ref AACTAAGAAGCT AACTAAGAAGCT ? 44 0 -31 L1ME3E:L1:40.5 20 1.17 N +2567 2 chr1 118980 118991 hom ref = = = -29 1.17 N +2568 2 chr1 118991 118995 half ref TATA TATA ? 35 0 7 L1ME3E:L1:40.5 20 1.17 N +2569 2 chr1 118995 119005 hom ref = = = 22 1.17 N +2570 2 chr1 119005 119044 no-call complex = ? ? -34 1.17 N +2571 2 chr1 119044 119062 hom ref = = = 15 1.17 N +2572 2 chr1 119062 119062 half ref ? 20 0 1091 1092 30 L1ME3E:L1:40.5 20 1.17 N +2573 2 chr1 119062 119065 hom ref = = = 9 1.17 N +2574 2 chr1 119065 119066 half ref A A N 32 24 1091 1092 9 L1ME3E:L1:40.5 20 1.17 N +2575 2 chr1 119066 119068 hom ref = = = 9 1.17 N +2576 2 chr1 119068 119069 half ref T T N 49 49 1091 1092 10 L1ME3E:L1:40.5 20 1.17 N +2577 2 chr1 119069 119077 hom ref = = = -10 1.17 N +2578 2 chr1 119077 119078 half ref T T N 49 21 1093 1094 -10 L1ME3E:L1:40.5 20 1.17 N +2579 2 chr1 119078 119081 hom ref = = = -10 1.17 N +2580 2 chr1 119081 119081 half ref ? 25 0 1093 1094 30 L1ME3E:L1:40.5 20 1.17 N +2581 2 chr1 119081 119083 hom ref = = = 24 1.17 N +2582 2 chr1 119083 119083 half ref ? 25 0 1093 1094 24 L1ME3E:L1:40.5 20 1.17 N +2583 2 chr1 119083 119089 hom ref = = = -24 1.17 N +2584 2 chr1 119089 119090 half ref A A N 49 24 1093 1094 24 L1ME3E:L1:40.5 20 1.17 N +2585 2 chr1 119090 119093 hom ref = = = 26 1.17 N +2586 2 chr1 119093 119094 half ref A A ? 49 0 1093 1094 31 L1ME3E:L1:40.5 20 1.17 N +2587 2 chr1 119094 119102 hom ref = = = 4 1.17 N +2588 2 chr1 119102 119103 half ref G G ? 31 0 4 20 1.17 N +2589 2 chr1 119103 119142 hom ref = = = 4 1.17 N +2590 2 chr1 119142 119182 no-call complex = ? ? -37 1.17 N +2591 2 chr1 119182 119199 hom ref = = = 4 1.17 N +2592 2 chr1 119199 119200 half ref T T ? 122 0 4 20 1.17 N +2593 2 chr1 119200 119210 hom ref = = = 4 1.17 N +2594 2 chr1 119210 119425 no-call complex = ? ? -69 1.17 N +2595 2 chr1 119425 119431 hom ref = = = 11 1.17 N +2596 2 chr1 119431 119506 no-call complex = ? ? -135 1.17 N +2597 2 chr1 119506 119521 hom ref = = = 13 1.17 N +2598 2 chr1 119521 119558 no-call complex = ? ? -43 1.17 N +2599 2 chr1 119558 119605 hom ref = = = 12 1.17 N +2600 2 chr1 119605 119623 no-call complex = ? ? -3 1.17 N +2601 2 chr1 119623 119628 hom ref = = = 18 1.17 N +2602 2 chr1 119628 119668 no-call complex = ? ? -67 1.17 N +2603 2 chr1 119668 119685 hom ref = = = 9 1.17 N +2604 2 chr1 119685 119686 half ref A A N 35 123 1103 1104 9 THE1C:ERVL-MaLR:20.3 20 1.17 N +2605 2 chr1 119686 119697 hom ref = = = 9 1.17 N +2606 2 chr1 119697 119698 half ref A A N 53 123 1103 1104 11 THE1C:ERVL-MaLR:20.3 20 1.17 N +2607 2 chr1 119698 119702 hom ref = = = 11 1.17 N +2608 2 chr1 119702 119703 half ref G G ? 55 0 1103 1104 15 THE1C:ERVL-MaLR:20.3 20 1.17 N +2609 2 chr1 119703 119713 hom ref = = = 4 1.17 N +2610 2 chr1 119713 119721 half ref AGCTTCTT AGCTTCTT ? 43 0 1103 1104 -8 THE1C:ERVL-MaLR:20.3 20 1.17 N +2611 2 chr1 119721 119728 hom ref = = = -1 1.17 N +2612 2 chr1 119728 119729 half ref C C N 65 123 1103 1104 -1 THE1C:ERVL-MaLR:20.3 20 1.17 N +2613 2 chr1 119729 119737 hom ref = = = -1 1.17 N +2614 2 chr1 119737 119778 no-call complex = ? ? -28 1.17 N +2615 2 chr1 119778 119793 hom ref = = = 17 1.17 N +2616 2 chr1 119793 119806 no-call complex = ? ? 2 1.17 N +2617 2 chr1 119806 119929 hom ref = = = -8 1.17 N +2618 2 chr1 119929 119936 no-call complex = ? ? -56 1.17 N +2619 2 chr1 119936 119964 hom ref = = = -31 1.17 N +2620 2 chr1 119964 119964 half ref ? 35 0 1105 1106 -31 20 1.17 N +2621 2 chr1 119964 119990 hom ref = = = -31 1.17 N +2622 2 chr1 119990 119995 half ref TTATA TTATA ? 41 0 1105 1106 0 20 1.17 N +2623 2 chr1 119995 120012 hom ref = = = 5 1.17 N +2624 2 chr1 120012 120059 no-call complex = ? ? -118 1.17 N +2625 2 chr1 120059 120096 hom ref = = = 15 1.17 N +2626 2 chr1 120096 120136 no-call complex = ? ? -53 1.17 N +2627 2 chr1 120136 120182 hom ref = = = 18 1.17 N +2628 2 chr1 120182 120190 no-call complex = ? ? -124 1.17 N +2629 2 chr1 120190 120351 hom ref = = = -23 1.17 N +2630 2 chr1 120351 120352 half ref A A ? 120 0 1 20 1.17 N +2631 2 chr1 120352 120367 hom ref = = = 1 1.17 N +2632 2 chr1 120367 120392 no-call complex = ? ? -254 1.17 N +2633 2 chr1 120392 120451 hom ref = = = 13 1.17 N +2634 2 chr1 120451 120486 no-call complex = ? ? -114 1.17 N +2635 2 chr1 120486 120493 hom ref = = = 14 1.17 N +2636 2 chr1 120493 120549 no-call complex = ? ? -146 1.17 N +2637 2 chr1 120549 120611 hom ref = = = 15 1.17 N +2638 2 chr1 120611 120641 no-call complex = ? ? -46 1.17 N +2639 2 chr1 120641 120663 hom ref = = = 18 1.17 N +2640 2 chr1 120663 120675 no-call complex CTTAAAAGTTTT CTTANAAGTTTT? ? 0 0 -8 20 1.17 N +2641 2 chr1 120675 120685 hom ref = = = 17 1.17 N +2642 2 chr1 120685 120722 no-call complex = ? ? -94 1.17 N +2643 2 chr1 120722 120729 hom ref = = = 20 1.17 N +2644 2 chr1 120729 120744 no-call complex = ? ? -1 1.17 N +2645 2 chr1 120744 120774 hom ref = = = 11 1.17 N +2646 2 chr1 120774 120798 no-call complex = ? ? -8 1.17 N +2647 2 chr1 120798 120810 hom ref = = = 13 1.17 N +2648 2 chr1 120810 120830 no-call complex = ? ? -30 1.17 N +2649 2 chr1 120830 120843 hom ref = = = 11 1.17 N +2650 2 chr1 120843 120853 half ref TTTCTGAATG TTTCTGAATG ? 26 0 1115 1116 8 20 1.17 N +2651 2 chr1 120853 120857 hom ref = = = 8 1.17 N +2652 2 chr1 120857 120858 half ref A A N 119 119 1115 1116 9 20 1.17 N +2653 2 chr1 120858 120876 hom ref = = = 9 1.17 N +2654 2 chr1 120876 120914 no-call complex = ? ? -22 1.17 N +2655 2 chr1 120914 120929 hom ref = = = 13 1.17 N +2656 2 chr1 120929 120947 no-call complex CAGCTAGAAAAAAATTAA CAGCTAGAAAAAAA?TAA ? 0 0 -6 20 1.17 N +2657 2 chr1 120947 120957 hom ref = = = 10 1.17 N +2658 2 chr1 120957 121200 no-call complex = ? ? -100 1.17 N +2659 2 chr1 121200 121208 hom ref = = = 19 1.17 N +2660 2 chr1 121208 121215 half ref TGACCAT TGACCAT ? 22 0 1117 1118 -2 21 1.17 N +2661 2 chr1 121215 121219 hom ref = = = 11 1.17 N +2662 2 chr1 121219 121220 half ref C C ? 71 0 1117 1118 11 21 1.17 N +2663 2 chr1 121220 121223 hom ref = = = 8 1.17 N +2664 2 chr1 121223 121227 half ref AATT AATT ? 26 0 1117 1118 -16 21 1.17 N +2665 2 chr1 121227 121232 hom ref = = = 9 1.17 N +2666 2 chr1 121232 121235 half ref ACT ACT NCN 25 54 1117 1118 9 21 1.17 N +2667 2 chr1 121235 121254 hom ref = = = 14 1.17 N +2668 2 chr1 121254 121533 no-call complex = ? ? -121 1.17 N +2669 2 chr1 121533 121538 hom ref = = = 13 1.17 N +2670 2 chr1 121538 121582 no-call complex = ? ? -88 1.17 N +2671 2 chr1 121582 121601 hom ref = = = 18 1.17 N +2672 2 chr1 121601 121620 no-call complex = ? ? -122 1.17 N +2673 2 chr1 121620 121635 hom ref = = = 16 1.17 N +2674 2 chr1 121635 121745 no-call complex = ? ? -74 1.17 N +2675 2 chr1 121745 121750 hom ref = = = 10 1.17 N +2676 2 chr1 121750 121789 no-call complex = ? ? -70 1.17 N +2677 2 chr1 121789 121801 hom ref = = = 14 1.17 N +2678 2 chr1 121801 121836 no-call complex = ? ? -13 1.17 N +2679 2 chr1 121836 121861 hom ref = = = 11 1.17 N +2680 2 chr1 121861 121888 no-call complex = ? ? -124 1.17 N +2681 2 chr1 121888 121907 hom ref = = = 12 1.17 N +2682 2 chr1 121907 121950 no-call complex = ? ? -314 1.17 N +2683 2 chr1 121950 121957 hom ref = = = 15 1.17 N +2684 2 chr1 121957 122008 no-call complex = ? ? -35 1.17 N +2685 2 chr1 122008 122016 hom ref = = = 11 1.17 N +2686 2 chr1 122016 122049 no-call complex = ? ? -14 1.17 N +2687 2 chr1 122049 122066 hom ref = = = 14 1.17 N +2688 2 chr1 122066 122108 no-call complex = ? ? -74 1.17 N +2689 2 chr1 122108 122182 hom ref = = = 12 1.17 N +2690 2 chr1 122182 122195 no-call complex = ? ? -89 1.17 N +2691 2 chr1 122195 122220 hom ref = = = 11 1.17 N +2692 2 chr1 122220 122243 no-call complex = ? ? -56 1.17 N +2693 2 chr1 122243 122275 hom ref = = = 7 1.17 N +2694 2 chr1 122275 122278 half ref AGA AGA NNN 35 121 1133 1134 2 21 1.17 N +2695 2 chr1 122278 122281 hom ref = = = 2 1.17 N +2696 2 chr1 122281 122282 half ref A A N 121 121 1133 1134 4 21 1.17 N +2697 2 chr1 122282 122379 hom ref = = = -3 1.17 N +2698 2 chr1 122379 122425 no-call complex = ? ? -108 1.17 N +2699 2 chr1 122425 122447 hom ref = = = -12 1.17 N +2700 2 chr1 122447 122448 half ref A A N 41 120 1137 1138 -12 21 1.17 N +2701 2 chr1 122448 122466 hom ref = = = -30 1.17 N +2702 2 chr1 122466 122466 half ref ? 30 0 1137 1138 -30 21 1.17 N +2703 2 chr1 122466 122526 hom ref = = = -30 1.17 N +2704 2 chr1 122526 122552 no-call complex = ? ? -329 1.17 N +2705 2 chr1 122552 122584 hom ref = = = 15 1.17 N +2706 2 chr1 122584 122614 no-call complex = ? ? -1 1.17 N +2707 2 chr1 122614 122621 hom ref = = = 31 1.17 N +2708 2 chr1 122621 122675 no-call complex = ? ? -293 1.17 N +2709 2 chr1 122675 122687 hom ref = = = 16 1.17 N +2710 2 chr1 122687 122725 no-call complex = ? ? -32 1.17 N +2711 2 chr1 122725 122744 hom ref = = = 16 1.17 N +2712 2 chr1 122744 122781 no-call complex = ? ? -94 1.17 N +2713 2 chr1 122781 122810 hom ref = = = -22 1.17 N +2714 2 chr1 122810 122810 half ref ? 23 0 1147 1148 17 20 1.17 N +2715 2 chr1 122810 122812 hom ref = = = 8 1.17 N +2716 2 chr1 122812 122813 half ref T T N 37 120 1147 1148 8 20 1.17 N +2717 2 chr1 122813 122868 hom ref = = = 8 1.17 N +2718 2 chr1 122868 122893 no-call complex = ? ? -89 1.17 N +2719 2 chr1 122893 122908 hom ref = = = 16 1.17 N +2720 2 chr1 122908 122915 no-call complex = ? ? -270 1.17 N +2721 2 chr1 122915 122928 hom ref = = = 16 1.17 N +2722 2 chr1 122928 122982 no-call complex = ? ? -75 1.17 N +2723 2 chr1 122982 122994 hom ref = = = 17 1.17 N +2724 2 chr1 122994 123028 no-call complex = ? ? -25 1.17 N +2725 2 chr1 123028 123033 hom ref = = = 26 1.17 N +2726 2 chr1 123033 123069 no-call complex = ? ? -11 1.17 N +2727 2 chr1 123069 123084 hom ref = = = 10 1.17 N +2728 2 chr1 123084 123180 no-call complex = ? ? -31 1.17 N +2729 2 chr1 123180 123197 hom ref = = = 15 1.17 N +2730 2 chr1 123197 123229 no-call complex = ? ? -11 1.17 N +2731 2 chr1 123229 123274 hom ref = = = 13 1.17 N +2732 2 chr1 123274 123316 no-call complex = ? ? -96 1.17 N +2733 2 chr1 123316 123328 hom ref = = = 12 1.17 N +2734 2 chr1 123328 123335 half ref ATGTAAA ATGTAAA ? 50 0 9 19 1.17 N +2735 2 chr1 123335 123375 hom ref = = = 11 1.17 N +2736 2 chr1 123375 123382 half ref TATGAGA TATGAGA ? 29 0 8 20 1.17 N +2737 2 chr1 123382 123389 hom ref = = = 13 1.17 N +2738 2 chr1 123389 123445 no-call complex = ? ? -17 1.17 N +2739 2 chr1 123445 123454 hom ref = = = 28 1.17 N +2740 2 chr1 123454 123484 no-call complex = ? ? -58 1.17 N +2741 2 chr1 123484 123505 hom ref = = = 34 1.17 N +2742 2 chr1 123505 123514 no-call complex = ? ? -298 1.17 N +2743 2 chr1 123514 123531 hom ref = = = 24 1.17 N +2744 2 chr1 123531 123561 no-call complex = ? ? -20 1.17 N +2745 2 chr1 123561 123632 hom ref = = = 8 1.17 N +2746 2 chr1 123632 123647 no-call complex = ? ? -261 1.17 N +2747 2 chr1 123647 123706 hom ref = = = 10 1.17 N +2748 2 chr1 123706 123752 no-call complex = ? ? -96 1.17 N +2749 2 chr1 123752 123846 hom ref = = = 10 1.17 N +2750 2 chr1 123846 123868 no-call complex = ? ? -20 1.17 N +2751 2 chr1 123868 123885 hom ref = = = 23 1.17 N +2752 2 chr1 123885 123931 no-call complex = ? ? -5 1.17 N +2753 2 chr1 123931 123938 hom ref = = = 11 1.17 N +2754 2 chr1 123938 123957 no-call complex = ? ? -84 1.17 N +2755 2 chr1 123957 124000 hom ref = = = 14 1.17 N +2756 2 chr1 124000 124021 no-call complex = ? ? -19 1.17 N +2757 2 chr1 124021 124051 hom ref = = = 13 1.17 N +2758 2 chr1 124051 124074 no-call complex = ? ? -29 1.17 N +2759 2 chr1 124074 124105 hom ref = = = 10 1.17 N +2760 2 chr1 124105 124132 no-call complex = ? ? -26 1.17 N +2761 2 chr1 124132 124138 hom ref = = = 12 1.17 N +2762 2 chr1 124138 124237 no-call complex = ? ? -41 1.17 N +2763 2 chr1 124237 124265 hom ref = = = 11 1.17 N +2764 2 chr1 124265 124306 no-call complex = ? ? -15 1.17 N +2765 2 chr1 124306 124316 hom ref = = = 15 1.17 N +2766 2 chr1 124316 124347 no-call complex = ? ? -52 1.17 N +2767 2 chr1 124347 124356 hom ref = = = 14 1.17 N +2768 2 chr1 124356 124393 no-call complex = ? ? -79 1.17 N +2769 2 chr1 124393 124411 hom ref = = = 23 1.17 N +2770 2 chr1 124411 124434 no-call complex = ? ? -50 1.17 N +2771 2 chr1 124434 124453 hom ref = = = 15 1.17 N +2772 2 chr1 124453 124462 no-call complex = ? ? -266 1.17 N +2773 2 chr1 124462 124494 hom ref = = = 14 1.17 N +2774 2 chr1 124494 124537 no-call complex = ? ? -23 1.17 N +2775 2 chr1 124537 124544 hom ref = = = 10 1.17 N +2776 2 chr1 124544 124590 no-call complex = ? ? -93 1.17 N +2777 2 chr1 124590 124606 hom ref = = = 16 1.17 N +2778 2 chr1 124606 124619 no-call complex = ? ? -12 1.17 N +2779 2 chr1 124619 124657 hom ref = = = -3 1.17 N +2780 2 chr1 124657 124658 half ref G G N 59 130 -3 AluJb:Alu:18.1 22 1.17 N +2781 2 chr1 124658 124670 hom ref = = = -3 1.17 N +2782 2 chr1 124670 124714 no-call complex = ? ? -151 1.17 N +2783 2 chr1 124714 124725 hom ref = = = 14 1.17 N +2784 2 chr1 124725 124762 no-call complex = ? ? -7 1.17 N +2785 2 chr1 124762 124775 hom ref = = = 13 1.17 N +2786 2 chr1 124775 124812 no-call complex = ? ? -4 1.17 N +2787 2 chr1 124812 124838 hom ref = = = 13 1.17 N +2788 2 chr1 124838 124874 no-call complex = ? ? -34 1.17 N +2789 2 chr1 124874 124990 hom ref = = = -9 1.17 N +2790 2 chr1 124990 125018 no-call complex = ? ? -35 1.17 N +2791 2 chr1 125018 125039 hom ref = = = 10 1.17 N +2792 2 chr1 125039 125049 no-call complex = ? ? -5 1.17 N +2793 2 chr1 125049 125093 hom ref = = = -3 1.17 N +2794 2 chr1 125093 125094 half ref C C N 22 120 -3 22 1.17 N +2795 2 chr1 125094 125114 hom ref = = = -8 1.17 N +2796 2 chr1 125114 125147 no-call complex = ? ? -47 1.17 N +2797 2 chr1 125147 125164 hom ref = = = 14 1.17 N +2798 2 chr1 125164 125210 no-call complex = ? ? -79 1.17 N +2799 2 chr1 125210 125221 hom ref = = = 17 1.17 N +2800 2 chr1 125221 125228 no-call complex = ? ? -41 1.17 N +2801 2 chr1 125228 125238 hom ref = = = 13 1.17 N +2802 2 chr1 125238 125276 no-call complex = ? ? -67 1.17 N +2803 2 chr1 125276 125337 hom ref = = = 7 1.17 N +2804 2 chr1 125337 125361 no-call complex = ? ? -7 1.17 N +2805 2 chr1 125361 125429 hom ref = = = 5 1.17 N +2806 2 chr1 125429 125430 half ref T T N 120 120 5 20 1.17 N +2807 2 chr1 125430 125458 hom ref = = = 5 1.17 N +2808 2 chr1 125458 125498 no-call complex = ? ? -72 1.17 N +2809 2 chr1 125498 125507 hom ref = = = 12 1.17 N +2810 2 chr1 125507 125555 no-call complex = ? ? -48 1.17 N +2811 2 chr1 125555 125567 hom ref = = = 5 1.17 N +2812 2 chr1 125567 125567 half ref ? 32 0 1191 1192 5 20 1.17 N +2813 2 chr1 125567 125570 hom ref = = = 5 1.17 N +2814 2 chr1 125570 125576 no-call complex TTATTT TT?ATTT ? 0 0 1191 1192 0 20 1.17 N +2815 2 chr1 125576 125579 hom ref = = = 0 1.17 N +2816 2 chr1 125579 125580 half ref T T N 55 55 1191 1192 0 20 1.17 N +2817 2 chr1 125580 125592 hom ref = = = 0 1.17 N +2818 2 chr1 125592 125620 no-call complex = ? ? -12 1.17 N +2819 2 chr1 125620 125652 hom ref = = = 11 1.17 N +2820 2 chr1 125652 125695 no-call complex = ? ? -24 1.17 N +2821 2 chr1 125695 125718 hom ref = = = 7 1.17 N +2822 2 chr1 125718 125719 half ref C C N 120 120 1193 1194 7 20 1.17 N +2823 2 chr1 125719 125724 hom ref = = = 7 1.17 N +2824 2 chr1 125724 125734 half ref TTCATACAAG TTCATACAAG ? 34 0 1193 1194 2 20 1.17 N +2825 2 chr1 125734 125757 hom ref = = = -7 1.17 N +2826 2 chr1 125757 125758 half ref A A N 69 69 1195 1196 -7 20 1.17 N +2827 2 chr1 125758 125762 hom ref = = = -7 1.17 N +2828 2 chr1 125762 125763 half ref A A N 69 69 1195 1196 -7 20 1.17 N +2829 2 chr1 125763 125770 hom ref = = = -7 1.17 N +2830 2 chr1 125770 125778 half ref TTATTGAA TTATTGAA ? 45 0 1195 1196 13 20 1.17 N +2831 2 chr1 125778 125782 hom ref = = = -12 1.17 N +2832 2 chr1 125782 125783 half ref T T N 22 69 1195 1196 -12 20 1.17 N +2833 2 chr1 125783 125786 hom ref = = = -12 1.17 N +2834 2 chr1 125786 125789 half ref AGA AGA ? 22 0 1195 1196 0 20 1.17 N +2835 2 chr1 125789 125798 hom ref = = = 14 1.17 N +2836 2 chr1 125798 125867 no-call complex = ? ? -37 1.17 N +2837 2 chr1 125867 125873 hom ref = = = 22 1.17 N +2838 2 chr1 125873 125909 no-call complex = ? ? -32 1.17 N +2839 2 chr1 125909 125940 hom ref = = = 11 1.17 N +2840 2 chr1 125940 126071 no-call complex = ? ? -138 1.17 N +2841 2 chr1 126071 126097 hom ref = = = 12 1.17 N +2842 2 chr1 126097 126123 no-call complex = ? ? -66 1.17 N +2843 2 chr1 126123 126141 hom ref = = = 17 1.17 N +2844 2 chr1 126141 126145 half ref CCTT CCTT ? 34 0 1201 1202 -3 L1MA5:L1:20.3 20 1.17 N +2845 2 chr1 126145 126154 hom ref = = = -3 1.17 N +2846 2 chr1 126154 126155 half ref C C N 27 124 1201 1202 11 L1MA5:L1:20.3 20 1.17 N +2847 2 chr1 126155 126158 hom ref = = = 5 1.17 N +2848 2 chr1 126158 126159 half ref G G N 31 124 1201 1202 5 L1MA5:L1:20.3 20 1.17 N +2849 2 chr1 126159 126205 hom ref = = = 5 1.17 N +2850 2 chr1 126205 126222 no-call complex TACAATTATTTGTCTCA TACAAT?TTTGTCTC?A ? 0 0 1203 1204 -2 L1MA5:L1:20.3 20 1.17 N +2851 2 chr1 126222 126228 hom ref = = = 3 1.17 N +2852 2 chr1 126228 126235 half ref AACAAAA AACAAAA ? 23 0 1203 1204 -6 L1MA5:L1:20.3 23 1.17 N +2853 2 chr1 126235 126257 hom ref = = = 10 1.17 N +2854 2 chr1 126257 126285 no-call complex = ? ? -127 1.17 N +2855 2 chr1 126285 126313 hom ref = = = 12 1.17 N +2856 2 chr1 126313 126372 no-call complex = ? ? -125 1.17 N +2857 2 chr1 126372 126392 hom ref = = = 12 1.17 N +2858 2 chr1 126392 126479 no-call complex = ? ? -40 1.17 N +2859 2 chr1 126479 126484 hom ref = = = 16 1.17 N +2860 2 chr1 126484 126538 no-call complex = ? ? -20 1.17 N +2861 2 chr1 126538 126554 hom ref = = = -6 1.17 N +2862 2 chr1 126554 126556 half ref AT AT NN 28 115 -6 L1M4c:L1:28.4 24 1.17 N +2863 2 chr1 126556 126594 hom ref = = = 1 1.17 N +2864 2 chr1 126594 126595 half ref T T N 32 77 1211 1212 3 L1M4c:L1:28.4 24 1.17 N +2865 2 chr1 126595 126604 hom ref = = = -5 1.17 N +2866 2 chr1 126604 126604 half ref ? 24 0 1211 1212 -5 L1M4c:L1:28.4 24 1.17 N +2867 2 chr1 126604 126621 hom ref = = = -22 1.17 N +2868 2 chr1 126621 126622 half ref T T N 27 77 1211 1212 -22 L1M4c:L1:28.4 24 1.17 N +2869 2 chr1 126622 126641 hom ref = = = -22 1.17 N +2870 2 chr1 126641 126685 no-call complex = ? ? -2 1.17 N +2871 2 chr1 126685 126690 hom ref = = = 14 1.17 N +2872 2 chr1 126690 126715 no-call complex = ? ? -3 1.17 N +2873 2 chr1 126715 126742 hom ref = = = 11 1.17 N +2874 2 chr1 126742 126743 half ref A A N 37 122 1217 1218 14 L1M4c:L1:28.4 24 1.17 N +2875 2 chr1 126743 126751 hom ref = = = -3 1.17 N +2876 2 chr1 126751 126752 half ref C C N 31 122 1217 1218 -3 L1M4c:L1:28.4 24 1.17 N +2877 2 chr1 126752 126770 hom ref = = = -3 1.17 N +2878 2 chr1 126770 126770 half ref ? 20 0 -2 L1M4c:L1:28.4 24 1.17 N +2879 2 chr1 126770 126782 hom ref = = = -2 1.17 N +2880 2 chr1 126782 126790 no-call complex ATATATAG ATNTATAG? ? 0 0 -20 L1M4c:L1:28.4 24 1.17 N +2881 2 chr1 126790 126802 hom ref = = = 4 1.17 N +2882 2 chr1 126802 126826 no-call complex = ? ? -15 1.17 N +2883 2 chr1 126826 126837 hom ref = = = 10 1.17 N +2884 2 chr1 126837 126875 no-call complex = ? ? -83 1.17 N +2885 2 chr1 126875 126882 hom ref = = = 14 1.17 N +2886 2 chr1 126882 126924 no-call complex = ? ? -90 1.17 N +2887 2 chr1 126924 126938 hom ref = = = 9 1.17 N +2888 2 chr1 126938 126940 half ref AA AA ? 55 0 1225 1226 9 L1M4c:L1:28.4 24 1.17 N +2889 2 chr1 126940 126951 hom ref = = = 5 1.17 N +2890 2 chr1 126951 126951 half ref ? 21 0 1225 1226 5 L1M4c:L1:28.4 24 1.17 N +2891 2 chr1 126951 126969 hom ref = = = 1 1.17 N +2892 2 chr1 126969 126970 half ref T T ? 55 0 1225 1226 1 L1M4c:L1:28.4 24 1.17 N +2893 2 chr1 126970 126977 hom ref = = = 10 1.17 N +2894 2 chr1 126977 126977 half ref ? 36 0 1227 1228 10 L1M4c:L1:28.4 24 1.17 N +2895 2 chr1 126977 126980 hom ref = = = 8 1.17 N +2896 2 chr1 126980 126981 half ref T T N 35 120 1227 1228 8 L1M4c:L1:28.4 24 1.17 N +2897 2 chr1 126981 126996 hom ref = = = 8 1.17 N +2898 2 chr1 126996 127000 no-call complex TGGC TGGN ? 59 0 6 L1M4c:L1:28.4 24 1.17 N +2899 2 chr1 127000 127017 hom ref = = = 6 1.17 N +2900 2 chr1 127017 127058 no-call complex = ? ? -15 1.17 N +2901 2 chr1 127058 127063 hom ref = = = 18 1.17 N +2902 2 chr1 127063 127124 no-call complex = ? ? -34 1.17 N +2903 2 chr1 127124 127129 hom ref = = = 18 1.17 N +2904 2 chr1 127129 127156 no-call complex = ? ? -4 1.17 N +2905 2 chr1 127156 127185 hom ref = = = 3 1.17 N +2906 2 chr1 127185 127186 half ref G G N 46 120 3 24 1.17 N +2907 2 chr1 127186 127207 hom ref = = = 3 1.17 N +2908 2 chr1 127207 127243 no-call complex = ? ? -39 1.17 N +2909 2 chr1 127243 127261 hom ref = = = 25 1.17 N +2910 2 chr1 127261 127288 no-call complex = ? ? -13 1.17 N +2911 2 chr1 127288 127294 hom ref = = = 11 1.17 N +2912 2 chr1 127294 127358 no-call complex = ? ? -19 1.17 N +2913 2 chr1 127358 127379 hom ref = = = 10 1.17 N +2914 2 chr1 127379 127395 no-call complex = ? ? -109 1.17 N +2915 2 chr1 127395 127518 hom ref = = = 5 1.17 N +2916 2 chr1 127518 127519 half ref T T N 125 125 6 24 1.17 N +2917 2 chr1 127519 127560 hom ref = = = 6 1.17 N +2918 2 chr1 127560 127640 no-call complex = ? ? -22 1.17 N +2919 2 chr1 127640 127652 hom ref = = = 12 1.17 N +2920 2 chr1 127652 127726 no-call complex = ? ? -75 1.17 N +2921 2 chr1 127726 127731 hom ref = = = 22 1.17 N +2922 2 chr1 127731 127754 no-call complex = ? ? -91 1.17 N +2923 2 chr1 127754 127769 hom ref = = = 16 1.17 N +2924 2 chr1 127769 127801 no-call complex = ? ? -15 1.17 N +2925 2 chr1 127801 127850 hom ref = = = 13 1.17 N +2926 2 chr1 127850 127895 no-call complex = ? ? -90 1.17 N +2927 2 chr1 127895 127904 hom ref = = = 14 1.17 N +2928 2 chr1 127904 127945 no-call complex = ? ? -191 1.17 N +2929 2 chr1 127945 127952 hom ref = = = 14 1.17 N +2930 2 chr1 127952 127976 no-call complex = ? ? -20 1.17 N +2931 2 chr1 127976 127993 hom ref = = = 11 1.17 N +2932 2 chr1 127993 127998 half ref CATCT CATCT NNNCN 33 68 7 AluSz:Alu:13.0 24 1.17 N +2933 2 chr1 127998 128043 hom ref = = = 3 1.17 N +2934 2 chr1 128043 128074 no-call complex = ? ? 6 1.17 N +2935 2 chr1 128074 128138 hom ref = = = 2 1.17 N +2936 2 chr1 128138 128139 half ref T T N 63 120 2 24 1.17 N +2937 2 chr1 128139 128225 hom ref = = = 2 1.17 N +2938 2 chr1 128225 128273 no-call complex = ? ? -49 1.17 N +2939 2 chr1 128273 128292 hom ref = = = 15 1.17 N +2940 2 chr1 128292 128299 no-call complex = ? ? -88 1.17 N +2941 2 chr1 128299 128320 hom ref = = = 13 1.17 N +2942 2 chr1 128320 128343 no-call complex = ? ? -39 1.17 N +2943 2 chr1 128343 128401 hom ref = = = -6 1.17 N +2944 2 chr1 128401 128402 half ref A A N 125 125 -6 24 1.17 N +2945 2 chr1 128402 128422 hom ref = = = -6 1.17 N +2946 2 chr1 128422 128463 no-call complex = ? ? -16 1.17 N +2947 2 chr1 128463 128531 hom ref = = = -14 1.17 N +2948 2 chr1 128531 128567 no-call complex = ? ? -9 1.17 N +2949 2 chr1 128567 128591 hom ref = = = 13 1.17 N +2950 2 chr1 128591 128621 no-call complex = ? ? -8 1.17 N +2951 2 chr1 128621 128681 hom ref = = = 19 1.17 N +2952 2 chr1 128681 128713 no-call complex = ? ? 7 1.17 N +2953 2 chr1 128713 128765 hom ref = = = 11 1.17 N +2954 2 chr1 128765 128828 no-call complex = ? ? -24 1.17 N +2955 2 chr1 128828 128851 hom ref = = = 3 1.17 N +2956 2 chr1 128851 128852 half ref C C N 25 120 1261 1262 3 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC AluSq2:Alu:12.1 24 1.17 N +2957 2 chr1 128852 128854 hom ref = = = 3 1.17 N +2958 2 chr1 128854 128855 half ref A A N 120 120 1261 1262 -35 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC AluSq2:Alu:12.1 24 1.17 N +2959 2 chr1 128855 128879 hom ref = = = -35 1.17 N +2960 2 chr1 128879 128893 no-call complex = ? ? -152 1.17 N +2961 2 chr1 128893 128978 hom ref = = = 3 1.17 N +2962 2 chr1 128978 129022 no-call complex = ? ? -91 1.17 N +2963 2 chr1 129022 129059 hom ref = = = 23 1.17 N +2964 2 chr1 129059 129098 no-call complex = ? ? -17 1.17 N +2965 2 chr1 129098 129108 hom ref = = = 14 1.17 N +2966 2 chr1 129108 129167 no-call complex = ? ? -58 1.17 N +2967 2 chr1 129167 129211 hom ref = = = -21 1.17 N +2968 2 chr1 129211 129212 no-call complex C N N 121 121 -21 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 24 1.17 N +2969 2 chr1 129212 129217 hom ref = = = -21 1.17 N +2970 2 chr1 129217 129218 half ref C C N 121 121 5 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::UTR:UNKNOWN-INC 24 1.17 N +2971 2 chr1 129218 129281 hom ref = = = 0 1.17 N +2972 2 chr1 129281 129308 no-call complex = ? ? -265 1.17 N +2973 2 chr1 129308 129325 hom ref = = = 17 1.17 N +2974 2 chr1 129325 129359 no-call complex = ? ? -6 1.17 N +2975 2 chr1 129359 129374 hom ref = = = 16 1.17 N +2976 2 chr1 129374 129413 no-call complex = ? ? -42 1.17 N +2977 2 chr1 129413 129443 hom ref = = = 6 1.17 N +2978 2 chr1 129443 129444 half ref A A N 121 121 6 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC AluSx:Alu:17.4 23 1.17 N +2979 2 chr1 129444 129473 hom ref = = = 6 1.17 N +2980 2 chr1 129473 129492 no-call complex = ? ? -60 1.17 N +2981 2 chr1 129492 129542 hom ref = = = -1 1.17 N +2982 2 chr1 129542 129543 half ref C C N 27 115 -1 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC AluSx:Alu:17.4 23 1.17 N +2983 2 chr1 129543 129581 hom ref = = = -1 1.17 N +2984 2 chr1 129581 129582 half ref T T ? 58 0 8 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC AluSx:Alu:17.4 23 1.17 N +2985 2 chr1 129582 129605 hom ref = = = -1 1.17 N +2986 2 chr1 129605 129635 no-call complex = ? ? -11 1.17 N +2987 2 chr1 129635 129673 hom ref = = = -1 1.17 N +2988 2 chr1 129673 129685 half ref AGACTTTTTTTT AGACTTTTTTTT ? 28 0 1 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC AluSx:Alu:17.4;FLAM_C:Alu:14.4 23 1.17 N +2989 2 chr1 129685 129743 hom ref = = = 0 1.17 N +2990 2 chr1 129743 129744 half ref A A N 115 115 1269 1270 5 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC FLAM_C:Alu:14.4 22 1.17 N +2991 2 chr1 129744 129748 hom ref = = = 6 1.17 N +2992 2 chr1 129748 129757 half ref AAGTGATCC AAGTGATCC ? 21 0 1269 1270 -5 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC FLAM_C:Alu:14.4 22 1.17 N +2993 2 chr1 129757 129770 hom ref = = = -5 1.17 N +2994 2 chr1 129770 129775 half ref TCCCA TCCCA NNCNN 23 30 1271 1272 3 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC FLAM_C:Alu:14.4 22 1.17 N +2995 2 chr1 129775 129782 hom ref = = = 4 1.17 N +2996 2 chr1 129782 129784 half ref GG GG ? 70 0 1271 1272 5 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC FLAM_C:Alu:14.4 22 1.17 N +2997 2 chr1 129784 129821 hom ref = = = 6 1.17 N +2998 2 chr1 129821 129864 no-call complex = ? ? -26 1.17 N +2999 2 chr1 129864 129873 hom ref = = = 23 1.17 N +3000 2 chr1 129873 129880 no-call complex = ? ? -100 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 1.17 N +3001 2 chr1 129880 129933 hom ref = = = 15 1.17 N +3002 2 chr1 129933 129985 no-call complex = ? ? -139 1.17 N +3003 2 chr1 129985 130034 hom ref = = = 11 1.17 N +3004 2 chr1 130034 130080 no-call complex = ? ? -52 1.17 N +3005 2 chr1 130080 130112 hom ref = = = 16 1.17 N +3006 2 chr1 130112 130139 no-call complex = ? ? -19 1.17 N +3007 2 chr1 130139 130147 hom ref = = = 21 1.17 N +3008 2 chr1 130147 130181 no-call complex = ? ? -61 1.17 N +3009 2 chr1 130181 130190 hom ref = = = 17 1.17 N +3010 2 chr1 130190 130234 no-call complex = ? ? -66 1.17 N +3011 2 chr1 130234 130256 hom ref = = = 1 1.17 N +3012 2 chr1 130256 130256 half ref ? 26 0 27 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC AluSg:Alu:14.9 21 1.17 N +3013 2 chr1 130256 130276 hom ref = = = 9 1.17 N +3014 2 chr1 130276 130326 no-call complex = ? ? -87 1.17 N +3015 2 chr1 130326 130386 hom ref = = = 6 1.17 N +3016 2 chr1 130386 130405 no-call complex = ? ? -101 1.17 N +3017 2 chr1 130405 130419 hom ref = = = 16 1.17 N +3018 2 chr1 130419 130449 no-call complex = ? ? -5 1.17 N +3019 2 chr1 130449 130483 hom ref = = = 4 1.17 N +3020 2 chr1 130483 130484 half ref C C N 51 120 4 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC L1M2:L1:49.5 23 1.17 N +3021 2 chr1 130484 130513 hom ref = = = -20 1.17 N +3022 2 chr1 130513 130514 half ref T T N 79 79 -20 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC L1M2:L1:49.5 23 1.17 N +3023 2 chr1 130514 130581 hom ref = = = -20 1.17 N +3024 2 chr1 130581 130604 no-call complex = ? ? -116 1.17 N +3025 2 chr1 130604 130741 hom ref = = = -15 1.17 N +3026 2 chr1 130741 130790 no-call complex = ? ? -102 1.17 N +3027 2 chr1 130790 130797 hom ref = = = 14 1.17 N +3028 2 chr1 130797 130829 no-call complex = ? ? -10 1.17 N +3029 2 chr1 130829 130864 hom ref = = = 12 1.17 N +3030 2 chr1 130864 130890 no-call complex = ? ? -22 1.17 N +3031 2 chr1 130890 130895 hom ref = = = 17 1.17 N +3032 2 chr1 130895 130927 no-call complex = ? ? 1 1.17 N +3033 2 chr1 130927 130951 hom ref = = = 12 1.17 N +3034 2 chr1 130951 130996 no-call complex = ? ? -161 1.17 N +3035 2 chr1 130996 131033 hom ref = = = 10 1.17 N +3036 2 chr1 131033 131083 no-call complex = ? ? -178 1.17 N +3037 2 chr1 131083 131098 hom ref = = = 10 1.17 N +3038 2 chr1 131098 131162 no-call complex = ? ? -230 1.17 N +3039 2 chr1 131162 131183 hom ref = = = 13 1.17 N +3040 2 chr1 131183 131206 no-call complex = ? ? -57 1.17 N +3041 2 chr1 131206 131217 hom ref = = = 23 1.17 N +3042 2 chr1 131217 131250 no-call complex = ? ? -57 1.17 N +3043 2 chr1 131250 131273 hom ref = = = 11 1.17 N +3044 2 chr1 131273 131295 no-call complex = ? ? -52 1.17 N +3045 2 chr1 131295 131300 hom ref = = = 11 1.17 N +3046 2 chr1 131300 131354 no-call complex = ? ? -24 1.17 N +3047 2 chr1 131354 131360 hom ref = = = 17 1.17 N +3048 2 chr1 131360 131402 no-call complex = ? ? -3 1.17 N +3049 2 chr1 131402 131417 hom ref = = = 12 1.17 N +3050 2 chr1 131417 131427 no-call complex = ? ? -47 1.17 N +3051 2 chr1 131427 131451 hom ref = = = 10 1.17 N +3052 2 chr1 131451 131509 no-call complex = ? ? -82 1.17 N +3053 2 chr1 131509 131545 hom ref = = = 10 1.17 N +3054 2 chr1 131545 131554 no-call complex = ? ? -58 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 1.17 N +3055 2 chr1 131554 131588 hom ref = = = 12 1.17 N +3056 2 chr1 131588 131621 no-call complex = ? ? -15 1.17 N +3057 2 chr1 131621 131633 hom ref = = = 13 1.17 N +3058 2 chr1 131633 131678 no-call complex = ? ? -45 1.17 N +3059 2 chr1 131678 131683 hom ref = = = 11 1.17 N +3060 2 chr1 131683 131802 no-call complex = ? ? -41 1.17 N +3061 2 chr1 131802 131824 hom ref = = = 10 1.17 N +3062 2 chr1 131824 131852 no-call complex = ? ? -33 1.17 N +3063 2 chr1 131852 131863 hom ref = = = 10 1.17 N +3064 2 chr1 131863 131931 no-call complex = ? ? -128 1.17 N +3065 2 chr1 131931 131946 hom ref = = = 17 1.17 N +3066 2 chr1 131946 131973 no-call complex = ? ? -147 1.17 N +3067 2 chr1 131973 132022 hom ref = = = 8 1.17 N +3068 2 chr1 132022 132044 no-call complex = ? ? -15 1.17 N +3069 2 chr1 132044 132050 hom ref = = = 10 1.17 N +3070 2 chr1 132050 132074 no-call complex = ? ? -57 1.17 N +3071 2 chr1 132074 132079 hom ref = = = 11 1.17 N +3072 2 chr1 132079 132123 no-call complex = ? ? -37 1.17 N +3073 2 chr1 132123 132134 hom ref = = = 10 1.17 N +3074 2 chr1 132134 132141 no-call complex = ? ? -82 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 1.17 N +3075 2 chr1 132141 132152 hom ref = = = 11 1.17 N +3076 2 chr1 132152 132186 no-call complex = ? ? -165 1.17 N +3077 2 chr1 132186 132212 hom ref = = = 12 1.17 N +3078 2 chr1 132212 132219 no-call complex = ? ? -9 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 1.17 N +3079 2 chr1 132219 132225 hom ref = = = 12 1.17 N +3080 2 chr1 132225 132308 no-call complex = ? ? -30 1.17 N +3081 2 chr1 132308 132350 hom ref = = = -15 1.17 N +3082 2 chr1 132350 132351 half ref A A N 40 120 -15 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 27 1.17 N +3083 2 chr1 132351 132406 hom ref = = = -15 1.17 N +3084 2 chr1 132406 132460 no-call complex = ? ? -125 1.17 N +3085 2 chr1 132460 132468 hom ref = = = 11 1.17 N +3086 2 chr1 132468 132497 no-call complex = ? ? -44 1.17 N +3087 2 chr1 132497 132506 hom ref = = = 13 1.17 N +3088 2 chr1 132506 132565 no-call complex = ? ? -32 1.17 N +3089 2 chr1 132565 132576 hom ref = = = 13 1.17 N +3090 2 chr1 132576 132610 no-call complex = ? ? -43 1.17 N +3091 2 chr1 132610 132624 hom ref = = = -31 1.17 N +3092 2 chr1 132624 132624 half ref ? 