Mercurial > repos > miller-lab > snp_analysis_conversion
changeset 1:1d8b23a21735
Deleted all files.
| author | cathy |
|---|---|
| date | Tue, 28 May 2013 17:44:08 -0400 |
| parents | 3871157bc013 |
| children | 35c20b109be5 |
| files | snp_analysis_conversion/dividePgSnpAlleles.pl snp_analysis_conversion/dividePgSnpAlleles.xml snp_analysis_conversion/gd_snp2vcf.pl snp_analysis_conversion/gd_snp2vcf.xml snp_analysis_conversion/master2gd_snp.pl snp_analysis_conversion/master2gd_snp.xml snp_analysis_conversion/master2pg.pl snp_analysis_conversion/master2pg.xml snp_analysis_conversion/pgSnp2gd_snp.pl snp_analysis_conversion/pgSnp2gd_snp.xml snp_analysis_conversion/test-data/dividePgSnp_input.pgSnp snp_analysis_conversion/test-data/dividePgSnp_output.txt snp_analysis_conversion/test-data/master2snp_output.txt snp_analysis_conversion/test-data/masterVarTest.txt snp_analysis_conversion/test-data/masterVar_output.txt snp_analysis_conversion/test-data/pgSnp2snp_output.txt snp_analysis_conversion/test-data/pgSnpTest.ref.txt snp_analysis_conversion/test-data/sample.gd_snp snp_analysis_conversion/test-data/snpsForSubmission.text snp_analysis_conversion/test-data/snpsForSubmission.vcf snp_analysis_conversion/test-data/vcf2pgSnp_input.vcf snp_analysis_conversion/test-data/vcf2pgSnp_output.pgSnp snp_analysis_conversion/vcf2pgSnp.pl snp_analysis_conversion/vcf2pgSnp.xml snp_analysis_conversion/vcf2pgSnpMult.pl |
| diffstat | 25 files changed, 0 insertions(+), 27568 deletions(-) [+] |
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--- a/snp_analysis_conversion/dividePgSnpAlleles.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -#!/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; -
--- a/snp_analysis_conversion/dividePgSnpAlleles.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -<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>
--- a/snp_analysis_conversion/gd_snp2vcf.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,197 +0,0 @@ -#!/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=$t"; - } - } - #PMID? -##INFO=<ID=PMID,Number=.,Type=Integer,Description="PubMed ID linked to variation if available."> - - return @h; -} -####End -
--- a/snp_analysis_conversion/gd_snp2vcf.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,141 +0,0 @@ -<tool id="gd_snp2vcf" name="gd_snp to VCF" version="1.0.0" force_history_refresh="True"> - <description>: Convert from gd_snp to VCF format, for submission to dbSNP</description> - - <command interpreter="perl"> - gd_snp2vcf.pl "$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>
--- a/snp_analysis_conversion/master2gd_snp.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,221 +0,0 @@ -#!/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
--- a/snp_analysis_conversion/master2gd_snp.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -<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>
--- a/snp_analysis_conversion/master2pg.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ -#!/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;
--- a/snp_analysis_conversion/master2pg.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -<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>
--- a/snp_analysis_conversion/pgSnp2gd_snp.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,208 +0,0 @@ -#!/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 -
--- a/snp_analysis_conversion/pgSnp2gd_snp.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -<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>
--- a/snp_analysis_conversion/test-data/dividePgSnp_input.pgSnp Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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
--- a/snp_analysis_conversion/test-data/dividePgSnp_output.txt Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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
--- a/snp_analysis_conversion/test-data/master2snp_output.txt Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#{"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
--- a/snp_analysis_conversion/test-data/masterVarTest.txt Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5000 +0,0 @@ -#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
--- a/snp_analysis_conversion/test-data/masterVar_output.txt Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -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
--- a/snp_analysis_conversion/test-data/pgSnp2snp_output.txt Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10002 +0,0 @@ -#{"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 -chr1 7911301 C T -1 8 9 1 0.8736 -chr1 7954646 C T -1 12 8 1 0.8490 -chr1 8027386 C T -1 15 21 1 0.8528 -chr1 8549302 C T -1 8 7 1 0.8633 -chr1 8932179 G T -1 13 12 1 0.8594 -chr1 9016389 C T -1 0 14 0 0.8590 -chr1 9494443 C T -1 0 6 0 0.8567 -chr1 10615774 T C -1 0 15 0 0.8684 -chr1 10622975 C T -1 0 4 0 0.8001 -chr1 10782207 C T -1 0 3 0 0.8402 -chr1 12238146 G A -1 9 4 1 0.8560 -chr1 12429037 A G -1 8 6 1 0.8863 -chr1 12669902 T C -1 24 10 1 0.8495 -chr1 13189040 A T -1 8 4 1 0.8868 -chr1 14208570 G A -1 8 10 1 0.8646 -chr1 14501554 G A -1 26 17 1 0.8646 -chr1 15063865 G A -1 18 9 1 0.8571 -chr1 15286095 A G -1 0 21 0 0.8600 -chr1 15441925 C T -1 0 17 0 0.8402 -chr1 15712178 G A -1 0 14 0 0.8694 -chr1 16207687 C G -1 0 16 0 0.8512 -chr1 16314956 T A -1 0 31 0 0.8639 -chr1 16476823 C T -1 5 8 1 0.8898 -chr1 16730581 C G -1 0 9 0 0.8232 -chr1 17053721 G T -1 0 66 0 0.8916 -chr1 17053765 G A -1 11 19 1 0.8246 -chr1 17408311 G C -1 0 22 0 0.8786 -chr1 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-chr1 90534457 90534458 C/T 2 5,4 0.8810,0.8699 C -chr1 90758097 90758098 A/C 2 4,3 0.8683,0.7675 A -chr1 91075848 91075849 A/G 2 13,11 0.8765,0.8441 G -chr1 91340680 91340681 C 1 22 0.8896 T -chr1 91547663 91547664 C/T 2 4,4 0.8439,0.9119 T -chr1 91750910 91750911 A 1 6 0.8562 C -chr1 92019170