24 0 26 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 27 1.17 N +3093 2 chr1 132624 132643 hom ref = = = 10 1.17 N +3094 2 chr1 132643 132688 no-call complex = ? ? -58 1.17 N +3095 2 chr1 132688 132699 hom ref = = = 10 1.17 N +3096 2 chr1 132699 132700 half ref G G N 120 120 1339 1340 -9 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 27 1.17 N +3097 2 chr1 132700 132703 hom ref = = = -9 1.17 N +3098 2 chr1 132703 132704 half ref T T N 120 120 1339 1340 6 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::INTRON:UNKNOWN-INC 27 1.17 N +3099 2 chr1 132704 132719 hom ref = = = 6 1.17 N +3100 2 chr1 132719 132798 no-call complex = ? ? -82 1.17 N +3101 2 chr1 132798 132810 hom ref = = = 13 1.17 N +3102 2 chr1 132810 132860 no-call complex = ? ? -59 1.17 N +3103 2 chr1 132860 132868 hom ref = = = 13 1.17 N +3104 2 chr1 132868 132902 no-call complex = ? ? 3 1.17 N +3105 2 chr1 132902 132939 hom ref = = = -8 1.17 N +3106 2 chr1 132939 132969 no-call complex = ? ? -10 1.17 N +3107 2 chr1 132969 132977 hom ref = = = 11 1.17 N +3108 2 chr1 132977 133036 no-call complex = ? ? -131 1.17 N +3109 2 chr1 133036 133052 hom ref = = = 12 1.17 N +3110 2 chr1 133052 133074 no-call complex = ? ? 0 1.17 N +3111 2 chr1 133074 133080 hom ref = = = 18 1.17 N +3112 2 chr1 133080 133155 no-call complex = ? ? -114 1.17 N +3113 2 chr1 133155 133238 hom ref = = = 0 1.17 N +3114 2 chr1 133238 133281 no-call complex = ? ? -12 1.17 N +3115 2 chr1 133281 133292 hom ref = = = 11 1.17 N +3116 2 chr1 133292 133381 no-call complex = ? ? -265 1.17 N +3117 2 chr1 133381 133409 hom ref = = = 10 1.17 N +3118 2 chr1 133409 133420 no-call complex = ? ? 15 1.17 N +3119 2 chr1 133420 133433 hom ref = = = 23 1.17 N +3120 2 chr1 133433 133486 no-call complex = ? ? -20 1.17 N +3121 2 chr1 133486 133492 hom ref = = = 20 1.17 N +3122 2 chr1 133492 133536 no-call complex = ? ? -141 1.17 N +3123 2 chr1 133536 133583 hom ref = = = -9 1.17 N +3124 2 chr1 133583 133650 no-call complex = ? ? -19 1.17 N +3125 2 chr1 133650 133658 hom ref = = = 13 1.17 N +3126 2 chr1 133658 133674 no-call complex = ? ? -85 1.17 N +3127 2 chr1 133674 133702 hom ref = = = 13 1.17 N +3128 2 chr1 133702 133753 no-call complex = ? ? -88 1.17 N +3129 2 chr1 133753 133811 hom ref = = = 0 1.17 N +3130 2 chr1 133811 133812 half ref T T N 85 85 1371 1372 0 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3131 2 chr1 133812 133838 hom ref = = = 0 1.17 N +3132 2 chr1 133838 133839 half ref T T ? 85 0 1371 1372 6 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3133 2 chr1 133839 133855 hom ref = = = 6 1.17 N +3134 2 chr1 133855 133886 no-call complex = ? ? 7 1.17 N +3135 2 chr1 133886 133906 hom ref = = = 11 1.17 N +3136 2 chr1 133906 133913 no-call complex = ? ? -40 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 1.17 N +3137 2 chr1 133913 133945 hom ref = = = 15 1.17 N +3138 2 chr1 133945 133963 no-call complex = ? ? -45 1.17 N +3139 2 chr1 133963 133977 hom ref = = = 16 1.17 N +3140 2 chr1 133977 134025 no-call complex = ? ? -86 1.17 N +3141 2 chr1 134025 134031 hom ref = = = 14 1.17 N +3142 2 chr1 134031 134127 no-call complex = ? ? -334 1.17 N +3143 2 chr1 134127 134133 hom ref = = = 15 1.17 N +3144 2 chr1 134133 134179 no-call complex = ? ? -29 1.17 N +3145 2 chr1 134179 134265 hom ref = = = -21 1.17 N +3146 2 chr1 134265 134266 half ref G G N 106 73 -6 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC AluSg:Alu:10.7 27 1.17 N +3147 2 chr1 134266 134311 hom ref = = = -12 1.17 N +3148 2 chr1 134311 134377 no-call complex = ? ? -110 1.17 N +3149 2 chr1 134377 134394 hom ref = = = 6 1.17 N +3150 2 chr1 134394 134452 no-call complex = ? ? -72 1.17 N +3151 2 chr1 134452 134458 hom ref = = = 10 1.17 N +3152 2 chr1 134458 134467 no-call complex = ? ? -115 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 1.17 N +3153 2 chr1 134467 134477 hom ref = = = 16 1.17 N +3154 2 chr1 134477 134519 no-call complex = ? ? -22 1.17 N +3155 2 chr1 134519 134548 hom ref = = = 11 1.17 N +3156 2 chr1 134548 134615 no-call complex = ? ? -156 1.17 N +3157 2 chr1 134615 134632 hom ref = = = 14 1.17 N +3158 2 chr1 134632 134674 no-call complex = ? ? -48 1.17 N +3159 2 chr1 134674 134701 hom ref = = = 0 1.17 N +3160 2 chr1 134701 134702 half ref A A N 31 58 1391 1392 9 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3161 2 chr1 134702 134710 hom ref = = = 9 1.17 N +3162 2 chr1 134710 134711 half ref A A N 29 58 1391 1392 10 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3163 2 chr1 134711 134718 hom ref = = = 10 1.17 N +3164 2 chr1 134718 134719 half ref T T ? 37 0 1391 1392 11 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3165 2 chr1 134719 134739 hom ref = = = 7 1.17 N +3166 2 chr1 134739 134793 no-call complex = ? ? -124 1.17 N +3167 2 chr1 134793 134804 hom ref = = = 10 1.17 N +3168 2 chr1 134804 134828 no-call complex = ? ? -12 1.17 N +3169 2 chr1 134828 134834 hom ref = = = 16 1.17 N +3170 2 chr1 134834 134878 no-call complex = ? ? -22 1.17 N +3171 2 chr1 134878 134933 hom ref = = = 15 1.17 N +3172 2 chr1 134933 134977 no-call complex = ? ? -70 1.17 N +3173 2 chr1 134977 134995 hom ref = = = 12 1.17 N +3174 2 chr1 134995 135059 no-call complex = ? ? -8 1.17 N +3175 2 chr1 135059 135084 hom ref = = = 0 1.17 N +3176 2 chr1 135084 135086 half ref CC CC ? 24 0 1403 1404 3 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3177 2 chr1 135086 135094 hom ref = = = -22 1.17 N +3178 2 chr1 135094 135095 half ref C C N 30 55 1403 1404 -22 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3179 2 chr1 135095 135100 hom ref = = = -22 1.17 N +3180 2 chr1 135100 135101 half ref G G N 36 55 1403 1404 7 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3181 2 chr1 135101 135109 hom ref = = = 7 1.17 N +3182 2 chr1 135109 135110 half ref T T N 55 55 11 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3183 2 chr1 135110 135115 hom ref = = = 3 1.17 N +3184 2 chr1 135115 135116 half ref T T N 55 55 9 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 27 1.17 N +3185 2 chr1 135116 135162 hom ref = = = -19 1.17 N +3186 2 chr1 135162 135264 no-call complex = ? ? -214 1.17 N +3187 2 chr1 135264 135291 hom ref = = = 3 1.17 N +3188 2 chr1 135291 135327 no-call complex = ? ? -26 1.17 N +3189 2 chr1 135327 135371 hom ref = = = 13 1.17 N +3190 2 chr1 135371 135427 no-call complex = ? ? -125 1.17 N +3191 2 chr1 135427 135448 hom ref = = = 2 1.17 N +3192 2 chr1 135448 135449 half ref A A N 121 121 2 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 23 1.17 N +3193 2 chr1 135449 135483 hom ref = = = 2 1.17 N +3194 2 chr1 135483 135503 no-call complex = ? ? -95 1.17 N +3195 2 chr1 135503 135535 hom ref = = = 17 1.17 N +3196 2 chr1 135535 135569 no-call complex = ? ? -206 1.17 N +3197 2 chr1 135569 135603 hom ref = = = 10 1.17 N +3198 2 chr1 135603 135621 no-call complex = ? ? -150 1.17 N +3199 2 chr1 135621 135659 hom ref = = = 16 1.17 N +3200 2 chr1 135659 135676 no-call complex = ? ? -339 1.17 N +3201 2 chr1 135676 135719 hom ref = = = 13 1.17 N +3202 2 chr1 135719 135745 no-call complex = ? ? -124 1.17 N +3203 2 chr1 135745 135773 hom ref = = = 16 1.17 N +3204 2 chr1 135773 135792 no-call complex = ? ? -21 1.17 N +3205 2 chr1 135792 135799 hom ref = = = 23 1.17 N +3206 2 chr1 135799 135839 no-call complex = ? ? -56 1.17 N +3207 2 chr1 135839 135965 hom ref = = = -1 1.17 N +3208 2 chr1 135965 135995 no-call complex = ? ? -89 1.17 N +3209 2 chr1 135995 136013 hom ref = = = 12 1.17 N +3210 2 chr1 136013 136032 no-call complex = ? ? -219 1.17 N +3211 2 chr1 136032 136044 hom ref = = = 19 1.17 N +3212 2 chr1 136044 136075 no-call complex = ? ? -24 1.17 N +3213 2 chr1 136075 136094 hom ref = = = 15 1.17 N +3214 2 chr1 136094 136103 no-call complex = ? ? 4 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::INTRON:UNKNOWN-INC 1.17 N +3215 2 chr1 136103 136137 hom ref = = = 12 1.17 N +3216 2 chr1 136137 136176 no-call complex = ? ? -54 1.17 N +3217 2 chr1 136176 136194 hom ref = = = 15 1.17 N +3218 2 chr1 136194 136214 no-call complex = ? ? -74 1.17 N +3219 2 chr1 136214 136225 hom ref = = = 10 1.17 N +3220 2 chr1 136225 136560 no-call complex = ? ? -71 1.17 N +3221 2 chr1 136560 136565 hom ref = = = 11 1.17 N +3222 2 chr1 136565 136587 no-call complex = ? ? -18 1.17 N +3223 2 chr1 136587 136592 hom ref = = = 12 1.17 N +3224 2 chr1 136592 136720 no-call complex = ? ? -75 1.17 N +3225 2 chr1 136720 136729 hom ref = = = 13 1.17 N +3226 2 chr1 136729 136974 no-call complex = ? ? -37 1.17 N +3227 2 chr1 136974 136983 hom ref = = = 10 1.17 N +3228 2 chr1 136983 137440 no-call complex = ? ? -81 1.17 N +3229 2 chr1 137440 137504 hom ref = = = -9 1.17 N +3230 2 chr1 137504 137511 no-call complex = ? ? -32 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::INTRON:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::INTRON:UNKNOWN-INC 1.17 N +3231 2 chr1 137511 137532 hom ref = = = 10 1.17 N +3232 2 chr1 137532 137571 no-call complex = ? ? -59 1.17 N +3233 2 chr1 137571 137577 hom ref = = = 25 1.17 N +3234 2 chr1 137577 137612 no-call complex = ? ? -216 1.17 N +3235 2 chr1 137612 137624 hom ref = = = 25 1.17 N +3236 2 chr1 137624 137680 no-call complex = ? ? -10 1.17 N +3237 2 chr1 137680 137694 hom ref = = = 14 1.17 N +3238 2 chr1 137694 137701 no-call complex = ? ? -43 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC 1.17 N +3239 2 chr1 137701 137714 hom ref = = = 10 1.17 N +3240 2 chr1 137714 137745 no-call complex = ? ? -49 1.17 N +3241 2 chr1 137745 137761 hom ref = = = 12 1.17 N +3242 2 chr1 137761 137779 no-call complex = ? ? -51 1.17 N +3243 2 chr1 137779 137864 hom ref = = = 2 1.17 N +3244 2 chr1 137864 137893 no-call complex = ? ? -18 1.17 N +3245 2 chr1 137893 137903 hom ref = = = 30 1.17 N +3246 2 chr1 137903 137940 no-call complex = ? ? -95 1.17 N +3247 2 chr1 137940 137949 hom ref = = = 16 1.17 N +3248 2 chr1 137949 137983 no-call complex = ? ? -2 1.17 N +3249 2 chr1 137983 138063 hom ref = = = -2 1.17 N +3250 2 chr1 138063 138064 half ref C C N 120 120 1441 1442 -2 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 12 1.17 N +3251 2 chr1 138064 138079 hom ref = = = -2 1.17 N +3252 2 chr1 138079 138080 half ref C C ? 120 0 1441 1442 12 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 12 1.17 N +3253 2 chr1 138080 138123 hom ref = = = 5 1.17 N +3254 2 chr1 138123 138159 no-call complex = ? ? -265 1.17 N +3255 2 chr1 138159 138259 hom ref = = = -1 1.17 N +3256 2 chr1 138259 138282 no-call complex = ? ? -164 1.17 N +3257 2 chr1 138282 138295 hom ref = = = 11 1.17 N +3258 2 chr1 138295 138302 no-call complex = ? ? -99 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 1.17 N +3259 2 chr1 138302 138323 hom ref = = = 14 1.17 N +3260 2 chr1 138323 138359 no-call complex = ? ? -105 1.17 N +3261 2 chr1 138359 138417 hom ref = = = -11 1.17 N +3262 2 chr1 138417 138418 half ref A A N 83 123 1449 1450 -11 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 11 1.17 N +3263 2 chr1 138418 138427 hom ref = = = -29 1.17 N +3264 2 chr1 138427 138428 half ref T T N 123 123 1449 1450 -29 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 11 1.17 N +3265 2 chr1 138428 138453 hom ref = = = -29 1.17 N +3266 2 chr1 138453 138478 no-call complex = ? ? -93 1.17 N +3267 2 chr1 138478 138502 hom ref = = = 12 1.17 N +3268 2 chr1 138502 138509 no-call complex = ? ? -76 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 100287060:XR_078212.1:LOC100287060::::TSS-UPSTREAM:UNKNOWN-INC;653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR3:UNKNOWN-INC 1.17 N +3269 2 chr1 138509 138544 hom ref = = = 12 1.17 N +3270 2 chr1 138544 138577 no-call complex = ? ? -39 1.17 N +3271 2 chr1 138577 138583 hom ref = = = 10 1.17 N +3272 2 chr1 138583 138625 no-call complex = ? ? -186 1.17 N +3273 2 chr1 138625 138655 hom ref = = = 11 1.17 N +3274 2 chr1 138655 138662 no-call complex = ? ? -107 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 1.17 N +3275 2 chr1 138662 138677 hom ref = = = 19 1.17 N +3276 2 chr1 138677 138717 no-call complex = ? ? -40 1.17 N +3277 2 chr1 138717 138750 hom ref = = = 12 1.17 N +3278 2 chr1 138750 138764 no-call complex = ? ? -26 1.17 N +3279 2 chr1 138764 138812 hom ref = = = 10 1.17 N +3280 2 chr1 138812 138842 no-call complex = ? ? -30 1.17 N +3281 2 chr1 138842 138851 hom ref = = = -12 1.17 N +3282 2 chr1 138851 138852 half ref C C ? 21 0 1461 1462 -12 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 11 1.17 N +3283 2 chr1 138852 138855 hom ref = = = -8 1.17 N +3284 2 chr1 138855 138856 half ref A A ? 120 0 1461 1462 -8 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 11 1.17 N +3285 2 chr1 138856 138874 hom ref = = = -8 1.17 N +3286 2 chr1 138874 138875 half ref G G N 120 120 1461 1462 0 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 11 1.17 N +3287 2 chr1 138875 138886 hom ref = = = 0 1.17 N +3288 2 chr1 138886 138933 no-call complex = ? ? -71 1.17 N +3289 2 chr1 138933 138967 hom ref = = = 18 1.17 N +3290 2 chr1 138967 138984 no-call complex = ? ? -8 1.17 N +3291 2 chr1 138984 139039 hom ref = = = 7 1.17 N +3292 2 chr1 139039 139071 no-call complex = ? ? 6 1.17 N +3293 2 chr1 139071 139079 hom ref = = = 12 1.17 N +3294 2 chr1 139079 139129 no-call complex = ? ? -101 1.17 N +3295 2 chr1 139129 139171 hom ref = = = 12 1.17 N +3296 2 chr1 139171 139239 no-call complex = ? ? -90 1.17 N +3297 2 chr1 139239 139265 hom ref = = = 8 1.17 N +3298 2 chr1 139265 139266 half ref T T N 122 122 11 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 11 1.17 N +3299 2 chr1 139266 139302 hom ref = = = 8 1.17 N +3300 2 chr1 139302 139326 no-call complex = ? ? -150 1.17 N +3301 2 chr1 139326 139403 hom ref = = = 17 1.17 N +3302 2 chr1 139403 139410 no-call complex = ? ? -29 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 1.17 N +3303 2 chr1 139410 139459 hom ref = = = 0 1.17 N +3304 2 chr1 139459 139460 half ref A A N 29 120 0 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 11 1.17 N +3305 2 chr1 139460 139536 hom ref = = = 0 1.17 N +3306 2 chr1 139536 139543 no-call complex = ? ? -20 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 1.17 N +3307 2 chr1 139543 139557 hom ref = = = 11 1.17 N +3308 2 chr1 139557 139588 no-call complex = ? ? -27 1.17 N +3309 2 chr1 139588 139654 hom ref = = = 1 1.17 N +3310 2 chr1 139654 139655 half ref G G N 46 148 1 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:NO-CHANGE 653340:XR_039243.2:LOC653340::::UTR:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::CDS:UNKNOWN-VNC 18 1.17 N +3311 2 chr1 139655 139699 hom ref = = = 1 1.17 N +3312 2 chr1 139699 139725 no-call complex = ? ? -38 1.17 N +3313 2 chr1 139725 139740 hom ref = = = 28 1.17 N +3314 2 chr1 139740 139747 no-call complex = ? ? -44 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 1.17 N +3315 2 chr1 139747 139760 hom ref = = = 19 1.17 N +3316 2 chr1 139760 139809 no-call complex = ? ? -89 1.17 N +3317 2 chr1 139809 139874 hom ref = = = -12 1.17 N +3318 2 chr1 139874 139875 half ref T T N 49 121 -7 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:22.6 18 1.17 N +3319 2 chr1 139875 139919 hom ref = = = -7 1.17 N +3320 2 chr1 139919 139932 no-call complex = ? ? -14 1.17 N +3321 2 chr1 139932 139939 hom ref = = = 17 1.17 N +3322 2 chr1 139939 140003 no-call complex = ? ? -29 1.17 N +3323 2 chr1 140003 140034 hom ref = = = 10 1.17 N +3324 2 chr1 140034 140084 no-call complex = ? ? -235 1.17 N +3325 2 chr1 140084 140094 hom ref = = = 10 1.17 N +3326 2 chr1 140094 140128 no-call complex = ? ? -42 1.17 N +3327 2 chr1 140128 140139 hom ref = = = 17 1.17 N +3328 2 chr1 140139 140162 no-call complex = ? ? -67 1.17 N +3329 2 chr1 140162 140175 hom ref = = = -3 1.17 N +3330 2 chr1 140175 140177 half ref CA CA NN 31 120 -24 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 18 1.17 N +3331 2 chr1 140177 140300 hom ref = = = -24 1.17 N +3332 2 chr1 140300 140346 no-call complex = ? ? -15 1.17 N +3333 2 chr1 140346 140365 hom ref = = = 14 1.17 N +3334 2 chr1 140365 140372 no-call complex = ? ? -42 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 1.17 N +3335 2 chr1 140372 140427 hom ref = = = 19 1.17 N +3336 2 chr1 140427 140472 no-call complex = ? ? -145 1.17 N +3337 2 chr1 140472 140496 hom ref = = = 17 1.17 N +3338 2 chr1 140496 140539 no-call complex = ? ? -249 1.17 N +3339 2 chr1 140539 140561 hom ref = = = 22 1.17 N +3340 2 chr1 140561 140583 no-call complex = ? ? -153 1.17 N +3341 2 chr1 140583 140637 hom ref = = = 10 1.17 N +3342 2 chr1 140637 140644 no-call complex = ? ? -5 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 1.17 N +3343 2 chr1 140644 140702 hom ref = = = 21 1.17 N +3344 2 chr1 140702 140715 no-call complex = ? ? -80 1.17 N +3345 2 chr1 140715 140751 hom ref = = = 14 1.17 N +3346 2 chr1 140751 140800 no-call complex = ? ? -94 1.17 N +3347 2 chr1 140800 140814 hom ref = = = 11 1.17 N +3348 2 chr1 140814 140857 no-call complex = ? ? -130 1.17 N +3349 2 chr1 140857 140914 hom ref = = = -1 1.17 N +3350 2 chr1 140914 140950 no-call complex = ? ? -144 1.17 N +3351 2 chr1 140950 141028 hom ref = = = -35 1.17 N +3352 2 chr1 141028 141065 no-call complex = ? ? 1 1.17 N +3353 2 chr1 141065 141175 hom ref = = = 4 1.17 N +3354 2 chr1 141175 141176 half ref A A N 110 110 5 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER21C:ERVL:31.5 21 1.17 N +3355 2 chr1 141176 141194 hom ref = = = 5 1.17 N +3356 2 chr1 141194 141198 half ref AGGG AGGG ? 63 0 1491 1492 7 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER21C:ERVL:31.5 21 1.17 N +3357 2 chr1 141198 141221 hom ref = = = 5 1.17 N +3358 2 chr1 141221 141222 half ref G G N 44 120 1491 1492 17 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER21C:ERVL:31.5 21 1.17 N +3359 2 chr1 141222 141224 hom ref = = = 1 1.17 N +3360 2 chr1 141224 141225 half ref G G N 120 120 1491 1492 1 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER21C:ERVL:31.5 21 1.17 N +3361 2 chr1 141225 141256 hom ref = = = 1 1.17 N +3362 2 chr1 141256 141299 no-call complex = ? ? -13 1.17 N +3363 2 chr1 141299 141320 hom ref = = = 11 1.17 N +3364 2 chr1 141320 141362 no-call complex = ? ? -8 1.17 N +3365 2 chr1 141362 141371 hom ref = = = 10 1.17 N +3366 2 chr1 141371 141407 no-call complex = ? ? -73 1.17 N +3367 2 chr1 141407 141445 hom ref = = = 16 1.17 N +3368 2 chr1 141445 141484 no-call complex = ? ? -238 1.17 N +3369 2 chr1 141484 141515 hom ref = = = 18 1.17 N +3370 2 chr1 141515 141559 no-call complex = ? ? -33 1.17 N +3371 2 chr1 141559 141610 hom ref = = = 6 1.17 N +3372 2 chr1 141610 141660 no-call complex = ? ? -82 1.17 N +3373 2 chr1 141660 141687 hom ref = = = 12 1.17 N +3374 2 chr1 141687 141729 no-call complex = ? ? -40 1.17 N +3375 2 chr1 141729 141743 hom ref = = = 15 1.17 N +3376 2 chr1 141743 141769 no-call complex = ? ? -33 1.17 N +3377 2 chr1 141769 141777 hom ref = = = 10 1.17 N +3378 2 chr1 141777 141797 no-call complex = ? ? -64 1.17 N +3379 2 chr1 141797 141932 hom ref = = = 6 1.17 N +3380 2 chr1 141932 141933 half ref A A N 24 69 7 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC AluJr:Alu:20.4 21 1.17 N +3381 2 chr1 141933 141950 hom ref = = = 7 1.17 N +3382 2 chr1 141950 141985 no-call complex = ? ? -2 1.17 N +3383 2 chr1 141985 142003 hom ref = = = 11 1.17 N +3384 2 chr1 142003 142044 no-call complex = ? ? -57 1.17 N +3385 2 chr1 142044 142075 hom ref = = = 22 1.17 N +3386 2 chr1 142075 142089 no-call complex = ? ? -4 1.17 N +3387 2 chr1 142089 142111 hom ref = = = 13 1.17 N +3388 2 chr1 142111 142130 no-call complex = ? ? -8 1.17 N +3389 2 chr1 142130 142191 hom ref = = = -4 1.17 N +3390 2 chr1 142191 142206 no-call complex = ? ? -78 1.17 N +3391 2 chr1 142206 142211 hom ref = = = 15 1.17 N +3392 2 chr1 142211 142263 no-call complex = ? ? -33 1.17 N +3393 2 chr1 142263 142327 hom ref = = = 6 1.17 N +3394 2 chr1 142327 142327 half ref ? 26 0 1511 1512 18 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MIRb:MIR:44.9 21 1.17 N +3395 2 chr1 142327 142329 hom ref = = = 18 1.17 N +3396 2 chr1 142329 142329 half ref ? 32 0 1511 1512 24 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MIRb:MIR:44.9 21 1.17 N +3397 2 chr1 142329 142355 hom ref = = = 5 1.17 N +3398 2 chr1 142355 142405 no-call complex = ? ? -25 1.17 N +3399 2 chr1 142405 142487 hom ref = = = -59 1.17 N +3400 2 chr1 142487 142509 no-call complex = ? ? -41 1.17 N +3401 2 chr1 142509 142564 hom ref = = = -19 1.17 N +3402 2 chr1 142564 142565 half ref A A N 121 121 -19 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 21 1.17 N +3403 2 chr1 142565 142587 hom ref = = = -5 1.17 N +3404 2 chr1 142587 142625 no-call complex = ? ? -19 1.17 N +3405 2 chr1 142625 142674 hom ref = = = -4 1.17 N +3406 2 chr1 142674 142697 no-call complex = ? ? -24 1.17 N +3407 2 chr1 142697 142715 hom ref = = = 10 1.17 N +3408 2 chr1 142715 142756 no-call complex = ? ? -60 1.17 N +3409 2 chr1 142756 142770 hom ref = = = 11 1.17 N +3410 2 chr1 142770 142799 no-call complex = ? ? -87 1.17 N +3411 2 chr1 142799 142909 hom ref = = = -7 1.17 N +3412 2 chr1 142909 142927 no-call complex = ? ? -59 1.17 N +3413 2 chr1 142927 143004 hom ref = = = -25 1.17 N +3414 2 chr1 143004 143005 half ref G G N 113 113 -25 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 21 1.17 N +3415 2 chr1 143005 143151 hom ref = = = -32 1.17 N +3416 2 chr1 143151 143190 no-call complex = ? ? -44 1.17 N +3417 2 chr1 143190 143265 hom ref = = = -1 1.17 N +3418 2 chr1 143265 143304 no-call complex = ? ? -42 1.17 N +3419 2 chr1 143304 143317 hom ref = = = 20 1.17 N +3420 2 chr1 143317 143357 no-call complex = ? ? -20 1.17 N +3421 2 chr1 143357 143390 hom ref = = = 23 1.17 N +3422 2 chr1 143390 143417 no-call complex = ? ? -109 1.17 N +3423 2 chr1 143417 143518 hom ref = = = 10 1.17 N +3424 2 chr1 143518 143568 no-call complex = ? ? -29 1.17 N +3425 2 chr1 143568 143576 hom ref = = = 28 1.17 N +3426 2 chr1 143576 143616 no-call complex = ? ? -81 1.17 N +3427 2 chr1 143616 143629 hom ref = = = 20 1.17 N +3428 2 chr1 143629 143661 no-call complex = ? ? -20 1.17 N +3429 2 chr1 143661 143729 hom ref = = = 5 1.17 N +3430 2 chr1 143729 143770 no-call complex = ? ? -29 1.17 N +3431 2 chr1 143770 143797 hom ref = = = 12 1.17 N +3432 2 chr1 143797 143815 no-call complex = ? ? -37 1.17 N +3433 2 chr1 143815 143824 hom ref = = = 5 1.17 N +3434 2 chr1 143824 143825 half ref T T N 57 120 1537 1538 5 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:13.6 20 1.17 N +3435 2 chr1 143825 143837 hom ref = = = 0 1.17 N +3436 2 chr1 143837 143838 half ref C C N 120 120 1537 1538 0 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:13.6 20 1.17 N +3437 2 chr1 143838 143842 hom ref = = = 0 1.17 N +3438 2 chr1 143842 143843 half ref G G N 41 120 1537 1538 2 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:13.6 20 1.17 N +3439 2 chr1 143843 143848 hom ref = = = 2 1.17 N +3440 2 chr1 143848 143849 half ref T T ? 120 0 1537 1538 8 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:13.6 20 1.17 N +3441 2 chr1 143849 143855 hom ref = = = -1 1.17 N +3442 2 chr1 143855 143856 half ref C C N 120 120 1537 1538 -1 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::INTRON:UNKNOWN-INC MER1A:hAT-Charlie:13.6 20 1.17 N +3443 2 chr1 143856 143878 hom ref = = = -1 1.17 N +3444 2 chr1 143878 143888 no-call complex = ? ? -62 1.17 N +3445 2 chr1 143888 143905 hom ref = = = 10 1.17 N +3446 2 chr1 143905 143954 no-call complex = ? ? -86 1.17 N +3447 2 chr1 143954 143964 hom ref = = = 17 1.17 N +3448 2 chr1 143964 143982 no-call complex = ? ? -8 1.17 N +3449 2 chr1 143982 144014 hom ref = = = 15 1.17 N +3450 2 chr1 144014 144061 no-call complex = ? ? -78 1.17 N +3451 2 chr1 144061 144070 hom ref = = = 13 1.17 N +3452 2 chr1 144070 144115 no-call complex = ? ? -32 1.17 N +3453 2 chr1 144115 144143 hom ref = = = -6 1.17 N +3454 2 chr1 144143 144144 half ref G G N 43 137 -6 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 20 1.17 N +3455 2 chr1 144144 144180 hom ref = = = -6 1.17 N +3456 2 chr1 144180 144201 no-call complex = ? ? -71 1.17 N +3457 2 chr1 144201 144220 hom ref = = = -11 1.17 N +3458 2 chr1 144220 144220 half ref ? 21 0 1545 1546 -11 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC LTR41:ERVL:35.6 20 1.17 N +3459 2 chr1 144220 144222 hom ref = = = -11 1.17 N +3460 2 chr1 144222 144223 half ref T T N 120 120 1545 1546 17 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC LTR41:ERVL:35.6 20 1.17 N +3461 2 chr1 144223 144264 hom ref = = = 8 1.17 N +3462 2 chr1 144264 144265 half ref A A N 50 50 1547 1548 11 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3463 2 chr1 144265 144268 hom ref = = = 11 1.17 N +3464 2 chr1 144268 144283 half ref CTGGGAGGCCAAGGT CTGGGAGGCCAAGGT ? 22 0 1547 1548 -9 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3465 2 chr1 144283 144293 hom ref = = = -9 1.17 N +3466 2 chr1 144293 144295 half ref CT CT ? 50 0 1549 1550 -9 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3467 2 chr1 144295 144298 hom ref = = = 8 1.17 N +3468 2 chr1 144298 144299 half ref A A ? 30 0 1549 1550 9 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::UTR5:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3469 2 chr1 144299 144308 hom ref = = = 9 1.17 N +3470 2 chr1 144308 144368 no-call complex = ? ? -47 1.17 N +3471 2 chr1 144368 144377 hom ref = = = 6 1.17 N +3472 2 chr1 144377 144378 half ref G G ? 120 0 6 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3473 2 chr1 144378 144412 hom ref = = = 6 1.17 N +3474 2 chr1 144412 144415 half ref CTG CTG ? 78 0 1553 1554 9 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3475 2 chr1 144415 144419 hom ref = = = -25 1.17 N +3476 2 chr1 144419 144434 half ref AGGAGAATTGCTTGA AGGAGAATTGCTTGA ? 24 0 1553 1554 -4 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluJb:Alu:16.1 20 1.17 N +3477 2 chr1 144434 144447 hom ref = = = 5 1.17 N +3478 2 chr1 144447 144463 no-call complex = ? ? -8 1.17 N +3479 2 chr1 144463 144515 hom ref = = = 22 1.17 N +3480 2 chr1 144515 144605 no-call complex = ? ? -57 1.17 N +3481 2 chr1 144605 144628 hom ref = = = -3 1.17 N +3482 2 chr1 144628 144628 half ref ? 21 0 23 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 653340:XR_039243.2:LOC653340::::TSS-UPSTREAM:UNKNOWN-INC;729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluSp:Alu:10.2 20 1.17 N +3483 2 chr1 144628 144641 hom ref = = = 13 1.17 N +3484 2 chr1 144641 144691 no-call complex = ? ? -50 1.17 N +3485 2 chr1 144691 144701 hom ref = = = 15 1.17 N +3486 2 chr1 144701 144913 no-call complex = ? ? -38 1.17 N +3487 2 chr1 144913 144971 hom ref = = = 11 1.17 N +3488 2 chr1 144971 144978 no-call complex = ? ? -57 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3489 2 chr1 144978 145044 hom ref = = = -18 1.17 N +3490 2 chr1 145044 145051 no-call complex = ? ? -67 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3491 2 chr1 145051 145115 hom ref = = = 14 1.17 N +3492 2 chr1 145115 145165 no-call complex = ? ? -7 1.17 N +3493 2 chr1 145165 145181 hom ref = = = 14 1.17 N +3494 2 chr1 145181 145184 half ref AGA AGA ? 37 0 1 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluJr:Alu:19.5 20 1.17 N +3495 2 chr1 145184 145201 hom ref = = = 13 1.17 N +3496 2 chr1 145201 145259 no-call complex = ? ? -79 1.17 N +3497 2 chr1 145259 145295 hom ref = = = -38 1.17 N +3498 2 chr1 145295 145296 half ref T T N 56 120 -12 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 20 1.17 N +3499 2 chr1 145296 145356 hom ref = = = -12 1.17 N +3500 2 chr1 145356 145378 no-call complex = ? ? -88 1.17 N +3501 2 chr1 145378 145429 hom ref = = = 11 1.17 N +3502 2 chr1 145429 145472 no-call complex = ? ? -40 1.17 N +3503 2 chr1 145472 145484 hom ref = = = 16 1.17 N +3504 2 chr1 145484 145514 no-call complex = ? ? -56 1.17 N +3505 2 chr1 145514 145549 hom ref = = = 0 1.17 N +3506 2 chr1 145549 145550 half ref T T N 35 93 0 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 20 1.17 N +3507 2 chr1 145550 145645 hom ref = = = -17 1.17 N +3508 2 chr1 145645 145652 half ref TGCAAGG TGCAAGG ? 37 0 1565 1566 -8 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 20 1.17 N +3509 2 chr1 145652 145660 hom ref = = = -8 1.17 N +3510 2 chr1 145660 145661 half ref C C ? 120 0 1565 1566 10 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC L2b:L2:43.7 20 1.17 N +3511 2 chr1 145661 145676 hom ref = = = -4 1.17 N +3512 2 chr1 145676 145712 no-call complex = ? ? -80 1.17 N +3513 2 chr1 145712 145718 hom ref = = = 15 1.17 N +3514 2 chr1 145718 145752 no-call complex = ? ? -81 1.17 N +3515 2 chr1 145752 145857 hom ref = = = -20 1.17 N +3516 2 chr1 145857 145858 half ref T T N 36 66 1571 1572 14 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC L2b:L2:43.7 20 1.17 N +3517 2 chr1 145858 145861 hom ref = = = 9 1.17 N +3518 2 chr1 145861 145862 half ref A A N 66 66 1571 1572 13 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC L2b:L2:43.7 20 1.17 N +3519 2 chr1 145862 145871 hom ref = = = 11 1.17 N +3520 2 chr1 145871 145874 half ref TAT TAT ? 25 0 1571 1572 -8 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC L2b:L2:43.7 20 1.17 N +3521 2 chr1 145874 145903 hom ref = = = 1 1.17 N +3522 2 chr1 145903 145947 no-call complex = ? ? -121 1.17 N +3523 2 chr1 145947 145997 hom ref = = = 7 1.17 N +3524 2 chr1 145997 146032 no-call complex = ? ? -188 1.17 N +3525 2 chr1 146032 146048 hom ref = = = 16 1.17 N +3526 2 chr1 146048 146088 no-call complex = ? ? -25 1.17 N +3527 2 chr1 146088 146110 hom ref = = = 16 1.17 N +3528 2 chr1 146110 146117 no-call complex = ? ? -66 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3529 2 chr1 146117 146165 hom ref = = = 12 1.17 N +3530 2 chr1 146165 146210 no-call complex = ? ? -43 1.17 N +3531 2 chr1 146210 146221 hom ref = = = 16 1.17 N +3532 2 chr1 146221 146229 no-call complex = ? ? -72 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3533 2 chr1 146229 146307 hom ref = = = -25 1.17 N +3534 2 chr1 146307 146354 no-call complex = ? ? -10 1.17 N +3535 2 chr1 146354 146389 hom ref = = = 21 1.17 N +3536 2 chr1 146389 146396 no-call complex = ? ? -1 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3537 2 chr1 146396 146503 hom ref = = = 6 1.17 N +3538 2 chr1 146503 146526 no-call complex = ? ? -35 1.17 N +3539 2 chr1 146526 146536 hom ref = = = 16 1.17 N +3540 2 chr1 146536 146564 no-call complex = ? ? -65 1.17 N +3541 2 chr1 146564 146580 hom ref = = = 11 1.17 N +3542 2 chr1 146580 146607 no-call complex = ? ? -31 1.17 N +3543 2 chr1 146607 146865 hom ref = = = -7 1.17 N +3544 2 chr1 146865 146900 no-call complex = ? ? -20 1.17 N +3545 2 chr1 146900 146923 hom ref = = = 15 1.17 N +3546 2 chr1 146923 146930 no-call complex = ? ? -38 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 1.17 N +3547 2 chr1 146930 146956 hom ref = = = 19 1.17 N +3548 2 chr1 146956 147003 no-call complex = ? ? -50 1.17 N +3549 2 chr1 147003 147033 hom ref = = = -7 1.17 N +3550 2 chr1 147033 147105 no-call complex = ? ? -97 1.17 N +3551 2 chr1 147105 147128 hom ref = = = 30 1.17 N +3552 2 chr1 147128 147141 no-call complex = ? ? -297 1.17 N +3553 2 chr1 147141 147285 hom ref = = = -33 1.17 N +3554 2 chr1 147285 147323 no-call complex = ? ? -44 1.17 N +3555 2 chr1 147323 147332 hom ref = = = 19 1.17 N +3556 2 chr1 147332 147351 no-call complex = ? ? -195 1.17 N +3557 2 chr1 147351 147400 hom ref = = = -16 1.17 N +3558 2 chr1 147400 147401 half ref T T N 121 121 -16 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluSx:Alu:16.3 20 1.17 N +3559 2 chr1 147401 147423 hom ref = = = -16 1.17 N +3560 2 chr1 147423 147479 no-call complex = ? ? -109 1.17 N +3561 2 chr1 147479 147528 hom ref = = = 12 1.17 N +3562 2 chr1 147528 147540 no-call complex = ? ? -106 1.17 N +3563 2 chr1 147540 147564 hom ref = = = 26 1.17 N +3564 2 chr1 147564 147612 no-call complex = ? ? -65 1.17 N +3565 2 chr1 147612 147675 hom ref = = = 19 1.17 N +3566 2 chr1 147675 147707 no-call complex = ? ? -42 1.17 N +3567 2 chr1 147707 147739 hom ref = = = 13 1.17 N +3568 2 chr1 147739 147753 no-call complex = ? ? -5 1.17 N +3569 2 chr1 147753 147917 hom ref = = = -27 1.17 N +3570 2 chr1 147917 147917 half ref ? 23 0 2 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC AluJb:Alu:20.2;L1MB8:L1:30.7 20 1.17 N +3571 2 chr1 147917 148011 hom ref = = = 2 1.17 N +3572 2 chr1 148011 148040 no-call complex = ? ? -21 1.17 N +3573 2 chr1 148040 148172 hom ref = = = 5 1.17 N +3574 2 chr1 148172 148201 no-call complex = ? ? -65 1.17 N +3575 2 chr1 148201 148224 hom ref = = = 22 1.17 N +3576 2 chr1 148224 148262 no-call complex = ? ? -93 1.17 N +3577 2 chr1 148262 148306 hom ref = = = -79 1.17 N +3578 2 chr1 148306 148347 no-call complex = ? ? -99 1.17 N +3579 2 chr1 148347 148478 hom ref = = = -2 1.17 N +3580 2 chr1 148478 148523 no-call complex = ? ? -105 1.17 N +3581 2 chr1 148523 148541 hom ref = = = 11 1.17 N +3582 2 chr1 148541 148590 no-call complex = ? ? -26 1.17 N +3583 2 chr1 148590 148612 hom ref = = = 25 1.17 N +3584 2 chr1 148612 148623 no-call complex = ? ? -32 1.17 N +3585 2 chr1 148623 148653 hom ref = = = 14 1.17 N +3586 2 chr1 148653 148688 no-call complex = ? ? -27 1.17 N +3587 2 chr1 148688 148702 hom ref = = = 11 1.17 N +3588 2 chr1 148702 148797 no-call complex = ? ? -174 1.17 N +3589 2 chr1 148797 148823 hom ref = = = 12 1.17 N +3590 2 chr1 148823 148856 no-call complex = ? ? -45 1.17 N +3591 2 chr1 148856 148924 hom ref = = = 4 1.17 N +3592 2 chr1 148924 148962 no-call complex = ? ? -97 1.17 N +3593 2 chr1 148962 149112 hom ref = = = -5 1.17 N +3594 2 chr1 149112 149113 half ref G G N 42 120 1605 1606 2 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC Tigger12c:TcMar-Tigger:35.6 19 1.17 N +3595 2 chr1 149113 149118 hom ref = = = -13 1.17 N +3596 2 chr1 149118 149119 half ref G G N 120 120 1605 1606 -13 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC 729737:XM_001133863.2:LOC729737::::TSS-UPSTREAM:UNKNOWN-INC Tigger12c:TcMar-Tigger:35.6 19 1.17 N +3597 2 chr1 149119 149168 hom ref = = = -13 1.17 N +3598 2 chr1 149168 149188 no-call complex = ? ? -7 1.17 N +3599 2 chr1 149188 149200 hom ref = = = 12 1.17 N +3600 2 chr1 149200 149244 no-call complex = ? ? -70 1.17 N +3601 2 chr1 149244 149458 hom ref = = = -1 1.17 N +3602 2 chr1 149458 149506 no-call complex = ? ? -6 1.17 N +3603 2 chr1 149506 149542 hom ref = = = -9 1.17 N +3604 2 chr1 149542 149578 no-call complex = ? ? -51 1.17 N +3605 2 chr1 149578 149629 hom ref = = = 13 1.17 N +3606 2 chr1 149629 149636 no-call complex = ? ? -30 1.17 N +3607 2 chr1 149636 149675 hom ref = = = 14 1.17 N +3608 2 chr1 149675 149720 no-call complex = ? ? -244 1.17 N +3609 2 chr1 149720 149785 hom ref = = = -13 1.17 N +3610 2 chr1 149785 149786 half ref C C N 44 120 -13 19 1.17 N +3611 2 chr1 149786 149870 hom ref = = = -19 1.17 N +3612 2 chr1 149870 149912 no-call complex = ? ? -66 1.17 N +3613 2 chr1 149912 150015 hom ref = = = 12 1.17 N +3614 2 chr1 150015 150064 no-call complex = ? ? -68 1.17 N +3615 2 chr1 150064 150083 hom ref = = = 23 1.17 N +3616 2 chr1 150083 150114 no-call complex = ? ? -25 1.17 N +3617 2 chr1 150114 150127 hom ref = = = 19 1.17 N +3618 2 chr1 150127 150176 no-call complex = ? ? -7 1.17 N +3619 2 chr1 150176 150334 hom ref = = = -5 1.17 N +3620 2 chr1 150334 150355 no-call complex = ? ? -8 1.17 N +3621 2 chr1 150355 150416 hom ref = = = 17 1.17 N +3622 2 chr1 150416 150435 no-call complex = ? ? -51 1.17 N +3623 2 chr1 150435 150449 hom ref = = = 22 1.17 N +3624 2 chr1 150449 150494 no-call complex = ? ? -24 1.17 N +3625 2 chr1 150494 150656 hom ref = = = 3 1.17 N +3626 2 chr1 150656 150701 no-call complex = ? ? -122 1.17 N +3627 2 chr1 150701 150739 hom ref = = = 17 1.17 N +3628 2 chr1 150739 150786 no-call complex = ? ? -70 1.17 N +3629 2 chr1 150786 150823 hom ref = = = 32 1.17 N +3630 2 chr1 150823 150834 no-call complex = ? ? -39 1.17 N +3631 2 chr1 150834 150848 hom ref = = = 33 1.17 N +3632 2 chr1 150848 150881 no-call complex = ? ? -21 1.17 N +3633 2 chr1 150881 150976 hom ref = = = -19 1.17 N +3634 2 chr1 150976 151021 no-call complex = ? ? -108 1.17 N +3635 2 chr1 151021 151033 hom ref = = = 18 1.17 N +3636 2 chr1 151033 151058 no-call complex = ? ? -80 1.17 N +3637 2 chr1 151058 151239 hom ref = = = -1 1.17 N +3638 2 chr1 151239 151276 no-call complex = ? ? -100 1.17 N +3639 2 chr1 151276 151312 hom ref = = = 13 1.17 N +3640 2 chr1 151312 151313 half ref C C N 44 88 13 L2a:L2:37.0 19 1.17 N +3641 2 chr1 151313 151341 hom ref = = = 5 1.17 N +3642 2 chr1 151341 151342 half ref A A N 88 88 1633 1634 5 AluJb:Alu:23.3 19 1.17 N +3643 2 chr1 151342 151353 hom ref = = = 5 1.17 N +3644 2 chr1 151353 151354 half ref T T N 88 88 1633 1634 19 AluJb:Alu:23.3 19 1.17 N +3645 2 chr1 151354 151475 hom ref = = = 8 1.17 N +3646 2 chr1 151475 151542 no-call complex = ? ? -318 1.17 N +3647 2 chr1 151542 151586 hom ref = = = 11 1.17 N +3648 2 chr1 151586 151597 no-call complex = ? ? -28 1.17 N +3649 2 chr1 151597 151714 hom ref = = = -32 1.17 N +3650 2 chr1 151714 151790 no-call complex = ? ? -93 1.17 N +3651 2 chr1 151790 151809 hom ref = = = -27 1.17 N +3652 2 chr1 151809 151810 half ref C C N 85 122 -27 AluJb:Alu:23.3 18 1.17 N +3653 2 chr1 151810 151838 hom ref = = = -27 1.17 N +3654 2 chr1 151838 151874 no-call complex = ? ? -44 1.17 N +3655 2 chr1 151874 151885 hom ref = = = 20 1.17 N +3656 2 chr1 151885 151929 no-call complex = ? ? -40 1.17 N +3657 2 chr1 151929 151953 hom ref = = = 18 1.17 N +3658 2 chr1 151953 151960 no-call complex = ? ? -13 1.17 N +3659 2 chr1 151960 151998 hom ref = = = 18 1.17 N +3660 2 chr1 151998 152028 no-call complex = ? ? -52 1.17 N +3661 2 chr1 152028 152119 hom ref = = = 11 1.17 N +3662 2 chr1 152119 152151 no-call complex = ? ? -30 1.17 N +3663 2 chr1 152151 152203 hom ref = = = 11 1.17 N +3664 2 chr1 152203 152236 no-call complex = ? ? -3 1.17 N +3665 2 chr1 152236 152378 hom ref = = = -9 1.17 N +3666 2 chr1 152378 152379 half ref T T N 76 120 -9 AluJr:Alu:21.7 17 1.17 N +3667 2 chr1 152379 152463 hom ref = = = -11 1.17 N +3668 2 chr1 152463 152464 half ref T T N 39 120 -11 AluJr:Alu:21.7 17 1.17 N +3669 2 chr1 152464 152529 hom ref = = = -25 1.17 N +3670 2 chr1 152529 152570 no-call complex = ? ? -27 1.17 N +3671 2 chr1 152570 152586 hom ref = = = -12 1.17 N +3672 2 chr1 152586 152587 half ref G G N 59 120 -12 MER21C:ERVL:33.0 17 1.17 N +3673 2 chr1 152587 152729 hom ref = = = -44 1.17 N +3674 2 chr1 152729 152748 no-call complex = ? ? -56 1.17 N +3675 2 chr1 152748 152758 hom ref = = = 21 1.17 N +3676 2 chr1 152758 152783 no-call complex = ? ? -75 1.17 N +3677 2 chr1 152783 152821 hom ref = = = 22 1.17 N +3678 2 chr1 152821 152844 no-call complex = ? ? -29 1.17 N +3679 2 chr1 152844 152867 hom ref = = = 10 1.17 N +3680 2 chr1 152867 152919 no-call complex = ? ? -35 1.17 N +3681 2 chr1 152919 152932 hom ref = = = 21 1.17 N +3682 2 chr1 152932 152978 no-call complex = ? ? -6 1.17 N +3683 2 chr1 152978 152999 hom ref = = = -10 1.17 N +3684 2 chr1 152999 152999 half ref ? 27 0 1659 1660 32 AluSq2:Alu:14.9 17 1.17 N +3685 2 chr1 152999 153007 hom ref = = = 2 1.17 N +3686 2 chr1 153007 153010 half ref CGG CGG NGN 38 118 1659 1660 2 AluSq2:Alu:14.9 17 1.17 N +3687 2 chr1 153010 153030 hom ref = = = 12 1.17 N +3688 2 chr1 153030 153037 no-call complex = ? ? -56 1.17 N +3689 2 chr1 153037 153069 hom ref = = = 20 1.17 N +3690 2 chr1 153069 153095 no-call complex = ? ? -312 1.17 N +3691 2 chr1 153095 153105 hom ref = = = 24 1.17 N +3692 2 chr1 153105 153169 no-call complex = ? ? -61 1.17 N +3693 2 chr1 153169 153265 hom ref = = = -8 1.17 N +3694 2 chr1 153265 153266 half ref A A N 121 121 1 MER21C:ERVL:33.0 17 1.17 N +3695 2 chr1 153266 153281 hom ref = = = 1 1.17 N +3696 2 chr1 153281 153328 no-call complex = ? ? -13 1.17 N +3697 2 chr1 153328 153519 hom ref = = = -7 1.17 N +3698 2 chr1 153519 153559 no-call complex = ? ? -85 1.17 N +3699 2 chr1 153559 153640 hom ref = = = 11 1.17 N +3700 2 chr1 153640 153694 no-call complex = ? ? -50 1.17 N +3701 2 chr1 153694 153740 hom ref = = = 13 1.17 N +3702 2 chr1 153740 153779 no-call complex = ? ? -179 1.17 N +3703 2 chr1 153779 153798 hom ref = = = 17 1.17 N +3704 2 chr1 153798 153828 no-call complex = ? ? -167 1.17 N +3705 2 chr1 153828 153860 hom ref = = = 19 1.17 N +3706 2 chr1 153860 153892 no-call complex = ? ? -43 1.17 N +3707 2 chr1 153892 153951 hom ref = = = 19 1.17 N +3708 2 chr1 153951 153999 no-call complex = ? ? -33 1.17 N +3709 2 chr1 153999 154068 hom ref = = = 15 1.17 N +3710 2 chr1 154068 154130 no-call complex = ? ? -22 1.17 N +3711 2 chr1 154130 154148 hom ref = = = 18 1.17 N +3712 2 chr1 154148 154191 no-call complex = ? ? -131 1.17 N +3713 2 chr1 154191 154224 hom ref = = = 8 1.17 N +3714 2 chr1 154224 154225 half ref C C ? 120 0 1673 1674 8 MER11B:ERVK:25.5 17 1.17 N +3715 2 chr1 154225 154227 hom ref = = = 0 1.17 N +3716 2 chr1 154227 154228 half ref T T N 120 120 1673 1674 0 MER11B:ERVK:25.5 17 1.17 N +3717 2 chr1 154228 154327 hom ref = = = 0 1.17 N +3718 2 chr1 154327 154328 half ref G G N 93 93 1675 1676 10 MER11B:ERVK:25.5 17 1.17 N +3719 2 chr1 154328 154338 hom ref = = = -2 1.17 N +3720 2 chr1 154338 154340 half ref AA AA NN 93 93 1675 1676 -2 MER11B:ERVK:25.5 17 1.17 N +3721 2 chr1 154340 154441 hom ref = = = 1 1.17 N +3722 2 chr1 154441 154448 no-call complex = ? ? -72 1.17 N +3723 2 chr1 154448 154556 hom ref = = = -24 1.17 N +3724 2 chr1 154556 154564 half ref AGGCCTCT AGGCCTCT ? 21 0 -17 MER11B:ERVK:25.5 18 1.17 N +3725 2 chr1 154564 154597 hom ref = = = -17 1.17 N +3726 2 chr1 154597 154605 no-call complex = ? ? -18 1.17 N +3727 2 chr1 154605 154615 hom ref = = = 18 1.17 N +3728 2 chr1 154615 154651 no-call complex = ? ? -46 1.17 N +3729 2 chr1 154651 154668 hom ref = = = 16 1.17 N +3730 2 chr1 154668 154675 no-call complex = ? ? -149 1.17 N +3731 2 chr1 154675 154775 hom ref = = = 12 1.17 N +3732 2 chr1 154775 154789 no-call complex = ? ? -264 1.17 N +3733 2 chr1 154789 154927 hom ref = = = -7 1.17 N +3734 2 chr1 154927 154965 no-call complex = ? ? -272 1.17 N +3735 2 chr1 154965 154971 hom ref = = = 11 1.17 N +3736 2 chr1 154971 154978 no-call complex = ? ? -70 1.17 N +3737 2 chr1 154978 154987 hom ref = = = 21 1.17 N +3738 2 chr1 154987 155060 no-call complex = ? ? -71 1.17 N +3739 2 chr1 155060 155073 hom ref = = = 16 1.17 N +3740 2 chr1 155073 155099 no-call complex = ? ? -12 1.17 N +3741 2 chr1 155099 155231 hom ref = = = 0 1.17 N +3742 2 chr1 155231 155277 no-call complex = ? ? -128 1.17 N +3743 2 chr1 155277 155413 hom ref = = = 6 1.17 N +3744 2 chr1 155413 155445 no-call complex = ? ? -35 1.17 N +3745 2 chr1 155445 155461 hom ref = = = 12 1.17 N +3746 2 chr1 155461 155509 no-call complex = ? ? -20 1.17 N +3747 2 chr1 155509 155521 hom ref = = = 11 1.17 N +3748 2 chr1 155521 155528 no-call complex = ? ? -11 1.17 N +3749 2 chr1 155528 155544 hom ref = = = 24 1.17 N +3750 2 chr1 155544 155574 no-call complex = ? ? -206 1.17 N +3751 2 chr1 155574 155600 hom ref = = = 10 1.17 N +3752 2 chr1 155600 155651 no-call complex = ? ? -15 1.17 N +3753 2 chr1 155651 155673 hom ref = = = 9 1.17 N +3754 2 chr1 155673 155725 no-call complex = ? ? -41 1.17 N +3755 2 chr1 155725 155731 hom ref = = = 14 1.17 N +3756 2 chr1 155731 155771 no-call complex = ? ? -53 1.17 N +3757 2 chr1 155771 155783 hom ref = = = 15 1.17 N +3758 2 chr1 155783 155811 no-call complex = ? ? -81 1.17 N +3759 2 chr1 155811 155830 hom ref = = = 20 1.17 N +3760 2 chr1 155830 155830 half ref ? 35 0 27 18 1.17 N +3761 2 chr1 155830 155848 hom ref = = = 9 1.17 N +3762 2 chr1 155848 155884 no-call complex = ? ? -98 1.17 N +3763 2 chr1 155884 155892 hom ref = = = 15 1.17 N +3764 2 chr1 155892 155934 no-call complex = ? ? -10 1.17 N +3765 2 chr1 155934 155941 hom ref = = = 24 1.17 N +3766 2 chr1 155941 155970 no-call complex = ? ? -67 1.17 N +3767 2 chr1 155970 155993 hom ref = = = -33 1.17 N +3768 2 chr1 155993 155993 half ref ? 42 0 1711 1712 -33 18 1.17 N +3769 2 chr1 155993 155999 hom ref = = = -36 1.17 N +3770 2 chr1 155999 156000 half ref A A ? 32 0 1711 1712 -34 AluJb:Alu:20.8 18 1.17 N +3771 2 chr1 156000 156078 hom ref = = = -34 1.17 N +3772 2 chr1 156078 156079 half ref G G N 120 120 1713 1714 17 AluJb:Alu:20.8 18 1.17 N +3773 2 chr1 156079 156096 hom ref = = = -2 1.17 N +3774 2 chr1 156096 156097 half ref T T N 120 120 1713 1714 -2 AluJb:Alu:20.8 18 1.17 N +3775 2 chr1 156097 156116 hom ref = = = -2 1.17 N +3776 2 chr1 156116 156126 no-call complex = ? ? -26 1.17 N +3777 2 chr1 156126 156136 hom ref = = = 13 1.17 N +3778 2 chr1 156136 156140 half ref TGCA TGCA NGNN 21 54 1715 1716 -6 AluJo:Alu:26.0 18 1.17 N +3779 2 chr1 156140 156150 hom ref = = = -6 1.17 N +3780 2 chr1 156150 156152 half ref TA TA NN 22 63 1715 1716 3 AluJo:Alu:26.0 18 1.17 N +3781 2 chr1 156152 156180 hom ref = = = -7 1.17 N +3782 2 chr1 156180 156181 half ref T T N 63 63 1715 1716 -7 AluJo:Alu:26.0 18 1.17 N +3783 2 chr1 156181 156219 hom ref = = = -7 1.17 N +3784 2 chr1 156219 156220 half ref C C N 35 120 1717 1718 -5 AluJo:Alu:26.0 18 1.17 N +3785 2 chr1 156220 156225 hom ref = = = -5 1.17 N +3786 2 chr1 156225 156226 half ref T T N 120 120 1717 1718 -5 AluJo:Alu:26.0 18 1.17 N +3787 2 chr1 156226 156269 hom ref = = = -5 1.17 N +3788 2 chr1 156269 156302 no-call complex = ? ? -66 1.17 N +3789 2 chr1 156302 156386 hom ref = = = 6 1.17 N +3790 2 chr1 156386 156448 no-call complex = ? ? -18 1.17 N +3791 2 chr1 156448 156459 hom ref = = = 17 1.17 N +3792 2 chr1 156459 156471 no-call complex = ? ? -41 1.17 N +3793 2 chr1 156471 156488 hom ref = = = 14 1.17 N +3794 2 chr1 156488 156573 no-call complex = ? ? -48 1.17 N +3795 2 chr1 156573 156586 hom ref = = = 19 1.17 N +3796 2 chr1 156586 156615 no-call complex = ? ? -65 1.17 N +3797 2 chr1 156615 156670 hom ref = = = 11 1.17 N +3798 2 chr1 156670 156699 no-call complex = ? ? -29 1.17 N +3799 2 chr1 156699 156723 hom ref = = = 6 1.17 N +3800 2 chr1 156723 156731 half ref TAAAAGTA TAAAAGTA ? 24 0 1727 1728 4 AT_rich:Low_complexity:5.1 18 1.17 N +3801 2 chr1 156731 156742 hom ref = = = 7 1.17 N +3802 2 chr1 156742 156756 half ref TATAATTTAATAAA TATAATTTAATAAA ? 22 0 1727 1728 -3 AT_rich:Low_complexity:5.1 18 1.17 N +3803 2 chr1 156756 156843 hom ref = = = -14 1.17 N +3804 2 chr1 156843 156858 no-call complex ATGCTTATAATACCA NTGCTTATAATACCA NNNNTNNNNATNCCN 43 21 1729 1730 -14 AluJr:Alu:25.3 18 1.17 N +3805 2 chr1 156858 156862 hom ref = = = -1 1.17 N +3806 2 chr1 156862 156864 half ref TT TT NN 120 120 1729 1730 -1 AluJr:Alu:25.3 18 1.17 N +3807 2 chr1 156864 156868 hom ref = = = 3 1.17 N +3808 2 chr1 156868 156869 half ref A A N 64 73 1729 1730 16 AluJr:Alu:25.3 18 1.17 N +3809 2 chr1 156869 156878 hom ref = = = 10 1.17 N +3810 2 chr1 156878 156897 no-call complex = ? ? -27 1.17 N +3811 2 chr1 156897 156947 hom ref = = = 20 1.17 N +3812 2 chr1 156947 156954 no-call complex = ? ? 6 1.17 N +3813 2 chr1 156954 156994 hom ref = = = 7 1.17 N +3814 2 chr1 156994 156995 half ref T T N 48 120 7 AluJr:Alu:25.3 18 1.17 N +3815 2 chr1 156995 157100 hom ref = = = -5 1.17 N +3816 2 chr1 157100 157101 half ref T T N 48 48 1731 1732 -5 AluJr:Alu:25.3 18 1.17 N +3817 2 chr1 157101 157105 hom ref = = = -5 1.17 N +3818 2 chr1 157105 157114 no-call complex TCAAAAAAA TCAAAAAAA? ? 0 0 1731 1732 -1 AluJr:Alu:25.3 18 1.17 N +3819 2 chr1 157114 157137 hom ref = = = -1 1.17 N +3820 2 chr1 157137 157148 no-call complex = ? ? -21 1.17 N +3821 2 chr1 157148 157161 hom ref = = = 18 1.17 N +3822 2 chr1 157161 157209 no-call complex = ? ? -137 1.17 N +3823 2 chr1 157209 157277 hom ref = = = 18 1.17 N +3824 2 chr1 157277 157322 no-call complex = ? ? -96 1.17 N +3825 2 chr1 157322 157392 hom ref = = = 16 1.17 N +3826 2 chr1 157392 157397 no-call complex ATTAT ATTNT ? 22 0 -13 L1M5:L1:39.2 18 1.17 N +3827 2 chr1 157397 157437 hom ref = = = 8 1.17 N +3828 2 chr1 157437 157466 no-call complex = ? ? -142 1.17 N +3829 2 chr1 157466 157479 hom ref = = = 10 1.17 N +3830 2 chr1 157479 157510 no-call complex = ? ? -39 1.17 N +3831 2 chr1 157510 157532 hom ref = = = 5 1.17 N +3832 2 chr1 157532 157533 half ref G G N 64 121 5 AluJr4:Alu:29.2 18 1.17 N +3833 2 chr1 157533 157574 hom ref = = = -12 1.17 N +3834 2 chr1 157574 157575 half ref C C N 121 121 3 AluJr4:Alu:29.2 18 1.17 N +3835 2 chr1 157575 157615 hom ref = = = 2 1.17 N +3836 2 chr1 157615 157641 no-call complex = ? ? -342 1.17 N +3837 2 chr1 157641 157663 hom ref = = = 25 1.17 N +3838 2 chr1 157663 157702 no-call complex = ? ? -4 1.17 N +3839 2 chr1 157702 157742 hom ref = = = 16 1.17 N +3840 2 chr1 157742 157749 no-call complex = ? ? -185 1.17 N +3841 2 chr1 157749 157759 hom ref = = = 16 1.17 N +3842 2 chr1 157759 157794 no-call complex = ? ? -51 1.17 N +3843 2 chr1 157794 157875 hom ref = = = 6 1.17 N +3844 2 chr1 157875 157913 no-call complex = ? ? -3 1.17 N +3845 2 chr1 157913 157983 hom ref = = = 10 1.17 N +3846 2 chr1 157983 158015 no-call complex = ? ? -107 1.17 N +3847 2 chr1 158015 158084 hom ref = = = 10 1.17 N +3848 2 chr1 158084 158091 no-call complex = ? ? -9 1.17 N +3849 2 chr1 158091 158173 hom ref = = = 7 1.17 N +3850 2 chr1 158173 158198 no-call complex = ? ? -13 1.17 N +3851 2 chr1 158198 158360 hom ref = = = -24 1.17 N +3852 2 chr1 158360 158396 no-call complex = ? ? -112 1.17 N +3853 2 chr1 158396 158460 hom ref = = = -6 1.17 N +3854 2 chr1 158460 158483 no-call complex = ? ? -38 1.17 N +3855 2 chr1 158483 158581 hom ref = = = 3 1.17 N +3856 2 chr1 158581 158610 no-call complex = ? ? -184 1.17 N +3857 2 chr1 158610 158635 hom ref = = = 11 1.17 N +3858 2 chr1 158635 158642 no-call complex = ? ? -104 1.17 N +3859 2 chr1 158642 158694 hom ref = = = 8 1.17 N +3860 2 chr1 158694 158697 half ref CAT CAT NNN 33 84 3 18 1.17 N +3861 2 chr1 158697 158734 hom ref = = = 3 1.17 N +3862 2 chr1 158734 158780 no-call complex = ? ? -69 1.17 N +3863 2 chr1 158780 158832 hom ref = = = 16 1.17 N +3864 2 chr1 158832 158862 no-call complex = ? ? -65 1.17 N +3865 2 chr1 158862 158909 hom ref = = = 6 1.17 N +3866 2 chr1 158909 158910 half ref G G N 138 138 6 AluJr:Alu:19.6 18 1.17 N +3867 2 chr1 158910 158985 hom ref = = = 5 1.17 N +3868 2 chr1 158985 159051 no-call complex = ? ? -145 1.17 N +3869 2 chr1 159051 159094 hom ref = = = 2 1.17 N +3870 2 chr1 159094 159095 half ref G G N 120 120 30 18 1.17 N +3871 2 chr1 159095 159155 hom ref = = = -2 1.17 N +3872 2 chr1 159155 159186 no-call complex = ? ? -87 1.17 N +3873 2 chr1 159186 159214 hom ref = = = 11 1.17 N +3874 2 chr1 159214 159249 no-call complex = ? ? -40 1.17 N +3875 2 chr1 159249 159264 hom ref = = = 26 1.17 N +3876 2 chr1 159264 159271 no-call complex = ? ? -5 1.17 N +3877 2 chr1 159271 159392 hom ref = = = -32 1.17 N +3878 2 chr1 159392 159433 no-call complex = ? ? -75 1.17 N +3879 2 chr1 159433 159478 hom ref = = = -50 1.17 N +3880 2 chr1 159478 159478 half ref ? 31 0 1763 1764 -50 AluSx1:Alu:7.1 18 1.17 N +3881 2 chr1 159478 159481 hom ref = = = -50 1.17 N +3882 2 chr1 159481 159482 half ref A A ? 38 0 1763 1764 17 AluSx1:Alu:7.1 18 1.17 N +3883 2 chr1 159482 159524 hom ref = = = 9 1.17 N +3884 2 chr1 159524 159574 no-call complex = ? ? -44 1.17 N +3885 2 chr1 159574 159712 hom ref = = = -32 1.17 N +3886 2 chr1 159712 159714 half ref GA GA NN 56 120 -16 18 1.17 N +3887 2 chr1 159714 159795 hom ref = = = -11 1.17 N +3888 2 chr1 159795 159803 no-call complex = ? ? -17 1.17 N +3889 2 chr1 159803 159949 hom ref = = = -15 1.17 N +3890 2 chr1 159949 159975 no-call complex = ? ? -103 1.17 N +3891 2 chr1 159975 160000 hom ref = = = 20 1.17 N +3892 2 chr1 160000 160007 no-call complex = ? ? -10 1.17 N +3893 2 chr1 160007 160077 hom ref = = = 10 1.17 N +3894 2 chr1 160077 160096 no-call complex = ? ? 8 1.17 N +3895 2 chr1 160096 160110 hom ref = = = 18 1.17 N +3896 2 chr1 160110 160117 no-call complex = ? ? -100 1.17 N +3897 2 chr1 160117 160203 hom ref = = = 10 1.17 N +3898 2 chr1 160203 160223 no-call complex = ? ? -1 1.17 N +3899 2 chr1 160223 160255 hom ref = = = 1 1.17 N +3900 2 chr1 160255 160256 half ref G G N 29 120 1771 1772 1 18 1.17 N +3901 2 chr1 160256 160300 hom ref = = = -23 1.17 N +3902 2 chr1 160300 160300 half ref ? 27 0 1771 1772 30 18 1.17 N +3903 2 chr1 160300 160323 hom ref = = = 23 1.17 N +3904 2 chr1 160323 160353 no-call complex = ? ? -120 1.17 N +3905 2 chr1 160353 160427 hom ref = = = 2 1.17 N +3906 2 chr1 160427 160457 no-call complex = ? ? -52 1.17 N +3907 2 chr1 160457 160467 hom ref = = = 13 1.17 N +3908 2 chr1 160467 160491 no-call complex = ? ? 5 1.17 N +3909 2 chr1 160491 160541 hom ref = = = 13 1.17 N +3910 2 chr1 160541 160565 no-call complex = ? ? -28 1.17 N +3911 2 chr1 160565 160613 hom ref = = = 13 1.17 N +3912 2 chr1 160613 160620 no-call complex = ? ? -129 1.17 N +3913 2 chr1 160620 160674 hom ref = = = -8 1.17 N +3914 2 chr1 160674 160675 half ref A A N 49 107 8 18 1.17 N +3915 2 chr1 160675 160696 hom ref = = = 8 1.17 N +3916 2 chr1 160696 160733 no-call complex = ? ? -55 1.17 N +3917 2 chr1 160733 160752 hom ref = = = 0 1.17 N +3918 2 chr1 160752 160753 half ref T T N 120 120 0 18 1.17 N +3919 2 chr1 160753 160813 hom ref = = = 0 1.17 N +3920 2 chr1 160813 160853 no-call complex = ? ? -20 1.17 N +3921 2 chr1 160853 160942 hom ref = = = -3 1.17 N +3922 2 chr1 160942 160979 no-call complex = ? ? -44 1.17 N +3923 2 chr1 160979 161095 hom ref = = = -43 1.17 N +3924 2 chr1 161095 161096 half ref T T N 25 119 -9 18 1.17 N +3925 2 chr1 161096 161169 hom ref = = = -9 1.17 N +3926 2 chr1 161169 161178 no-call complex = ? ? -53 1.17 N +3927 2 chr1 161178 161204 hom ref = = = 14 1.17 N +3928 2 chr1 161204 161223 no-call complex = ? ? -46 1.17 N +3929 2 chr1 161223 161283 hom ref = = = 5 1.17 N +3930 2 chr1 161283 161331 no-call complex = ? ? -94 1.17 N +3931 2 chr1 161331 161346 hom ref = = = 18 1.17 N +3932 2 chr1 161346 161384 no-call complex = ? ? -111 1.17 N +3933 2 chr1 161384 161402 hom ref = = = 12 1.17 N +3934 2 chr1 161402 161429 no-call complex = ? ? -147 1.17 N +3935 2 chr1 161429 161445 hom ref = = = 18 1.17 N +3936 2 chr1 161445 161493 no-call complex = ? ? -113 1.17 N +3937 2 chr1 161493 161498 hom ref = = = 10 1.17 N +3938 2 chr1 161498 161512 no-call complex = ? ? -4 1.17 N +3939 2 chr1 161512 161575 hom ref = = = 6 1.17 N +3940 2 chr1 161575 161576 half ref A A ? 120 0 6 L1MC4:L1:39.4 18 1.17 N +3941 2 chr1 161576 161621 hom ref = = = 6 1.17 N +3942 2 chr1 161621 161660 no-call complex = ? ? -42 1.17 N +3943 2 chr1 161660 161908 hom ref = = = -16 1.17 N +3944 2 chr1 161908 161909 half ref A A N 50 100 -6 17 1.17 N +3945 2 chr1 161909 161943 hom ref = = = -6 1.17 N +3946 2 chr1 161943 161950 no-call complex = ? ? -23 1.17 N +3947 2 chr1 161950 162047 hom ref = = = -45 1.17 N +3948 2 chr1 162047 162054 no-call complex = ? ? -95 1.17 N +3949 2 chr1 162054 162103 hom ref = = = -160 1.17 N +3950 2 chr1 162103 162103 half ref ? 24 0 -160 17 1.17 N +3951 2 chr1 162103 162122 hom ref = = = -160 1.17 N +3952 2 chr1 162122 162148 no-call complex = ? ? -7 1.17 N +3953 2 chr1 162148 162167 hom ref = = = -3 1.17 N +3954 2 chr1 162167 162167 half ref ? 21 0 4 MSTD:ERVL-MaLR:18.2 17 1.17 N +3955 2 chr1 162167 162279 hom ref = = = -46 1.17 N +3956 2 chr1 162279 162349 no-call complex = ? ? -50 1.17 N +3957 2 chr1 162349 162377 hom ref = = = 22 1.17 N +3958 2 chr1 162377 162419 no-call complex = ? ? -12 1.17 N +3959 2 chr1 162419 162427 hom ref = = = 17 1.17 N +3960 2 chr1 162427 162466 no-call complex = ? ? -323 1.17 N +3961 2 chr1 162466 162488 hom ref = = = 18 1.17 N +3962 2 chr1 162488 162519 no-call complex = ? ? -44 1.17 N +3963 2 chr1 162519 162568 hom ref = = = -6 1.17 N +3964 2 chr1 162568 162575 no-call complex = ? ? -139 1.17 N +3965 2 chr1 162575 162598 hom ref = = = 15 1.17 N +3966 2 chr1 162598 162632 no-call complex = ? ? -25 1.17 N +3967 2 chr1 162632 162685 hom ref = = = 9 1.17 N +3968 2 chr1 162685 162685 half ref ? 30 0 1797 1798 12 MSTD:ERVL-MaLR:28.3 17 1.17 N +3969 2 chr1 162685 162687 hom ref = = = -50 1.17 N +3970 2 chr1 162687 162688 half ref G G ? 114 0 1797 1798 -50 MSTD:ERVL-MaLR:28.3 17 1.17 N +3971 2 chr1 162688 162788 hom ref = = = -50 1.17 N +3972 2 chr1 162788 162814 no-call complex = ? ? -123 1.17 N +3973 2 chr1 162814 162871 hom ref = = = 7 1.17 N +3974 2 chr1 162871 162897 no-call complex = ? ? -42 1.17 N +3975 2 chr1 162897 162941 hom ref = = = 10 1.17 N +3976 2 chr1 162941 162989 no-call complex = ? ? -19 1.17 N +3977 2 chr1 162989 163005 hom ref = = = 29 1.17 N +3978 2 chr1 163005 163047 no-call complex = ? ? -21 1.17 N +3979 2 chr1 163047 163059 hom ref = = = 20 1.17 N +3980 2 chr1 163059 163106 no-call complex = ? ? -6 1.17 N +3981 2 chr1 163106 163157 hom ref = = = -8 1.17 N +3982 2 chr1 163157 163158 half ref G G N 120 120 -8 17 1.17 N +3983 2 chr1 163158 163185 hom ref = = = -11 1.17 N +3984 2 chr1 163185 163192 no-call complex = ? ? -23 1.17 N +3985 2 chr1 163192 163216 hom ref = = = 13 1.17 N +3986 2 chr1 163216 163260 no-call complex = ? ? -14 1.17 N +3987 2 chr1 163260 163323 hom ref = = = 10 1.17 N +3988 2 chr1 163323 163370 no-call complex = ? ? -29 1.17 N +3989 2 chr1 163370 163406 hom ref = = = 19 1.17 N +3990 2 chr1 163406 163421 no-call complex = ? ? -80 1.17 N +3991 2 chr1 163421 163512 hom ref = = = 13 1.17 N +3992 2 chr1 163512 163524 no-call complex = ? ? -183 1.17 N +3993 2 chr1 163524 163618 hom ref = = = 0 1.17 N +3994 2 chr1 163618 163633 no-call complex = ? ? -30 1.17 N +3995 2 chr1 163633 163652 hom ref = = = 16 1.17 N +3996 2 chr1 163652 163683 no-call complex = ? ? -77 1.17 N +3997 2 chr1 163683 163708 hom ref = = = -24 1.17 N +3998 2 chr1 163708 163709 half ref G G ? 120 0 32 17 1.17 N +3999 2 chr1 163709 163777 hom ref = = = 0 1.17 N +4000 2 chr1 163777 163836 no-call complex = ? ? -70 1.17 N +4001 2 chr1 163836 163854 hom ref = = = -32 1.17 N +4002 2 chr1 163854 163855 half ref C C N 170 170 -32 AluSq2:Alu:15.3 16 1.17 N +4003 2 chr1 163855 163882 hom ref = = = -32 1.17 N +4004 2 chr1 163882 163904 no-call complex = ? ? -7 1.17 N +4005 2 chr1 163904 163957 hom ref = = = 10 1.17 N +4006 2 chr1 163957 163992 no-call complex = ? ? -36 1.17 N +4007 2 chr1 163992 164001 hom ref = = = 16 1.17 N +4008 2 chr1 164001 164034 no-call complex = ? ? -9 1.17 N +4009 2 chr1 164034 164083 hom ref = = = 13 1.17 N +4010 2 chr1 164083 164126 no-call complex = ? ? -4 1.17 N +4011 2 chr1 164126 164150 hom ref = = = 14 1.17 N +4012 2 chr1 164150 164186 no-call complex = ? ? -13 1.17 N +4013 2 chr1 164186 164218 hom ref = = = 40 1.17 N +4014 2 chr1 164218 164235 no-call complex = ? ? -75 1.17 N +4015 2 chr1 164235 164259 hom ref = = = 18 1.17 N +4016 2 chr1 164259 164299 no-call complex = ? ? -165 1.17 N +4017 2 chr1 164299 164338 hom ref = = = 22 1.17 N +4018 2 chr1 164338 164380 no-call complex = ? ? -76 1.17 N +4019 2 chr1 164380 164399 hom ref = = = 11 1.17 N +4020 2 chr1 164399 164443 no-call complex = ? ? -7 1.17 N +4021 2 chr1 164443 164530 hom ref = = = -6 1.17 N +4022 2 chr1 164530 164531 half ref A A N 75 122 -6 AluSq2:Alu:21.4 15 1.17 N +4023 2 chr1 164531 164652 hom ref = = = -6 1.17 N +4024 2 chr1 164652 164653 half ref T T N 38 109 -3 AluSq2:Alu:21.4 15 1.17 N +4025 2 chr1 164653 164668 hom ref = = = -3 1.17 N +4026 2 chr1 164668 164708 no-call complex = ? ? -7 1.17 N +4027 2 chr1 164708 164715 hom ref = = = 14 1.17 N +4028 2 chr1 164715 164755 no-call complex = ? ? -142 1.17 N +4029 2 chr1 164755 164761 hom ref = = = 26 1.17 N +4030 2 chr1 164761 164798 no-call complex = ? ? -110 1.17 N +4031 2 chr1 164798 164810 hom ref = = = 19 1.17 N +4032 2 chr1 164810 164817 no-call complex = ? ? -125 1.17 N +4033 2 chr1 164817 164868 hom ref = = = 0 1.17 N +4034 2 chr1 164868 164869 half ref C C N 40 120 1825 1826 0 15 1.17 N +4035 2 chr1 164869 164875 hom ref = = = 0 1.17 N +4036 2 chr1 164875 164876 half ref T T ? 120 0 1825 1826 22 15 1.17 N +4037 2 chr1 164876 164940 hom ref = = = -33 1.17 N +4038 2 chr1 164940 164941 half ref T T N 25 83 -33 15 1.17 N +4039 2 chr1 164941 165055 hom ref = = = -33 1.17 N +4040 2 chr1 165055 165093 no-call complex = ? ? -33 1.17 N +4041 2 chr1 165093 165127 hom ref = = = 10 1.17 N +4042 2 chr1 165127 165166 no-call complex = ? ? -16 1.17 N +4043 2 chr1 165166 165199 hom ref = = = 13 1.17 N +4044 2 chr1 165199 165234 no-call complex = ? ? -53 1.17 N +4045 2 chr1 165234 165258 hom ref = = = 23 1.17 N +4046 2 chr1 165258 165318 no-call complex = ? ? -71 1.17 N +4047 2 chr1 165318 165390 hom ref = = = -17 1.17 N +4048 2 chr1 165390 165391 half ref A A ? 63 0 -17 15 1.17 N +4049 2 chr1 165391 165442 hom ref = = = -17 1.17 N +4050 2 chr1 165442 165463 no-call complex = ? ? -13 1.17 N +4051 2 chr1 165463 165492 hom ref = = = 14 1.17 N +4052 2 chr1 165492 165522 no-call complex = ? ? -118 1.17 N +4053 2 chr1 165522 165564 hom ref = = = 19 1.17 N +4054 2 chr1 165564 165571 no-call complex = ? ? -261 1.17 N +4055 2 chr1 165571 165595 hom ref = = = 30 1.17 N +4056 2 chr1 165595 165620 no-call complex = ? ? -411 1.17 N +4057 2 chr1 165620 165690 hom ref = = = 15 1.17 N +4058 2 chr1 165690 165712 no-call complex = ? ? -12 1.17 N +4059 2 chr1 165712 165763 hom ref = = = 1 1.17 N +4060 2 chr1 165763 165764 half ref T T N 120 120 1837 1838 5 15 1.17 N +4061 2 chr1 165764 165771 hom ref = = = -3 1.17 N +4062 2 chr1 165771 165774 half ref GAC GAC NAN 30 120 1837 1838 -14 15 1.17 N +4063 2 chr1 165774 165853 hom ref = = = -14 1.17 N +4064 2 chr1 165853 165882 no-call complex = ? ? -55 1.17 N +4065 2 chr1 165882 165953 hom ref = = = 6 1.17 N +4066 2 chr1 165953 165999 no-call complex = ? ? -36 1.17 N +4067 2 chr1 165999 166007 hom ref = = = 32 1.17 N +4068 2 chr1 166007 166059 no-call complex = ? ? -102 1.17 N +4069 2 chr1 166059 166079 hom ref = = = 10 1.17 N +4070 2 chr1 166079 166082 half ref GTA GTA ? 40 0 1845 1846 0 AluSx1:Alu:12.2 15 1.17 N +4071 2 chr1 166082 166087 hom ref = = = 14 1.17 N +4072 2 chr1 166087 166088 half ref A A N 23 113 1845 1846 22 AluSx1:Alu:12.2 15 1.17 N +4073 2 chr1 166088 166091 hom ref = = = 22 1.17 N +4074 2 chr1 166091 166094 half ref GTT GTT NTN 45 30 1845 1846 -3 AluSx1:Alu:12.2 15 1.17 N +4075 2 chr1 166094 166096 hom ref = = = -9 1.17 N +4076 2 chr1 166096 166097 half ref G G N 113 53 1845 1846 -9 AluSx1:Alu:12.2 15 1.17 N +4077 2 chr1 166097 166102 hom ref = = = -9 1.17 N +4078 2 chr1 166102 166107 half ref CGAGG CGAGG ? 41 0 1845 1846 -24 AluSx1:Alu:12.2 15 1.17 N +4079 2 chr1 166107 166132 hom ref = = = -24 1.17 N +4080 2 chr1 166132 166140 no-call complex = ? ? -3 1.17 N +4081 2 chr1 166140 166219 hom ref = = = -20 1.17 N +4082 2 chr1 166219 166242 no-call complex = ? ? -118 1.17 N +4083 2 chr1 166242 166351 hom ref = = = 13 1.17 N +4084 2 chr1 166351 166394 no-call complex = ? ? -1 1.17 N +4085 2 chr1 166394 166437 hom ref = = = -4 1.17 N +4086 2 chr1 166437 166438 half ref A A N 64 129 -4 MIRb:MIR:47.0 15 1.17 N +4087 2 chr1 166438 166490 hom ref = = = -4 1.17 N +4088 2 chr1 166490 166506 no-call complex = ? ? -149 1.17 N +4089 2 chr1 166506 166516 hom ref = = = 24 1.17 N +4090 2 chr1 166516 166545 no-call complex = ? ? -108 1.17 N +4091 2 chr1 166545 166552 hom ref = = = 18 1.17 N +4092 2 chr1 166552 166568 no-call complex = ? ? -13 1.17 N +4093 2 chr1 166568 166599 hom ref = = = -21 1.17 N +4094 2 chr1 166599 166601 half ref CC CC ? 91 0 -9 15 1.17 N +4095 2 chr1 166601 166620 hom ref = = = -23 1.17 N +4096 2 chr1 166620 166621 half ref G G N 91 91 -23 15 1.17 N +4097 2 chr1 166621 166673 hom ref = = = -35 1.17 N +4098 2 chr1 166673 166673 half ref ? 86 0 1857 1858 -35 15 1.17 N +4099 2 chr1 166673 166695 hom ref = = = -35 1.17 N +4100 2 chr1 166695 166696 half ref A A N 41 111 1857 1858 -24 15 1.17 N +4101 2 chr1 166696 166802 hom ref = = = -24 1.17 N +4102 2 chr1 166802 166844 no-call complex = ? ? -71 1.17 N +4103 2 chr1 166844 166872 hom ref = = = 17 1.17 N +4104 2 chr1 166872 166922 no-call complex = ? ? -107 1.17 N +4105 2 chr1 166922 166938 hom ref = = = 5 1.17 N +4106 2 chr1 166938 166938 half ref ? 31 0 12 15 1.17 N +4107 2 chr1 166938 166955 hom ref = = = 12 1.17 N +4108 2 chr1 166955 167017 no-call complex = ? ? -386 1.17 N +4109 2 chr1 167017 167103 hom ref = = = 3 1.17 N +4110 2 chr1 167103 167111 no-call complex = ? ? -7 1.17 N +4111 2 chr1 167111 167134 hom ref = = = 17 1.17 N +4112 2 chr1 167134 167181 no-call complex = ? ? -10 1.17 N +4113 2 chr1 167181 167237 hom ref = = = 23 1.17 N +4114 2 chr1 167237 167260 no-call complex = ? ? -71 1.17 N +4115 2 chr1 167260 167284 hom ref = = = 23 1.17 N +4116 2 chr1 167284 167315 no-call complex = ? ? -2 1.17 N +4117 2 chr1 167315 167354 hom ref = = = 12 1.17 N +4118 2 chr1 167354 167390 no-call complex = ? ? -123 1.17 N +4119 2 chr1 167390 167486 hom ref = = = -26 1.17 N +4120 2 chr1 167486 167486 half ref ? 41 0 1 15 1.17 N +4121 2 chr1 167486 167569 hom ref = = = -12 1.17 N +4122 2 chr1 167569 167569 half ref ? 23 0 21 AluSg7:Alu:8.7 15 1.17 N +4123 2 chr1 167569 167617 hom ref = = = -34 1.17 N +4124 2 chr1 167617 167617 half ref ? 31 0 -32 AluSg7:Alu:8.7 15 1.17 N +4125 2 chr1 167617 167663 hom ref = = = -32 1.17 N +4126 2 chr1 167663 167671 no-call complex = ? ? -215 1.17 N +4127 2 chr1 167671 167690 hom ref = = = 16 1.17 N +4128 2 chr1 167690 167748 no-call complex = ? ? -82 1.17 N +4129 2 chr1 167748 167756 hom ref = = = 13 1.17 N +4130 2 chr1 167756 167785 no-call complex = ? ? -40 1.17 N +4131 2 chr1 167785 167862 hom ref = = = -38 1.17 N +4132 2 chr1 167862 167872 no-call complex = ? ? -6 1.17 N +4133 2 chr1 167872 167940 hom ref = = = -21 1.17 N +4134 2 chr1 167940 167941 half ref G G ? 40 0 16 14 1.17 N +4135 2 chr1 167941 168051 hom ref = = = 15 1.17 N +4136 2 chr1 168051 168069 no-call complex = ? ? -110 1.17 N +4137 2 chr1 168069 168094 hom ref = = = 13 1.17 N +4138 2 chr1 168094 168137 no-call complex = ? ? -335 1.17 N +4139 2 chr1 168137 168144 hom ref = = = 26 1.17 N +4140 2 chr1 168144 168151 no-call complex = ? ? -72 1.17 N +4141 2 chr1 168151 168222 hom ref = = = 21 1.17 N +4142 2 chr1 168222 168255 no-call complex = ? ? -79 1.17 N +4143 2 chr1 168255 168294 hom ref = = = -35 1.17 N +4144 2 chr1 168294 168294 half ref ? 29 0 -35 14 1.17 N +4145 2 chr1 168294 168344 hom ref = = = -35 1.17 N +4146 2 chr1 168344 168396 no-call complex = ? ? -33 1.17 N +4147 2 chr1 168396 168467 hom ref = = = 10 1.17 N +4148 2 chr1 168467 168507 no-call complex = ? ? 3 1.17 N +4149 2 chr1 168507 168527 hom ref = = = 16 1.17 N +4150 2 chr1 168527 168529 half ref GC GC ? 89 0 1879 1880 20 AluSx1:Alu:24.1 14 1.17 N +4151 2 chr1 168529 168539 hom ref = = = -24 1.17 N +4152 2 chr1 168539 168540 half ref G G ? 119 0 1879 1880 -24 AluSx1:Alu:24.1 14 1.17 N +4153 2 chr1 168540 168556 hom ref = = = -24 1.17 N +4154 2 chr1 168556 168613 no-call complex = ? ? -93 1.17 N +4155 2 chr1 168613 168622 hom ref = = = -24 1.17 N +4156 2 chr1 168622 168622 half ref ? 21 0 1885 1886 -24 AluSx1:Alu:24.1 14 1.17 N +4157 2 chr1 168622 168635 hom ref = = = -24 1.17 N +4158 2 chr1 168635 168640 half ref TGGCG TGGCG ? 31 0 1885 1886 -11 AluSx1:Alu:24.1 14 1.17 N +4159 2 chr1 168640 168650 hom ref = = = -11 1.17 N +4160 2 chr1 168650 168651 half ref G G N 21 80 1885 1886 1 AluSx1:Alu:24.1 14 1.17 N +4161 2 chr1 168651 168667 hom ref = = = -4 1.17 N +4162 2 chr1 168667 168670 half ref GGC GGC ? 48 0 6 AluSx1:Alu:24.1 14 1.17 N +4163 2 chr1 168670 168690 hom ref = = = 6 1.17 N +4164 2 chr1 168690 168691 half ref A A N 46 112 1887 1888 6 AluSx1:Alu:24.1 14 1.17 N +4165 2 chr1 168691 168693 hom ref = = = 6 1.17 N +4166 2 chr1 168693 168693 half ref ? 31 0 1887 1888 18 AluSx1:Alu:24.1 14 1.17 N +4167 2 chr1 168693 168696 hom ref = = = -6 1.17 N +4168 2 chr1 168696 168697 half ref G G ? 51 0 1887 1888 4 AluSx1:Alu:24.1 14 1.17 N +4169 2 chr1 168697 168706 hom ref = = = 4 1.17 N +4170 2 chr1 168706 168707 half ref A A N 58 112 1887 1888 13 AluSx1:Alu:24.1 14 1.17 N +4171 2 chr1 168707 168710 hom ref = = = 13 1.17 N +4172 2 chr1 168710 168712 half ref CA CA ? 53 0 1887 1888 14 AluSx1:Alu:24.1 14 1.17 N +4173 2 chr1 168712 168716 hom ref = = = -7 1.17 N +4174 2 chr1 168716 168717 half ref G G N 25 112 1887 1888 -7 AluSx1:Alu:24.1 14 1.17 N +4175 2 chr1 168717 168746 hom ref = = = -7 1.17 N +4176 2 chr1 168746 168778 no-call complex = ? ? -54 1.17 N +4177 2 chr1 168778 168804 hom ref = = = 13 1.17 N +4178 2 chr1 168804 168826 no-call complex = ? ? -40 1.17 N +4179 2 chr1 168826 168838 hom ref = = = 8 1.17 N +4180 2 chr1 168838 168839 half ref C C N 120 112 1893 1894 8 14 1.17 N +4181 2 chr1 168839 168845 hom ref = = = 8 1.17 N +4182 2 chr1 168845 168846 half ref A A ? 120 0 1893 1894 45 14 1.17 N +4183 2 chr1 168846 168949 hom ref = = = -14 1.17 N +4184 2 chr1 168949 168996 no-call complex = ? ? -36 1.17 N +4185 2 chr1 168996 169029 hom ref = = = 22 1.17 N +4186 2 chr1 169029 169036 no-call complex = ? ? -40 1.17 N +4187 2 chr1 169036 169055 hom ref = = = 19 1.17 N +4188 2 chr1 169055 169091 no-call complex = ? ? -185 1.17 N +4189 2 chr1 169091 169163 hom ref = = = 0 1.17 N +4190 2 chr1 169163 169208 no-call complex = ? ? -11 1.17 N +4191 2 chr1 169208 169221 hom ref = = = 17 1.17 N +4192 2 chr1 169221 169234 no-call complex = ? ? -26 1.17 N +4193 2 chr1 169234 169261 hom ref = = = 30 1.17 N +4194 2 chr1 169261 169273 no-call complex = ? ? -19 1.17 N +4195 2 chr1 169273 169360 hom ref = = = -13 1.17 N +4196 2 chr1 169360 169362 half ref AC AC ? 49 0 6 14 1.17 N +4197 2 chr1 169362 169402 hom ref = = = 1 1.17 N +4198 2 chr1 169402 169429 no-call complex = ? ? -7 1.17 N +4199 2 chr1 169429 169484 hom ref = = = 8 1.17 N +4200 2 chr1 169484 169516 no-call complex = ? ? -52 1.17 N +4201 2 chr1 169516 169577 hom ref = = = 5 1.17 N +4202 2 chr1 169577 169586 no-call complex = ? ? -156 1.17 N +4203 2 chr1 169586 169679 hom ref = = = -16 1.17 N +4204 2 chr1 169679 169679 half ref ? 23 0 -16 AluSz:Alu:13.1 15 1.17 N +4205 2 chr1 169679 169710 hom ref = = = -16 1.17 N +4206 2 chr1 169710 169743 no-call complex = ? ? -443 1.17 N +4207 2 chr1 169743 169757 hom ref = = = 4 1.17 N +4208 2 chr1 169757 169758 half ref C C N 122 122 4 15 1.17 N +4209 2 chr1 169758 169855 hom ref = = = 4 1.17 N +4210 2 chr1 169855 169894 no-call complex = ? ? -33 1.17 N +4211 2 chr1 169894 169918 hom ref = = = 11 1.17 N +4212 2 chr1 169918 169952 no-call complex = ? ? -85 1.17 N +4213 2 chr1 169952 170119 hom ref = = = -21 1.17 N +4214 2 chr1 170119 170120 half ref C C N 93 120 1911 1912 17 AluSz6:Alu:17.8 15 1.17 N +4215 2 chr1 170120 170125 hom ref = = = 8 1.17 N +4216 2 chr1 170125 170126 half ref T T N 110 120 1911 1912 8 AluSz6:Alu:17.8 15 1.17 N +4217 2 chr1 170126 170167 hom ref = = = 16 1.17 N +4218 2 chr1 170167 170211 no-call complex = ? ? -192 1.17 N +4219 2 chr1 170211 170304 hom ref = = = -44 1.17 N +4220 2 chr1 170304 170305 half ref T T N 120 120 1913 1914 -44 15 1.17 N +4221 2 chr1 170305 170309 hom ref = = = -44 1.17 N +4222 2 chr1 170309 170310 half ref C C N 43 120 1913 1914 -6 15 1.17 N +4223 2 chr1 170310 170336 hom ref = = = -6 1.17 N +4224 2 chr1 170336 170337 half ref T T N 35 120 9 15 1.17 N +4225 2 chr1 170337 170374 hom ref = = = 9 1.17 N +4226 2 chr1 170374 170393 no-call complex = ? ? -180 1.17 N +4227 2 chr1 170393 170410 hom ref = = = 11 1.17 N +4228 2 chr1 170410 170448 no-call complex = ? ? -275 1.17 N +4229 2 chr1 170448 170459 hom ref = = = 28 1.17 N +4230 2 chr1 170459 170509 no-call complex = ? ? -60 1.17 N +4231 2 chr1 170509 170524 hom ref = = = 10 1.17 N +4232 2 chr1 170524 170580 no-call complex = ? ? -35 1.17 N +4233 2 chr1 170580 170588 hom ref = = = 3 1.17 N +4234 2 chr1 170588 170589 half ref C C N 46 125 3 15 1.17 N +4235 2 chr1 170589 170626 hom ref = = = 3 1.17 N +4236 2 chr1 170626 170674 no-call complex = ? ? -37 1.17 N +4237 2 chr1 170674 170693 hom ref = = = 0 1.17 N +4238 2 chr1 170693 170695 half ref GG GG NN 120 120 1921 1922 0 15 1.17 N +4239 2 chr1 170695 170697 hom ref = = = -6 1.17 N +4240 2 chr1 170697 170698 half ref C C N 120 120 1921 1922 -6 15 1.17 N +4241 2 chr1 170698 170726 hom ref = = = 3 1.17 N +4242 2 chr1 170726 170748 no-call complex = ? ? -33 1.17 N +4243 2 chr1 170748 170763 hom ref = = = 12 1.17 N +4244 2 chr1 170763 170786 no-call complex = ? ? -29 1.17 N +4245 2 chr1 170786 170846 hom ref = = = 19 1.17 N +4246 2 chr1 170846 170853 no-call complex = ? ? -56 1.17 N +4247 2 chr1 170853 170868 hom ref = = = 14 1.17 N +4248 2 chr1 170868 170897 no-call complex = ? ? -68 1.17 N +4249 2 chr1 170897 170930 hom ref = = = 21 1.17 N +4250 2 chr1 170930 170972 no-call complex = ? ? -71 1.17 N +4251 2 chr1 170972 171050 hom ref = = = 0 1.17 N +4252 2 chr1 171050 171051 half ref T T N 120 120 0 AluSq2:Alu:13.0 15 1.17 N +4253 2 chr1 171051 171102 hom ref = = = 0 1.17 N +4254 2 chr1 171102 171134 no-call complex = ? ? -84 1.17 N +4255 2 chr1 171134 171159 hom ref = = = -11 1.17 N +4256 2 chr1 171159 171160 half ref T T N 31 120 -2 AluSq2:Alu:13.0 15 1.17 N +4257 2 chr1 171160 171174 hom ref = = = -2 1.17 N +4258 2 chr1 171174 171222 no-call complex = ? ? -58 1.17 N +4259 2 chr1 171222 171235 hom ref = = = 22 1.17 N +4260 2 chr1 171235 171242 no-call complex = ? ? 0 1.17 N +4261 2 chr1 171242 171418 hom ref = = = 8 1.17 N +4262 2 chr1 171418 171419 half ref A A N 47 120 4 14 1.17 N +4263 2 chr1 171419 171510 hom ref = = = 4 1.17 N +4264 2 chr1 171510 171577 no-call complex = ? ? -27 1.17 N +4265 2 chr1 171577 171584 hom ref = = = 11 1.17 N +4266 2 chr1 171584 171591 no-call complex = ? ? -57 1.17 N +4267 2 chr1 171591 171719 hom ref = = = -5 1.17 N +4268 2 chr1 171719 171726 no-call complex = ? ? -98 1.17 N +4269 2 chr1 171726 171773 hom ref = = = 18 1.17 N +4270 2 chr1 171773 171794 no-call complex = ? ? -18 1.17 N +4271 2 chr1 171794 171830 hom ref = = = 10 1.17 N +4272 2 chr1 171830 171851 no-call complex = ? ? -58 1.17 N +4273 2 chr1 171851 172068 hom ref = = = -44 1.17 N +4274 2 chr1 172068 172075 no-call complex = ? ? -48 1.17 N +4275 2 chr1 172075 172091 hom ref = = = 14 1.17 N +4276 2 chr1 172091 172139 no-call complex = ? ? -66 1.17 N +4277 2 chr1 172139 172198 hom ref = = = 10 1.17 N +4278 2 chr1 172198 172230 no-call complex = ? ? -56 1.17 N +4279 2 chr1 172230 172373 hom ref = = = -20 1.17 N +4280 2 chr1 172373 172393 no-call complex = ? ? -45 1.17 N +4281 2 chr1 172393 172497 hom ref = = = 5 1.17 N +4282 2 chr1 172497 172499 half ref GC GC NN 46 120 5 14 1.17 N +4283 2 chr1 172499 172516 hom ref = = = 17 1.17 N +4284 2 chr1 172516 172548 no-call complex = ? ? -7 1.17 N +4285 2 chr1 172548 172557 hom ref = = = 15 1.17 N +4286 2 chr1 172557 172609 no-call complex = ? ? -29 1.17 N +4287 2 chr1 172609 172628 hom ref = = = 12 1.17 N +4288 2 chr1 172628 172636 no-call complex = ? ? -22 1.17 N +4289 2 chr1 172636 172704 hom ref = = = 4 1.17 N +4290 2 chr1 172704 172711 no-call complex = ? ? -159 1.17 N +4291 2 chr1 172711 172857 hom ref = = = -24 1.17 N +4292 2 chr1 172857 172880 no-call complex = ? ? -61 1.17 N +4293 2 chr1 172880 172931 hom ref = = = 9 1.17 N +4294 2 chr1 172931 172954 no-call complex = ? ? -61 1.17 N +4295 2 chr1 172954 172966 hom ref = = = 16 1.17 N +4296 2 chr1 172966 172995 no-call complex = ? ? -221 1.17 N +4297 2 chr1 172995 173043 hom ref = = = -10 1.17 N +4298 2 chr1 173043 173061 no-call complex = ? ? -19 1.17 N +4299 2 chr1 173061 173069 hom ref = = = 20 1.17 N +4300 2 chr1 173069 173102 no-call complex = ? ? -47 1.17 N +4301 2 chr1 173102 173123 hom ref = = = 20 1.17 N +4302 2 chr1 173123 173138 no-call complex = ? ? -135 1.17 N +4303 2 chr1 173138 173149 hom ref = = = 10 1.17 N +4304 2 chr1 173149 173218 no-call complex = ? ? -73 1.17 N +4305 2 chr1 173218 173241 hom ref = = = 5 1.17 N +4306 2 chr1 173241 173243 half ref CA CA ? 75 0 1955 1956 17 14 1.17 N +4307 2 chr1 173243 173253 hom ref = = = -12 1.17 N +4308 2 chr1 173253 173253 half ref ? 20 0 1955 1956 -12 14 1.17 N +4309 2 chr1 173253 173302 hom ref = = = -12 1.17 N +4310 2 chr1 173302 173350 no-call complex = ? ? -56 1.17 N +4311 2 chr1 173350 173396 hom ref = = = 14 1.17 N +4312 2 chr1 173396 173430 no-call complex = ? ? -29 1.17 N +4313 2 chr1 173430 173442 hom ref = = = 12 1.17 N +4314 2 chr1 173442 173470 no-call complex = ? ? -1 1.17 N +4315 2 chr1 173470 173512 hom ref = = = 17 1.17 N +4316 2 chr1 173512 173549 no-call complex = ? ? -10 1.17 N +4317 2 chr1 173549 173581 hom ref = = = 10 1.17 N +4318 2 chr1 173581 173606 no-call complex = ? ? -168 1.17 N +4319 2 chr1 173606 173633 hom ref = = = 13 1.17 N +4320 2 chr1 173633 173656 no-call complex = ? ? -368 1.17 N +4321 2 chr1 173656 173679 hom ref = = = 20 1.17 N +4322 2 chr1 173679 173686 no-call complex = ? ? -1 1.17 N +4323 2 chr1 173686 173697 hom ref = = = 11 1.17 N +4324 2 chr1 173697 173745 no-call complex = ? ? -296 1.17 N +4325 2 chr1 173745 173772 hom ref = = = 19 1.17 N +4326 2 chr1 173772 173796 no-call complex = ? ? -129 1.17 N +4327 2 chr1 173796 173837 hom ref = = = 18 1.17 N +4328 2 chr1 173837 173867 no-call complex = ? ? -10 1.17 N +4329 2 chr1 173867 173988 hom ref = = = 1 1.17 N +4330 2 chr1 173988 173995 no-call complex = ? ? -68 1.17 N +4331 2 chr1 173995 174057 hom ref = = = 4 1.17 N +4332 2 chr1 174057 174058 half ref G G N 120 120 6 15 1.17 N +4333 2 chr1 174058 174188 hom ref = = = -22 1.17 N +4334 2 chr1 174188 174226 no-call complex = ? ? -78 1.17 N +4335 2 chr1 174226 174237 hom ref = = = -13 1.17 N +4336 2 chr1 174237 174238 half ref G G N 121 121 -13 15 1.17 N +4337 2 chr1 174238 174376 hom ref = = = -18 1.17 N +4338 2 chr1 174376 174409 no-call complex = ? ? -44 1.17 N +4339 2 chr1 174409 174423 hom ref = = = 10 1.17 N +4340 2 chr1 174423 174465 no-call complex = ? ? -30 1.17 N +4341 2 chr1 174465 174497 hom ref = = = 20 1.17 N +4342 2 chr1 174497 174540 no-call complex = ? ? -48 1.17 N +4343 2 chr1 174540 174557 hom ref = = = 18 1.17 N +4344 2 chr1 174557 174591 no-call complex = ? ? -38 1.17 N +4345 2 chr1 174591 174615 hom ref = = = 13 1.17 N +4346 2 chr1 174615 174632 no-call complex = ? ? -19 1.17 N +4347 2 chr1 174632 174687 hom ref = = = 20 1.17 N +4348 2 chr1 174687 174727 no-call complex = ? ? -20 1.17 N +4349 2 chr1 174727 174756 hom ref = = = 11 1.17 N +4350 2 chr1 174756 174790 no-call complex = ? ? -71 1.17 N +4351 2 chr1 174790 174795 hom ref = = = 10 1.17 N +4352 2 chr1 174795 174817 no-call complex = ? ? -16 1.17 N +4353 2 chr1 174817 174839 hom ref = = = 10 1.17 N +4354 2 chr1 174839 174867 no-call complex = ? ? -74 1.17 N +4355 2 chr1 174867 174897 hom ref = = = 13 1.17 N +4356 2 chr1 174897 174977 no-call complex = ? ? -34 1.17 N +4357 2 chr1 174977 175039 hom ref = = = 10 1.17 N +4358 2 chr1 175039 175076 no-call complex = ? ? -236 1.17 N +4359 2 chr1 175076 175185 hom ref = = = -5 1.17 N +4360 2 chr1 175185 175186 half ref G G ? 121 0 3 AluSx:Alu:10.2 13 1.17 N +4361 2 chr1 175186 175200 hom ref = = = 15 1.17 N +4362 2 chr1 175200 175237 no-call complex = ? ? -64 1.17 N +4363 2 chr1 175237 175243 hom ref = = = 11 1.17 N +4364 2 chr1 175243 175248 half ref TCGAG TCGAG NCNAN 22 49 -8 AluSx:Alu:10.2 13 1.17 N +4365 2 chr1 175248 175311 hom ref = = = -8 1.17 N +4366 2 chr1 175311 175352 no-call complex = ? ? -247 1.17 N +4367 2 chr1 175352 175369 hom ref = = = 11 1.17 N +4368 2 chr1 175369 175412 no-call complex = ? ? -42 1.17 N +4369 2 chr1 175412 175427 hom ref = = = 20 1.17 N +4370 2 chr1 175427 175462 no-call complex = ? ? -105 1.17 N +4371 2 chr1 175462 175524 hom ref = = = 16 1.17 N +4372 2 chr1 175524 175531 no-call complex = ? ? -192 1.17 N +4373 2 chr1 175531 175606 hom ref = = = -8 1.17 N +4374 2 chr1 175606 175606 half ref ? 30 0 -8 AluSp:Alu:11.9 13 1.17 N +4375 2 chr1 175606 175633 hom ref = = = -8 1.17 N +4376 2 chr1 175633 175667 no-call complex = ? ? -28 1.17 N +4377 2 chr1 175667 175727 hom ref = = = -26 1.17 N +4378 2 chr1 175727 175728 half ref G G N 25 89 1991 1992 -26 AluSp:Alu:11.9 14 1.17 N +4379 2 chr1 175728 175730 hom ref = = = -26 1.17 N +4380 2 chr1 175730 175731 half ref T T N 89 89 1991 1992 -10 AluSp:Alu:11.9 14 1.17 N +4381 2 chr1 175731 175779 hom ref = = = -10 1.17 N +4382 2 chr1 175779 175817 no-call complex = ? ? -30 1.17 N +4383 2 chr1 175817 175838 hom ref = = = 10 1.17 N +4384 2 chr1 175838 175845 no-call complex = ? ? -124 1.17 N +4385 2 chr1 175845 175919 hom ref = = = 10 1.17 N +4386 2 chr1 175919 175973 no-call complex = ? ? -30 1.17 N +4387 2 chr1 175973 176036 hom ref = = = 6 1.17 N +4388 2 chr1 176036 176042 half ref AATATA AATATA ? 36 0 3 AluSx:Alu:15.8 14 1.17 N +4389 2 chr1 176042 176058 hom ref = = = 12 1.17 N +4390 2 chr1 176058 176086 no-call complex = ? ? -59 1.17 N +4391 2 chr1 176086 176091 hom ref = = = 13 1.17 N +4392 2 chr1 176091 176117 no-call complex = ? ? -19 1.17 N +4393 2 chr1 176117 176128 hom ref = = = 11 1.17 N +4394 2 chr1 176128 176160 no-call complex = ? ? -31 1.17 N +4395 2 chr1 176160 176181 hom ref = = = 18 1.17 N +4396 2 chr1 176181 176188 no-call complex = ? ? -23 1.17 N +4397 2 chr1 176188 176198 hom ref = = = 18 1.17 N +4398 2 chr1 176198 176250 no-call complex = ? ? -132 1.17 N +4399 2 chr1 176250 176265 hom ref = = = 26 1.17 N +4400 2 chr1 176265 176335 no-call complex = ? ? -114 1.17 N +4401 2 chr1 176335 176344 hom ref = = = 9 1.17 N +4402 2 chr1 176344 176346 half ref AA AA ? 25 0 9 14 1.17 N +4403 2 chr1 176346 176365 hom ref = = = 14 1.17 N +4404 2 chr1 176365 176400 no-call complex = ? ? -58 1.17 N +4405 2 chr1 176400 176407 hom ref = = = 22 1.17 N +4406 2 chr1 176407 176448 no-call complex = ? ? -464 1.17 N +4407 2 chr1 176448 176537 hom ref = = = 9 1.17 N +4408 2 chr1 176537 176548 no-call complex = ? ? -376 1.17 N +4409 2 chr1 176548 176645 hom ref = = = 13 1.17 N +4410 2 chr1 176645 176697 no-call complex = ? ? -112 1.17 N +4411 2 chr1 176697 176707 hom ref = = = 15 1.17 N +4412 2 chr1 176707 176743 no-call complex = ? ? -76 1.17 N +4413 2 chr1 176743 176761 hom ref = = = 14 1.17 N +4414 2 chr1 176761 176768 no-call complex = ? ? -18 1.17 N +4415 2 chr1 176768 176773 hom ref = = = 21 1.17 N +4416 2 chr1 176773 176813 no-call complex = ? ? -66 1.17 N +4417 2 chr1 176813 176863 hom ref = = = -25 1.17 N +4418 2 chr1 176863 176863 half ref ? 24 0 2007 2008 -25 7 1.17 N +4419 2 chr1 176863 176882 hom ref = = = -25 1.17 N +4420 2 chr1 176882 176882 half ref ? 23 0 2007 2008 8 7 1.17 N +4421 2 chr1 176882 176928 hom ref = = = 4 1.17 N +4422 2 chr1 176928 176949 no-call complex = ? ? -432 1.17 N +4423 2 chr1 176949 176976 hom ref = = = 11 1.17 N +4424 2 chr1 176976 177007 no-call complex = ? ? -202 1.17 N +4425 2 chr1 177007 177083 hom ref = = = 15 1.17 N +4426 2 chr1 177083 177111 no-call complex = ? ? -222 1.17 N +4427 2 chr1 177111 177129 hom ref = = = 16 1.17 N +4428 2 chr1 177129 177173 no-call complex = ? ? -113 1.17 N +4429 2 chr1 177173 177192 hom ref = = = 7 1.17 N +4430 2 chr1 177192 177193 half ref A A N 26 115 2013 2014 7 7 1.17 N +4431 2 chr1 177193 177198 hom ref = = = 1 1.17 N +4432 2 chr1 177198 177199 half ref A A N 115 115 2013 2014 1 7 1.17 N +4433 2 chr1 177199 177231 hom ref = = = 9 1.17 N +4434 2 chr1 177231 177280 no-call complex = ? ? -4 1.17 N +4435 2 chr1 177280 177288 hom ref = = = 17 1.17 N +4436 2 chr1 177288 177334 no-call complex = ? ? -59 1.17 N +4437 2 chr1 177334 177360 hom ref = = = 11 1.17 N +4438 2 chr1 177360 177365 half ref AAGAT AAGAT ? 28 0 17 7 1.17 N +4439 2 chr1 177365 177381 hom ref = = = 15 1.17 N +4440 2 chr1 177381 177417 no-call complex = ? ? -20 1.17 N +4441 2 chr1 177417 227417 no-call complex = ? ? -2 +4442 2 chr1 227417 227435 no-call complex = ? ? -12 1.17 N +4443 2 chr1 227435 227460 hom ref = = = -16 1.17 N +4444 2 chr1 227460 227461 half ref C C N 45 121 2023 2024 -16 MLT2B3:ERVL:25.0 9 1.17 N +4445 2 chr1 227461 227466 hom ref = = = -15 1.17 N +4446 2 chr1 227466 227468 half ref GA GA NN 44 121 2023 2024 -15 MLT2B3:ERVL:25.0 9 1.17 N +4447 2 chr1 227468 227489 hom ref = = = -6 1.17 N +4448 2 chr1 227489 227533 no-call complex = ? ? -154 1.17 N +4449 2 chr1 227533 227538 hom ref = = = 16 1.17 N +4450 2 chr1 227538 227604 no-call complex = ? ? -47 1.17 N +4451 2 chr1 227604 227610 hom ref = = = 17 1.17 N +4452 2 chr1 227610 227690 no-call complex = ? ? -27 1.17 N +4453 2 chr1 227690 227733 hom ref = = = 21 1.17 N +4454 2 chr1 227733 227784 no-call complex = ? ? -81 1.17 N +4455 2 chr1 227784 227840 hom ref = = = -1 1.17 N +4456 2 chr1 227840 227860 no-call complex = ? ? -7 1.17 N +4457 2 chr1 227860 227883 hom ref = = = 19 1.17 N +4458 2 chr1 227883 227937 no-call complex = ? ? -77 1.17 N +4459 2 chr1 227937 227952 hom ref = = = 14 1.17 N +4460 2 chr1 227952 227983 no-call complex = ? ? -14 1.17 N +4461 2 chr1 227983 228092 hom ref = = = 5 1.17 N +4462 2 chr1 228092 228116 no-call complex = ? ? -41 1.17 N +4463 2 chr1 228116 228177 hom ref = = = -6 1.17 N +4464 2 chr1 228177 228195 no-call complex = ? ? -82 1.17 N +4465 2 chr1 228195 228215 hom ref = = = 11 1.17 N +4466 2 chr1 228215 228231 no-call complex = ? ? -88 1.17 N +4467 2 chr1 228231 228239 hom ref = = = 24 1.17 N +4468 2 chr1 228239 228276 no-call complex = ? ? -6 1.17 N +4469 2 chr1 228276 228311 hom ref = = = 14 1.17 N +4470 2 chr1 228311 228342 no-call complex = ? ? -13 1.17 N +4471 2 chr1 228342 228414 hom ref = = = 32 1.17 N +4472 2 chr1 228414 228421 no-call complex = ? ? -62 1.17 N +4473 2 chr1 228421 228459 hom ref = = = 20 1.17 N +4474 2 chr1 228459 228471 no-call complex = ? ? -40 1.17 N +4475 2 chr1 228471 228490 hom ref = = = 12 1.17 N +4476 2 chr1 228490 228512 no-call complex = ? ? -98 1.17 N +4477 2 chr1 228512 228527 hom ref = = = 13 1.17 N +4478 2 chr1 228527 228542 no-call complex = ? ? -107 1.17 N +4479 2 chr1 228542 228589 hom ref = = = 12 1.17 N +4480 2 chr1 228589 228622 no-call complex = ? ? -264 1.17 N +4481 2 chr1 228622 228643 hom ref = = = 15 1.17 N +4482 2 chr1 228643 228687 no-call complex = ? ? -56 1.17 N +4483 2 chr1 228687 228704 hom ref = = = 37 1.17 N +4484 2 chr1 228704 228766 no-call complex = ? ? -38 1.17 N +4485 2 chr1 228766 228785 hom ref = = = 12 1.17 N +4486 2 chr1 228785 228792 no-call complex = ? ? -34 1.17 N +4487 2 chr1 228792 228855 hom ref = = = 12 1.17 N +4488 2 chr1 228855 228880 no-call complex = ? ? 5 1.17 N +4489 2 chr1 228880 228891 hom ref = = = 24 1.17 N +4490 2 chr1 228891 228928 no-call complex = ? ? -70 1.17 N +4491 2 chr1 228928 229016 hom ref = = = 10 1.17 N +4492 2 chr1 229016 229049 no-call complex = ? ? -79 1.17 N +4493 2 chr1 229049 229070 hom ref = = = 19 1.17 N +4494 2 chr1 229070 229100 no-call complex = ? ? -20 1.17 N +4495 2 chr1 229100 229135 hom ref = = = 13 1.17 N +4496 2 chr1 229135 229142 no-call complex = ? ? -3 1.17 N +4497 2 chr1 229142 229180 hom ref = = = 33 1.17 N +4498 2 chr1 229180 229213 no-call complex = ? ? -63 1.17 N +4499 2 chr1 229213 229223 hom ref = = = 20 1.17 N +4500 2 chr1 229223 229253 no-call complex = ? ? -24 1.17 N +4501 2 chr1 229253 229268 hom ref = = = 10 1.17 N +4502 2 chr1 229268 229308 no-call complex = ? ? -36 1.17 N +4503 2 chr1 229308 229327 hom ref = = = 11 1.17 N +4504 2 chr1 229327 229362 no-call complex = ? ? -17 1.17 N +4505 2 chr1 229362 229385 hom ref = = = -1 1.17 N +4506 2 chr1 229385 229386 half ref G G N 140 140 -1 MER31-int:ERV1:33.3 14 1.17 N +4507 2 chr1 229386 229409 hom ref = = = -22 1.17 N +4508 2 chr1 229409 229411 half ref TA TA ? 30 0 2065 2066 -22 MER31-int:ERV1:33.3 14 1.17 N +4509 2 chr1 229411 229418 hom ref = = = 5 1.17 N +4510 2 chr1 229418 229421 half ref AGA AGA NGN 31 97 2065 2066 8 MER31-int:ERV1:33.3 14 1.17 N +4511 2 chr1 229421 229424 hom ref = = = 7 1.17 N +4512 2 chr1 229424 229425 half ref T T N 121 121 2065 2066 11 MER31-int:ERV1:33.3 14 1.17 N +4513 2 chr1 229425 229455 hom ref = = = -75 1.17 N +4514 2 chr1 229455 229456 half ref C C N 61 167 -75 MER31-int:ERV1:33.3 14 1.17 N +4515 2 chr1 229456 229475 hom ref = = = -75 1.17 N +4516 2 chr1 229475 229512 no-call complex = ? ? -66 1.17 N +4517 2 chr1 229512 229553 hom ref = = = 15 1.17 N +4518 2 chr1 229553 229580 no-call complex = ? ? -41 1.17 N +4519 2 chr1 229580 229647 hom ref = = = 12 1.17 N +4520 2 chr1 229647 229708 no-call complex = ? ? -121 1.17 N +4521 2 chr1 229708 229760 hom ref = = = -26 1.17 N +4522 2 chr1 229760 229761 half ref C C N 120 120 28 AluY:Alu:10.4 14 1.17 N +4523 2 chr1 229761 229784 hom ref = = = 9 1.17 N +4524 2 chr1 229784 229829 no-call complex = ? ? -66 1.17 N +4525 2 chr1 229829 230035 hom ref = = = -10 1.17 N +4526 2 chr1 230035 230079 no-call complex = ? ? -28 1.17 N +4527 2 chr1 230079 230110 hom ref = = = -35 1.17 N +4528 2 chr1 230110 230111 half ref G G N 120 120 -35 MER31-int:ERV1:27.1 19 1.17 N +4529 2 chr1 230111 230217 hom ref = = = -35 1.17 N +4530 2 chr1 230217 230253 no-call complex = ? ? -150 1.17 N +4531 2 chr1 230253 230297 hom ref = = = 33 1.17 N +4532 2 chr1 230297 230323 no-call complex = ? ? -139 1.17 N +4533 2 chr1 230323 230428 hom ref = = = 11 1.17 N +4534 2 chr1 230428 230466 no-call complex = ? ? -6 1.17 N +4535 2 chr1 230466 230493 hom ref = = = 12 1.17 N +4536 2 chr1 230493 230517 no-call complex = ? ? -78 1.17 N +4537 2 chr1 230517 230522 hom ref = = = 22 1.17 N +4538 2 chr1 230522 230571 no-call complex = ? ? -57 1.17 N +4539 2 chr1 230571 230624 hom ref = = = -36 1.17 N +4540 2 chr1 230624 230625 half ref A A N 39 110 -36 L1MC3:L1:42.1 19 1.17 N +4541 2 chr1 230625 230639 hom ref = = = -36 1.17 N +4542 2 chr1 230639 230679 no-call complex = ? ? -35 1.17 N +4543 2 chr1 230679 230757 hom ref = = = -16 1.17 N +4544 2 chr1 230757 230758 half ref A A N 20 80 -16 MSTB1:ERVL-MaLR:28.6 19 1.17 N +4545 2 chr1 230758 230766 hom ref = = = -16 1.17 N +4546 2 chr1 230766 230864 no-call complex = ? ? -271 1.17 N +4547 2 chr1 230864 230874 hom ref = = = 13 1.17 N +4548 2 chr1 230874 230897 no-call complex = ? ? 5 1.17 N +4549 2 chr1 230897 230909 hom ref = = = 25 1.17 N +4550 2 chr1 230909 230953 no-call complex = ? ? -117 1.17 N +4551 2 chr1 230953 230968 hom ref = = = 21 1.17 N +4552 2 chr1 230968 230983 no-call complex = ? ? -215 1.17 N +4553 2 chr1 230983 230989 hom ref = = = 10 1.17 N +4554 2 chr1 230989 231036 no-call complex = ? ? -61 1.17 N +4555 2 chr1 231036 231042 hom ref = = = 57 1.17 N +4556 2 chr1 231042 231073 no-call complex = ? ? -155 1.17 N +4557 2 chr1 231073 231087 hom ref = = = 21 1.17 N +4558 2 chr1 231087 231094 no-call complex = ? ? -136 1.17 N +4559 2 chr1 231094 231119 hom ref = = = 21 1.17 N +4560 2 chr1 231119 231160 no-call complex = ? ? -183 1.17 N +4561 2 chr1 231160 231171 hom ref = = = 40 1.17 N +4562 2 chr1 231171 231178 no-call complex = ? ? -74 1.17 N +4563 2 chr1 231178 231201 hom ref = = = 30 1.17 N +4564 2 chr1 231201 231232 no-call complex = ? ? -173 1.17 N +4565 2 chr1 231232 231242 hom ref = = = 38 1.17 N +4566 2 chr1 231242 231250 no-call complex = ? ? -407 1.17 N +4567 2 chr1 231250 231303 hom ref = = = 19 1.17 N +4568 2 chr1 231303 231329 no-call complex = ? ? -114 1.17 N +4569 2 chr1 231329 231361 hom ref = = = 8 1.17 N +4570 2 chr1 231361 231397 no-call complex = ? ? -77 1.17 N +4571 2 chr1 231397 231500 hom ref = = = -23 1.17 N +4572 2 chr1 231500 231507 no-call complex = ? ? -143 1.17 N +4573 2 chr1 231507 231560 hom ref = = = 27 1.17 N +4574 2 chr1 231560 231581 no-call complex = ? ? -8 1.17 N +4575 2 chr1 231581 231671 hom ref = = = 15 1.17 N +4576 2 chr1 231671 231694 no-call complex = ? ? -56 1.17 N +4577 2 chr1 231694 231781 hom ref = = = 1 1.17 N +4578 2 chr1 231781 231782 half ref A A N 169 169 1 L1MC3:L1:42.1 18 1.17 N +4579 2 chr1 231782 231813 hom ref = = = 1 1.17 N +4580 2 chr1 231813 231848 no-call complex = ? ? -99 1.17 N +4581 2 chr1 231848 231936 hom ref = = = 12 1.17 N +4582 2 chr1 231936 231977 no-call complex = ? ? -110 1.17 N +4583 2 chr1 231977 232048 hom ref = = = 20 1.17 N +4584 2 chr1 232048 232055 no-call complex = ? ? -56 1.17 N +4585 2 chr1 232055 232164 hom ref = = = 0 1.17 N +4586 2 chr1 232164 232171 no-call complex = ? ? -27 1.17 N +4587 2 chr1 232171 232204 hom ref = = = 16 1.17 N +4588 2 chr1 232204 232227 no-call complex = ? ? -117 1.17 N +4589 2 chr1 232227 232430 hom ref = = = -43 1.17 N +4590 2 chr1 232430 232475 no-call complex = ? ? -34 1.17 N +4591 2 chr1 232475 232521 hom ref = = = 22 1.17 N +4592 2 chr1 232521 232545 no-call complex = ? ? -46 1.17 N +4593 2 chr1 232545 232652 hom ref = = = -16 1.17 N +4594 2 chr1 232652 232685 no-call complex = ? ? -40 1.17 N +4595 2 chr1 232685 232782 hom ref = = = -2 1.17 N +4596 2 chr1 232782 232823 no-call complex = ? ? -30 1.17 N +4597 2 chr1 232823 232876 hom ref = = = -13 1.17 N +4598 2 chr1 232876 232879 half ref CAA CAA NAN 120 120 18 20 1.17 N +4599 2 chr1 232879 232956 hom ref = = = 4 1.17 N +4600 2 chr1 232956 232993 no-call complex = ? ? -37 1.17 N +4601 2 chr1 232993 233000 hom ref = = = 47 1.17 N +4602 2 chr1 233000 233007 no-call complex = ? ? -138 1.17 N +4603 2 chr1 233007 233052 hom ref = = = 11 1.17 N +4604 2 chr1 233052 233089 no-call complex = ? ? -120 1.17 N +4605 2 chr1 233089 233217 hom ref = = = 15 1.17 N +4606 2 chr1 233217 233224 no-call complex = ? ? 4 1.17 N +4607 2 chr1 233224 233351 hom ref = = = -28 1.17 N +4608 2 chr1 233351 233352 half ref T T N 72 120 -21 21 1.17 N +4609 2 chr1 233352 233390 hom ref = = = -21 1.17 N +4610 2 chr1 233390 233408 no-call complex = ? ? -65 1.17 N +4611 2 chr1 233408 233472 hom ref = = = -154 1.17 N +4612 2 chr1 233472 233473 het-ref snp C G C 118 118 dbsnp.130:rs66974659 1522 21 42 0 63 -154 MER4A1:ERV1:18.8 21 1.17 N +4613 2 chr1 233473 233511 hom ref = = = -154 1.17 N +4614 2 chr1 233511 233557 no-call complex = ? ? -72 1.17 N +4615 2 chr1 233557 233617 hom ref = = = 12 1.17 N +4616 2 chr1 233617 233662 no-call complex = ? ? -74 1.17 N +4617 2 chr1 233662 233680 hom ref = = = 17 1.17 N +4618 2 chr1 233680 233704 no-call complex = ? ? -316 1.17 N +4619 2 chr1 233704 233752 hom ref = = = 10 1.17 N +4620 2 chr1 233752 233785 no-call complex = ? ? -101 1.17 N +4621 2 chr1 233785 233805 hom ref = = = 23 1.17 N +4622 2 chr1 233805 233847 no-call complex = ? ? -54 1.17 N +4623 2 chr1 233847 234020 hom ref = = = -18 1.17 N +4624 2 chr1 234020 234038 no-call complex = ? ? -18 1.17 N +4625 2 chr1 234038 234077 hom ref = = = 36 1.17 N +4626 2 chr1 234077 234101 no-call complex = ? ? -11 1.17 N +4627 2 chr1 234101 234146 hom ref = = = 11 1.17 N +4628 2 chr1 234146 234147 half ref C C N 120 120 2109 2110 11 20 1.17 N +4629 2 chr1 234147 234158 hom ref = = = -24 1.17 N +4630 2 chr1 234158 234159 half ref A A N 120 120 2109 2110 -24 20 1.17 N +4631 2 chr1 234159 234187 hom ref = = = -43 1.17 N +4632 2 chr1 234187 234188 half ref T T N 117 120 -43 19 1.17 N +4633 2 chr1 234188 234205 hom ref = = = -43 1.17 N +4634 2 chr1 234205 234205 half ref ? 50 0 15 19 1.17 N +4635 2 chr1 234205 234366 hom ref = = = -10 1.17 N +4636 2 chr1 234366 234373 no-call complex = ? ? -35 1.17 N +4637 2 chr1 234373 234442 hom ref = = = 29 1.17 N +4638 2 chr1 234442 234484 no-call complex = ? ? -216 1.17 N +4639 2 chr1 234484 234538 hom ref = = = 22 1.17 N +4640 2 chr1 234538 234578 no-call complex = ? ? -172 1.17 N +4641 2 chr1 234578 234591 hom ref = = = 58 1.17 N +4642 2 chr1 234591 234615 no-call complex = ? ? -8 1.17 N +4643 2 chr1 234615 234709 hom ref = = = -36 1.17 N +4644 2 chr1 234709 234716 no-call complex = ? ? -34 1.17 N +4645 2 chr1 234716 234756 hom ref = = = 35 1.17 N +4646 2 chr1 234756 234763 no-call complex = ? ? -50 1.17 N +4647 2 chr1 234763 235017 hom ref = = = -38 1.17 N +4648 2 chr1 235017 235066 no-call complex = ? ? -73 1.17 N +4649 2 chr1 235066 235088 hom ref = = = -47 1.17 N +4650 2 chr1 235088 235088 half ref ? 108 0 -47 MLT1I:ERVL-MaLR:40.6 17 1.17 N +4651 2 chr1 235088 235157 hom ref = = = -47 1.17 N +4652 2 chr1 235157 235183 no-call complex = ? ? -326 1.17 N +4653 2 chr1 235183 235199 hom ref = = = 45 1.17 N +4654 2 chr1 235199 235217 no-call complex = ? ? -22 1.17 N +4655 2 chr1 235217 235420 hom ref = = = -40 1.17 N +4656 2 chr1 235420 235428 no-call complex = ? ? -115 1.17 N +4657 2 chr1 235428 235840 hom ref = = = 11 1.17 N +4658 2 chr1 235840 235847 no-call complex = ? ? -418 1.17 N +4659 2 chr1 235847 235916 hom ref = = = 38 1.17 N +4660 2 chr1 235916 235932 no-call complex = ? ? -174 1.17 N +4661 2 chr1 235932 235972 hom ref = = = 38 1.17 N +4662 2 chr1 235972 235979 no-call complex = ? ? -172 1.17 N +4663 2 chr1 235979 236256 hom ref = = = -31 1.17 N +4664 2 chr1 236256 236289 no-call complex = ? ? -55 1.17 N +4665 2 chr1 236289 236302 hom ref = = = 56 1.17 N +4666 2 chr1 236302 236309 no-call complex = ? ? -126 1.17 N +4667 2 chr1 236309 236484 hom ref = = = -11 1.17 N +4668 2 chr1 236484 236485 half ref C C N 122 122 -11 MLT1H2:ERVL-MaLR:28.7 7 1.17 N +4669 2 chr1 236485 236633 hom ref = = = -11 1.17 N +4670 2 chr1 236633 236673 no-call complex = ? ? -267 1.17 N +4671 2 chr1 236673 236684 hom ref = = = 10 1.17 N +4672 2 chr1 236684 236715 no-call complex = ? ? -151 1.17 N +4673 2 chr1 236715 236726 hom ref = = = 16 1.17 N +4674 2 chr1 236726 236729 half ref GTT GTT ? 33 0 2121 2122 4 7 1.17 N +4675 2 chr1 236729 236733 hom ref = = = -4 1.17 N +4676 2 chr1 236733 236734 half ref T T ? 123 0 2121 2122 -4 7 1.17 N +4677 2 chr1 236734 236782 hom ref = = = -4 1.17 N +4678 2 chr1 236782 236796 no-call complex = ? ? -228 1.17 N +4679 2 chr1 236796 236844 hom ref = = = 32 1.17 N +4680 2 chr1 236844 236851 no-call complex = ? ? -261 1.17 N +4681 2 chr1 236851 236887 hom ref = = = 43 1.17 N +4682 2 chr1 236887 236894 no-call complex = ? ? -86 1.17 N +4683 2 chr1 236894 237219 hom ref = = = 2 1.17 N +4684 2 chr1 237219 237226 no-call complex = ? ? -104 1.17 N +4685 2 chr1 237226 237268 hom ref = = = 61 1.17 N +4686 2 chr1 237268 237305 no-call complex = ? ? -252 1.17 N +4687 2 chr1 237305 237362 hom ref = = = 16 1.17 N +4688 2 chr1 237362 237369 no-call complex = ? ? -46 1.17 N +4689 2 chr1 237369 237422 hom ref = = = -28 1.17 N +4690 2 chr1 237422 237423 half ref T T N 76 126 -28 AluY:Alu:9.1 7 1.17 N +4691 2 chr1 237423 237486 hom ref = = = -28 1.17 N +4692 2 chr1 237486 237493 no-call complex = ? ? -114 1.17 N +4693 2 chr1 237493 237524 hom ref = = = 57 1.17 N +4694 2 chr1 237524 237567 no-call complex = ? ? -52 1.17 N +4695 2 chr1 237567 237801 hom ref = = = 10 1.17 N +4696 2 chr1 237801 237808 no-call complex = ? ? -24 1.17 N +4697 2 chr1 237808 237842 hom ref = = = 19 1.17 N +4698 2 chr1 237842 237884 no-call complex = ? ? -17 1.17 N +4699 2 chr1 237884 237944 hom ref = = = 28 1.17 N +4700 2 chr1 237944 237969 no-call complex = ? ? -61 1.17 N +4701 2 chr1 237969 238263 hom ref = = = 3 1.17 N +4702 2 chr1 238263 238270 no-call complex = ? ? -36 1.17 N +4703 2 chr1 238270 238306 hom ref = = = 54 1.17 N +4704 2 chr1 238306 238313 no-call complex = ? ? -11 1.17 N +4705 2 chr1 238313 238580 hom ref = = = -16 1.17 N +4706 2 chr1 238580 238587 no-call complex = ? ? -214 1.17 N +4707 2 chr1 238587 238986 hom ref = = = -18 1.17 N +4708 2 chr1 238986 239020 no-call complex = ? ? -18 1.17 N +4709 2 chr1 239020 239118 hom ref = = = 33 1.17 N +4710 2 chr1 239118 239125 no-call complex = ? ? -39 1.17 N +4711 2 chr1 239125 239210 hom ref = = = 26 1.17 N +4712 2 chr1 239210 239243 no-call complex = ? ? -58 1.17 N +4713 2 chr1 239243 239506 hom ref = = = -23 1.17 N +4714 2 chr1 239506 239535 no-call complex = ? ? -279 1.17 N +4715 2 chr1 239535 239692 hom ref = = = -32 1.17 N +4716 2 chr1 239692 239738 no-call complex = ? ? -63 1.17 N +4717 2 chr1 239738 239896 hom ref = = = -18 1.17 N +4718 2 chr1 239896 239936 no-call complex = ? ? -114 1.17 N +4719 2 chr1 239936 240232 hom ref = = = -19 1.17 N +4720 2 chr1 240232 240245 no-call complex = ? ? -61 1.17 N +4721 2 chr1 240245 240388 hom ref = = = -19 1.17 N +4722 2 chr1 240388 240389 half ref C C N 58 120 -19 14 1.17 N +4723 2 chr1 240389 240566 hom ref = = = -19 1.17 N +4724 2 chr1 240566 240567 half ref G G N 82 122 34 L2:L2:41.6 14 1.17 N +4725 2 chr1 240567 240849 hom ref = = = -87 1.17 N +4726 2 chr1 240849 240879 no-call complex = ? ? -125 1.17 N +4727 2 chr1 240879 240892 hom ref = = = 27 1.17 N +4728 2 chr1 240892 240901 no-call complex = ? ? -111 1.17 N +4729 2 chr1 240901 240976 hom ref = = = -11 1.17 N +4730 2 chr1 240976 240977 half ref T T N 226 226 -11 MLT1H:ERVL-MaLR:42.0 14 1.17 N +4731 2 chr1 240977 241023 hom ref = = = -11 1.17 N +4732 2 chr1 241023 241030 no-call complex = ? ? -94 1.17 N +4733 2 chr1 241030 241132 hom ref = = = 30 1.17 N +4734 2 chr1 241132 241184 no-call complex = ? ? -37 1.17 N +4735 2 chr1 241184 241190 hom ref = = = 14 1.17 N +4736 2 chr1 241190 241197 no-call complex = ? ? -109 1.17 N +4737 2 chr1 241197 241236 hom ref = = = 28 1.17 N +4738 2 chr1 241236 241255 no-call complex = ? ? -35 1.17 N +4739 2 chr1 241255 241316 hom ref = = = -4 1.17 N +4740 2 chr1 241316 241385 no-call complex = ? ? -80 1.17 N +4741 2 chr1 241385 241423 hom ref = = = 34 1.17 N +4742 2 chr1 241423 241430 no-call complex = ? ? -34 1.17 N +4743 2 chr1 241430 241523 hom ref = = = 13 1.17 N +4744 2 chr1 241523 241530 no-call complex = ? ? -78 1.17 N +4745 2 chr1 241530 241930 hom ref = = = -19 1.17 N +4746 2 chr1 241930 241960 no-call complex = ? ? -24 1.17 N +4747 2 chr1 241960 242032 hom ref = = = -23 1.17 N +4748 2 chr1 242032 242033 half ref C C N 120 120 2133 2134 25 14 1.17 N +4749 2 chr1 242033 242060 hom ref = = = -29 1.17 N +4750 2 chr1 242060 242061 half ref C C N 68 120 2133 2134 -29 14 1.17 N +4751 2 chr1 242061 242264 hom ref = = = -29 1.17 N +4752 2 chr1 242264 242271 no-call complex = ? ? -118 1.17 N +4753 2 chr1 242271 242306 hom ref = = = 14 1.17 N +4754 2 chr1 242306 242338 no-call complex = ? ? -50 1.17 N +4755 2 chr1 242338 242506 hom ref = = = 3 1.17 N +4756 2 chr1 242506 242517 no-call complex = ? ? 0 1.17 N +4757 2 chr1 242517 242563 hom ref = = = 33 1.17 N +4758 2 chr1 242563 242604 no-call complex = ? ? -10 1.17 N +4759 2 chr1 242604 242706 hom ref = = = 18 1.17 N +4760 2 chr1 242706 242743 no-call complex = ? ? -152 1.17 N +4761 2 chr1 242743 242797 hom ref = = = 13 1.17 N +4762 2 chr1 242797 242804 no-call complex = ? ? -3 1.17 N +4763 2 chr1 242804 242946 hom ref = = = 1 1.17 N +4764 2 chr1 242946 242946 half ref ? 27 0 2143 2144 1 14 1.17 N +4765 2 chr1 242946 242959 hom ref = = = -6 1.17 N +4766 2 chr1 242959 242960 half ref T T N 36 120 2143 2144 -6 14 1.17 N +4767 2 chr1 242960 243070 hom ref = = = -14 1.17 N +4768 2 chr1 243070 243077 no-call complex = ? ? -10 1.17 N +4769 2 chr1 243077 243132 hom ref = = = 15 1.17 N +4770 2 chr1 243132 243140 no-call complex = ? ? 1 1.17 N +4771 2 chr1 243140 243149 hom ref = = = 15 1.17 N +4772 2 chr1 243149 243190 no-call complex = ? ? -129 1.17 N +4773 2 chr1 243190 243352 hom ref = = = -16 1.17 N +4774 2 chr1 243352 243390 no-call complex = ? ? -101 1.17 N +4775 2 chr1 243390 243503 hom ref = = = -49 1.17 N +4776 2 chr1 243503 243504 half ref G G N 121 121 -31 14 1.17 N +4777 2 chr1 243504 243691 hom ref = = = -31 1.17 N +4778 2 chr1 243691 243692 half ref A A N 76 121 12 14 1.17 N +4779 2 chr1 243692 243799 hom ref = = = -4 1.17 N +4780 2 chr1 243799 243806 no-call complex = ? ? -13 1.17 N +4781 2 chr1 243806 244191 hom ref = = = -18 1.17 N +4782 2 chr1 244191 244207 no-call complex = ? ? -6 1.17 N +4783 2 chr1 244207 244284 hom ref = = = 15 1.17 N +4784 2 chr1 244284 244291 no-call complex = ? ? -39 1.17 N +4785 2 chr1 244291 244695 hom ref = = = -25 1.17 N +4786 2 chr1 244695 244721 no-call complex = ? ? -88 1.17 N +4787 2 chr1 244721 244788 hom ref = = = 18 1.17 N +4788 2 chr1 244788 244819 no-call complex = ? ? -87 1.17 N +4789 2 chr1 244819 244843 hom ref = = = 14 1.17 N +4790 2 chr1 244843 244852 no-call complex = ? ? -1 1.17 N +4791 2 chr1 244852 244966 hom ref = = = -90 1.17 N +4792 2 chr1 244966 244966 half ref ? 34 0 -90 14 1.17 N +4793 2 chr1 244966 245020 hom ref = = = -90 1.17 N +4794 2 chr1 245020 245027 no-call complex = ? ? -471 1.17 N +4795 2 chr1 245027 245128 hom ref = = = 13 1.17 N +4796 2 chr1 245128 245143 no-call complex = ? ? -287 1.17 N +4797 2 chr1 245143 245198 hom ref = = = 10 1.17 N +4798 2 chr1 245198 245245 no-call complex = ? ? -103 1.17 N +4799 2 chr1 245245 245257 hom ref = = = 40 1.17 N +4800 2 chr1 245257 245268 no-call complex = ? ? -139 1.17 N +4801 2 chr1 245268 245330 hom ref = = = 15 1.17 N +4802 2 chr1 245330 245381 no-call complex = ? ? -248 1.17 N +4803 2 chr1 245381 245400 hom ref = = = 12 1.17 N +4804 2 chr1 245400 245458 no-call complex = ? ? -280 1.17 N +4805 2 chr1 245458 245559 hom ref = = = 0 1.17 N +4806 2 chr1 245559 245581 no-call complex = ? ? -12 1.17 N +4807 2 chr1 245581 245620 hom ref = = = 22 1.17 N +4808 2 chr1 245620 245643 no-call complex = ? ? -125 1.17 N +4809 2 chr1 245643 245853 hom ref = = = 0 1.17 N +4810 2 chr1 245853 245884 no-call complex = ? ? -32 1.17 N +4811 2 chr1 245884 245929 hom ref = = = -65 1.17 N +4812 2 chr1 245929 245929 half ref ? 34 0 -64 14 1.17 N +4813 2 chr1 245929 246067 hom ref = = = -64 1.17 N +4814 2 chr1 246067 246087 no-call complex = ? ? -158 1.17 N +4815 2 chr1 246087 246142 hom ref = = = 5 1.17 N +4816 2 chr1 246142 246192 no-call complex = ? ? -96 1.17 N +4817 2 chr1 246192 246222 hom ref = = = 27 1.17 N +4818 2 chr1 246222 246235 no-call complex = ? ? -18 1.17 N +4819 2 chr1 246235 246556 hom ref = = = -18 1.17 N +4820 2 chr1 246556 246586 no-call complex = ? ? -6 1.17 N +4821 2 chr1 246586 246642 hom ref = = = 10 1.17 N +4822 2 chr1 246642 246667 no-call complex = ? ? -43 1.17 N +4823 2 chr1 246667 246801 hom ref = = = 24 1.17 N +4824 2 chr1 246801 246818 no-call complex = ? ? -228 1.17 N +4825 2 chr1 246818 246973 hom ref = = = 6 1.17 N +4826 2 chr1 246973 247001 no-call complex = ? ? -126 1.17 N +4827 2 chr1 247001 247171 hom ref = = = 10 1.17 N +4828 2 chr1 247171 247196 no-call complex = ? ? -133 1.17 N +4829 2 chr1 247196 247297 hom ref = = = -20 1.17 N +4830 2 chr1 247297 247298 half ref A A N 120 70 -20 14 1.17 N +4831 2 chr1 247298 247408 hom ref = = = -20 1.17 N +4832 2 chr1 247408 247431 no-call complex = ? ? -7 1.17 N +4833 2 chr1 247431 247538 hom ref = = = 10 1.17 N +4834 2 chr1 247538 247566 no-call complex = ? ? -24 1.17 N +4835 2 chr1 247566 247581 hom ref = = = 32 1.17 N +4836 2 chr1 247581 247606 no-call complex = ? ? -34 1.17 N +4837 2 chr1 247606 247648 hom ref = = = 23 1.17 N +4838 2 chr1 247648 247687 no-call complex = ? ? -22 1.17 N +4839 2 chr1 247687 247715 hom ref = = = -10 1.17 N +4840 2 chr1 247715 247715 half ref ? 20 0 2175 2176 -9 14 1.17 N +4841 2 chr1 247715 247718 hom ref = = = -9 1.17 N +4842 2 chr1 247718 247719 half ref T T N 89 89 2175 2176 -2 14 1.17 N +4843 2 chr1 247719 247884 hom ref = = = -2 1.17 N +4844 2 chr1 247884 247891 no-call complex = ? ? -188 1.17 N +4845 2 chr1 247891 247910 hom ref = = = 4 1.17 N +4846 2 chr1 247910 247911 half ref A A N 29 39 2177 2178 4 AluJr:Alu:23.8 14 1.17 N +4847 2 chr1 247911 247920 hom ref = = = 4 1.17 N +4848 2 chr1 247920 247922 half ref GT GT ? 71 0 2177 2178 17 AluJr:Alu:23.8 14 1.17 N +4849 2 chr1 247922 247925 hom ref = = = 23 1.17 N +4850 2 chr1 247925 247926 half ref G G ? 55 0 2177 2178 8 AluJr:Alu:23.8 14 1.17 N +4851 2 chr1 247926 247936 hom ref = = = 6 1.17 N +4852 2 chr1 247936 247937 half ref A A N 58 85 2177 2178 3 AluJr:Alu:23.8 14 1.17 N +4853 2 chr1 247937 247945 hom ref = = = 3 1.17 N +4854 2 chr1 247945 247947 half ref CA CA ? 75 0 2177 2178 37 AluJr:Alu:23.8 14 1.17 N +4855 2 chr1 247947 247987 hom ref = = = 9 1.17 N +4856 2 chr1 247987 248010 no-call complex = ? ? -63 1.17 N +4857 2 chr1 248010 248028 hom ref = = = 20 1.17 N +4858 2 chr1 248028 248055 no-call complex = ? ? -21 1.17 N +4859 2 chr1 248055 248108 hom ref = = = 16 1.17 N +4860 2 chr1 248108 248133 no-call complex = ? ? -11 1.17 N +4861 2 chr1 248133 248194 hom ref = = = 16 1.17 N +4862 2 chr1 248194 248234 no-call complex = ? ? -304 1.17 N +4863 2 chr1 248234 248255 hom ref = = = -92 1.17 N +4864 2 chr1 248255 248256 half ref C C ? 60 0 -92 AluSx:Alu:14.3 14 1.17 N +4865 2 chr1 248256 248300 hom ref = = = -92 1.17 N +4866 2 chr1 248300 248323 no-call complex = ? ? -84 1.17 N +4867 2 chr1 248323 248337 hom ref = = = 12 1.17 N +4868 2 chr1 248337 248344 no-call complex = ? ? 7 1.17 N +4869 2 chr1 248344 248646 hom ref = = = -6 1.17 N +4870 2 chr1 248646 248653 no-call complex = ? ? -169 1.17 N +4871 2 chr1 248653 248760 hom ref = = = 12 1.17 N +4872 2 chr1 248760 248761 half ref T T ? 125 0 -22 14 1.17 N +4873 2 chr1 248761 248976 hom ref = = = -22 1.17 N +4874 2 chr1 248976 248983 no-call complex = ? ? -11 1.17 N +4875 2 chr1 248983 249103 hom ref = = = 45 1.17 N +4876 2 chr1 249103 249134 no-call complex = ? ? -30 1.17 N +4877 2 chr1 249134 249263 hom ref = = = -6 1.17 N +4878 2 chr1 249263 249309 no-call complex = ? ? -159 1.17 N +4879 2 chr1 249309 249323 hom ref = = = -13 1.17 N +4880 2 chr1 249323 249324 half ref A A N 155 155 -13 AluSx:Alu:12.1 14 1.17 N +4881 2 chr1 249324 249400 hom ref = = = -13 1.17 N +4882 2 chr1 249400 249426 no-call complex = ? ? -22 1.17 N +4883 2 chr1 249426 249501 hom ref = = = 11 1.17 N +4884 2 chr1 249501 249519 no-call complex = ? ? -33 1.17 N +4885 2 chr1 249519 249554 hom ref = = = 11 1.17 N +4886 2 chr1 249554 249561 no-call complex = ? ? -45 1.17 N +4887 2 chr1 249561 249697 hom ref = = = -28 1.17 N +4888 2 chr1 249697 249705 no-call complex = ? ? -44 1.17 N +4889 2 chr1 249705 249788 hom ref = = = 20 1.17 N +4890 2 chr1 249788 249795 no-call complex = ? ? -145 1.17 N +4891 2 chr1 249795 249858 hom ref = = = 12 1.17 N +4892 2 chr1 249858 249889 no-call complex = ? ? -69 1.17 N +4893 2 chr1 249889 249922 hom ref = = = 14 1.17 N +4894 2 chr1 249922 249952 no-call complex = ? ? -45 1.17 N +4895 2 chr1 249952 250057 hom ref = = = 40 1.17 N +4896 2 chr1 250057 250079 no-call complex = ? ? -500 1.17 N +4897 2 chr1 250079 250179 hom ref = = = -33 1.17 N +4898 2 chr1 250179 250195 no-call complex = ? ? -13 1.17 N +4899 2 chr1 250195 250299 hom ref = = = -3 1.17 N +4900 2 chr1 250299 250300 half ref C C N 94 120 -3 MSTB1:ERVL-MaLR:24.9 15 1.17 N +4901 2 chr1 250300 250331 hom ref = = = -3 1.17 N +4902 2 chr1 250331 250353 no-call complex = ? ? -197 1.17 N +4903 2 chr1 250353 250385 hom ref = = = 29 1.17 N +4904 2 chr1 250385 250428 no-call complex = ? ? -645 1.17 N +4905 2 chr1 250428 250473 hom ref = = = 13 1.17 N +4906 2 chr1 250473 250518 no-call complex = ? ? -80 1.17 N +4907 2 chr1 250518 250536 hom ref = = = 23 1.17 N +4908 2 chr1 250536 250561 no-call complex = ? ? -88 1.17 N +4909 2 chr1 250561 250619 hom ref = = = 41 1.17 N +4910 2 chr1 250619 250667 no-call complex = ? ? -549 1.17 N +4911 2 chr1 250667 250722 hom ref = = = 27 1.17 N +4912 2 chr1 250722 250729 no-call complex = ? ? -822 1.17 N +4913 2 chr1 250729 250863 hom ref = = = 6 1.17 N +4914 2 chr1 250863 250870 no-call complex = ? ? -497 1.17 N +4915 2 chr1 250870 250925 hom ref = = = 36 1.17 N +4916 2 chr1 250925 250950 no-call complex = ? ? -52 1.17 N +4917 2 chr1 250950 251008 hom ref = = = 23 1.17 N +4918 2 chr1 251008 251038 no-call complex = ? ? -112 1.17 N +4919 2 chr1 251038 251139 hom ref = = = 18 1.17 N +4920 2 chr1 251139 251177 no-call complex = ? ? -52 1.17 N +4921 2 chr1 251177 251253 hom ref = = = 23 1.17 N +4922 2 chr1 251253 251268 no-call complex = ? ? -76 1.17 N +4923 2 chr1 251268 251434 hom ref = = = 8 1.17 N +4924 2 chr1 251434 251441 no-call complex = ? ? -946 1.17 N +4925 2 chr1 251441 251492 hom ref = = = 30 1.17 N +4926 2 chr1 251492 251513 no-call complex = ? ? -341 1.17 N +4927 2 chr1 251513 251524 hom ref = = = 45 1.17 N +4928 2 chr1 251524 251539 no-call complex = ? ? -118 1.17 N +4929 2 chr1 251539 251590 hom ref = = = 25 1.17 N +4930 2 chr1 251590 251597 no-call complex = ? ? -372 1.17 N +4931 2 chr1 251597 251624 hom ref = = = 60 1.17 N +4932 2 chr1 251624 251666 no-call complex = ? ? -251 1.17 N +4933 2 chr1 251666 251747 hom ref = = = 47 1.17 N +4934 2 chr1 251747 251763 no-call complex = ? ? -104 1.17 N +4935 2 chr1 251763 251790 hom ref = = = 47 1.17 N +4936 2 chr1 251790 251807 no-call complex = ? ? -1220 1.17 N +4937 2 chr1 251807 251925 hom ref = = = 11 1.17 N +4938 2 chr1 251925 251952 no-call complex = ? ? -286 1.17 N +4939 2 chr1 251952 252011 hom ref = = = 22 1.17 N +4940 2 chr1 252011 252034 no-call complex = ? ? -554 1.17 N +4941 2 chr1 252034 252043 hom ref = = = 32 1.17 N +4942 2 chr1 252043 252055 no-call complex = ? ? -117 1.17 N +4943 2 chr1 252055 252088 hom ref = = = 18 1.17 N +4944 2 chr1 252088 252109 no-call complex = ? ? -336 1.17 N +4945 2 chr1 252109 252178 hom ref = = = 41 1.17 N +4946 2 chr1 252178 252208 no-call complex = ? ? -173 1.17 N +4947 2 chr1 252208 252288 hom ref = = = -16 1.17 N +4948 2 chr1 252288 252306 no-call complex = ? ? -65 1.17 N +4949 2 chr1 252306 252329 hom ref = = = 14 1.17 N +4950 2 chr1 252329 252374 no-call complex = ? ? -323 1.17 N +4951 2 chr1 252374 252468 hom ref = = = 0 1.17 N +4952 2 chr1 252468 252482 no-call complex = ? ? -203 1.17 N +4953 2 chr1 252482 252635 hom ref = = = 23 1.17 N +4954 2 chr1 252635 252662 no-call complex = ? ? -295 1.17 N +4955 2 chr1 252662 252675 hom ref = = = 38 1.17 N +4956 2 chr1 252675 252682 no-call complex = ? ? -13 1.17 N +4957 2 chr1 252682 252721 hom ref = = = 11 1.17 N +4958 2 chr1 252721 252752 no-call complex = ? ? -257 1.17 N +4959 2 chr1 252752 252792 hom ref = = = 31 1.17 N +4960 2 chr1 252792 252806 no-call complex = ? ? -362 1.17 N +4961 2 chr1 252806 252849 hom ref = = = 31 1.17 N +4962 2 chr1 252849 252882 no-call complex = ? ? -193 1.17 N +4963 2 chr1 252882 252915 hom ref = = = -60 1.17 N +4964 2 chr1 252915 252915 half ref ? 61 0 -59 10 1.17 N +4965 2 chr1 252915 252952 hom ref = = = -59 1.17 N +4966 2 chr1 252952 252991 no-call complex = ? ? -373 1.17 N +4967 2 chr1 252991 253167 hom ref = = = 18 1.17 N +4968 2 chr1 253167 253203 no-call complex = ? ? -108 1.17 N +4969 2 chr1 253203 253224 hom ref = = = 73 1.17 N +4970 2 chr1 253224 253270 no-call complex = ? ? -1017 1.17 N +4971 2 chr1 253270 253281 hom ref = = = 51 1.17 N +4972 2 chr1 253281 253288 no-call complex = ? ? -32 1.17 N +4973 2 chr1 253288 253470 hom ref = = = -37 1.17 N +4974 2 chr1 253470 253471 half ref C C N 76 120 35 10 1.17 N +4975 2 chr1 253471 253546 hom ref = = = 35 1.17 N +4976 2 chr1 253546 253590 no-call complex = ? ? -235 1.17 N +4977 2 chr1 253590 253663 hom ref = = = 52 1.17 N +4978 2 chr1 253663 253670 no-call complex = ? ? -287 1.17 N +4979 2 chr1 253670 253775 hom ref = = = 23 1.17 N +4980 2 chr1 253775 253782 no-call complex = ? ? -207 1.17 N
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masterVar_output.txt Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,27 @@ +chr1 41980 41981 G 1 1 76 +chr1 51672 51673 C 1 1 53 +chr1 52237 52238 G 1 7 63 +chr1 53205 53206 C/G 2 7,30 93,127 +chr1 54042 54043 T/C 2 3,10 66,84 +chr1 54585 54586 C/T 2 9,19 94,94 +chr1 55163 55164 A 1 9 76 +chr1 55301 55302 T/C 2 15,19 87,95 +chr1 55321 55322 T/C 2 12,12 95,95 +chr1 55325 55326 C/T 2 12,11 95,95 +chr1 55925 55926 C 1 12 66 +chr1 57951 57952 C 1 2 72 +chr1 58210 58211 G 1 11 98 +chr1 59050 59051 G/A 2 6,21 66,91 +chr1 59343 59344 T/C 2 25,23 57,120 +chr1 59497 59498 C/T 2 12,15 74,120 +chr1 60828 60829 T/C 2 1,11 60,97 +chr1 61441 61442 G 1 8 23 +chr1 68305 68306 T/C 2 27,20 44,44 +chr1 68315 68316 C/T 2 27,20 44,44 +chr1 69452 69453 A/G 2 6,37 61,121 +chr1 69510 69511 G 1 3 123 +chr1 69551 69552 C/G 2 4,27 98,98 +chr1 69568 69569 C/T 2 3,29 98,98 +chr1 77461 77462 A 1 4 26 +chr1 82733 82734 C/T 2 18,17 42,118 +chr1 233472 233473 G/C 2 21,42 118,118
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pgSnp2snp_output.txt Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,10002 @@ +#{"column_names":["chr","pos","A","B","Q","1A","1B","1G","1Q"], +#"individuals":[["na",6]], +#"dbkey":"hg19","pos":2,"rPos":2,"ref":1,"scaffold":1,"species":"hg19"} +chr1 1888681 T C -1 3 4 1 0.8893 +chr1 3118325 C T -1 0 8 0 0.8796 +chr1 3211457 A C -1 17 10 1 0.8576 +chr1 3222692 G A -1 10 14 1 0.8694 +chr1 3281273 G A -1 5 4 1 0.8210 +chr1 3630475 C T -1 12 12 1 0.8430 +chr1 4599834 C T -1 0 18 0 0.8797 +chr1 5287107 T G -1 0 6 0 0.8443 +chr1 5307765 C T -1 22 12 1 0.8505 +chr1 5341621 A C -1 5 3 1 0.9001 +chr1 5478586 A G -1 0 11 0 0.8997 +chr1 5680961 A C -1 16 10 1 0.8135 +chr1 5736051 G A -1 34 57 1 0.8655 +chr1 5831207 C T -1 5 10 1 0.8575 +chr1 6200884 A C -1 0 13 0 0.8346 +chr1 6307254 T C -1 0 11 0 0.8723 +chr1 6621228 G T -1 10 11 1 0.8336 +chr1 7094424 G A -1 0 4 0 0.8578 +chr1 7392593 C T -1 15 25 1 0.8644 +chr1 7500089 C G -1 0 13 0 0.8508 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2 7,13 0.8616,0.8676 T +chr2 9143011 9143012 A/T 2 5,10 0.8248,0.8300 A +chr2 9178379 9178380 T 1 29 0.8553 C +chr2 9773585 9773586 C/T 2 15,10 0.8741,0.8891 T +chr2 9805099 9805100 A/G 2 7,20 0.8302,0.8403 G +chr2 9967765 9967766 A/G 2 12,9 0.8679,0.8972 A +chr2 9970017 9970018 C/T 2 12,15 0.8615,0.8724 T +chr2 10356139 10356140 C/T 2 8,5 0.8023,0.8023 C +chr2 10613283 10613284 A 1 29 0.8376 G +chr2 11643829 11643830 A 1 15 0.7810 G +chr2 11834046 11834047 A 1 6 0.8677 G +chr2 11966615 11966616 A 1 4 0.8999 G +chr2 12146868 12146869 C/T 2 10,16 0.8749,0.8683 T +chr2 12227796 12227797 A/G 2 14,11 0.8742,0.8405 A +chr2 12364227 12364228 T 1 41 0.8428 C +chr2 13148264 13148265 C/T 2 4,14 0.8687,0.8741 T +chr2 13211442 13211443 C/T 2 19,8 0.8446,0.8316 T +chr2 13261985 13261986 T 1 13 0.8172 C +chr2 13520956 13520957 A/G 2 6,5 0.8646,0.8587 A +chr2 13653170 13653171 C/T 2 11,10 0.8684,0.8426 C +chr2 14331715 14331716 A/G 2 7,8 0.8851,0.8871 A +chr2 14904075 14904076 A 1 19 0.8775 G +chr2 14968580 14968581 G 1 19 0.9066 A +chr2 15085258 15085259 A/G 2 13,10 0.8449,0.8460 A +chr2 15164713 15164714 C 1 4 0.8366 T +chr2 15655479 15655480 G 1 32 0.8694 A +chr2 15697409 15697410 G 1 18 0.8645 A +chr2 16176893 16176894 C 1 41 0.8711 T +chr2 16380856 16380857 C/G 2 3,6 0.8209,0.8881 G +chr2 17545574 17545575 G/T 2 8,10 0.8689,0.8355 G +chr2 17897837 17897838 C/T 2 18,12 0.8014,0.8034 C +chr2 18235610 18235611 A 1 24 0.8539 C +chr2 18310861 18310862 C/G 2 17,17 0.8883,0.8960 G +chr2 18555627 18555628 G/T 2 4,9 0.7988,0.8279 T +chr2 18807785 18807786 A/G 2 20,16 0.8430,0.8607 A +chr2 19390486 19390487 A/C 2 9,6 0.8374,0.8094 A +chr2 19725690 19725691 C 1 23 0.8739 T +chr2 19760402 19760403 C/T 2 15,7 0.8496,0.8665 C +chr2 19774004 19774005 C/G 2 7,7 0.8438,0.8253 G +chr2 19878193 19878194 A/C 2 12,24 0.8802,0.8621 C +chr2 19989060 19989061 A/T 2 8,13 0.9021,0.8653 A +chr2 20289567 20289568 C/G 2 4,8 0.8610,0.8880 G +chr2 21129428 21129429 C 1 9 0.8852 T +chr2 21873183 21873184 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A +chr2 54913630 54913631 C/G 2 5,5 0.7846,0.7695 C +chr2 55075545 55075546 G 1 42 0.8782 A +chr2 55251373 55251374 A 1 51 0.8503 G +chr2 55307996 55307997 A 1 4 0.8707 G +chr2 55370488 55370489 C/G 2 13,12 0.8836,0.9030 G +chr2 56201625 56201626 A 1 34 0.8180 G +chr2 56724178 56724179 A/T 2 3,4 0.6182,0.7791 T +chr2 57600075 57600076 C/T 2 11,13 0.8644,0.8626 C +chr2 58296325 58296326 C 1 36 0.8607 A +chr2 58510033 58510034 T 1 22 0.8861 C +chr2 58589194 58589195 T 1 29 0.8725 C +chr2 58779120 58779121 T 1 2 0.8633 C +chr2 58792231 58792232 T 1 13 0.8380 C +chr2 59066562 59066563 G 1 24 0.8339 A +chr2 59293312 59293313 C/G 2 18,11 0.8240,0.8519 G +chr2 60071276 60071277 C/T 2 10,14 0.8460,0.8585 T +chr2 60519256 60519257 C/T 2 13,13 0.8735,0.8543 C +chr2 60547566 60547567 G 1 22 0.8584 A +chr2 60817253 60817254 C/T 2 12,11 0.8823,0.8863 C +chr2 61311118 61311119 A/G 2 6,9 0.8739,0.8454 G +chr2 61374148 61374149 C 1 8 0.8641 T +chr2 61932435 61932436 A 1 17 0.8533 G +chr2 62023583 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242323119 C/T 2 9,20 0.8814,0.8456 T +chr2 242625733 242625734 G 1 21 0.8778 C +chr2 242787513 242787514 C/T 2 11,9 0.8774,0.8763 C +chr3 614688 614689 C/T 2 14,8 0.8778,0.8334 C +chr3 750388 750389 C/T 2 3,4 0.8882,0.8724 C +chr3 888994 888995 T 1 14 0.8456 G +chr3 1328767 1328768 G 1 8 0.9129 T +chr3 1348569 1348570 A/T 2 8,9 0.8716,0.8623 A +chr3 1587859 1587860 C/T 2 13,10 0.8723,0.8819 T +chr3 1756870 1756871 C/G 2 21,10 0.8555,0.8576 G +chr3 1862779 1862780 C/T 2 7,6 0.8652,0.8616 C +chr3 1970016 1970017 C/T 2 13,24 0.8324,0.8259 T +chr3 1994643 1994644 A 1 11 0.8751 C +chr3 2032901 2032902 C/T 2 5,5 0.8223,0.8057 C +chr3 2139921 2139922 C 1 8 0.8561 A +chr3 2275005 2275006 C/T 2 18,14 0.8521,0.8677 C +chr3 2317280 2317281 A 1 9 0.8385 G +chr3 2470718 2470719 G 1 14 0.9008 A +chr3 2744662 2744663 C/G 2 11,11 0.8255,0.8100 G +chr3 2875926 2875927 C/G 2 12,7 0.8411,0.8453 C +chr3 2890537 2890538 A/G 2 10,16 0.8511,0.8660 G +chr3 2907096 2907097 A 1 14 0.8760 G +chr3 2953325 2953326 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51201411 51201412 C 1 28 0.8655 T +chr3 52720079 52720080 C 1 15 0.8341 A +chr3 52971578 52971579 A/G 2 8,18 0.8434,0.8282 G +chr3 53084288 53084289 G 1 9 0.8820 T +chr3 54228290 54228291 A/T 2 15,13 0.8335,0.7837 A +chr3 54267623 54267624 C/T 2 14,22 0.8790,0.8801 T +chr3 54499049 54499050 T 1 9 0.9304 C +chr3 54926622 54926623 A 1 10 0.8497 C +chr3 54929650 54929651 A/C 2 16,20 0.8356,0.8377 C +chr3 55119275 55119276 A/G 2 21,14 0.8659,0.8879 G +chr3 55181875 55181876 C/T 2 2,4 0.9610,0.8514 T +chr3 55492049 55492050 T 1 26 0.8568 C +chr3 55936700 55936701 A/G 2 15,24 0.8447,0.8462 A +chr3 56135450 56135451 A/G 2 9,18 0.8532,0.8599 A +chr3 56161289 56161290 A 1 30 0.8452 T +chr3 56228601 56228602 A/G 2 8,6 0.7838,0.8678 G +chr3 56263255 56263256 C 1 22 0.8632 T +chr3 56502077 56502078 T 1 12 0.8276 G +chr3 56650707 56650708 A 1 16 0.9014 G +chr3 57278672 57278673 G 1 26 0.8841 A +chr3 57394484 57394485 C 1 4 0.8452 T +chr3 57455696 57455697 C/T 2 10,6 0.8550,0.7793 C +chr3 57701936 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2 11,3 0.8728,0.8114 T +chr4 154162668 154162669 C/T 2 11,20 0.8884,0.8761 T +chr4 154492165 154492166 A/G 2 10,8 0.8857,0.8432 A +chr4 154706015 154706016 A/G 2 16,15 0.8330,0.8504 G +chr4 154714115 154714116 A/T 2 4,6 0.8315,0.8646 A +chr4 154829155 154829156 A/G 2 23,20 0.8610,0.8954 G +chr4 155162788 155162789 A/G 2 5,7 0.8406,0.8365 A +chr4 155430934 155430935 A 1 4 0.8594 T +chr4 156281668 156281669 C/T 2 4,4 0.8742,0.7787 C +chr4 157108351 157108352 A/C 2 6,9 0.8964,0.8525 A +chr4 157233214 157233215 C/T 2 12,19 0.8571,0.8818 T +chr4 157563568 157563569 C/T 2 17,15 0.8041,0.8083 C +chr4 157633621 157633622 T 1 13 0.8661 C +chr4 157746164 157746165 C/T 2 11,7 0.8252,0.8430 C +chr4 157811440 157811441 A/G 2 9,9 0.8133,0.8443 G +chr4 157984813 157984814 T 1 23 0.8748 C +chr4 158394831 158394832 C 1 31 0.8581 T +chr4 158932875 158932876 G 1 24 0.8827 T +chr4 159032439 159032440 A 1 23 0.8567 G +chr4 159541402 159541403 G 1 28 0.8530 A +chr4 159545147 159545148 A 1 3 0.8041 G +chr4 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36765429 36765430 T 1 20 0.8605 G +chr7 36819600 36819601 C/T 2 16,18 0.8593,0.8347 C +chr7 36904522 36904523 A/G 2 12,15 0.8723,0.8962 A +chr7 36913156 36913157 A 1 38 0.8400 G +chr7 37031182 37031183 C/T 2 10,5 0.8807,0.8639 C +chr7 37103935 37103936 G/T 2 7,9 0.8557,0.8600 G +chr7 37304145 37304146 C 1 8 0.8485 G +chr7 37315679 37315680 C/T 2 18,13 0.8205,0.8182 C +chr7 37625070 37625071 T 1 17 0.8897 A +chr7 37879846 37879847 C/T 2 12,9 0.8384,0.8430 C +chr7 38394847 38394848 G 1 6 0.8634 T +chr7 38462178 38462179 C/T 2 3,5 0.8205,0.8423 T +chr7 38740877 38740878 A 1 31 0.8492 C +chr7 38820372 38820373 G 1 3 0.8067 C +chr7 38853943 38853944 A 1 42 0.8560 G +chr7 39480497 39480498 A/T 2 4,11 0.8201,0.8738 T +chr7 39754834 39754835 G/T 2 11,16 0.8444,0.8531 G +chr7 39878866 39878867 A/G 2 10,18 0.8362,0.8173 G +chr7 39961107 39961108 C 1 15 0.8669 T +chr7 40247130 40247131 A 1 12 0.8630 G +chr7 41029332 41029333 A/C 2 4,5 0.8586,0.9288 C +chr7 41309917 41309918 A/T 2 15,16 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2 9,7 0.8012,0.8147 C +chr8 3964313 3964314 C 1 7 0.8880 T +chr8 4031325 4031326 G 1 36 0.8619 C +chr8 4056479 4056480 T 1 3 0.8680 A +chr8 4349662 4349663 G 1 23 0.8687 C +chr8 4508702 4508703 A/G 2 12,11 0.8784,0.8711 A +chr8 4587366 4587367 C/T 2 5,7 0.8846,0.8801 T +chr8 4655592 4655593 C/G 2 6,3 0.8913,0.8942 C +chr8 4782051 4782052 G 1 2 0.8920 C +chr8 4844403 4844404 A/G 2 11,16 0.8211,0.8581 G +chr8 4951063 4951064 A 1 24 0.8352 G +chr8 5070850 5070851 A/G 2 12,13 0.8614,0.8400 G +chr8 5089024 5089025 G 1 6 0.7985 T +chr8 5105060 5105061 G 1 35 0.8594 T +chr8 5157362 5157363 C/T 2 15,13 0.8782,0.8760 T +chr8 5347119 5347120 A/G 2 9,8 0.8035,0.7895 A +chr8 5586185 5586186 C/T 2 5,6 0.8277,0.8825 C +chr8 5671310 5671311 C/T 2 22,8 0.8333,0.8486 C +chr8 5899513 5899514 T 1 28 0.8764 G +chr8 5976167 5976168 A/C 2 4,4 0.8620,0.8850 C +chr8 6024174 6024175 G 1 37 0.8582 A +chr8 6069171 6069172 T 1 5 0.8682 A +chr8 6165823 6165824 A/G 2 11,12 0.8334,0.8654 G +chr8 6251985 6251986 G/T 2 6,3 0.7772,0.8402 T +chr8 6463002 6463003 G 1 16 0.8656 A +chr8 6497752 6497753 C/G 2 16,8 0.8444,0.8525 C +chr8 6505704 6505705 A/T 2 10,3 0.8849,0.8805 A +chr8 6561255 6561256 A/G 2 4,3 0.8675,0.8333 G +chr8 6658469 6658470 C 1 4 0.8445 G +chr8 6684000 6684001 A/G 2 15,18 0.8797,0.8956 A +chr8 6722350 6722351 A 1 13 0.8478 T +chr8 6754918 6754919 G 1 24 0.8705 C +chr8 6781685 6781686 C 1 5 0.8968 T +chr8 6879884 6879885 C/T 2 20,7 0.8479,0.8676 C +chr8 7831188 7831189 G 1 2 0.8670 C +chr8 8192830 8192831 C/T 2 12,18 0.8517,0.8895 T +chr8 8271709 8271710 C/T 2 12,24 0.8669,0.8689 T +chr8 8319341 8319342 A/C 2 12,21 0.8463,0.8208 C +chr8 8543543 8543544 A/G 2 4,4 0.9012,0.8815 A +chr8 8610782 8610783 C 1 5 0.8035 A +chr8 8861183 8861184 A/C 2 20,16 0.8267,0.8540 C +chr8 8932550 8932551 C/G 2 17,24 0.8846,0.8732 C +chr8 9085514 9085515 A/C 2 5,6 0.9011,0.8698 C +chr8 9155684 9155685 C/T 2 7,3 0.8583,0.8748 C +chr8 9225846 9225847 A/G 2 8,9 0.8624,0.7734 A +chr8 9687552 9687553 C/G 2 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0.8664,0.8669 C +chr8 24580755 24580756 A/G 2 12,16 0.8642,0.8700 G +chr8 24716593 24716594 G 1 31 0.8490 A +chr8 24741724 24741725 A 1 30 0.8745 G +chr8 25054133 25054134 A/G 2 8,7 0.8235,0.8083 A +chr8 25227225 25227226 G/T 2 8,15 0.9057,0.8852 G +chr8 25645065 25645066 C/T 2 18,10 0.8428,0.8092 C +chr8 25654047 25654048 A/T 2 8,11 0.8762,0.8630 A +chr8 25760359 25760360 G/T 2 18,18 0.8845,0.8722 G +chr8 25900308 25900309 G/T 2 15,15 0.8661,0.8705 G +chr8 26355746 26355747 C/T 2 16,10 0.8496,0.8366 C +chr8 26369268 26369269 A/G 2 10,4 0.8525,0.8291 G +chr8 26543313 26543314 A 1 26 0.8548 G +chr8 26819162 26819163 C 1 33 0.8730 T +chr8 26881354 26881355 G/T 2 28,20 0.8715,0.8552 G +chr8 27077741 27077742 A/G 2 18,10 0.8961,0.8848 A +chr8 27234932 27234933 A/G 2 10,11 0.8716,0.8747 G +chr8 27563688 27563689 A/G 2 3,8 0.8026,0.8981 G +chr8 27600973 27600974 C/T 2 13,15 0.9085,0.8934 T +chr8 27633554 27633555 G 1 19 0.8634 A +chr8 27722399 27722400 A/G 2 6,6 0.8692,0.8361 A +chr8 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43778913 43778914 A 1 35 0.8743 G +chr8 43809875 43809876 A/T 2 3,3 0.8645,0.8400 A +chr8 43819477 43819478 C/T 2 11,20 0.8660,0.8231 T +chr8 47293346 47293347 C 1 20 0.8362 T +chr8 47335659 47335660 A/C 2 11,12 0.8452,0.8447 C +chr8 47416596 47416597 T 1 8 0.8295 C +chr8 47722128 47722129 C/T 2 10,4 0.8345,0.8699 C +chr8 47849420 47849421 A/C 2 14,20 0.8235,0.8594 A +chr8 47964870 47964871 C/T 2 4,9 0.8865,0.8173 C +chr8 48080667 48080668 C/T 2 14,17 0.8777,0.8893 T +chr8 48812003 48812004 C/T 2 13,11 0.8868,0.8831 T +chr8 49462728 49462729 A/G 2 11,7 0.8780,0.8780 A +chr8 49662317 49662318 C/T 2 15,9 0.8560,0.8461 C +chr8 49895441 49895442 G/T 2 15,7 0.8451,0.8495 G +chr8 50052764 50052765 G/T 2 13,11 0.8693,0.8939 T +chr8 50157479 50157480 C/G 2 11,9 0.8429,0.8760 G +chr8 50762457 50762458 A/T 2 12,28 0.8862,0.8534 T +chr8 51215498 51215499 A/C 2 13,21 0.8406,0.8445 C +chr8 51481016 51481017 A/G 2 14,12 0.8976,0.8861 G +chr8 51659192 51659193 A 1 8 0.8324 G +chr8 51779121 51779122 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132677772 132677773 A/C 2 7,19 0.8367,0.8560 A +chr10 132732325 132732326 A/G 2 17,7 0.8414,0.8452 A +chr10 132894880 132894881 G 1 16 0.8715 A +chr10 133150406 133150407 C/T 2 18,13 0.8377,0.8515 T +chr10 133218173 133218174 C/G 2 17,17 0.8620,0.8607 C +chr10 133371738 133371739 A 1 23 0.8212 G +chr10 133374746 133374747 G 1 23 0.8553 T +chr10 133829718 133829719 A/G 2 9,6 0.8646,0.8784 A +chr10 134070559 134070560 T 1 5 0.7892 C +chr10 134112531 134112532 A/G 2 12,5 0.7851,0.7941 A +chr10 134176984 134176985 C 1 11 0.8675 T +chr10 134287008 134287009 C/T 2 20,23 0.8773,0.8929 C +chr10 134309946 134309947 T 1 7 0.8718 A +chr10 134677721 134677722 A/C 2 4,5 0.8658,0.9170 C +chr11 243267 243268 G 1 3 0.8740 T +chr11 257307 257308 C/T 2 6,4 0.8636,0.8446 T +chr11 437400 437401 G 1 8 0.8243 C +chr11 699851 699852 A 1 12 0.8881 G +chr11 1016809 1016810 G/T 2 34,16 0.8304,0.8326 G +chr11 1142631 1142632 G 1 11 0.8992 C +chr11 1161200 1161201 A 1 15 0.8542 G +chr11 1764966 1764967 C/T 2 5,10 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C 1 20 0.8322 T +chr11 5349061 5349062 C/T 2 13,8 0.8541,0.8181 T +chr11 5987695 5987696 T 1 24 0.7884 C +chr11 6005758 6005759 A/G 2 17,11 0.8212,0.8210 G +chr11 6428016 6428017 A/C 2 8,9 0.8561,0.8779 C +chr11 6920772 6920773 C/G 2 10,10 0.8638,0.8563 G +chr11 7794975 7794976 A 1 16 0.8435 T +chr11 7850955 7850956 G 1 17 0.8430 C +chr11 7901367 7901368 T 1 20 0.8227 C +chr11 7916070 7916071 C/T 2 7,5 0.9275,0.8635 C +chr11 7927053 7927054 A/T 2 15,14 0.8726,0.8701 A +chr11 7970049 7970050 C/T 2 13,11 0.8427,0.9007 C +chr11 8104485 8104486 C/T 2 16,15 0.8869,0.8790 T +chr11 8269312 8269313 C/T 2 11,6 0.8576,0.8657 T +chr11 8529276 8529277 A 1 36 0.8565 G +chr11 8529837 8529838 T 1 8 0.8454 C +chr11 8549622 8549623 T 1 28 0.8390 C +chr11 9024851 9024852 A 1 19 0.8947 G +chr11 9674914 9674915 C/T 2 7,5 0.8088,0.8938 T +chr11 9697343 9697344 C/T 2 6,10 0.8843,0.8548 T +chr11 9882345 9882346 G 1 18 0.8532 A +chr11 10408115 10408116 G 1 13 0.7903 C +chr11 10769020 10769021 C/T 2 6,6 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93588311 A/G 2 16,13 0.8775,0.8773 A +chr11 93660731 93660732 G/T 2 8,11 0.8415,0.8379 T +chr11 93696669 93696670 A 1 14 0.8676 G +chr11 93854156 93854157 A/G 2 4,3 0.8732,0.7659 A +chr11 93954236 93954237 C/G 2 22,17 0.8299,0.8172 C +chr11 94616935 94616936 C 1 20 0.8639 G +chr11 94639736 94639737 A/C 2 18,10 0.8540,0.8748 A +chr11 94779013 94779014 C/T 2 15,6 0.8858,0.8253 T +chr11 94995736 94995737 T 1 19 0.8207 C +chr11 95283119 95283120 C/T 2 25,20 0.8660,0.8673 C +chr11 95715897 95715898 C/T 2 8,5 0.8877,0.8451 T +chr11 96058793 96058794 G/T 2 11,9 0.8339,0.8033 T +chr11 96515318 96515319 A/G 2 12,21 0.8155,0.8305 G +chr11 96674330 96674331 C/T 2 10,9 0.8432,0.8225 T +chr11 97270426 97270427 A/C 2 21,10 0.8841,0.8657 A +chr11 97348547 97348548 C/T 2 17,14 0.8025,0.8351 T +chr11 97744329 97744330 G 1 19 0.8591 A +chr11 98084889 98084890 A/T 2 10,14 0.8510,0.8847 T +chr11 98171236 98171237 A/G 2 8,10 0.8719,0.8810 G +chr11 98189079 98189080 A 1 22 0.8538 G +chr11 98435687 98435688 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65335512 T 1 6 0.8041 C +chr18 65471580 65471581 A/G 2 5,13 0.8305,0.8417 A +chr18 65615782 65615783 A/G 2 15,13 0.8661,0.8751 G +chr18 65703472 65703473 G 1 21 0.8406 A +chr18 66313773 66313774 C 1 18 0.8845 G +chr18 67186056 67186057 A 1 29 0.8573 G +chr18 67259873 67259874 A/T 2 9,5 0.8016,0.8197 T +chr18 67287028 67287029 G 1 21 0.8284 C +chr18 67354468 67354469 A 1 12 0.8768 G +chr18 67478876 67478877 A 1 3 0.8511 T +chr18 67489883 67489884 C/G 2 10,16 0.8126,0.8466 G +chr18 67507984 67507985 C 1 27 0.8426 T +chr18 67547413 67547414 G 1 16 0.8840 T +chr18 67852535 67852536 C/G 2 16,22 0.8744,0.8735 G +chr18 68033941 68033942 C/T 2 6,20 0.8258,0.8901 T +chr18 68501662 68501663 A/T 2 17,10 0.8421,0.8436 T +chr18 68718615 68718616 C/T 2 4,10 0.8403,0.8951 T +chr18 68757854 68757855 C 1 4 0.8020 T +chr18 68878233 68878234 G 1 18 0.8660 A +chr18 68906841 68906842 G/T 2 16,14 0.8335,0.8211 G +chr18 69021430 69021431 G/T 2 23,14 0.8670,0.8658 G +chr18 69038775 69038776 T 1 9 0.8336 G 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.gd_snp Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,402 @@ +#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist", +#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"} +Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 +Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 +Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 +Contig86_chr1_30984450_30985684 670 C T 365.0 chr1 30985133 C 9 0 2 54 10 0 2 57 13 0 2 66 3 0 2 36 9 0 2 54 7 0 2 48 Y 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18 0 2 81 14 0 2 69 17 0 2 78 12 0 2 63 14 0 2 69 Y 44 0.882 0 +Contig94_chr2_43869105_43870358 220 G A 888.0 chr2 43869333 G 12 0 2 63 18 0 2 81 11 0 2 60 15 0 2 72 12 0 2 63 13 0 2 66 Y 1 0.156 0 +Contig34_chr2_48444129_48444939 695 C T 134.0 chr2 48444828 C 14 0 2 69 8 0 2 51 16 0 2 75 17 0 2 78 9 0 2 54 15 0 2 72 Y 161 0.375 0 +Contig6_chr2_56859179_56859956 671 T C 999.9 chr2 56859851 T 15 0 2 72 18 0 2 81 20 0 2 90 19 0 2 84 19 0 2 84 24 0 2 99 N 28 5.308 1 +Contig115_chr2_61631913_61632510 310 G T 999.3 chr2 61632216 G 7 0 2 48 9 0 2 54 7 0 2 48 11 0 2 60 10 0 2 57 10 0 2 57 N 13 0.184 0 +Contig31_chr2_67331584_67331785 39 C T 999.0 chr2 67331623 C 11 0 2 60 10 0 2 57 7 0 2 48 9 0 2 54 2 0 2 33 4 0 2 39 N 110 0.647 1 +Contig92_chr2_75906683_75907774 773 T C 85.4 chr2 75907438 C 12 0 2 63 12 0 2 63 17 0 2 78 8 0 2 51 8 0 2 51 13 0 2 66 Y 93 0.166 0 +Contig163_chr2_76402959_76404830 221 C T 127.0 chr2 76403181 C 4 0 2 42 10 0 2 57 9 0 2 54 11 0 2 60 7 0 2 48 9 0 2 54 Y 54 0.178 1 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2 60 23 0 2 96 13 0 2 66 12 0 2 63 11 0 2 60 Y 36 3.583 2 +Contig97_chr3_49820354_49821631 1069 G A 44.1 chr3 49821402 G 9 0 2 54 9 0 2 54 6 0 2 45 10 0 2 57 5 0 2 42 8 0 2 51 N 6 0.201 2 +Contig1_chr3_51588422_51589409 926 A G 51.0 chr3 51589353 G 2 0 2 33 2 0 2 33 6 0 2 45 4 0 2 39 9 0 2 54 11 0 2 60 N 21 1.147 0 +Contig25_chr3_53260697_53262560 402 G A 211.0 chr3 53261095 G 17 0 2 78 14 0 2 69 15 0 2 75 12 0 2 63 14 0 2 69 12 0 2 63 Y 116 1.033 0 +Contig11_chr3_53992739_53995954 2392 G A 82.4 chr3 53995143 A 12 0 2 66 11 0 2 60 14 0 2 69 6 0 2 45 11 0 2 60 17 0 2 78 Y 358 0.321 1 +Contig236_chr3_72676275_72676473 128 G A 278.0 chr3 72676410 G 12 0 2 63 11 0 2 60 13 0 2 66 10 0 2 57 11 0 2 60 8 0 2 51 N 36 0.496 1 +Contig48_chr3_74792236_74792388 63 T C 111.0 chr3 74792289 - 17 0 2 78 9 0 2 54 9 0 2 54 5 0 2 42 11 0 2 60 9 0 2 54 N -1 3.528 0 +Contig65_chr3_80727952_80728283 39 T C 71.2 chr3 80727990 T 7 0 2 48 3 0 2 36 8 0 2 51 6 0 2 45 8 0 2 51 11 0 2 60 N 22 7.078 0 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5 0 2 42 4 0 2 39 2 0 2 33 2 0 2 33 N 33 0.499 0 +Contig16_chr4_30177226_30179725 621 C T 88.4 chr4 30177859 C 20 0 2 87 13 0 2 66 13 0 2 66 11 0 2 60 8 0 2 51 8 0 2 51 Y 45 0.797 1 +Contig30_chr4_46196500_46197672 1045 A C 33.4 chr4 46197522 C 16 0 2 75 9 0 2 54 4 0 2 39 7 0 2 48 14 0 2 69 6 0 2 45 Y 43 0.306 0 +Contig2_chr4_47039007_47039323 158 G C 35.1 chr4 47039160 - 8 0 2 51 9 0 2 54 13 0 2 66 8 0 2 51 10 0 2 60 9 0 2 54 N 0 0.131 0 +Contig17_chr4_61310346_61311158 267 C T 49.9 chr4 61310604 T 10 0 2 57 7 0 2 48 9 0 2 54 10 0 2 57 14 0 2 69 7 0 2 48 Y 219 0.098 0 +Contig26_chr4_64190783_64191295 64 A G 162.0 chr4 64190843 A 10 0 2 57 6 0 2 45 20 0 2 87 12 0 2 63 17 0 2 78 7 0 2 48 Y 306 7.428 0 +Contig11_chr4_65500960_65501654 634 T C 107.0 chr4 65501585 T 13 0 2 66 14 0 2 69 13 0 2 66 13 0 2 66 6 0 2 45 18 0 2 81 Y 10 6.849 0 +Contig38_chr4_67768488_67768982 113 A G 102.0 chr4 67768598 A 9 0 2 54 8 0 2 51 9 0 2 54 11 0 2 60 10 0 2 57 7 0 2 48 Y 188 3.175 0 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2 87 22 0 2 93 10 0 2 57 10 0 2 57 21 0 2 90 Y 182 2.013 0 +Contig5_chr5_23188121_23190168 1841 C T 141.0 chr5 23189975 C 20 0 2 87 19 0 2 84 22 0 2 93 16 0 2 75 18 0 2 81 14 0 2 69 N 45 0.355 0 +Contig6_chr5_26899813_26900498 97 A C 88.6 chr5 26899910 A 15 0 2 72 14 0 2 69 27 0 2 108 15 0 2 72 13 0 2 69 12 0 2 63 Y 92 7.370 3 +Contig314_chr5_34019166_34019319 72 C A 20.1 chr5 -1 N 6 0 2 45 9 0 2 54 4 0 2 39 4 0 2 39 9 0 2 54 5 0 2 42 N -1 +99. 4 +Contig147_chr5_38980258_38980559 221 C T 40.8 chr5 38980477 C 15 0 2 72 15 0 2 72 19 0 2 84 10 0 2 57 12 0 2 63 20 0 2 87 Y 11 4.576 0 +Contig115_chr5_48119079_48120169 151 C T 78.3 chr5 48119234 C 17 0 2 78 10 0 2 57 14 0 2 69 16 0 2 75 8 0 2 51 12 0 2 63 Y 205 0.320 0 +Contig45_chr5_50892738_50892968 169 C A 25.8 chr5 50892911 C 10 0 2 57 7 0 2 48 10 0 2 60 6 0 2 45 6 0 2 45 13 0 2 66 N 244 0.497 1 +Contig40_chr5_51484164_51484696 14 A G 53.3 chr5 51484180 A 6 0 2 45 4 0 2 39 4 0 2 39 3 0 2 36 0 0 2 13 3 0 2 36 N 63 +99. 1 +Contig40_chr5_51664286_51667573 861 C T 148.0 chr5 51665149 C 20 0 2 87 21 0 2 90 20 0 2 87 11 0 2 60 16 0 2 75 15 0 2 72 Y 207 0.080 1 +Contig15_chr5_51889708_51891244 882 A G 149.0 chr5 51890581 G 13 0 2 66 18 0 2 81 17 0 2 78 22 0 2 93 15 0 2 72 22 0 2 93 Y 7 0.025 1 +Contig143_chr5_57231364_57232010 294 T C 78.5 chr5 57231644 T 3 0 2 36 5 0 2 42 4 0 2 39 2 0 2 33 10 0 2 57 6 0 2 45 Y 73 0.337 2 +Contig13_chr5_57609985_57610584 496 C T 50.5 chr5 57610476 C 17 0 2 78 9 0 2 54 6 0 2 45 8 0 2 51 10 0 2 57 12 0 2 63 N 77 2.022 1 +Contig230_chr5_58486998_58487280 227 T C 192.0 chr5 58487232 T 3 0 2 36 4 0 2 39 9 0 2 54 6 0 2 45 4 0 2 39 7 0 2 48 N 24 0.100 2 +Contig385_chr5_60122961_60123128 15 C G 136.0 chr5 60122976 C 0 0 -1 0 0 0 -1 0 1 0 2 30 1 0 2 30 3 0 2 36 0 0 -1 0 N 100 +99. 2 +Contig143_chr5_65121393_65122035 558 C A 127.0 chr5 65121959 A 0 0 -1 0 5 0 2 42 3 0 2 36 4 0 2 39 0 0 -1 0 4 0 2 39 Y 285 0.391 1 +Contig32_chr5_70852360_70853289 282 G A 114.0 chr5 70852623 G 16 0 2 75 11 0 2 60 13 0 2 66 12 0 2 63 13 0 2 66 7 0 2 48 Y 33 0.276 0 +Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0 +Contig100_chr5_71189678_71190590 813 C T 30.8 chr5 71190523 C 11 0 2 60 11 0 2 60 9 0 2 54 10 0 2 57 6 0 2 45 13 0 2 66 Y 8 0.362 1 +Contig45_chr5_76133561_76134403 388 A G 103.0 chr5 76133941 G 3 0 2 36 8 0 2 51 8 0 2 51 5 0 2 42 6 0 2 45 7 0 2 48 Y 57 0.038 0 +Contig61_chr5_90202541_90204393 909 C T 101.0 chr5 90203461 T 7 0 2 48 5 0 2 42 14 0 2 69 3 0 2 36 5 0 2 42 8 0 2 51 Y 64 1.448 0 +Contig111_chr6_5821219_5822519 1060 A G 68.1 chr6 5822321 T 7 0 2 48 6 0 2 45 11 0 2 60 9 0 2 54 3 0 2 36 12 0 2 63 Y 7 0.231 1 +Contig220_chr6_10671338_10672441 999 T C 36.3 chr6 10672322 T 5 0 2 42 11 0 2 60 11 0 2 60 8 0 2 51 5 0 2 42 9 0 2 54 Y 1 1.667 0 +Contig226_chr6_17361986_17362884 418 G C 251.0 chr6 17362406 G 6 0 2 45 8 0 2 51 7 0 2 48 9 0 2 54 7 0 2 48 7 0 2 48 Y 7 0.147 0 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8 0 2 51 12 0 2 63 16 0 2 75 Y 15 0.145 1 +Contig112_chr6_51024554_51024851 100 A G 121.0 chr6 51024654 A 10 0 2 57 12 0 2 63 9 0 2 54 13 0 2 66 14 0 2 69 17 0 2 78 N 75 4.287 0 +Contig40_chr6_51412751_51413807 227 T C 94.5 chr6 51412975 C 5 0 2 42 8 0 2 51 7 0 2 48 9 0 2 54 11 0 2 60 10 0 2 57 Y 4 5.661 0 +Contig47_chr6_69073222_69074767 1315 T C 212.0 chr6 69074558 T 20 0 2 87 17 0 2 78 18 0 2 81 12 0 2 63 17 0 2 78 7 0 2 48 Y 9 0.652 0 +Contig30_chr6_74848932_74849059 57 C G 46.3 chr6 74848993 C 7 0 2 48 7 0 2 33 6 0 2 45 7 0 2 48 5 0 2 42 6 0 2 45 N -1 +99. 1 +Contig84_chr7_6648683_6650255 1297 G A 110.0 chr7 6649988 G 18 0 2 81 9 0 2 54 22 0 2 77 16 0 2 75 20 0 2 87 6 0 2 45 Y 83 0.166 0 +Contig239_chr7_13007379_13007700 275 A G 39.8 chr7 13007642 A 8 0 2 51 5 0 2 42 8 0 2 51 3 0 2 36 3 0 2 36 5 0 2 42 N 46 1.511 3 +Contig119_chr7_18310707_18310948 23 A T 133.0 chr7 18310729 A 6 0 2 45 5 0 2 42 10 0 2 57 5 0 2 42 2 0 2 33 2 0 2 33 N 4553 +99. 0 +Contig93_chr7_18513377_18513741 173 T C 130.0 chr7 18513533 C 15 0 2 72 11 0 2 60 18 0 2 81 6 0 2 45 10 0 2 57 14 0 2 69 Y 115 0.174 0 +Contig133_chr7_19603333_19603776 414 C G 31.9 chr7 19603734 G 10 0 2 57 4 0 2 39 4 0 2 39 5 0 2 42 9 0 2 54 9 0 2 54 N 78 +99. 5 +Contig132_chr7_20426224_20428145 1815 A G 28.3 chr7 20428041 A 11 1 2 43 12 0 2 63 19 0 2 84 23 0 2 96 14 0 2 69 10 0 2 57 N 11 0.264 0 +Contig206_chr7_26281823_26282074 103 C A 101.0 chr7 26281925 T 11 0 2 60 16 0 2 61 19 0 2 84 6 0 2 45 19 0 2 84 16 0 2 75 N -1 0.947 1 +Contig116_chr7_45858984_45859111 38 T C 73.2 chr7 -1 N 2 0 2 33 1 0 2 30 3 0 2 36 2 0 2 33 2 0 2 33 1 0 2 30 N -1 3.442 0 +Contig38_chr7_50681997_50682600 42 T C 92.4 chr7 50682037 G 6 0 2 45 2 0 2 33 10 0 2 57 12 0 2 63 5 0 2 42 6 0 2 45 Y 94 0.146 0 +Contig55_chr7_53147505_53148974 894 A G 68.4 chr7 53148397 G 22 0 2 93 13 0 2 66 16 0 2 75 8 0 2 51 16 0 2 75 11 0 2 60 Y 19 0.060 0 +Contig4_chr7_53685534_53688206 1709 C G 76.2 chr7 53687225 C 18 0 2 81 17 0 2 78 18 0 2 81 15 0 2 72 14 0 2 69 14 0 2 69 Y 32 0.659 1 +Contig61_chr7_55832923_55834065 506 T C 185.0 chr7 55833450 C 9 0 2 54 10 0 2 57 22 0 2 93 12 0 2 63 12 0 2 63 7 0 2 48 Y 1 0.019 0 +Contig91_chr8_12804505_12805470 409 C A 111.0 chr8 12804906 C 8 0 2 51 10 0 2 57 15 0 2 72 12 0 2 63 14 0 2 69 15 0 2 72 N 145 0.175 0 +Contig30_chr8_17147743_17147923 13 G A 105.0 chr8 17147756 A 1 3 1 19 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 3 0 2 36 N 6 +99. 0 +Contig8_chr8_27811135_27812620 333 C T 37.9 chr8 27811458 C 4 0 2 39 11 0 2 60 18 0 2 81 5 0 2 42 6 0 2 45 5 0 2 42 Y 1 0.272 0 +Contig66_chr8_28273102_28273660 175 G C 81.6 chr8 28273263 T 9 0 2 54 17 0 2 78 19 0 2 84 8 0 2 51 16 0 2 75 19 0 2 84 Y 3 2.735 0 +Contig84_chr8_31375511_31376456 443 T C 125.0 chr8 31375954 T 10 0 2 57 15 0 2 72 27 0 2 108 18 0 2 81 16 0 2 75 9 0 2 54 Y 2 0.650 0 +Contig18_chr8_32575859_32577431 264 T C 151.0 chr8 32576124 T 20 0 2 87 14 0 2 69 17 0 2 78 14 0 2 69 13 0 2 66 14 0 2 69 Y 17 0.915 1 +Contig54_chr8_40913908_40916451 1275 G A 175.0 chr8 40915190 G 10 0 2 57 8 0 2 51 11 0 2 60 7 0 2 48 8 0 2 51 9 0 2 54 Y 21 0.056 3 +Contig93_chr8_44658786_44659075 180 T G 55.3 chr8 44658964 T 4 0 2 39 3 0 2 36 6 0 2 45 5 0 2 45 5 0 2 42 4 0 2 39 N 14 0.188 0 +Contig17_chr8_57490059_57490498 69 G T 97.4 chr8 57490127 A 2 0 2 33 11 0 2 60 15 0 2 72 16 0 2 75 8 0 2 51 10 0 2 57 N 40 0.522 5 +Contig66_chr8_58562376_58563446 345 C G 5.74 chr8 58562721 C 14 0 2 69 12 0 2 63 9 0 2 57 10 0 2 57 9 0 2 54 10 0 2 57 Y 6 0.685 0 +Contig44_chr8_71186368_71188207 1455 G T 147.0 chr8 71187818 G 4 10 1 74 3 0 2 36 20 0 2 87 12 0 2 63 8 0 2 51 10 0 2 57 Y 88 0.036 0 +Contig73_chr9_29451535_29452248 616 A G 24.7 chr9 29452127 G 4 0 2 39 7 0 2 48 1 0 2 30 4 0 2 39 7 0 2 48 6 0 2 45 N 49 0.448 4 +Contig96_chr9_39008495_39009278 215 A C 98.7 chr9 39008708 C 7 0 2 48 13 0 2 66 28 0 2 111 16 0 2 75 17 0 2 78 17 0 2 78 Y 8 0.427 1 +Contig22_chr10_15505382_15505589 172 T C 38.5 chr10 15505548 T 2 0 2 33 6 0 2 45 8 0 2 51 8 0 2 51 9 0 2 54 12 0 2 63 N 284 2.861 0 +Contig69_chr10_40547265_40548153 371 G A 58.1 chr10 40547649 A 9 0 2 54 8 0 2 51 8 0 2 51 9 0 2 54 4 0 2 39 5 0 2 42 Y 20 0.138 4 +Contig63_chr10_42716594_42719945 1018 A G 88.7 chr10 42717616 G 13 0 2 66 14 0 2 69 13 0 2 66 12 0 2 63 18 0 2 81 5 0 2 42 Y 25 1.740 0 +Contig22_chr10_43255307_43255570 81 C A 37.2 chr10 43255383 C 15 0 2 72 18 0 2 81 22 0 2 93 16 0 2 75 11 0 2 60 12 0 2 63 N 62 0.450 0 +Contig9_chr10_51475063_51476054 770 C T 57.3 chr10 51475839 C 6 0 2 45 16 0 2 75 16 0 2 75 13 0 2 66 9 0 2 54 9 2 2 21 N 80 0.394 0 +Contig42_chr10_53816543_53818392 1642 G A 27.5 chr10 53818172 A 7 0 2 48 13 0 2 66 17 0 2 78 14 0 2 69 19 0 2 84 16 0 2 75 N 1 0.433 0 +Contig36_chr10_53992615_53993741 229 G C 86.2 chr10 53992846 G 17 0 2 78 14 0 2 69 13 0 2 66 15 0 2 72 12 0 2 63 15 0 2 72 N 23 1.912 0 +Contig20_chr10_58141129_58141750 575 C T 46.1 chr10 58141701 C 7 0 2 48 8 0 2 51 9 0 2 54 3 0 2 36 4 0 2 39 9 0 2 54 N 1 4.264 0 +Contig26_chr10_59510973_59511899 146 C A 29.0 chr10 59511126 C 8 0 2 51 13 0 2 66 18 0 2 81 13 0 2 66 10 0 2 57 7 0 2 48 Y 208 1.077 0 +Contig72_chr11_7142765_7143772 146 G A 152.0 chr11 7142911 A 8 0 2 51 8 0 2 51 24 0 2 99 10 0 2 57 17 0 2 78 11 0 2 60 Y 90 1.137 0 +Contig103_chr11_8844784_8845095 214 T G 135.0 chr11 8844993 T 1 1 2 12 10 0 2 57 5 4 1 26 2 3 1 13 2 7 1 34 1 1 2 13 Y 75 0.731 0 +Contig9_chr11_9904571_9905983 1284 C T 151.0 chr11 9905857 C 16 0 2 75 19 0 2 84 17 0 2 78 16 0 2 75 12 0 2 63 13 1 2 44 Y 11 0.422 1 +Contig35_chr11_22459883_22460855 714 T G 54.9 chr11 22460577 T 3 0 2 36 1 0 2 30 3 0 2 36 2 0 2 33 2 0 2 33 0 0 -1 0 N 24 0.382 0 +Contig7_chr11_40017076_40017630 352 C T 46.3 chr11 40017422 C 7 0 2 48 9 0 2 54 6 0 2 45 8 0 2 51 16 0 2 75 9 0 2 54 Y 44 0.336 0 +Contig108_chr11_42953408_42955156 367 A G 89.4 chr11 42953779 A 17 0 2 78 11 0 2 60 14 0 2 69 20 0 2 87 14 0 2 69 17 0 2 78 Y 118 0.784 1 +Contig82_chr11_43490732_43490862 60 C T 47.3 chr11 -1 N 0 0 -1 0 0 0 -1 0 1 0 2 30 3 0 2 36 1 1 2 19 1 0 2 30 N -1 6.763 0 +Contig16_chr11_53408448_53408790 187 A G 153.0 chr11 53408638 A 7 0 2 48 9 0 2 54 18 0 2 81 10 0 2 57 11 0 2 60 12 0 2 63 Y 116 1.367 0 +Contig21_chr12_18403415_18404381 586 G T 34.5 chr12 18403983 - 13 0 2 66 16 0 2 75 25 0 2 102 12 0 2 63 12 0 2 63 14 0 2 69 Y 12 0.068 0 +Contig33_chr12_19804073_19804529 178 T C 69.4 chr12 19804261 T 13 0 2 66 13 0 2 66 22 0 2 93 11 0 2 60 12 0 2 63 18 0 2 81 Y 11 1.571 0 +Contig41_chr12_25565452_25566993 475 G T 6.29 chr12 25565926 G 15 0 2 72 14 0 2 69 10 0 2 57 15 0 2 72 18 0 2 81 19 0 2 84 N 10 2.231 1 +Contig9_chr12_27204351_27204696 239 A G 145.0 chr12 27204587 A 7 0 2 48 8 0 2 51 12 0 2 63 8 0 2 51 11 0 2 60 11 0 2 60 Y 14 0.046 0 +Contig45_chr12_30548282_30550498 448 C T 124.0 chr12 30548703 - 9 0 2 54 11 0 2 60 22 0 2 93 19 0 2 84 12 0 2 63 12 0 2 63 Y 66 0.305 0 +Contig46_chr12_35571846_35572563 58 G C 83.2 chr12 35571906 G 4 0 2 39 10 0 2 57 11 0 2 60 6 0 2 45 10 0 2 57 6 0 2 45 Y 55 +99. 1 +Contig28_chr12_42075871_42076044 136 G A 134.0 chr12 42076006 A 6 0 2 45 5 0 2 42 7 0 2 48 7 0 2 48 2 0 2 33 4 0 2 39 N 3 9.479 0 +Contig16_chr12_42386141_42387454 194 A G 161.0 chr12 42386323 A 11 0 2 60 8 0 2 54 23 0 2 96 17 0 2 78 6 0 2 45 13 0 2 66 Y 7 0.927 1 +Contig42_chr12_44424628_44425829 255 A G 84.4 chr12 44424879 A 12 0 2 63 19 0 2 84 23 0 2 96 15 0 2 72 18 0 2 81 14 0 2 69 Y 18 1.190 2 +Contig10_chr12_44447953_44449698 63 C T 105.0 chr12 44448020 C 11 0 2 60 9 0 2 54 12 0 2 63 10 0 2 57 15 0 2 72 8 0 2 51 Y 31 11.791 0 +Contig5_chr12_53880670_53882675 1221 A C 99.4 chr12 53881888 A 16 0 2 75 18 0 2 81 23 0 2 96 10 0 2 57 15 0 2 72 17 0 2 78 Y 31 0.061 0 +Contig86_chr12_56715356_56716464 818 T C 166.0 chr12 56716164 T 20 0 2 87 16 0 2 75 16 0 2 75 14 0 2 69 13 0 2 66 7 0 2 48 Y 22 1.092 0 +Contig3_chr12_65021967_65024097 238 T G 92.6 chr12 65022205 T 17 0 2 78 14 0 2 69 16 0 2 75 9 0 2 54 13 0 2 66 15 0 2 72 Y 258 0.117 0 +Contig43_chr12_66499742_66500010 121 G T 41.5 chr12 66499866 G 12 0 2 63 4 0 2 39 8 0 2 51 6 0 2 45 10 0 2 57 6 0 2 45 N 42 0.421 0 +Contig14_chr12_71364692_71365311 20 A C 103.0 chr12 71364712 A 7 0 2 48 3 0 2 36 5 0 2 42 1 0 2 30 2 0 2 33 3 0 2 36 Y 35 +99. 0 +Contig37_chr13_15910164_15910426 245 G A 32.9 chr13 -1 N 3 4 1 41 4 0 2 39 3 0 2 36 4 0 2 39 3 0 2 36 10 0 2 57 N -1 2.159 1 +Contig107_chr13_26045881_26046290 341 C G 81.4 chr13 26046230 C 16 0 2 75 20 0 2 90 14 0 2 69 15 0 2 72 9 0 2 54 9 0 2 54 Y 51 4.510 0 +Contig251_chr13_28498333_28501066 864 T G 296.0 chr13 28499180 T 3 0 2 36 5 0 2 42 4 0 2 39 2 0 2 33 5 0 2 42 6 0 2 45 Y 9 0.068 0 +Contig154_chr13_36777857_36778736 356 G A 95.5 chr13 36778225 A 6 0 2 45 11 0 2 60 11 0 2 60 9 0 2 54 13 0 2 66 8 0 2 51 Y 59 0.192 0 +Contig37_chr13_42529793_42530857 150 G T 192.0 chr13 42529926 G 18 0 2 81 14 0 2 69 16 0 2 75 14 0 2 69 8 0 2 51 11 0 2 60 N 22 0.795 5 +Contig47_chr13_47045833_47046626 257 A C 28.5 chr13 47046097 A 13 0 2 66 10 0 2 57 17 0 2 78 20 0 2 87 15 0 2 72 9 0 2 57 N 129 0.468 0 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24132818 G 21 0 2 90 16 0 2 75 12 0 2 63 10 0 2 57 11 0 2 60 20 0 2 87 Y 36 0.347 0 +Contig28_chr14_26905747_26909514 975 G C 3.13 chr14 26906723 G 16 0 2 75 10 0 2 57 12 0 2 63 15 0 2 72 10 0 2 57 7 0 2 48 N 287 0.117 2 +Contig14_chr14_29616948_29618316 109 G A 80.3 chr14 29617053 - 17 0 2 78 16 0 2 75 16 0 2 75 10 0 2 57 17 0 2 78 19 0 2 84 Y 32 1.051 0 +Contig24_chr14_29728478_29728839 242 T A 107.0 chr14 29728724 T 2 0 2 33 12 0 2 63 10 0 2 57 12 0 2 63 5 0 2 42 9 0 2 54 N 70 2.712 0 +Contig76_chr14_30028102_30029179 1046 C T 38.5 chr14 30029169 T 3 0 2 36 6 0 2 45 9 0 2 54 7 0 2 48 9 0 2 54 8 0 2 51 Y 96 +99. 0 +Contig115_chr14_31417207_31417574 259 A G 12.1 chr14 31417454 G 13 0 2 66 15 0 2 72 21 0 2 90 12 0 2 63 13 0 2 66 9 0 2 54 N 28 5.379 2 +Contig70_chr14_46653662_46653790 111 G A 46.7 chr14 46653768 G 7 0 2 48 5 0 2 42 11 0 2 60 11 0 2 60 8 0 2 51 10 0 2 57 N 21 +99. 2 +Contig43_chr14_49991855_49993511 918 A G 112.0 chr14 49992767 G 15 0 2 72 10 0 2 57 11 0 2 63 9 0 2 54 12 0 2 63 9 0 2 54 Y 6 0.314 1 +Contig64_chr14_56768376_56768902 473 C T 29.0 chr14 56768832 C 15 0 2 72 11 0 2 60 14 0 2 69 14 0 2 69 7 0 2 48 9 0 2 54 Y 91 8.281 0 +Contig60_chr15_18493036_18494316 150 G A 92.6 chr15 18493188 G 9 0 2 54 13 0 2 66 9 0 2 54 6 0 2 45 5 0 2 42 12 0 2 63 Y 45 0.125 0 +Contig213_chr15_19567788_19568626 196 A C 13.9 chr15 19567992 A 4 0 2 39 2 0 2 33 7 0 2 48 4 0 2 39 4 0 2 39 6 0 2 45 Y 111 0.043 0 +Contig59_chr15_22138344_22138535 120 G C 142.0 chr15 22138470 C 11 0 2 60 10 0 2 57 18 0 2 81 4 0 2 39 10 0 2 57 15 0 2 72 N 8 2.553 0 +Contig112_chr15_26772864_26773267 374 C T 21.6 chr15 26773244 C 4 0 2 39 4 0 2 39 5 0 2 42 2 0 2 33 4 0 2 39 3 0 2 36 N 18 +99. 0 +Contig24_chr15_26894765_26895003 155 G A 87.6 chr15 -1 N 6 0 2 45 5 0 2 42 7 0 2 48 4 0 2 39 4 0 2 39 2 0 2 33 N -1 0.178 0 +Contig2_chr15_33944796_33947182 1860 G A 99.5 chr15 33946654 G 10 0 2 57 11 0 2 60 16 0 2 75 14 0 2 69 14 0 2 69 16 0 2 75 Y 16 0.252 0 +Contig73_chr15_34690052_34691332 714 T C 130.0 chr15 34690769 T 7 0 2 48 7 0 2 48 17 0 2 78 9 0 2 54 9 0 2 54 4 0 2 39 Y 7 6.003 0 +Contig68_chr15_37747190_37747426 126 G A 130.0 chr15 37747331 G 14 0 2 69 14 0 2 69 11 0 2 63 19 0 2 84 13 0 2 66 21 0 2 90 N 229 0.255 0 +Contig35_chr15_41400484_41400672 160 A C 143.0 chr15 -1 N 1 0 2 30 2 0 2 33 0 0 -1 0 2 0 2 33 3 0 2 36 2 0 2 33 N -1 +99. 0 +Contig104_chr15_45106954_45107158 70 A T 64.4 chr15 45107015 A 6 0 2 45 6 0 2 45 19 0 2 84 7 0 2 48 7 0 2 48 3 0 2 36 N 202 4.319 0 +Contig119_chr16_6160274_6160477 180 G A 54.8 chr16 6160457 G 7 0 2 48 6 0 2 45 12 0 2 63 3 0 2 36 11 0 2 60 10 0 2 57 N 42 +99. 0 +Contig126_chr16_10611887_10612152 150 G T 145.0 chr16 10612037 G 14 0 2 69 9 0 2 54 11 0 2 63 8 0 2 51 8 0 2 51 11 0 2 60 N 15 0.104 6 +Contig114_chr16_12565220_12565676 10 G A 134.0 chr16 12565230 G 0 0 -1 0 2 0 2 33 2 0 2 33 0 0 -1 0 1 0 2 30 1 0 2 30 N 333 +99. 0 +Contig43_chr16_20200090_20200514 70 A G 58.6 chr16 20200154 A 11 0 2 60 15 0 2 72 15 0 2 72 6 0 2 45 9 0 2 54 12 0 2 63 Y 2 0.466 1 +Contig60_chr16_28079136_28080263 588 T G 157.0 chr16 28079739 T 22 0 2 93 20 0 2 87 22 0 2 93 17 0 2 78 12 0 2 63 10 0 2 57 Y 105 5.999 1 +Contig70_chr16_33758668_33759655 104 A T 58.1 chr16 33758772 A 6 0 2 45 7 0 2 48 17 0 2 78 14 0 2 69 8 0 2 51 10 0 2 57 N 54 0.162 0 +Contig66_chr16_37935682_37935831 116 T C 99.2 chr16 37935802 C 12 0 2 63 6 0 2 45 19 0 2 84 12 0 2 63 13 0 2 66 17 0 2 78 N 266 +99. 2 +Contig16_chr16_40451506_40451643 84 A G 59.8 chr16 40451592 A 7 0 2 48 5 0 2 42 7 0 2 48 13 0 2 66 14 0 2 69 19 0 2 84 N 45 5.061 0 +Contig53_chr16_49888293_49888587 260 G A 108.0 chr16 49888550 A 4 0 2 39 1 0 2 30 3 0 2 36 5 0 2 42 2 0 2 33 2 0 2 33 Y 9 0.261 1 +Contig31_chr17_12128267_12129637 205 G A 90.5 chr17 12128484 G 7 0 2 48 6 0 2 45 6 0 2 45 11 0 2 60 7 0 2 48 4 0 2 39 Y 10 0.246 0 +Contig50_chr17_12247973_12249183 889 G T 47.6 chr17 12248878 G 0 1 2 9 8 0 2 51 9 2 2 21 7 2 2 21 15 0 2 72 0 3 0 9 Y 1 1.181 0 +Contig1_chr17_12979232_12980380 808 G T 12.3 chr17 12980028 G 18 0 2 81 12 0 2 63 21 0 2 90 13 0 2 66 22 0 2 93 18 0 2 81 Y 9 0.336 1 +Contig63_chr17_14186372_14186928 54 C T 70.7 chr17 14186427 C 6 0 2 45 2 0 2 33 5 0 2 42 6 0 2 45 3 0 2 36 3 0 2 36 Y 11 0.560 3 +Contig42_chr17_23434859_23438330 2100 C T 39.5 chr17 23436985 T 4 0 2 39 7 0 2 48 7 0 2 48 3 0 2 36 6 0 2 45 2 0 2 33 Y 25 0.344 0 +Contig63_chr17_23796320_23796814 220 A G 54.0 chr17 23796536 G 6 0 2 45 4 0 2 39 5 0 2 42 6 0 2 45 4 0 2 39 6 0 2 45 Y 139 0.067 1 +Contig76_chr17_24107434_24107834 316 T C 141.0 chr17 24107726 T 19 0 2 84 15 0 2 72 20 0 2 87 16 0 2 75 11 0 2 60 18 0 2 81 Y 30 0.175 2 +Contig99_chr17_26021506_26022200 505 C T 88.8 chr17 26022017 T 15 0 2 72 13 0 2 66 19 0 2 84 9 0 2 54 10 0 2 57 11 0 2 60 Y 1 0.172 1 +Contig59_chr17_26790302_26795045 287 C T 45.1 chr17 26790582 C 8 0 2 51 6 0 2 45 13 0 2 66 6 0 2 45 15 0 2 72 12 0 2 63 Y 75 0.019 1 +Contig99_chr17_27018324_27019378 446 G A 31.1 chr17 27018776 G 14 0 2 69 12 0 2 63 14 0 2 69 10 0 2 57 9 0 2 54 11 0 2 60 Y 13 0.290 4 +Contig125_chr17_27739115_27739410 63 G A 107.0 chr17 27739177 G 8 0 2 51 11 0 2 60 16 0 2 75 8 0 2 51 4 0 2 39 15 0 2 72 N 100 0.819 0 +Contig115_chr17_37489899_37490101 159 G A 62.4 chr17 37490067 G 4 0 2 39 3 0 2 36 4 0 2 39 4 0 2 39 3 0 2 36 6 0 2 45 N 4 1.411 1 +Contig180_chr17_45154356_45154925 524 A G 146.0 chr17 45154886 G 7 0 2 48 9 0 2 54 7 0 2 48 9 0 2 54 4 0 2 39 8 0 2 51 Y 11 +99. 2 +Contig61_chr17_48221795_48223545 1404 T A 177.0 chr17 48223216 T 15 0 2 72 14 0 2 69 24 0 2 99 17 0 2 78 18 0 2 81 24 0 2 99 Y 161 0.633 2 +Contig27_chr17_61713766_61716585 1056 G C 40.0 chr17 61714821 G 4 0 2 39 8 0 2 51 10 0 2 57 6 0 2 45 6 0 2 45 3 0 2 36 N 6 2.200 4 +Contig229_chr18_3706523_3708577 1076 A G 83.9 chr18 3707630 A 11 0 2 60 13 0 2 66 26 0 2 105 11 0 2 60 15 0 2 72 17 0 2 78 Y 63 0.445 0 +Contig24_chr18_14049894_14050480 24 A G 123.0 chr18 14049918 A 5 0 2 42 5 0 2 42 4 0 2 39 6 0 2 45 7 0 2 48 5 0 2 42 Y 17 +99. 0 +Contig30_chr18_18771753_18772121 39 C G 48.5 chr18 18771787 C 2 0 2 33 5 0 2 42 2 0 2 33 6 0 2 45 3 0 2 36 2 0 2 33 N 5 0.135 0 +Contig123_chr18_19916160_19916379 116 G A 79.2 chr18 19916272 A 14 0 2 69 12 0 2 63 14 0 2 69 6 0 2 45 11 0 2 60 10 0 2 57 N 26 0.172 0 +Contig82_chr18_27305489_27306229 566 C T 49.5 chr18 27306051 A 6 0 2 45 6 0 2 45 10 0 2 57 11 0 2 60 6 0 2 45 7 0 2 48 N 1 0.349 0 +Contig71_chr18_34324706_34326687 136 G A 151.0 chr18 34324841 G 9 0 2 54 9 0 2 54 17 0 2 78 8 0 2 51 11 0 2 60 10 0 2 57 Y 2 2.129 2 +Contig16_chr18_34672093_34673044 538 T C 58.2 chr18 34672635 T 8 0 2 51 15 0 2 72 16 0 2 75 15 0 2 72 9 0 2 57 18 0 2 81 Y 8 0.214 1 +Contig96_chr18_38492535_38493333 624 G A 119.0 chr18 38493162 T 17 0 2 78 12 0 2 63 13 0 2 66 16 0 2 75 8 0 2 51 15 0 2 72 Y 127 0.131 0 +Contig226_chr18_47753756_47754666 427 T C 21.1 chr18 47754215 T 10 0 2 57 4 0 2 39 8 0 2 51 5 0 2 42 6 0 2 45 7 0 2 48 Y 42 0.522 0 +Contig170_chr18_49411558_49412230 94 C A 74.3 chr18 49411655 C 14 0 2 69 10 0 2 57 9 0 2 54 10 0 2 57 3 0 2 36 3 0 2 36 N 9 1.457 0 +Contig192_chr18_49419342_49420737 1058 C T 42.8 chr18 49420381 A 3 0 2 36 4 0 2 39 5 0 2 42 8 0 2 51 3 0 2 36 3 0 2 36 Y 34 2.107 2 +Contig64_chr18_55979770_55980315 49 G A 89.1 chr18 55979824 G 3 0 2 36 9 0 2 54 7 0 2 51 4 0 2 39 3 0 2 36 3 0 2 36 Y -1 2.124 0 +Contig20_chr18_58130301_58130735 112 A G 74.4 chr18 58130413 A 12 0 2 66 11 0 2 60 11 0 2 60 12 0 2 63 6 0 2 45 6 0 2 45 Y 10 0.290 0 +Contig146_chr19_5221790_5223013 143 A G 114.0 chr19 5221916 - 1 0 2 30 4 0 2 39 3 0 2 36 5 0 2 42 2 0 2 33 5 0 2 42 Y 12 0.870 0 +Contig13_chr19_7739961_7740118 26 C G 220.0 chr19 -1 N 3 0 2 36 1 0 2 30 2 0 2 33 3 0 2 36 1 0 2 30 2 0 2 33 N -1 +99. 0 +Contig67_chr19_12398520_12399367 499 C T 161.0 chr19 12399017 C 10 0 2 57 11 0 2 60 20 0 2 87 14 0 2 69 24 0 2 99 8 0 2 51 Y 137 5.634 0 +Contig66_chr19_16285672_16287223 996 C T 190.0 chr19 16286674 C 9 0 2 57 14 0 2 69 16 0 2 78 17 0 2 78 8 0 2 51 22 0 2 93 Y 40 0.110 0 +Contig129_chr19_25541958_25542221 202 T C 68.1 chr19 25542154 C 11 0 2 60 19 0 2 84 10 0 2 60 17 0 2 78 9 0 2 54 12 0 2 63 N -1 2.551 1 +Contig152_chr19_34274440_34275622 1072 C T 48.0 chr19 34275509 T 1 0 2 30 2 0 2 33 1 0 2 30 1 0 2 30 4 0 2 39 5 0 2 42 N 71 0.309 0 +Contig29_chr19_37339947_37341911 1692 C T 211.0 chr19 37341631 C 15 0 2 72 20 0 2 87 11 0 2 60 15 0 2 72 3 0 2 36 12 0 2 63 Y 7 0.096 0 +Contig39_chr19_47709708_47711327 444 C T 36.8 chr19 47710148 T 10 0 2 57 4 0 2 39 8 0 2 51 9 0 2 54 6 0 2 45 6 0 2 45 Y 95 1.251 1 +Contig60_chr19_54013816_54014398 281 A G 138.0 chr19 54014103 C 6 0 2 45 15 0 2 72 7 0 2 48 10 0 2 57 15 0 2 72 10 0 2 57 Y 188 1.271 0 +Contig251_chr19_56559098_56559626 452 T C 3.36 chr19 56559549 T 12 0 2 63 13 0 2 66 21 0 2 90 15 0 2 72 14 0 2 69 11 0 2 60 N 1 0.117 0 +Contig50_chr20_12138509_12141975 3206 C A 248.0 chr20 12141763 C 8 0 2 51 15 0 2 72 14 0 2 69 6 0 2 45 10 0 2 57 7 0 2 48 Y 2 0.384 0 +Contig36_chr20_32631363_32632049 176 G A 24.1 chr20 32631526 G 7 0 2 48 14 0 2 69 19 0 2 84 14 0 2 69 15 0 2 72 16 0 2 75 N 50 1.150 0 +Contig39_chr20_36316398_36316498 57 C T 30.3 chr20 36316455 C 2 0 2 33 0 1 2 8 0 0 -1 0 0 1 2 10 0 0 -1 0 0 0 -1 0 N -483 +99. 0 +Contig32_chr20_36468058_36468869 66 C T 40.4 chr20 36468127 C 6 0 2 45 3 0 2 36 4 0 2 39 5 0 2 42 3 0 2 36 4 0 2 39 N 59 0.281 0 +Contig24_chr20_38203888_38204900 834 C T 132.0 chr20 38204731 C 9 0 2 54 17 0 2 78 20 0 2 87 8 0 2 51 11 0 2 60 17 0 2 78 Y 14 0.397 0 +Contig79_chr20_44263127_44264103 456 G T 31.5 chr20 44263573 G 22 0 2 93 16 0 2 75 15 0 2 72 19 0 2 84 13 0 2 66 26 0 2 105 Y 8 3.250 0 +Contig26_chr20_45878482_45878787 197 A G 160.0 chr20 45878672 A 17 0 2 78 15 0 2 72 11 0 2 63 17 0 2 78 12 0 2 63 10 0 2 57 N 14 0.535 0 +Contig119_chr20_46550670_46551383 609 G A 139.0 chr20 46551277 G 7 0 2 48 17 0 2 78 19 0 2 84 20 0 2 87 9 0 2 54 15 0 2 72 Y 7 0.488 1 +Contig50_chr21_4178523_4178687 121 G A 362.0 chr21 4178640 G 8 0 2 51 14 0 2 69 5 0 2 42 3 0 2 36 11 0 2 60 4 0 2 39 N 392 0.483 0 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3 0 2 36 2 0 2 33 1 0 2 30 0 0 -1 0 3 0 2 36 1 0 2 30 N -1 +99. 1 +Contig159_chr22_7896450_7896974 109 G C 151.0 chr22 7896570 G 16 0 2 75 5 7 1 62 14 0 2 69 16 0 2 75 13 0 2 66 13 0 2 66 Y 16 0.465 0 +Contig46_chr22_9416920_9417467 381 G A 145.0 chr22 9417259 G 10 0 2 57 9 0 2 54 10 0 2 57 6 0 2 45 13 0 2 66 7 0 2 48 Y 154 0.242 0 +Contig86_chr22_9440787_9441725 713 T G 119.0 chr22 9441488 G 6 0 2 45 12 0 2 63 10 0 2 57 11 0 2 60 13 0 2 66 16 0 2 75 Y 132 0.218 0 +Contig16_chr22_15636960_15637372 236 A C 9.79 chr22 15637192 T 4 0 2 39 5 0 2 42 12 0 2 63 7 0 2 48 6 0 2 45 11 0 2 60 Y 5 2.163 0 +Contig4_chr22_16114310_16114546 128 G C 101.0 chr22 16114432 G 10 0 2 57 13 0 2 66 20 0 2 87 20 0 2 87 16 0 2 75 9 0 2 54 N 19 0.526 0 +Contig23_chr22_34612023_34612568 167 C G 92.3 chr22 34612181 C 11 0 2 60 18 0 2 81 13 0 2 66 8 0 2 51 12 0 2 63 14 0 2 69 Y 7 0.409 0 +Contig4_chr22_38252245_38253712 799 A C 159.0 chr22 38253064 A 18 0 2 81 15 0 2 72 15 0 2 72 20 0 2 87 27 0 2 108 15 0 2 72 Y 90 4.330 0 +Contig122_chr22_48412466_48414788 1888 C T 125.0 chr22 48414355 T 16 0 2 75 15 0 2 72 16 0 2 75 14 0 2 72 12 0 2 63 7 0 2 48 N 42 0.122 0 +Contig77_chr22_49764414_49764875 353 C A 148.0 chr22 49764777 C 7 4 1 65 18 0 2 81 16 0 2 75 20 0 2 87 4 3 1 52 9 4 1 67 Y 12 0.941 0 +Contig26_chr22_57817664_57819633 1453 A G 150.0 chr22 57819121 G 9 0 2 54 9 0 2 54 13 0 2 66 15 0 2 72 11 0 2 60 14 0 2 69 N 15 0.471 1 +Contig348_chr22_62406104_62406495 189 C A 134.0 chr22 62406302 A 9 0 2 54 14 0 2 69 11 0 2 60 10 0 2 57 12 0 2 63 6 0 2 45 Y 5 0.912 0 +Contig133_chr23_3525134_3526502 1223 A G 201.0 chr23 3526387 A 11 0 2 60 13 0 2 66 23 0 2 96 21 0 2 90 13 0 2 66 10 0 2 57 Y 61 1.359 0 +Contig111_chr23_7058063_7058181 107 G A 108.0 chr23 7058162 A 8 0 2 51 8 0 2 51 7 0 2 48 2 0 2 33 5 0 2 42 6 0 2 45 N 3 +99. 0 +Contig79_chr23_7844129_7844837 110 C A 141.0 chr23 7844237 T 13 0 2 66 15 0 2 72 17 0 2 78 12 0 2 63 15 0 2 72 16 0 2 75 Y 40 0.339 0 +Contig38_chr23_9201002_9201725 597 C T 155.0 chr23 9201609 T 17 0 2 78 8 0 2 51 13 0 2 66 5 0 2 42 11 0 2 60 7 0 2 48 Y 167 0.633 1 +Contig33_chr23_20672540_20674320 347 T A 91.4 chr23 20672885 A 11 0 2 60 14 0 2 69 15 0 2 72 7 0 2 48 12 0 2 63 18 0 2 81 Y 31 0.452 1 +Contig35_chr23_28447813_28449115 70 T A 21.3 chr23 28447881 T 9 0 2 54 8 0 2 51 10 0 2 57 9 0 2 54 10 0 2 57 12 0 2 63 N 251 0.163 1 +Contig51_chr23_30590939_30591162 140 C T 142.0 chr23 30591080 C 14 0 2 69 4 0 2 39 10 0 2 57 12 0 2 63 14 0 2 69 4 0 2 39 N 13 1.658 0 +Contig57_chr23_32216351_32216721 179 T G 143.0 chr23 32216534 T 15 0 2 72 15 0 2 72 23 0 2 96 13 0 2 66 16 0 2 75 15 0 2 72 N 32 1.387 1 +Contig93_chr23_35744841_35745791 40 A T 30.4 chr23 35744880 T 6 0 2 45 7 0 2 48 7 0 2 48 2 0 2 33 5 0 2 42 5 0 2 42 Y 50 2.173 0 +Contig99_chr23_42543966_42544147 14 G A 357.0 chr23 42543980 G 4 0 2 39 2 0 2 33 3 0 2 36 3 0 2 36 1 0 2 30 2 0 2 33 N 69 +99. 0 +Contig32_chr23_48285289_48286638 186 T C 176.0 chr23 48285470 T 18 0 2 81 12 0 2 63 16 0 2 75 13 0 2 66 9 0 2 54 9 0 2 54 Y 4 4.238 1 +Contig50_chr24_22515247_22516072 761 C T 243.0 chr24 22515981 T 11 0 2 60 10 0 2 57 8 0 2 51 9 0 2 54 18 0 2 81 8 0 2 51 Y 1 0.190 0 +Contig92_chr24_28935897_28936321 13 G A 47.1 chr24 -1 N 2 0 2 33 1 0 2 30 0 0 -1 0 0 0 -1 0 1 0 2 30 0 0 -1 0 Y -1 +99. 2 +Contig84_chr24_29196623_29199644 466 C T 126.0 chr24 29197091 T 7 0 2 48 11 0 2 60 8 0 2 51 7 0 2 48 11 0 2 60 15 0 2 72 Y 42 0.215 0 +Contig35_chr24_30150986_30151507 492 A C 114.0 chr24 30151448 A 5 0 2 42 2 0 2 33 2 0 2 33 3 0 2 36 3 0 2 36 5 0 2 42 N 41 2.587 6 +Contig61_chr24_30465488_30465834 149 G T 68.2 chr24 30465637 G 13 0 2 66 4 2 2 11 18 0 2 81 11 0 2 60 11 0 2 60 9 0 2 54 N 99 0.105 2 +Contig145_chr24_34778364_34778898 163 T C 372.0 chr24 34778541 C 10 0 2 57 8 0 2 51 12 0 2 63 12 0 2 63 6 1 2 31 7 0 2 48 Y 40 0.037 0 +Contig34_chr24_36147443_36150244 2679 C T 140.0 chr24 36150125 C 13 0 2 66 7 0 2 48 14 0 2 69 14 0 2 69 10 0 2 57 13 0 2 66 N 282 0.099 1 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0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 N 27 +99. 1 +Contig59_chr25_18196776_18197707 785 G A 112.0 chr25 18197551 G 8 10 1 42 27 0 2 108 21 0 2 90 18 0 2 81 10 0 2 57 14 0 2 69 N 36 3.625 0 +Contig103_chr25_38891221_38892140 407 G A 131.0 chr25 38891644 G 8 0 2 51 14 0 2 69 18 0 2 81 8 0 2 51 8 0 2 51 11 0 2 60 Y 149 0.167 4 +Contig84_chr25_42407960_42408708 55 C T 119.0 chr25 42408013 C 6 0 2 45 9 0 2 54 11 0 2 60 9 0 2 54 7 0 2 48 8 0 2 51 Y 11 0.121 0 +Contig73_chr25_43562500_43564110 955 T C 52.1 chr25 43563469 C 9 0 2 57 4 0 2 39 6 0 2 45 5 0 2 42 7 0 2 48 10 0 2 57 Y 4 1.406 0 +Contig37_chr25_51074433_51074885 170 A G 102.0 chr25 51074589 G 11 0 2 60 7 0 2 48 6 0 2 45 15 0 2 72 9 0 2 54 7 0 2 48 Y 68 0.207 1 +Contig204_chr26_4311195_4311778 170 C T 16.9 chr26 4311363 T 20 0 2 87 8 0 2 51 13 0 2 66 18 0 2 81 11 0 2 60 14 0 2 69 N 35 0.085 0 +Contig122_chr26_7622321_7623491 106 C G 139.0 chr26 7622423 C 3 0 2 36 9 0 2 54 10 0 2 57 12 0 2 63 9 0 2 54 5 0 2 42 N 19 0.458 0 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2 30 7 0 2 48 14 0 2 69 13 0 2 66 9 0 2 54 3 0 2 36 Y 8 0.071 0 +Contig135_chr27_6853874_6854079 158 C T 116.0 chr27 6854032 T 18 0 2 81 19 0 2 84 13 0 2 66 7 0 2 48 8 0 2 51 11 0 2 60 N 4 0.060 1 +Contig47_chr27_11777710_11777915 25 A G 67.3 chr27 11777731 A 3 0 2 36 5 0 2 42 6 0 2 45 10 0 2 57 9 0 2 54 6 0 2 45 N 97 +99. 0 +Contig23_chr27_14633002_14633153 23 G A 128.0 chr27 14633023 A 3 0 2 36 4 0 2 39 5 0 2 42 5 0 2 42 3 0 2 36 2 0 2 33 N 240 3.881 0 +Contig31_chr27_14987233_14988055 630 A G 48.5 chr27 14987850 G 10 0 2 57 2 0 2 33 4 0 2 39 4 0 2 39 1 0 2 30 4 0 2 39 Y 9 0.089 1 +Contig29_chr27_15428166_15429413 380 T C 140.0 chr27 15428539 T 15 0 2 72 15 0 2 72 17 0 2 78 15 0 2 72 15 0 2 72 15 0 2 72 Y 47 0.916 1 +Contig31_chr27_19519489_19520891 129 G T 14.9 chr27 19519624 T 12 0 2 63 19 0 2 84 20 0 2 87 16 0 2 75 10 0 2 57 11 0 2 60 Y 48 2.756 0 +Contig64_chr27_34654435_34654621 132 C A 115.0 chr27 34654567 T 2 0 2 33 2 0 2 33 5 0 2 42 3 0 2 36 3 0 2 36 8 0 2 51 N 12 0.297 1 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36340213 T 4 0 2 39 0 0 -1 0 2 0 2 33 2 0 2 33 3 0 2 36 4 0 2 39 N 4 0.183 0 +Contig175_chr28_36441165_36441915 68 T C 3.83 chr28 36441234 T 4 4 1 15 6 0 2 45 12 0 2 63 15 0 2 72 6 0 2 45 9 0 2 54 N 4 1.610 2 +Contig29_chr29_4726399_4727143 559 A T 163.0 chr29 4726955 A 15 0 2 72 18 0 2 81 18 0 2 81 16 0 2 75 11 0 2 60 14 0 2 72 Y 161 3.114 0 +Contig48_chr29_13129286_13130137 232 A G 92.2 chr29 13129514 G 13 0 2 66 11 0 2 60 19 0 2 84 16 0 2 75 11 0 2 60 17 0 2 78 Y 337 2.581 1 +Contig64_chr29_15736891_15737257 344 T C 40.4 chr29 15737233 C 1 0 2 30 0 0 -1 0 0 0 -1 0 2 0 2 33 0 0 -1 0 0 0 -1 0 N 58 +99. 0 +Contig33_chr29_17000374_17000921 71 C T 48.6 chr29 17000441 - 4 0 2 39 9 0 2 54 12 0 2 66 10 0 2 57 7 0 2 48 4 0 2 39 N 26 5.491 0 +Contig34_chr29_17581796_17584016 2105 C T 126.0 chr29 17583890 T 14 0 2 69 11 0 2 60 18 0 2 81 12 0 2 63 10 0 2 57 10 0 2 57 Y 22 2.208 0 +Contig19_chr29_20976080_20977761 1007 G A 115.0 chr29 20977076 G 19 0 2 84 22 0 2 93 22 0 2 93 22 0 2 93 11 0 2 60 13 0 2 66 Y 4 1.915 0 +Contig51_chr29_21149853_21150467 266 C T 146.0 chr29 21150118 C 12 0 2 63 12 0 2 63 23 0 2 96 14 0 2 69 13 0 2 66 10 0 2 57 Y 4 0.051 0 +Contig1_chr30_5992217_5993068 106 C T 129.0 chr30 5992319 C 10 0 2 57 11 0 2 60 7 0 2 48 11 0 2 60 10 0 2 57 12 0 2 63 Y 76 1.079 0 +Contig1_chr30_8232878_8233406 402 C T 127.0 chr30 8233264 C 8 0 2 51 19 0 2 84 16 0 2 75 18 0 2 81 10 0 2 57 14 0 2 69 Y 358 5.283 0 +Contig108_chr30_9436961_9437520 546 C T 39.8 chr30 9437502 C 7 0 2 48 5 0 2 42 2 0 2 33 7 0 2 48 5 0 2 42 7 0 2 48 Y 64 +99. 0 +Contig165_chr30_25804389_25804926 190 T C 126.0 chr30 25804592 C 3 0 2 36 8 0 2 51 7 0 2 48 10 0 2 57 7 0 2 48 4 0 2 39 Y 113 0.329 0 +Contig193_chr30_27495616_27496125 434 C A 234.0 chr30 27496024 C 13 0 2 66 16 0 2 75 25 0 2 102 16 0 2 75 13 0 2 66 14 0 2 69 Y 76 2.621 0 +Contig114_chr30_33636712_33637208 34 C T 142.0 chr30 33636744 C 7 0 2 48 4 1 2 20 6 0 2 45 6 0 2 45 3 4 1 29 5 0 2 42 Y 14 8.028 0 +Contig38_chr31_5164423_5166573 2074 C T 134.0 chr31 5166501 T 13 0 2 66 10 0 2 57 17 0 2 78 11 0 2 60 17 0 2 78 10 0 2 57 Y 58 +99. 0 +Contig6_chr31_9649308_9650149 431 G T 162.0 chr31 9649742 G 31 0 2 120 23 0 2 96 17 0 2 78 17 0 2 78 10 0 2 57 16 0 2 75 Y 98 2.200 0 +Contig85_chr31_12242872_12245082 38 G C 92.4 chr31 12242910 G 1 0 2 30 6 0 2 45 9 0 2 54 8 0 2 51 5 0 2 42 9 0 2 54 N 2 2.340 0 +Contig7_chr31_12384974_12386400 305 C T 69.6 chr31 12385267 C 6 0 2 45 10 0 2 57 11 0 2 60 11 0 2 60 9 0 2 54 12 0 2 63 Y 44 1.165 0 +Contig90_chr31_17267583_17267778 81 C A 143.0 chr31 17267665 C 20 0 2 87 6 0 2 45 14 0 2 72 22 0 2 93 17 0 2 78 15 0 2 72 N 7 0.565 0 +Contig68_chr31_20000241_20000597 215 C T 131.0 chr31 20000454 T 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 0 0 -1 0 Y 5 3.383 1 +Contig137_chr31_23357653_23358568 885 G A 119.0 chr31 23358545 G 5 0 2 42 3 0 2 36 3 0 2 36 2 0 2 33 3 0 2 36 4 0 2 39 Y 11 +99. 0 +Contig17_chr31_26433828_26434459 498 T C 9.79 chr31 26434322 T 18 0 2 81 10 0 2 57 15 0 2 72 13 0 2 66 16 0 2 75 15 0 2 72 Y 137 4.814 0 +Contig9_chr32_19479532_19479735 12 A G 20.7 chr32 19479544 A 1 0 2 30 2 0 2 33 1 0 2 30 5 0 2 42 3 0 2 36 3 0 2 36 N 17 +99. 0 +Contig30_chr32_25902721_25905783 208 C G 162.0 chr32 25902927 G 11 0 2 60 13 0 2 66 11 0 2 60 12 0 2 63 7 0 2 48 11 0 2 60 Y 145 0.322 2 +Contig7_chr32_27789513_27789926 20 G A 7.19 chr32 27789530 A 0 0 -1 0 4 0 2 39 4 0 2 39 4 0 2 39 2 0 2 33 6 0 2 45 Y 14 +99. 0 +Contig42_chr32_38900713_38901320 320 A G 134.0 chr32 38901021 T 12 0 2 63 10 0 2 57 9 11 1 104 5 0 2 42 19 0 2 84 7 6 1 56 Y 71 0.165 0 +Contig18_chr33_22207246_22209159 1363 G T 51.5 chr33 22208619 - 16 0 2 75 8 0 2 51 11 0 2 60 10 0 2 57 15 0 2 72 12 0 2 63 Y 59 2.560 0 +Contig104_chr33_22483642_22484187 424 C T 140.0 chr33 22484054 T 13 0 2 66 16 0 2 75 9 0 2 54 15 0 2 72 13 0 2 66 10 0 2 57 Y 36 0.404 0 +Contig170_chr33_26189421_26189940 292 T C 98.4 chr33 26189703 T 21 0 2 90 13 0 2 66 15 0 2 72 13 0 2 66 19 0 2 84 13 0 2 66 Y 23 0.307 0 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42800126 T 5 0 2 42 7 0 2 48 6 0 2 45 7 0 2 48 6 0 2 45 2 0 2 33 Y 5 2.787 0 +Contig47_chr35_3666773_3667898 348 G T 124.0 chr35 3667121 G 9 0 2 54 20 0 2 87 18 0 2 81 15 0 2 72 12 0 2 63 14 0 2 69 Y 285 0.235 0 +Contig195_chr35_15722500_15722741 205 G A 4.08 chr35 15722718 G 3 0 2 36 5 0 2 42 1 0 2 30 6 0 2 45 1 0 2 30 1 0 2 30 N 43 +99. 0 +Contig101_chr35_19513178_19513697 62 C T 112.0 chr35 19513238 C 12 0 2 63 7 0 2 48 13 0 2 66 7 0 2 48 5 0 2 42 8 0 2 51 N 115 3.135 0 +Contig19_chr35_23887144_23888282 90 C A 10.1 chr35 23887242 - 3 3 1 12 4 4 1 19 8 6 1 37 4 3 1 11 8 3 2 7 9 3 2 11 Y 105 0.199 0 +Contig47_chr35_24382042_24382526 33 G A 87.0 chr35 24382076 G 5 0 2 42 4 0 2 39 6 0 2 45 7 0 2 48 4 0 2 39 2 0 2 33 Y 71 +99. 0 +Contig77_chr35_24796947_24797172 65 A G 52.1 chr35 24797009 A 7 0 2 48 5 0 2 42 8 0 2 51 6 0 2 45 12 0 2 63 10 0 2 57 N 11 1.401 3 +Contig74_chr35_25394343_25394813 303 A T 221.0 chr35 25394646 G 23 0 2 96 15 0 2 72 25 0 2 105 7 7 1 49 18 0 2 81 16 0 2 75 Y 58 4.298 0 +Contig5_chr36_4562983_4563634 343 C T 151.0 chr36 4563324 T 20 0 2 87 20 0 2 87 23 0 2 96 24 0 2 99 9 0 2 54 8 0 2 51 Y 40 1.169 0 +Contig75_chr36_7885319_7885588 53 G A 25.7 chr36 7885372 G 10 0 2 57 8 0 2 51 13 0 2 66 7 0 2 48 4 0 2 39 7 0 2 48 N 7 2.653 0 +Contig184_chr36_18956191_18958552 187 A G 11.5 chr36 18956371 G 10 0 2 57 11 0 2 60 21 0 2 90 14 0 2 69 7 0 2 48 4 0 2 39 N 278 1.434 2 +Contig12_chr36_21557176_21557828 513 T A 159.0 chr36 21557695 A 11 0 2 60 14 0 2 69 21 0 2 90 12 0 2 63 15 0 2 72 11 0 2 60 Y 55 0.222 0 +Contig2_chr36_22436067_22436794 653 C T 73.0 chr36 22436730 C 11 0 2 60 16 0 2 75 13 0 2 66 11 0 2 60 21 0 2 90 21 0 2 90 Y 9 0.534 0 +Contig133_chr36_32954045_32955409 136 A G 116.0 chr36 32954182 A 16 0 2 75 15 0 2 72 20 0 2 87 11 0 2 60 18 0 2 81 13 0 2 66 Y 74 3.772 1 +Contig53_chr37_6665763_6665919 116 C T 111.0 chr37 6665875 C 9 0 2 54 9 0 2 54 5 0 2 42 9 0 2 54 8 0 2 51 10 0 2 57 N 15 10.875 1 +Contig42_chr37_9589176_9591269 252 G A 25.1 chr37 9589430 G 10 0 2 40 13 0 2 66 18 0 2 81 21 0 2 90 9 0 2 54 17 0 2 78 N 67 1.170 2 +Contig2_chr37_17134963_17136513 1140 A C 158.0 chr37 17136092 A 14 0 2 69 24 0 2 99 17 0 2 78 16 0 2 75 15 0 2 75 13 0 2 66 Y 12 0.053 1 +Contig18_chr37_17147806_17149851 291 T G 112.0 chr37 17148084 T 4 6 1 45 16 0 2 75 17 0 2 78 14 0 2 69 22 0 2 93 13 0 2 66 Y 41 4.442 0 +Contig64_chr37_17606895_17607534 565 C T 30.2 chr37 17607439 A 9 0 2 54 16 0 2 75 20 0 2 87 14 0 2 69 16 0 2 75 10 0 2 57 N 20 1.622 0 +Contig126_chr37_21587881_21590621 373 G T 132.0 chr37 21588256 G 11 0 2 60 11 0 2 60 23 0 2 96 12 0 2 63 8 0 2 51 18 0 2 81 Y 12 0.549 0 +Contig2_chr37_31197993_31198256 182 C T 39.6 chr37 31198171 T 6 0 2 45 10 0 2 57 7 0 2 48 9 0 2 54 10 0 2 57 12 0 2 63 N 2 0.595 0 +Contig46_chr37_31852376_31853555 825 A G 111.0 chr37 31853191 G 19 0 2 84 14 0 2 69 15 0 2 72 7 0 2 48 8 0 2 51 16 0 2 75 Y 17 0.128 1 +Contig7_chr38_12217200_12218387 1163 A T 44.4 chr38 12218353 A 11 0 2 60 13 0 2 66 17 0 2 78 10 0 2 57 11 0 2 60 11 0 2 60 Y 67 +99. 0 +Contig15_chr38_12282020_12282253 150 C T 156.0 chr38 12282164 A 17 0 2 78 11 0 2 60 19 0 2 84 14 0 2 69 5 0 2 42 14 0 2 69 Y 26 2.952 1 +Contig4_chr38_14807432_14807747 275 A G 36.5 chr38 14807715 G 1 0 2 30 2 0 2 33 2 0 2 33 4 0 2 39 1 0 2 30 0 0 -1 0 Y 28 +99. 1 +Contig6_chr38_16185744_16186110 325 A G 74.9 chr38 16186061 A 5 0 2 42 3 0 2 36 9 0 2 54 7 0 2 48 1 0 2 30 12 0 2 63 Y 40 +99. 0 +Contig265_chrX_2689247_2689484 114 C G 103.0 chrX 2689356 C 11 0 2 60 9 0 2 54 13 0 2 66 16 0 2 75 14 0 2 69 10 0 2 57 N 2 9.232 1 +Contig122_chrX_6026976_6027327 330 C T 79.4 chrX 6027303 C 3 0 2 36 3 0 2 36 3 0 2 36 4 0 2 39 3 0 2 36 6 0 2 45 Y 30 +99. 0 +Contig15_chrX_15659909_15660340 15 A C 14.9 chrX 15659924 C 1 0 2 30 1 0 2 30 3 0 2 36 6 0 2 45 2 0 2 33 0 0 -1 0 Y 216 +99. 1 +Contig12_chrX_23243561_23244412 479 C G 67.7 chrX 23244037 C 2 0 2 33 4 2 2 8 2 6 1 43 7 0 2 48 6 0 2 45 4 0 2 39 Y 208 1.620 0 +Contig113_chrX_26287829_26288398 385 C T 59.6 chrX 26288213 C 9 0 2 54 9 0 2 54 17 0 2 78 11 0 2 60 3 8 1 44 4 0 2 39 N 13 0.077 0 +Contig186_chrX_29118735_29118939 192 G A 7.01 chrX 29118931 G 1 0 2 30 7 0 2 48 4 0 2 39 5 0 2 42 8 0 2 51 4 0 2 39 N 50 +99. 0 +Contig237_chrX_31256648_31257654 165 T A 246.0 chrX 31256814 T 7 0 2 48 23 0 2 96 19 0 2 84 17 0 2 78 14 0 2 69 8 0 2 51 Y 37 1.481 0 +Contig25_chrX_40729418_40730089 332 C T 31.2 chrX 40729745 C 0 0 -1 0 2 0 2 33 4 0 2 39 5 0 2 42 3 0 2 36 3 0 2 36 Y 34 0.212 0 +Contig90_chrX_57430715_57431566 548 C T 116.0 chrX 57431266 T 9 0 2 54 18 0 2 81 13 0 2 66 14 0 2 69 8 0 2 54 7 0 2 48 Y 261 0.154 1 +Contig133_chrX_84833782_84834125 182 G A 69.7 chrX 84833962 G 5 0 2 42 18 0 2 81 12 0 2 63 19 0 2 84 6 3 1 27 7 0 2 48 N 619 0.278 0 +Contig129_chrX_90586053_90586467 135 A T 120.0 chrX 90586195 A 1 0 2 30 6 0 2 45 8 0 2 51 5 0 2 42 1 0 2 30 2 0 2 33 N 637 0.245 0 +Contig125_chrX_93319363_93320877 349 A C 145.0 chrX 93319721 A 4 0 2 39 6 0 2 45 11 0 2 60 10 0 2 57 13 0 2 66 6 0 2 45 Y 59 1.686 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpsForSubmission.text Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,29 @@ +TYPE: CONT +HANDLE: MyHandle +NAME: +FAX: +TEL: +EMAIL: +LAB: +INST: +ADDR: +|| +TYPE: METHOD +HANDLE: MyHandle +ID: +METHOD_CLASS: Sequence +TEMPLATE_TYPE: +METHOD: +|| +TYPE: SNPASSAY +HANDLE: MyHandle +BATCH: Test1 +MOLTYPE: +METHOD: +ORGANISM: +|| +TYPE: SNPPOPUSE | SNPINDUSE +HANDLE: MyHandle +BATCH: +METHOD: +||
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpsForSubmission.vcf Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,407 @@ +##fileformat=VCFv4.1 +##fileDate=2013520 +##handle=MyHandle +##batch=Test1 +##reference=pb_000001.1 +##INFO=<ID=VRT,Number=1,Type=Integer,Description="Variation type,1 - SNV: single nucleotide variation,2 - DIV: deletion/insertion variation,3 - HETEROZYGOUS: variable, but undefined at nucleotide level,4 - STR: short tandem repeat (microsatellite) variation, 5 - NAMED: insertion/deletion variation of named repetitive element,6 - NO VARIATON: sequence scanned for variation, but none observed,7 - MIXED: cluster contains submissions from 2 or more allelic classes (not used) ,8 - MNV: multiple nucleotide variation with all eles of common length greater than 1,9 - Exception"> +#CHROM POS ID REF ALT QUAL FILTER INFO +Contig161_chr1_4641264_4641879 115 Contig161_chr1_4641264_4641879;115 C T 73.5 . VRT=6 +Contig48_chr1_10150253_10151311 11 Contig48_chr1_10150253_10151311;11 A G 94.3 . VRT=6 +Contig20_chr1_21313469_21313570 66 Contig20_chr1_21313469_21313570;66 C T 54.0 . VRT=6 +Contig86_chr1_30984450_30985684 670 Contig86_chr1_30984450_30985684;670 C T 365.0 . VRT=6 +Contig5_chr1_32562160_32563940 1215 Contig5_chr1_32562160_32563940;1215 G T 163.0 . VRT=6 +Contig110_chr1_33385093_33386888 510 Contig110_chr1_33385093_33386888;510 C T 270.0 . VRT=6 +Contig100_chr1_33562920_33564288 743 Contig100_chr1_33562920_33564288;743 C T 178.0 . VRT=6 +Contig7_chr1_37302355_37302489 97 Contig7_chr1_37302355_37302489;97 A G 59.2 . VRT=6 +Contig62_chr1_41880715_41882180 1078 Contig62_chr1_41880715_41882180;1078 T G 57.6 . VRT=6 +Contig47_chr1_48409178_48409384 37 Contig47_chr1_48409178_48409384;37 C T 134.0 . VRT=6 +Contig119_chr1_49647683_49650077 1618 Contig119_chr1_49647683_49650077;1618 C A 99.7 . VRT=6 +Contig21_chr1_60697952_60699446 307 Contig21_chr1_60697952_60699446;307 G A 51.9 . VRT=6 +Contig131_chr1_62319542_62320564 169 Contig131_chr1_62319542_62320564;169 C G 103.0 . VRT=6 +Contig14_chr1_63450425_63450680 101 Contig14_chr1_63450425_63450680;101 T A 102.0 . VRT=6 +Contig83_chr1_63869778_63869942 40 Contig83_chr1_63869778_63869942;40 T C 23.7 . VRT=6 +Contig30_chr1_64702572_64703138 178 Contig30_chr1_64702572_64703138;178 A T 117.0 . VRT=6 +Contig101_chr1_69868406_69868872 287 Contig101_chr1_69868406_69868872;287 G A 14.6 . VRT=6 +Contig35_chr1_74482577_74482791 170 Contig35_chr1_74482577_74482791;170 G A 45.4 . VRT=6 +Contig49_chr1_83865731_83865944 85 Contig49_chr1_83865731_83865944;85 G A 34.1 . VRT=6 +Contig64_chr1_87343284_87345672 163 Contig64_chr1_87343284_87345672;163 T A 3.76 . VRT=6 +Contig20_chr1_110679280_110679687 181 Contig20_chr1_110679280_110679687;181 C T 87.4 . VRT=6 +Contig129_chr1_117547123_117548666 926 Contig129_chr1_117547123_117548666;926 G A 126.0 . VRT=6 +Contig7_chr1_125154638_125154844 190 Contig7_chr1_125154638_125154844;190 G T 130.0 . VRT=6 +Contig222_chr2_9817738_9818143 220 Contig222_chr2_9817738_9818143;220 C T 888.0 . VRT=6 +Contig47_chr2_25470778_25471576 126 Contig47_chr2_25470778_25471576;126 G A 888.0 . VRT=6 +Contig10_chr2_40859744_40860534 637 Contig10_chr2_40859744_40860534;637 G A 888.0 . VRT=6 +Contig52_chr2_41421981_41422725 604 Contig52_chr2_41421981_41422725;604 C A 888.0 . VRT=6 +Contig94_chr2_43869105_43870358 220 Contig94_chr2_43869105_43870358;220 G A 888.0 . VRT=6 +Contig34_chr2_48444129_48444939 695 Contig34_chr2_48444129_48444939;695 C T 134.0 . VRT=6 +Contig6_chr2_56859179_56859956 671 Contig6_chr2_56859179_56859956;671 T C 999.9 . VRT=6 +Contig115_chr2_61631913_61632510 310 Contig115_chr2_61631913_61632510;310 G T 999.3 . VRT=6 +Contig31_chr2_67331584_67331785 39 Contig31_chr2_67331584_67331785;39 C T 999.0 . VRT=6 +Contig92_chr2_75906683_75907774 773 Contig92_chr2_75906683_75907774;773 T C 85.4 . VRT=6 +Contig163_chr2_76402959_76404830 221 Contig163_chr2_76402959_76404830;221 C T 127.0 . VRT=6 +Contig177_chr2_79559305_79560033 168 Contig177_chr2_79559305_79560033;168 C T 5.67 . VRT=6 +Contig8_chr2_82945728_82945839 61 Contig8_chr2_82945728_82945839;61 T C 223.0 . VRT=6 +Contig59_chr2_85243022_85243758 506 Contig59_chr2_85243022_85243758;506 G A 96.3 . VRT=6 +Contig56_chr3_17326225_17327548 387 Contig56_chr3_17326225_17327548;387 G C 91.2 . VRT=6 +Contig108_chr3_46210055_46210874 367 Contig108_chr3_46210055_46210874;367 A G 21.0 . VRT=6 +Contig16_chr3_47113407_47114449 322 Contig16_chr3_47113407_47114449;322 G A 105.0 . VRT=6 +Contig3_chr3_47564810_47565251 262 Contig3_chr3_47564810_47565251;262 T G 112.0 . VRT=6 +Contig35_chr3_49662401_49662929 270 Contig35_chr3_49662401_49662929;270 A T 96.1 . VRT=6 +Contig97_chr3_49820354_49821631 1069 Contig97_chr3_49820354_49821631;1069 G A 44.1 . VRT=6 +Contig1_chr3_51588422_51589409 926 Contig1_chr3_51588422_51589409;926 A G 51.0 . VRT=6 +Contig25_chr3_53260697_53262560 402 Contig25_chr3_53260697_53262560;402 G A 211.0 . VRT=6 +Contig11_chr3_53992739_53995954 2392 Contig11_chr3_53992739_53995954;2392 G A 82.4 . VRT=6 +Contig236_chr3_72676275_72676473 128 Contig236_chr3_72676275_72676473;128 G A 278.0 . VRT=6 +Contig48_chr3_74792236_74792388 63 Contig48_chr3_74792236_74792388;63 T C 111.0 . VRT=6 +Contig65_chr3_80727952_80728283 39 Contig65_chr3_80727952_80728283;39 T C 71.2 . VRT=6 +Contig53_chr3_86407941_86409349 1406 Contig53_chr3_86407941_86409349;1406 G A 86.9 . VRT=6 +Contig13_chr3_92409738_92412300 718 Contig13_chr3_92409738_92412300;718 A G 23.3 . VRT=6 +Contig134_chr4_12145648_12148225 1326 Contig134_chr4_12145648_12148225;1326 C T 164.0 . VRT=6 +Contig88_chr4_15557471_15557833 268 Contig88_chr4_15557471_15557833;268 A G 145.0 . VRT=6 +Contig53_chr4_18823968_18824478 149 Contig53_chr4_18823968_18824478;149 A G 91.3 . VRT=6 +Contig86_chr4_24953866_24956222 1985 Contig86_chr4_24953866_24956222;1985 C T 76.4 . VRT=6 +Contig19_chr4_26233601_26233991 146 Contig19_chr4_26233601_26233991;146 G C 51.6 . VRT=6 +Contig78_chr4_28579975_28580134 30 Contig78_chr4_28579975_28580134;30 T G 19.6 . VRT=6 +Contig16_chr4_30177226_30179725 621 Contig16_chr4_30177226_30179725;621 C T 88.4 . VRT=6 +Contig30_chr4_46196500_46197672 1045 Contig30_chr4_46196500_46197672;1045 A C 33.4 . VRT=6 +Contig2_chr4_47039007_47039323 158 Contig2_chr4_47039007_47039323;158 G C 35.1 . VRT=6 +Contig17_chr4_61310346_61311158 267 Contig17_chr4_61310346_61311158;267 C T 49.9 . VRT=6 +Contig26_chr4_64190783_64191295 64 Contig26_chr4_64190783_64191295;64 A G 162.0 . VRT=6 +Contig11_chr4_65500960_65501654 634 Contig11_chr4_65500960_65501654;634 T C 107.0 . VRT=6 +Contig38_chr4_67768488_67768982 113 Contig38_chr4_67768488_67768982;113 A G 102.0 . VRT=6 +Contig30_chr4_70978564_70979580 596 Contig30_chr4_70978564_70979580;596 A G 164.0 . VRT=6 +Contig72_chr4_74225793_74226492 674 Contig72_chr4_74225793_74226492;674 A G 110.0 . VRT=6 +Contig32_chr4_75618955_75620254 301 Contig32_chr4_75618955_75620254;301 T C 333.0 . VRT=6 +Contig31_chr5_4734956_4736547 1166 Contig31_chr5_4734956_4736547;1166 C T 133.0 . VRT=6 +Contig113_chr5_11052263_11052603 28 Contig113_chr5_11052263_11052603;28 C T 38.2 . VRT=1 +Contig30_chr5_15698241_15699076 396 Contig30_chr5_15698241_15699076;396 G T 76.6 . VRT=6 +Contig36_chr5_17709244_17710004 373 Contig36_chr5_17709244_17710004;373 T C 281.0 . VRT=6 +Contig13_chr5_21881138_21881562 227 Contig13_chr5_21881138_21881562;227 A G 251.0 . VRT=6 +Contig5_chr5_23188121_23190168 1841 Contig5_chr5_23188121_23190168;1841 C T 141.0 . VRT=6 +Contig6_chr5_26899813_26900498 97 Contig6_chr5_26899813_26900498;97 A C 88.6 . VRT=6 +Contig314_chr5_34019166_34019319 72 Contig314_chr5_34019166_34019319;72 C A 20.1 . VRT=6 +Contig147_chr5_38980258_38980559 221 Contig147_chr5_38980258_38980559;221 C T 40.8 . VRT=6 +Contig115_chr5_48119079_48120169 151 Contig115_chr5_48119079_48120169;151 C T 78.3 . VRT=6 +Contig45_chr5_50892738_50892968 169 Contig45_chr5_50892738_50892968;169 C A 25.8 . VRT=6 +Contig40_chr5_51484164_51484696 14 Contig40_chr5_51484164_51484696;14 A G 53.3 . VRT=6 +Contig40_chr5_51664286_51667573 861 Contig40_chr5_51664286_51667573;861 C T 148.0 . VRT=6 +Contig15_chr5_51889708_51891244 882 Contig15_chr5_51889708_51891244;882 A G 149.0 . VRT=6 +Contig143_chr5_57231364_57232010 294 Contig143_chr5_57231364_57232010;294 T C 78.5 . VRT=6 +Contig13_chr5_57609985_57610584 496 Contig13_chr5_57609985_57610584;496 C T 50.5 . VRT=6 +Contig230_chr5_58486998_58487280 227 Contig230_chr5_58486998_58487280;227 T C 192.0 . VRT=6 +Contig385_chr5_60122961_60123128 15 Contig385_chr5_60122961_60123128;15 C G 136.0 . VRT=1 +Contig143_chr5_65121393_65122035 558 Contig143_chr5_65121393_65122035;558 C A 127.0 . VRT=1 +Contig32_chr5_70852360_70853289 282 Contig32_chr5_70852360_70853289;282 G A 114.0 . VRT=6 +Contig215_chr5_70946445_70947428 363 Contig215_chr5_70946445_70947428;363 T G 28.2 . VRT=6 +Contig100_chr5_71189678_71190590 813 Contig100_chr5_71189678_71190590;813 C T 30.8 . VRT=6 +Contig45_chr5_76133561_76134403 388 Contig45_chr5_76133561_76134403;388 A G 103.0 . VRT=6 +Contig61_chr5_90202541_90204393 909 Contig61_chr5_90202541_90204393;909 C T 101.0 . VRT=6 +Contig111_chr6_5821219_5822519 1060 Contig111_chr6_5821219_5822519;1060 A G 68.1 . VRT=6 +Contig220_chr6_10671338_10672441 999 Contig220_chr6_10671338_10672441;999 T C 36.3 . VRT=6 +Contig226_chr6_17361986_17362884 418 Contig226_chr6_17361986_17362884;418 G C 251.0 . VRT=6 +Contig380_chr6_18173971_18174169 180 Contig380_chr6_18173971_18174169;180 C T 4.87 . VRT=1 +Contig51_chr6_20231207_20231785 161 Contig51_chr6_20231207_20231785;161 A G 70.5 . VRT=6 +Contig102_chr6_30271329_30271577 39 Contig102_chr6_30271329_30271577;39 T G 139.0 . VRT=6 +Contig217_chr6_31393824_31394218 97 Contig217_chr6_31393824_31394218;97 G A 115.0 . VRT=6 +Contig186_chr6_31928098_31928245 73 Contig186_chr6_31928098_31928245;73 G A 117.0 . VRT=6 +Contig52_chr6_33188498_33188724 123 Contig52_chr6_33188498_33188724;123 G A 59.0 . VRT=6 +Contig102_chr6_38743009_38743435 290 Contig102_chr6_38743009_38743435;290 A G 178.0 . VRT=6 +Contig81_chr6_49018353_49019532 179 Contig81_chr6_49018353_49019532;179 C A 72.5 . VRT=6 +Contig112_chr6_51024554_51024851 100 Contig112_chr6_51024554_51024851;100 A G 121.0 . VRT=6 +Contig40_chr6_51412751_51413807 227 Contig40_chr6_51412751_51413807;227 T C 94.5 . VRT=6 +Contig47_chr6_69073222_69074767 1315 Contig47_chr6_69073222_69074767;1315 T C 212.0 . VRT=6 +Contig30_chr6_74848932_74849059 57 Contig30_chr6_74848932_74849059;57 C G 46.3 . VRT=6 +Contig84_chr7_6648683_6650255 1297 Contig84_chr7_6648683_6650255;1297 G A 110.0 . VRT=6 +Contig239_chr7_13007379_13007700 275 Contig239_chr7_13007379_13007700;275 A G 39.8 . VRT=6 +Contig119_chr7_18310707_18310948 23 Contig119_chr7_18310707_18310948;23 A T 133.0 . VRT=6 +Contig93_chr7_18513377_18513741 173 Contig93_chr7_18513377_18513741;173 T C 130.0 . VRT=6 +Contig133_chr7_19603333_19603776 414 Contig133_chr7_19603333_19603776;414 C G 31.9 . VRT=6 +Contig132_chr7_20426224_20428145 1815 Contig132_chr7_20426224_20428145;1815 A G 28.3 . VRT=6 +Contig206_chr7_26281823_26282074 103 Contig206_chr7_26281823_26282074;103 C A 101.0 . VRT=6 +Contig116_chr7_45858984_45859111 38 Contig116_chr7_45858984_45859111;38 T C 73.2 . VRT=6 +Contig38_chr7_50681997_50682600 42 Contig38_chr7_50681997_50682600;42 T C 92.4 . VRT=6 +Contig55_chr7_53147505_53148974 894 Contig55_chr7_53147505_53148974;894 A G 68.4 . VRT=6 +Contig4_chr7_53685534_53688206 1709 Contig4_chr7_53685534_53688206;1709 C G 76.2 . VRT=6 +Contig61_chr7_55832923_55834065 506 Contig61_chr7_55832923_55834065;506 T C 185.0 . VRT=6 +Contig91_chr8_12804505_12805470 409 Contig91_chr8_12804505_12805470;409 C A 111.0 . VRT=6 +Contig30_chr8_17147743_17147923 13 Contig30_chr8_17147743_17147923;13 G A 105.0 . VRT=1 +Contig8_chr8_27811135_27812620 333 Contig8_chr8_27811135_27812620;333 C T 37.9 . VRT=6 +Contig66_chr8_28273102_28273660 175 Contig66_chr8_28273102_28273660;175 G C 81.6 . VRT=6 +Contig84_chr8_31375511_31376456 443 Contig84_chr8_31375511_31376456;443 T C 125.0 . VRT=6 +Contig18_chr8_32575859_32577431 264 Contig18_chr8_32575859_32577431;264 T C 151.0 . VRT=6 +Contig54_chr8_40913908_40916451 1275 Contig54_chr8_40913908_40916451;1275 G A 175.0 . VRT=6 +Contig93_chr8_44658786_44659075 180 Contig93_chr8_44658786_44659075;180 T G 55.3 . VRT=6 +Contig17_chr8_57490059_57490498 69 Contig17_chr8_57490059_57490498;69 G T 97.4 . VRT=6 +Contig66_chr8_58562376_58563446 345 Contig66_chr8_58562376_58563446;345 C G 5.74 . VRT=6 +Contig44_chr8_71186368_71188207 1455 Contig44_chr8_71186368_71188207;1455 G T 147.0 . VRT=1 +Contig73_chr9_29451535_29452248 616 Contig73_chr9_29451535_29452248;616 A G 24.7 . VRT=6 +Contig96_chr9_39008495_39009278 215 Contig96_chr9_39008495_39009278;215 A C 98.7 . VRT=6 +Contig22_chr10_15505382_15505589 172 Contig22_chr10_15505382_15505589;172 T C 38.5 . VRT=6 +Contig69_chr10_40547265_40548153 371 Contig69_chr10_40547265_40548153;371 G A 58.1 . VRT=6 +Contig63_chr10_42716594_42719945 1018 Contig63_chr10_42716594_42719945;1018 A G 88.7 . VRT=6 +Contig22_chr10_43255307_43255570 81 Contig22_chr10_43255307_43255570;81 C A 37.2 . VRT=6 +Contig9_chr10_51475063_51476054 770 Contig9_chr10_51475063_51476054;770 C T 57.3 . VRT=6 +Contig42_chr10_53816543_53818392 1642 Contig42_chr10_53816543_53818392;1642 G A 27.5 . VRT=6 +Contig36_chr10_53992615_53993741 229 Contig36_chr10_53992615_53993741;229 G C 86.2 . VRT=6 +Contig20_chr10_58141129_58141750 575 Contig20_chr10_58141129_58141750;575 C T 46.1 . VRT=6 +Contig26_chr10_59510973_59511899 146 Contig26_chr10_59510973_59511899;146 C A 29.0 . VRT=6 +Contig72_chr11_7142765_7143772 146 Contig72_chr11_7142765_7143772;146 G A 152.0 . VRT=6 +Contig103_chr11_8844784_8845095 214 Contig103_chr11_8844784_8845095;214 T G 135.0 . VRT=6 +Contig9_chr11_9904571_9905983 1284 Contig9_chr11_9904571_9905983;1284 C T 151.0 . VRT=6 +Contig35_chr11_22459883_22460855 714 Contig35_chr11_22459883_22460855;714 T G 54.9 . VRT=6 +Contig7_chr11_40017076_40017630 352 Contig7_chr11_40017076_40017630;352 C T 46.3 . VRT=6 +Contig108_chr11_42953408_42955156 367 Contig108_chr11_42953408_42955156;367 A G 89.4 . VRT=6 +Contig82_chr11_43490732_43490862 60 Contig82_chr11_43490732_43490862;60 C T 47.3 . VRT=1 +Contig16_chr11_53408448_53408790 187 Contig16_chr11_53408448_53408790;187 A G 153.0 . VRT=6 +Contig21_chr12_18403415_18404381 586 Contig21_chr12_18403415_18404381;586 G T 34.5 . VRT=6 +Contig33_chr12_19804073_19804529 178 Contig33_chr12_19804073_19804529;178 T C 69.4 . VRT=6 +Contig41_chr12_25565452_25566993 475 Contig41_chr12_25565452_25566993;475 G T 6.29 . VRT=6 +Contig9_chr12_27204351_27204696 239 Contig9_chr12_27204351_27204696;239 A G 145.0 . VRT=6 +Contig45_chr12_30548282_30550498 448 Contig45_chr12_30548282_30550498;448 C T 124.0 . VRT=6 +Contig46_chr12_35571846_35572563 58 Contig46_chr12_35571846_35572563;58 G C 83.2 . VRT=6 +Contig28_chr12_42075871_42076044 136 Contig28_chr12_42075871_42076044;136 G A 134.0 . VRT=6 +Contig16_chr12_42386141_42387454 194 Contig16_chr12_42386141_42387454;194 A G 161.0 . VRT=6 +Contig42_chr12_44424628_44425829 255 Contig42_chr12_44424628_44425829;255 A G 84.4 . VRT=6 +Contig10_chr12_44447953_44449698 63 Contig10_chr12_44447953_44449698;63 C T 105.0 . VRT=6 +Contig5_chr12_53880670_53882675 1221 Contig5_chr12_53880670_53882675;1221 A C 99.4 . VRT=6 +Contig86_chr12_56715356_56716464 818 Contig86_chr12_56715356_56716464;818 T C 166.0 . VRT=6 +Contig3_chr12_65021967_65024097 238 Contig3_chr12_65021967_65024097;238 T G 92.6 . VRT=6 +Contig43_chr12_66499742_66500010 121 Contig43_chr12_66499742_66500010;121 G T 41.5 . VRT=6 +Contig14_chr12_71364692_71365311 20 Contig14_chr12_71364692_71365311;20 A C 103.0 . VRT=6 +Contig37_chr13_15910164_15910426 245 Contig37_chr13_15910164_15910426;245 G A 32.9 . VRT=1 +Contig107_chr13_26045881_26046290 341 Contig107_chr13_26045881_26046290;341 C G 81.4 . VRT=6 +Contig251_chr13_28498333_28501066 864 Contig251_chr13_28498333_28501066;864 T G 296.0 . VRT=6 +Contig154_chr13_36777857_36778736 356 Contig154_chr13_36777857_36778736;356 G A 95.5 . VRT=6 +Contig37_chr13_42529793_42530857 150 Contig37_chr13_42529793_42530857;150 G T 192.0 . VRT=6 +Contig47_chr13_47045833_47046626 257 Contig47_chr13_47045833_47046626;257 A C 28.5 . VRT=6 +Contig42_chr13_47730018_47730856 254 Contig42_chr13_47730018_47730856;254 A G 75.1 . VRT=6 +Contig55_chr13_53467708_53468101 221 Contig55_chr13_53467708_53468101;221 T G 132.0 . VRT=6 +Contig49_chr13_55103679_55105532 503 Contig49_chr13_55103679_55105532;503 G A 76.0 . VRT=6 +Contig42_chr13_64785759_64786045 14 Contig42_chr13_64785759_64786045;14 C G 22.8 . VRT=6 +Contig66_chr13_66021813_66022244 319 Contig66_chr13_66021813_66022244;319 C T 125.0 . VRT=6 +Contig48_chr14_11839435_11843272 3014 Contig48_chr14_11839435_11843272;3014 A G 163.0 . VRT=6 +Contig9_chr14_23353717_23354432 80 Contig9_chr14_23353717_23354432;80 G A 61.3 . VRT=6 +Contig14_chr14_24131180_24133488 1633 Contig14_chr14_24131180_24133488;1633 G A 131.0 . VRT=6 +Contig28_chr14_26905747_26909514 975 Contig28_chr14_26905747_26909514;975 G C 3.13 . VRT=6 +Contig14_chr14_29616948_29618316 109 Contig14_chr14_29616948_29618316;109 G A 80.3 . VRT=6 +Contig24_chr14_29728478_29728839 242 Contig24_chr14_29728478_29728839;242 T A 107.0 . VRT=6 +Contig76_chr14_30028102_30029179 1046 Contig76_chr14_30028102_30029179;1046 C T 38.5 . VRT=6 +Contig115_chr14_31417207_31417574 259 Contig115_chr14_31417207_31417574;259 A G 12.1 . VRT=6 +Contig70_chr14_46653662_46653790 111 Contig70_chr14_46653662_46653790;111 G A 46.7 . VRT=6 +Contig43_chr14_49991855_49993511 918 Contig43_chr14_49991855_49993511;918 A G 112.0 . VRT=6 +Contig64_chr14_56768376_56768902 473 Contig64_chr14_56768376_56768902;473 C T 29.0 . VRT=6 +Contig60_chr15_18493036_18494316 150 Contig60_chr15_18493036_18494316;150 G A 92.6 . VRT=6 +Contig213_chr15_19567788_19568626 196 Contig213_chr15_19567788_19568626;196 A C 13.9 . VRT=6 +Contig59_chr15_22138344_22138535 120 Contig59_chr15_22138344_22138535;120 G C 142.0 . VRT=6 +Contig112_chr15_26772864_26773267 374 Contig112_chr15_26772864_26773267;374 C T 21.6 . VRT=6 +Contig24_chr15_26894765_26895003 155 Contig24_chr15_26894765_26895003;155 G A 87.6 . VRT=6 +Contig2_chr15_33944796_33947182 1860 Contig2_chr15_33944796_33947182;1860 G A 99.5 . VRT=6 +Contig73_chr15_34690052_34691332 714 Contig73_chr15_34690052_34691332;714 T C 130.0 . VRT=6 +Contig68_chr15_37747190_37747426 126 Contig68_chr15_37747190_37747426;126 G A 130.0 . VRT=6 +Contig35_chr15_41400484_41400672 160 Contig35_chr15_41400484_41400672;160 A C 143.0 . VRT=6 +Contig104_chr15_45106954_45107158 70 Contig104_chr15_45106954_45107158;70 A T 64.4 . VRT=6 +Contig119_chr16_6160274_6160477 180 Contig119_chr16_6160274_6160477;180 G A 54.8 . VRT=6 +Contig126_chr16_10611887_10612152 150 Contig126_chr16_10611887_10612152;150 G T 145.0 . VRT=6 +Contig114_chr16_12565220_12565676 10 Contig114_chr16_12565220_12565676;10 G A 134.0 . VRT=1 +Contig43_chr16_20200090_20200514 70 Contig43_chr16_20200090_20200514;70 A G 58.6 . VRT=6 +Contig60_chr16_28079136_28080263 588 Contig60_chr16_28079136_28080263;588 T G 157.0 . VRT=6 +Contig70_chr16_33758668_33759655 104 Contig70_chr16_33758668_33759655;104 A T 58.1 . VRT=6 +Contig66_chr16_37935682_37935831 116 Contig66_chr16_37935682_37935831;116 T C 99.2 . VRT=6 +Contig16_chr16_40451506_40451643 84 Contig16_chr16_40451506_40451643;84 A G 59.8 . VRT=6 +Contig53_chr16_49888293_49888587 260 Contig53_chr16_49888293_49888587;260 G A 108.0 . VRT=6 +Contig31_chr17_12128267_12129637 205 Contig31_chr17_12128267_12129637;205 G A 90.5 . VRT=6 +Contig50_chr17_12247973_12249183 889 Contig50_chr17_12247973_12249183;889 G T 47.6 . VRT=6 +Contig1_chr17_12979232_12980380 808 Contig1_chr17_12979232_12980380;808 G T 12.3 . VRT=6 +Contig63_chr17_14186372_14186928 54 Contig63_chr17_14186372_14186928;54 C T 70.7 . VRT=6 +Contig42_chr17_23434859_23438330 2100 Contig42_chr17_23434859_23438330;2100 C T 39.5 . VRT=6 +Contig63_chr17_23796320_23796814 220 Contig63_chr17_23796320_23796814;220 A G 54.0 . VRT=6 +Contig76_chr17_24107434_24107834 316 Contig76_chr17_24107434_24107834;316 T C 141.0 . VRT=6 +Contig99_chr17_26021506_26022200 505 Contig99_chr17_26021506_26022200;505 C T 88.8 . VRT=6 +Contig59_chr17_26790302_26795045 287 Contig59_chr17_26790302_26795045;287 C T 45.1 . VRT=6 +Contig99_chr17_27018324_27019378 446 Contig99_chr17_27018324_27019378;446 G A 31.1 . VRT=6 +Contig125_chr17_27739115_27739410 63 Contig125_chr17_27739115_27739410;63 G A 107.0 . VRT=6 +Contig115_chr17_37489899_37490101 159 Contig115_chr17_37489899_37490101;159 G A 62.4 . VRT=6 +Contig180_chr17_45154356_45154925 524 Contig180_chr17_45154356_45154925;524 A G 146.0 . VRT=6 +Contig61_chr17_48221795_48223545 1404 Contig61_chr17_48221795_48223545;1404 T A 177.0 . VRT=6 +Contig27_chr17_61713766_61716585 1056 Contig27_chr17_61713766_61716585;1056 G C 40.0 . VRT=6 +Contig229_chr18_3706523_3708577 1076 Contig229_chr18_3706523_3708577;1076 A G 83.9 . VRT=6 +Contig24_chr18_14049894_14050480 24 Contig24_chr18_14049894_14050480;24 A G 123.0 . VRT=6 +Contig30_chr18_18771753_18772121 39 Contig30_chr18_18771753_18772121;39 C G 48.5 . VRT=6 +Contig123_chr18_19916160_19916379 116 Contig123_chr18_19916160_19916379;116 G A 79.2 . VRT=6 +Contig82_chr18_27305489_27306229 566 Contig82_chr18_27305489_27306229;566 C T 49.5 . VRT=6 +Contig71_chr18_34324706_34326687 136 Contig71_chr18_34324706_34326687;136 G A 151.0 . VRT=6 +Contig16_chr18_34672093_34673044 538 Contig16_chr18_34672093_34673044;538 T C 58.2 . VRT=6 +Contig96_chr18_38492535_38493333 624 Contig96_chr18_38492535_38493333;624 G A 119.0 . VRT=6 +Contig226_chr18_47753756_47754666 427 Contig226_chr18_47753756_47754666;427 T C 21.1 . VRT=6 +Contig170_chr18_49411558_49412230 94 Contig170_chr18_49411558_49412230;94 C A 74.3 . VRT=6 +Contig192_chr18_49419342_49420737 1058 Contig192_chr18_49419342_49420737;1058 C T 42.8 . VRT=6 +Contig64_chr18_55979770_55980315 49 Contig64_chr18_55979770_55980315;49 G A 89.1 . VRT=6 +Contig20_chr18_58130301_58130735 112 Contig20_chr18_58130301_58130735;112 A G 74.4 . VRT=6 +Contig146_chr19_5221790_5223013 143 Contig146_chr19_5221790_5223013;143 A G 114.0 . VRT=6 +Contig13_chr19_7739961_7740118 26 Contig13_chr19_7739961_7740118;26 C G 220.0 . VRT=6 +Contig67_chr19_12398520_12399367 499 Contig67_chr19_12398520_12399367;499 C T 161.0 . VRT=6 +Contig66_chr19_16285672_16287223 996 Contig66_chr19_16285672_16287223;996 C T 190.0 . VRT=6 +Contig129_chr19_25541958_25542221 202 Contig129_chr19_25541958_25542221;202 T C 68.1 . VRT=6 +Contig152_chr19_34274440_34275622 1072 Contig152_chr19_34274440_34275622;1072 C T 48.0 . VRT=6 +Contig29_chr19_37339947_37341911 1692 Contig29_chr19_37339947_37341911;1692 C T 211.0 . VRT=6 +Contig39_chr19_47709708_47711327 444 Contig39_chr19_47709708_47711327;444 C T 36.8 . VRT=6 +Contig60_chr19_54013816_54014398 281 Contig60_chr19_54013816_54014398;281 A G 138.0 . VRT=6 +Contig251_chr19_56559098_56559626 452 Contig251_chr19_56559098_56559626;452 T C 3.36 . VRT=6 +Contig50_chr20_12138509_12141975 3206 Contig50_chr20_12138509_12141975;3206 C A 248.0 . VRT=6 +Contig36_chr20_32631363_32632049 176 Contig36_chr20_32631363_32632049;176 G A 24.1 . VRT=6 +Contig39_chr20_36316398_36316498 57 Contig39_chr20_36316398_36316498;57 C T 30.3 . VRT=6 +Contig32_chr20_36468058_36468869 66 Contig32_chr20_36468058_36468869;66 C T 40.4 . VRT=6 +Contig24_chr20_38203888_38204900 834 Contig24_chr20_38203888_38204900;834 C T 132.0 . VRT=6 +Contig79_chr20_44263127_44264103 456 Contig79_chr20_44263127_44264103;456 G T 31.5 . VRT=6 +Contig26_chr20_45878482_45878787 197 Contig26_chr20_45878482_45878787;197 A G 160.0 . VRT=6 +Contig119_chr20_46550670_46551383 609 Contig119_chr20_46550670_46551383;609 G A 139.0 . VRT=6 +Contig50_chr21_4178523_4178687 121 Contig50_chr21_4178523_4178687;121 G A 362.0 . VRT=6 +Contig103_chr21_10177255_10177765 121 Contig103_chr21_10177255_10177765;121 G A 125.0 . VRT=6 +Contig1_chr21_10805534_10806399 766 Contig1_chr21_10805534_10806399;766 A G 146.0 . VRT=6 +Contig46_chr21_21029492_21030645 443 Contig46_chr21_21029492_21030645;443 C T 5.37 . VRT=6 +Contig129_chr21_31045749_31046924 381 Contig129_chr21_31045749_31046924;381 A G 129.0 . VRT=6 +Contig23_chr21_31651123_31651986 840 Contig23_chr21_31651123_31651986;840 C T 71.3 . VRT=6 +Contig64_chr21_43341847_43342031 84 Contig64_chr21_43341847_43342031;84 T C 114.0 . VRT=6 +Contig60_chr21_43475347_43475824 175 Contig60_chr21_43475347_43475824;175 C T 8.05 . VRT=6 +Contig64_chr21_45377513_45377872 19 Contig64_chr21_45377513_45377872;19 C T 60.7 . VRT=6 +Contig159_chr22_7896450_7896974 109 Contig159_chr22_7896450_7896974;109 G C 151.0 . VRT=6 +Contig46_chr22_9416920_9417467 381 Contig46_chr22_9416920_9417467;381 G A 145.0 . VRT=6 +Contig86_chr22_9440787_9441725 713 Contig86_chr22_9440787_9441725;713 T G 119.0 . VRT=6 +Contig16_chr22_15636960_15637372 236 Contig16_chr22_15636960_15637372;236 A C 9.79 . VRT=6 +Contig4_chr22_16114310_16114546 128 Contig4_chr22_16114310_16114546;128 G C 101.0 . VRT=6 +Contig23_chr22_34612023_34612568 167 Contig23_chr22_34612023_34612568;167 C G 92.3 . VRT=6 +Contig4_chr22_38252245_38253712 799 Contig4_chr22_38252245_38253712;799 A C 159.0 . VRT=6 +Contig122_chr22_48412466_48414788 1888 Contig122_chr22_48412466_48414788;1888 C T 125.0 . VRT=6 +Contig77_chr22_49764414_49764875 353 Contig77_chr22_49764414_49764875;353 C A 148.0 . VRT=1 +Contig26_chr22_57817664_57819633 1453 Contig26_chr22_57817664_57819633;1453 A G 150.0 . VRT=6 +Contig348_chr22_62406104_62406495 189 Contig348_chr22_62406104_62406495;189 C A 134.0 . VRT=6 +Contig133_chr23_3525134_3526502 1223 Contig133_chr23_3525134_3526502;1223 A G 201.0 . VRT=6 +Contig111_chr23_7058063_7058181 107 Contig111_chr23_7058063_7058181;107 G A 108.0 . VRT=6 +Contig79_chr23_7844129_7844837 110 Contig79_chr23_7844129_7844837;110 C A 141.0 . VRT=6 +Contig38_chr23_9201002_9201725 597 Contig38_chr23_9201002_9201725;597 C T 155.0 . VRT=6 +Contig33_chr23_20672540_20674320 347 Contig33_chr23_20672540_20674320;347 T A 91.4 . VRT=6 +Contig35_chr23_28447813_28449115 70 Contig35_chr23_28447813_28449115;70 T A 21.3 . VRT=6 +Contig51_chr23_30590939_30591162 140 Contig51_chr23_30590939_30591162;140 C T 142.0 . VRT=6 +Contig57_chr23_32216351_32216721 179 Contig57_chr23_32216351_32216721;179 T G 143.0 . VRT=6 +Contig93_chr23_35744841_35745791 40 Contig93_chr23_35744841_35745791;40 A T 30.4 . VRT=6 +Contig99_chr23_42543966_42544147 14 Contig99_chr23_42543966_42544147;14 G A 357.0 . VRT=6 +Contig32_chr23_48285289_48286638 186 Contig32_chr23_48285289_48286638;186 T C 176.0 . VRT=6 +Contig50_chr24_22515247_22516072 761 Contig50_chr24_22515247_22516072;761 C T 243.0 . VRT=6 +Contig92_chr24_28935897_28936321 13 Contig92_chr24_28935897_28936321;13 G A 47.1 . VRT=6 +Contig84_chr24_29196623_29199644 466 Contig84_chr24_29196623_29199644;466 C T 126.0 . VRT=6 +Contig35_chr24_30150986_30151507 492 Contig35_chr24_30150986_30151507;492 A C 114.0 . VRT=6 +Contig61_chr24_30465488_30465834 149 Contig61_chr24_30465488_30465834;149 G T 68.2 . VRT=6 +Contig145_chr24_34778364_34778898 163 Contig145_chr24_34778364_34778898;163 T C 372.0 . VRT=6 +Contig34_chr24_36147443_36150244 2679 Contig34_chr24_36147443_36150244;2679 C T 140.0 . VRT=6 +Contig164_chr24_46598127_46599206 84 Contig164_chr24_46598127_46599206;84 C T 105.0 . VRT=6 +Contig144_chr25_4011170_4013134 541 Contig144_chr25_4011170_4013134;541 A G 160.0 . VRT=6 +Contig81_chr25_6103472_6104760 699 Contig81_chr25_6103472_6104760;699 G A 378.0 . VRT=6 +Contig152_chr25_7486442_7487609 75 Contig152_chr25_7486442_7487609;75 A G 11.6 . VRT=6 +Contig24_chr25_7695778_7698612 2714 Contig24_chr25_7695778_7698612;2714 C T 130.0 . VRT=6 +Contig89_chr25_8635170_8636009 586 Contig89_chr25_8635170_8636009;586 G C 209.0 . VRT=6 +Contig77_chr25_10796299_10796481 2 Contig77_chr25_10796299_10796481;2 T C 17.3 . VRT=6 +Contig73_chr25_14177327_14177474 125 Contig73_chr25_14177327_14177474;125 A C 6.85 . VRT=1 +Contig59_chr25_18196776_18197707 785 Contig59_chr25_18196776_18197707;785 G A 112.0 . VRT=1 +Contig103_chr25_38891221_38892140 407 Contig103_chr25_38891221_38892140;407 G A 131.0 . VRT=6 +Contig84_chr25_42407960_42408708 55 Contig84_chr25_42407960_42408708;55 C T 119.0 . VRT=6 +Contig73_chr25_43562500_43564110 955 Contig73_chr25_43562500_43564110;955 T C 52.1 . VRT=6 +Contig37_chr25_51074433_51074885 170 Contig37_chr25_51074433_51074885;170 A G 102.0 . VRT=6 +Contig204_chr26_4311195_4311778 170 Contig204_chr26_4311195_4311778;170 C T 16.9 . VRT=6 +Contig122_chr26_7622321_7623491 106 Contig122_chr26_7622321_7623491;106 C G 139.0 . VRT=6 +Contig11_chr26_11062142_11062902 707 Contig11_chr26_11062142_11062902;707 C A 108.0 . VRT=6 +Contig133_chr26_17695661_17696368 39 Contig133_chr26_17695661_17696368;39 T G 98.7 . VRT=6 +Contig157_chr26_23894107_23895229 25 Contig157_chr26_23894107_23895229;25 C T 50.2 . VRT=1 +Contig146_chr26_26622638_26623906 574 Contig146_chr26_26622638_26623906;574 G A 186.0 . VRT=6 +Contig8_chr26_27834126_27834326 140 Contig8_chr26_27834126_27834326;140 G A 41.7 . VRT=6 +Contig78_chr26_31128839_31129005 123 Contig78_chr26_31128839_31129005;123 T C 145.0 . VRT=6 +Contig28_chr26_32935355_32935833 289 Contig28_chr26_32935355_32935833;289 T C 77.9 . VRT=6 +Contig36_chr26_36606876_36607240 115 Contig36_chr26_36606876_36607240;115 A T 139.0 . VRT=6 +Contig135_chr27_6853874_6854079 158 Contig135_chr27_6853874_6854079;158 C T 116.0 . VRT=6 +Contig47_chr27_11777710_11777915 25 Contig47_chr27_11777710_11777915;25 A G 67.3 . VRT=6 +Contig23_chr27_14633002_14633153 23 Contig23_chr27_14633002_14633153;23 G A 128.0 . VRT=6 +Contig31_chr27_14987233_14988055 630 Contig31_chr27_14987233_14988055;630 A G 48.5 . VRT=6 +Contig29_chr27_15428166_15429413 380 Contig29_chr27_15428166_15429413;380 T C 140.0 . VRT=6 +Contig31_chr27_19519489_19520891 129 Contig31_chr27_19519489_19520891;129 G T 14.9 . VRT=6 +Contig64_chr27_34654435_34654621 132 Contig64_chr27_34654435_34654621;132 C A 115.0 . VRT=6 +Contig35_chr27_40596169_40596445 20 Contig35_chr27_40596169_40596445;20 G C 133.0 . VRT=6 +Contig85_chr27_45471750_45472022 211 Contig85_chr27_45471750_45472022;211 G A 53.1 . VRT=6 +Contig131_chr28_6481806_6483783 138 Contig131_chr28_6481806_6483783;138 C T 36.2 . VRT=6 +Contig141_chr28_10027332_10028242 780 Contig141_chr28_10027332_10028242;780 T G 74.8 . VRT=6 +Contig144_chr28_15468203_15470548 743 Contig144_chr28_15468203_15470548;743 G A 20.0 . VRT=6 +Contig47_chr28_21311718_21312366 541 Contig47_chr28_21311718_21312366;541 G A 116.0 . VRT=6 +Contig60_chr28_30197166_30197364 92 Contig60_chr28_30197166_30197364;92 T C 164.0 . VRT=6 +Contig201_chr28_36339953_36341322 260 Contig201_chr28_36339953_36341322;260 C T 6.36 . VRT=6 +Contig175_chr28_36441165_36441915 68 Contig175_chr28_36441165_36441915;68 T C 3.83 . VRT=1 +Contig29_chr29_4726399_4727143 559 Contig29_chr29_4726399_4727143;559 A T 163.0 . VRT=6 +Contig48_chr29_13129286_13130137 232 Contig48_chr29_13129286_13130137;232 A G 92.2 . VRT=6 +Contig64_chr29_15736891_15737257 344 Contig64_chr29_15736891_15737257;344 T C 40.4 . VRT=6 +Contig33_chr29_17000374_17000921 71 Contig33_chr29_17000374_17000921;71 C T 48.6 . VRT=6 +Contig34_chr29_17581796_17584016 2105 Contig34_chr29_17581796_17584016;2105 C T 126.0 . VRT=6 +Contig19_chr29_20976080_20977761 1007 Contig19_chr29_20976080_20977761;1007 G A 115.0 . VRT=6 +Contig51_chr29_21149853_21150467 266 Contig51_chr29_21149853_21150467;266 C T 146.0 . VRT=6 +Contig1_chr30_5992217_5993068 106 Contig1_chr30_5992217_5993068;106 C T 129.0 . VRT=6 +Contig1_chr30_8232878_8233406 402 Contig1_chr30_8232878_8233406;402 C T 127.0 . VRT=6 +Contig108_chr30_9436961_9437520 546 Contig108_chr30_9436961_9437520;546 C T 39.8 . VRT=6 +Contig165_chr30_25804389_25804926 190 Contig165_chr30_25804389_25804926;190 T C 126.0 . VRT=6 +Contig193_chr30_27495616_27496125 434 Contig193_chr30_27495616_27496125;434 C A 234.0 . VRT=6 +Contig114_chr30_33636712_33637208 34 Contig114_chr30_33636712_33637208;34 C T 142.0 . VRT=6 +Contig38_chr31_5164423_5166573 2074 Contig38_chr31_5164423_5166573;2074 C T 134.0 . VRT=6 +Contig6_chr31_9649308_9650149 431 Contig6_chr31_9649308_9650149;431 G T 162.0 . VRT=6 +Contig85_chr31_12242872_12245082 38 Contig85_chr31_12242872_12245082;38 G C 92.4 . VRT=6 +Contig7_chr31_12384974_12386400 305 Contig7_chr31_12384974_12386400;305 C T 69.6 . VRT=6 +Contig90_chr31_17267583_17267778 81 Contig90_chr31_17267583_17267778;81 C A 143.0 . VRT=6 +Contig68_chr31_20000241_20000597 215 Contig68_chr31_20000241_20000597;215 C T 131.0 . VRT=1 +Contig137_chr31_23357653_23358568 885 Contig137_chr31_23357653_23358568;885 G A 119.0 . VRT=6 +Contig17_chr31_26433828_26434459 498 Contig17_chr31_26433828_26434459;498 T C 9.79 . VRT=6 +Contig9_chr32_19479532_19479735 12 Contig9_chr32_19479532_19479735;12 A G 20.7 . VRT=6 +Contig30_chr32_25902721_25905783 208 Contig30_chr32_25902721_25905783;208 C G 162.0 . VRT=6 +Contig7_chr32_27789513_27789926 20 Contig7_chr32_27789513_27789926;20 G A 7.19 . VRT=1 +Contig42_chr32_38900713_38901320 320 Contig42_chr32_38900713_38901320;320 A G 134.0 . VRT=6 +Contig18_chr33_22207246_22209159 1363 Contig18_chr33_22207246_22209159;1363 G T 51.5 . VRT=6 +Contig104_chr33_22483642_22484187 424 Contig104_chr33_22483642_22484187;424 C T 140.0 . VRT=6 +Contig170_chr33_26189421_26189940 292 Contig170_chr33_26189421_26189940;292 T C 98.4 . VRT=6 +Contig113_chr34_13341080_13341643 236 Contig113_chr34_13341080_13341643;236 C T 90.7 . VRT=6 +Contig405_chr34_14415672_14415979 59 Contig405_chr34_14415672_14415979;59 A G 36.2 . VRT=6 +Contig21_chr34_16422980_16425681 2009 Contig21_chr34_16422980_16425681;2009 G A 19.4 . VRT=1 +Contig41_chr34_16544482_16545449 46 Contig41_chr34_16544482_16545449;46 T C 102.0 . VRT=6 +Contig8_chr34_18474513_18475673 1122 Contig8_chr34_18474513_18475673;1122 C A 129.0 . VRT=6 +Contig152_chr34_31794848_31795540 242 Contig152_chr34_31794848_31795540;242 G A 93.2 . VRT=6 +Contig28_chr34_41708848_41712034 1381 Contig28_chr34_41708848_41712034;1381 A G 78.2 . VRT=6 +Contig85_chr34_42798284_42800584 1845 Contig85_chr34_42798284_42800584;1845 C T 171.0 . VRT=6 +Contig47_chr35_3666773_3667898 348 Contig47_chr35_3666773_3667898;348 G T 124.0 . VRT=6 +Contig195_chr35_15722500_15722741 205 Contig195_chr35_15722500_15722741;205 G A 4.08 . VRT=6 +Contig101_chr35_19513178_19513697 62 Contig101_chr35_19513178_19513697;62 C T 112.0 . VRT=6 +Contig19_chr35_23887144_23888282 90 Contig19_chr35_23887144_23888282;90 C A 10.1 . VRT=1 +Contig47_chr35_24382042_24382526 33 Contig47_chr35_24382042_24382526;33 G A 87.0 . VRT=6 +Contig77_chr35_24796947_24797172 65 Contig77_chr35_24796947_24797172;65 A G 52.1 . VRT=6 +Contig74_chr35_25394343_25394813 303 Contig74_chr35_25394343_25394813;303 A T 221.0 . VRT=6 +Contig5_chr36_4562983_4563634 343 Contig5_chr36_4562983_4563634;343 C T 151.0 . VRT=6 +Contig75_chr36_7885319_7885588 53 Contig75_chr36_7885319_7885588;53 G A 25.7 . VRT=6 +Contig184_chr36_18956191_18958552 187 Contig184_chr36_18956191_18958552;187 A G 11.5 . VRT=6 +Contig12_chr36_21557176_21557828 513 Contig12_chr36_21557176_21557828;513 T A 159.0 . VRT=6 +Contig2_chr36_22436067_22436794 653 Contig2_chr36_22436067_22436794;653 C T 73.0 . VRT=6 +Contig133_chr36_32954045_32955409 136 Contig133_chr36_32954045_32955409;136 A G 116.0 . VRT=6 +Contig53_chr37_6665763_6665919 116 Contig53_chr37_6665763_6665919;116 C T 111.0 . VRT=6 +Contig42_chr37_9589176_9591269 252 Contig42_chr37_9589176_9591269;252 G A 25.1 . VRT=6 +Contig2_chr37_17134963_17136513 1140 Contig2_chr37_17134963_17136513;1140 A C 158.0 . VRT=6 +Contig18_chr37_17147806_17149851 291 Contig18_chr37_17147806_17149851;291 T G 112.0 . VRT=1 +Contig64_chr37_17606895_17607534 565 Contig64_chr37_17606895_17607534;565 C T 30.2 . VRT=6 +Contig126_chr37_21587881_21590621 373 Contig126_chr37_21587881_21590621;373 G T 132.0 . VRT=6 +Contig2_chr37_31197993_31198256 182 Contig2_chr37_31197993_31198256;182 C T 39.6 . VRT=6 +Contig46_chr37_31852376_31853555 825 Contig46_chr37_31852376_31853555;825 A G 111.0 . VRT=6 +Contig7_chr38_12217200_12218387 1163 Contig7_chr38_12217200_12218387;1163 A T 44.4 . VRT=6 +Contig15_chr38_12282020_12282253 150 Contig15_chr38_12282020_12282253;150 C T 156.0 . VRT=6 +Contig4_chr38_14807432_14807747 275 Contig4_chr38_14807432_14807747;275 A G 36.5 . VRT=6 +Contig6_chr38_16185744_16186110 325 Contig6_chr38_16185744_16186110;325 A G 74.9 . VRT=6 +Contig265_chrX_2689247_2689484 114 Contig265_chrX_2689247_2689484;114 C G 103.0 . VRT=6 +Contig122_chrX_6026976_6027327 330 Contig122_chrX_6026976_6027327;330 C T 79.4 . VRT=6 +Contig15_chrX_15659909_15660340 15 Contig15_chrX_15659909_15660340;15 A C 14.9 . VRT=6 +Contig12_chrX_23243561_23244412 479 Contig12_chrX_23243561_23244412;479 C G 67.7 . VRT=6 +Contig113_chrX_26287829_26288398 385 Contig113_chrX_26287829_26288398;385 C T 59.6 . VRT=6 +Contig186_chrX_29118735_29118939 192 Contig186_chrX_29118735_29118939;192 G A 7.01 . VRT=6 +Contig237_chrX_31256648_31257654 165 Contig237_chrX_31256648_31257654;165 T A 246.0 . VRT=6 +Contig25_chrX_40729418_40730089 332 Contig25_chrX_40729418_40730089;332 C T 31.2 . VRT=1 +Contig90_chrX_57430715_57431566 548 Contig90_chrX_57430715_57431566;548 C T 116.0 . VRT=6 +Contig133_chrX_84833782_84834125 182 Contig133_chrX_84833782_84834125;182 G A 69.7 . VRT=6 +Contig129_chrX_90586053_90586467 135 Contig129_chrX_90586053_90586467;135 A T 120.0 . VRT=6 +Contig125_chrX_93319363_93320877 349 Contig125_chrX_93319363_93320877;349 A C 145.0 . VRT=6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2pgSnp_input.vcf Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,50 @@ +##fileformat=VCFv4.1 +##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD"> +##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder"> +##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder"> +##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder"> +##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder"> +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> +##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> +##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count"> +##ALT=<ID=DEL,Description="Deletion"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder"> +##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN"> +##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN"> +##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN"> +##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN"> +##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN"> +##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents"> +##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 +1 10523 . TCCG T 152 PASS VT=INDEL;RSQ=0.5246;ERATE=0.0023;AN=2184;AA=.;THETA=0.0172;AC=5;AVGPOST=0.9954;LDAF=0.0045;AF=0.00;AMR_AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.000:0.00,-1.50,-34.60 0|0:0.000:0.00,-0.90,-20.70 0|0:0.000:0.00,-1.50,-34.50 0|0:0.000:0.00,-0.30,-6.90 +1 10583 rs58108140 G A 100 PASS VT=SNP;SNPSOURCE=LOWCOV;AN=2184;AC=327;LDAF=0.2363;AVGPOST=0.7630;ERATE=0.0098;AA=.;RSQ=0.4161;THETA=0.0197;SNPSOURCE=LOWCOV;AF=0.15;ASN_AF=0.15;AMR_AF=0.18;AFR_AF=0.04;EUR_AF=0.21 GT:DS:GL 0|0:0.250:-0.18,-0.47,-2.42 0|0:0.200:-0.24,-0.44,-1.16 0|0:0.250:-0.15,-0.54,-3.12 0|1:0.750:-0.48,-0.48,-0.48 +1 10611 rs189107123 C G 100 PASS VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0048;RSQ=0.3814;AN=2184;AVGPOST=0.9427;ERATE=0.0024;LDAF=0.0420;AA=.;SNPSOURCE=LOWCOV;AC=39;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02 GT:DS:GL 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.350:-0.24,-0.44,-1.16 0|0:0.100:-0.22,-0.42,-1.80 0|0:0.100:-0.48,-0.48,-0.48 +1 10616 . CCGCCGTTGCAAAGGCGCGCCG C 2781 PASS VT=INDEL;RSQ=0.1048;AN=2184;LDAF=0.7052;AVGPOST=0.5674;ERATE=0.0146;AA=.;THETA=0.0195;AC=1972;AF=0.90;ASN_AF=0.88;AMR_AF=0.92;AFR_AF=0.89;EUR_AF=0.92 GT:DS:GL 1|1:1.450:0,0,0 1|1:1.750:0,0,0 1|1:1.200:0,0,0 0|1:1.150:0,0,0 +1 11540 . T TA 263 PASS VT=INDEL;AVGPOST=0.5915;LDAF=0.2676;AN=2184;RSQ=0.0831;AC=93;THETA=0.0011;AA=.;ERATE=0.0222;AF=0.04;ASN_AF=0.05;AMR_AF=0.04;AFR_AF=0.05;EUR_AF=0.04 GT:DS:GL 0|0:0.700:0,0,0 0|1:0.800:0,0,0 0|0:0.300:0,0,0 0|0:0.450:0,0,0 +1 13302 rs180734498 C T 100 PASS VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0159;LDAF=0.1562;AN=2184;AC=250;AA=.;RSQ=0.6272;ERATE=0.0116;SNPSOURCE=LOWCOV;AVGPOST=0.8877;AF=0.11;ASN_AF=0.02;AMR_AF=0.09;AFR_AF=0.21;EUR_AF=0.13 GT:DS:GL 0|0:0.250:-0.13,-0.58,-3.62 0|1:0.950:-2.45,-0.00,-5.00 0|0:0.450:-0.29,-0.32,-5.00 0|0:0.300:-0.48,-0.48,-0.48 +1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.6776;THETA=0.0189;AN=2184;AC=57;AA=.;LDAF=0.0342;AVGPOST=0.9733;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.03;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48 +1 13417 . C CGAGA 2788 PASS VT=INDEL;AVGPOST=0.7560;THETA=0.0061;AC=52;AN=2184;AA=.;RSQ=0.1970;LDAF=0.1542;ERATE=0.0127;AF=0.02;ASN_AF=0.02;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.050:0.00,-0.30,-5.60 0|0:0.250:0,0,0 0|0:0.400:0,0,0 0|0:0.350:0.00,-0.30,-5.60 +1 13957 . TC T 226 PASS VT=INDEL;RSQ=0.2600;AN=2184;AA=.;LDAF=0.0542;THETA=0.0144;AVGPOST=0.9144;ERATE=0.0029;AC=27;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 GT:DS:GL 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0,0,0 +1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0021;THETA=0.0096;RSQ=0.3995;AN=2184;AC=55;LDAF=0.0628;AVGPOST=0.9128;AA=.;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 +1 16226 . AG A 104 PASS VT=INDEL;THETA=0.0211;AN=2184;RSQ=0.6096;LDAF=0.0034;AVGPOST=0.9971;AA=A;ERATE=0.0008;AC=4;AF=0.00;AMR_AF=0.00;EUR_AF=0.00 GT:DS:GL 0|0:0.000:0.00,-1.50,-24.00 0|0:0.050:0,0,0 0|0:0.000:0.00,-0.30,-4.80 0|0:0.000:0.00,-0.90,-14.40 +1 17496 . AC A 209 PASS VT=INDEL;AC=7;AN=2184;ERATE=0.0009;AA=A;RSQ=0.7057;THETA=0.0221;AVGPOST=0.9968;LDAF=0.0045;AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.000:0.00,-3.30,-42.90 0|0:0.000:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0,0,0 +1 18869 . ACC A 126 PASS VT=INDEL;LDAF=0.2562;AC=52;AN=2184;ERATE=0.0162;AVGPOST=0.5962;AA=A;RSQ=0.0889;THETA=0.0107;AF=0.02;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.01 GT:DS:GL 0|0:0.400:0,0,0 0|0:0.350:0,0,0 0|0:0.250:0.00,-0.30,-2.90 0|0:0.550:0,0,0 +1 19083 . G GCA 139 PASS VT=INDEL;AVGPOST=0.7121;AN=2184;AC=13;AA=G;THETA=0.0077;ERATE=0.0123;RSQ=0.0826;LDAF=0.1645;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.00 GT:DS:GL 0|0:0.200:0,0,0 0|0:0.400:0,0,0 0|0:0.250:0,0,0 0|0:0.350:0,0,0 +1 19190 . GC G 815 PASS VT=INDEL;AC=131;LDAF=0.2531;AN=2184;AA=G;THETA=0.0161;AVGPOST=0.6408;RSQ=0.1696;ERATE=0.0188;AF=0.06;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.07;EUR_AF=0.04 GT:DS:GL 0|0:0.650:0,0,0 0|0:0.200:0,0,0 0|0:0.650:0,0,0 0|0:0.500:0,0,0 +1 20862 . A AG 78 PASS VT=INDEL;ERATE=0.0067;AVGPOST=0.8007;RSQ=0.0827;LDAF=0.8907;AN=2184;THETA=0.0095;AA=A;AC=2178;AF=1.00;ASN_AF=1.00;AMR_AF=1.00;AFR_AF=0.99;EUR_AF=1.00 GT:DS:GL 1|1:1.750:0,0,0 1|1:1.800:0,0,0 1|1:1.850:0,0,0 1|1:1.750:0,0,0 +1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5363;LDAF=0.6540;THETA=0.0078;AN=2184;AA=T;ERATE=0.0127;AC=1581;SNPSOURCE=LOWCOV;AVGPOST=0.7309;AF=0.72;ASN_AF=0.88;AMR_AF=0.81;AFR_AF=0.48;EUR_AF=0.72 GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48 +1 46402 . C CTGT 104 PASS VT=INDEL;RSQ=0.0943;AA=C;AN=2184;AVGPOST=0.8697;THETA=0.0108;AC=5;LDAF=0.0697;ERATE=0.0056;AF=0.00;ASN_AF=0.00;AMR_AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0 +1 47190 . G GA 868 PASS VT=INDEL;LDAF=0.2298;AN=2184;AC=45;AA=G;RSQ=0.1035;AVGPOST=0.6322;THETA=0.0141;ERATE=0.0127;AF=0.02;ASN_AF=0.00;AMR_AF=0.03;AFR_AF=0.05;EUR_AF=0.01 GT:DS:GL 0|0:0.350:0,0,0 0|0:0.500:0,0,0 0|0:0.550:0,0,0 0|0:0.400:0,0,0 +1 49514 . AG A 449 PASS VT=INDEL;THETA=0.0164;AC=52;AN=2184;RSQ=0.4892;AA=A;LDAF=0.0469;AVGPOST=0.9448;ERATE=0.0053;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.000:0.00,-0.90,-12.40 0|1:0.800:0,0,0 0|0:0.150:-0.10,0.00,0.00 0|0:0.000:0.00,-0.30,-4.20 +1 49515 . G GA 44 PASS VT=INDEL;THETA=0.0214;AN=2184;AC=13;AA=A;ERATE=0.0008;AVGPOST=0.9879;LDAF=0.0111;RSQ=0.5361;AF=0.01;ASN_AF=0.02;EUR_AF=0.01 GT:DS:GL 0|0:0.050:0.00,-0.90,-9.70 0|0:0.050:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0.00,-0.30,-3.20 +1 50481 . GGT G 2370 PASS VT=INDEL;RSQ=0.3702;THETA=0.0038;AN=2184;AA=G;ERATE=0.0177;AVGPOST=0.7981;AC=142;LDAF=0.1660;AF=0.07;ASN_AF=0.05;AMR_AF=0.13;AFR_AF=0.07;EUR_AF=0.04 GT:DS:GL 0|0:0.250:0,0,0 0|0:0.350:0,0,0 1|0:1.150:-3.00,-0.30,0.00 0|0:0.250:0,0,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2pgSnp_output.pgSnp Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,22 @@ +chr1 10522 10523 TCCG 1 8 0 +chr1 10582 10583 G/A 2 7,1 0,0 +chr1 10610 10611 C 1 8 0 +chr1 10615 10616 CCGCCGTTGCAAAGGCGCGCCG/C 2 1,7 0,0 +chr1 11539 11540 T/T 2 7,1 0,0 +chr1 13301 13302 C/T 2 7,1 0,0 +chr1 13326 13327 G/C 2 7,1 0,0 +chr1 13416 13417 C 1 8 0 +chr1 13956 13957 TC 1 8 0 +chr1 13979 13980 T/C 2 7,1 0,0 +chr1 16225 16226 AG 1 8 0 +chr1 17495 17496 AC 1 8 0 +chr1 18868 18869 ACC 1 8 0 +chr1 19082 19083 G 1 8 0 +chr1 19189 19190 GC 1 8 0 +chr1 20861 20862 A 1 8 0 +chr1 30922 30923 G/T 2 4,4 0,0 +chr1 46401 46402 C 1 8 0 +chr1 47189 47190 G 1 8 0 +chr1 49513 49514 AG/A 2 7,1 0,0 +chr1 49514 49515 G 1 8 0 +chr1 50480 50481 GGT/G 2 7,1 0,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2pgSnp.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,116 @@ +#!/usr/bin/perl -w +use strict; + +#convert from a vcf file to a pgSnp file. +#frequency count = chromosome count +#either a single column/individual +#or all columns as a population + +my $in; +my $stCol = 9; +my $endCol; +if (@ARGV && scalar @ARGV == 2) { + $stCol = shift @ARGV; + $in = shift @ARGV; + if ($stCol eq 'all') { $stCol = 10; } + else { $endCol = $stCol; } + $stCol--; #go from 1 based to zero based column number + if ($stCol < 9) { + print "ERROR genotype fields don't start until column 10\n"; + exit; + } +}elsif (@ARGV && scalar @ARGV == 1) { + $in = shift @ARGV; +}elsif (@ARGV) { + print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n"; + exit; +} + +open(FH, $in) or die "Couldn't open $in, $!\n"; +while (<FH>) { + chomp; + if (/^\s*#/) { next; } #skip comments/headers + if (/^\s*$/) { next; } #skip blank lines + my @f = split(/\t/); + #chr pos1base ID refNt altNt[,|D#|Int] quality filter info format geno1 ... + my $a; + my %nt; + my %all; + my $cnt = 0; + my $var; + if ($f[3] eq 'N') { next; } #ignore ref=N + if ($f[4] =~ /[DI]/ or $f[3] =~ /[DI]/) { next; } #don't do microsatellite + #if ($f[4] =~ /[ACTG],[ACTG]/) { next; } #only do positions with single alternate + if ($f[6] && !($f[6] eq '.' or $f[6] eq 'PASS')) { next; } #filtered for some reason + my $ind = 0; + if ($f[8] ne 'GT') { #more than just genotype + my @t = split(/:/, $f[8]); + foreach (@t) { if ($_ eq 'GT') { last; } $ind++; } + if ($ind == 0 && $f[8] !~ /^GT/) { die "ERROR couldn't find genotype in format $f[8]\n"; } + } + #count 0's, 1's, 2's + if (!$endCol) { $endCol = $#f; } + foreach my $col ($stCol .. $endCol) { + if ($ind > 0) { + my @t = split(/:/, $f[$col]); + $f[$col] = $t[$ind] . ":"; #only keep genotype part + } + if ($f[$col] =~ /^(0|1|2).(0|1|2)/) { + $nt{$1}++; + $nt{$2}++; + }elsif ($f[$col] =~ /^(0|1|2):/) { #chrY or male chrX, single + $nt{$1}++; + } #else ignore + } + if (%nt) { + if ($f[0] !~ /chr/) { $f[0] = "chr$f[0]"; } + print "$f[0]\t", ($f[1]-1), "\t$f[1]\t"; #position info + my $cnt = scalar(keys %nt); + my $fr; + my $sc; + my $all; + if (exists $nt{0}) { + $all = uc($f[3]); + $fr = $nt{0}; + $sc = 0; + } + if (!exists $nt{0} && exists $nt{1}) { + if ($f[4] =~ /([ACTG]),?/) { + $all = $1; + $fr = $nt{1}; + $sc = 0; + }else { die "bad variant nt $f[4] for nt 1"; } + }elsif (exists $nt{1}) { + if ($f[4] =~ /([ACTG]),?/) { + $all .= '/' . $1; + $fr .= ",$nt{1}"; + $sc .= ",0"; + }else { die "bad variant nt $f[4] for nt 1"; } + } + if (exists $nt{2}) { + if ($f[4] =~ /^[ACTG],([ACTG]),?/) { + $all .= '/' . $1; + $fr .= ",$nt{2}"; + $sc .= ",0"; + }else { die "bad variant nt $f[4] for nt 2"; } + } + if (exists $nt{3}) { + if ($f[4] =~ /^[ACTG],[ACTG],([ACTG])/) { + $all .= '/' . $1; + $fr .= ",$nt{3}"; + $sc .= ",0"; + }else { die "bad variant nt $f[4] for nt 3"; } + } + if (exists $nt{4}) { + if ($f[4] =~ /^[ACTG],[ACTG],[ACTG],([ACTG])/) { + $all .= '/' . $1; + $fr .= ",$nt{4}"; + $sc .= ",0"; + }else { die "bad variant nt $f[4] for nt 4"; } + } + print "$all\t$cnt\t$fr\t$sc\n"; + } +} +close FH; + +exit;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2pgSnp.xml Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,80 @@ +<tool id="vcf2pgSnp" name="VCF to pgSnp" version="1.0.0" hidden="false"> + <description>: Convert from VCF to pgSnp format</description> + <command interpreter="perl"> + #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1 + #else #vcf2pgSnp.pl $inType.ind_column $input1 > $out_file1 + #end if + </command> + <inputs> + <param format="vcf" name="input1" type="data" label="VCF dataset" /> + <conditional name="inType"> + <param name="how" type="select" label="How to treat individuals"> + <option value="all">Group all as a population</option> + <option value="one">Do just one individual</option> + </param> + <when value="one"> + <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" /> + </when> + <when value="all"> + <!-- do nothing --> + </when> + </conditional> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" /> + <param name="how" value="all" /> + <output name="output" file="vcf2pgSnp_output.pgSnp" /> + </test> + </tests> + + <help> + +**Dataset formats** + +The input dataset is in VCF_ format. +The output dataset is pgSnp_. (`Dataset missing?`_) + +.. _VCF: ./static/formatHelp.html#vcf +.. _pgSnp: ./static/formatHelp.html#pgSnp +.. _Dataset missing?: ./static/formatHelp.html + +----- + +**What it does** + +This converts a VCF dataset to pgSnp format, using chromosome counts for +the allele frequencies. If there is more than one column (individual) +of SNP data, it can either combine all columns as a population, or just +convert a single selected column. + +----- + +**Examples** + +- input:: + + 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48 + 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 + 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48 + etc. + +- output as a population:: + + chr1 13326 13327 G/C 2 7,1 0,0 + chr1 13979 13980 T/C 2 7,1 0,0 + chr1 30922 30923 G/T 2 4,4 0,0 + etc. + +- output for column 10:: + + chr1 13326 13327 G 1 2 0 + chr1 13979 13980 T 1 2 0 + chr1 30922 30923 T 1 2 0 + etc. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcf2pgSnpMult.pl Tue May 28 17:54:02 2013 -0400 @@ -0,0 +1,81 @@ +#!/usr/bin/perl -w +use strict; + +#convert from a vcf file to a pgSnp file with multiple sets of the allele +# specific columns +#frequency count = chromosome count + +my $in; +my $stCol = 9; +my $endCol; +if (@ARGV && scalar @ARGV == 1) { + $in = shift @ARGV; +}else { + print "usage: vcf2pgSnpMult.pl file.vcf > file.pgSnpMult\n"; + exit; +} + +if ($in =~ /.gz$/) { + open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; +}else { + open(FH, $in) or die "Couldn't open $in, $!\n"; +} +while (<FH>) { + chomp; + if (/^\s*#/) { next; } #skip comments/headers + if (/^\s*$/) { next; } #skip blank lines + my @f = split(/\t/); + #chr pos1base ID refNt altNt[,|D#|Int] quality filter info format geno1 ... + my $a; + my %nt; + my %all; + my $cnt = 0; + my $var; + if ($f[3] eq 'N') { next; } #ignore ref=N + if ($f[4] =~ /[DI]/ or $f[3] =~ /[DI]/) { next; } #don't do microsatellite + if ($f[6] && !($f[6] eq '.' or $f[6] eq 'PASS')) { next; } #filtered for some reason + my $ind = 0; + if ($f[8] ne 'GT') { #more than just genotype + my @t = split(/:/, $f[8]); + foreach (@t) { if ($_ eq 'GT') { last; } $ind++; } + if ($ind == 0 && $f[8] !~ /^GT/) { die "ERROR couldn't find genotype in format $f[8]\n"; } + } + if (!$endCol) { $endCol = $#f; } + #put f[3] => nt{0} and split f[4] for rest of nt{} + $nt{0} = $f[3]; + my @t = split(/,/, $f[4]); + for (my $i=0; $i<=$#t; $i++) { + my $j = $i + 1; + $nt{$j} = $t[$i]; + } + if ($f[0] !~ /chr/) { $f[0] = "chr$f[0]"; } + print "$f[0]\t", ($f[1]-1), "\t$f[1]"; #position info + foreach my $col ($stCol .. $endCol) { #add each individual (4 columns) + if ($ind > 0) { + my @t = split(/:/, $f[$col]); + $f[$col] = $t[$ind] . ":"; #only keep genotype part + } + print "\t"; + if ($f[$col] =~ /^(\d).(\d)/) { + my $a1 = $1; + my $a2 = $2; + if (!exists $nt{$a1}) { die "ERROR bad allele $a1 in $f[3] $f[4]\n"; } + if (!exists $nt{$a2}) { die "ERROR bad allele $a2 in $f[3] $f[4]\n"; } + if ($a1 eq $a2) { #homozygous + print "$nt{$a1}\t1\t2\t0"; + }else { #heterozygous + print "$nt{$a1}/$nt{$a2}\t2\t1,1\t0,0"; + } + }elsif ($f[$col] =~ /^(\d):/) { #chrY or male chrX, single + my $a1 = $1; + if (!exists $nt{$a1}) { die "ERROR bad allele $a1 in $f[3] $f[4]\n"; } + print "$nt{$a1}\t1\t1\t0"; + }else { #don't know how to parse + die "ERROR unknown genotype $f[$col]\n"; + } + } + print "\n"; #end this SNP +} +close FH; + +exit;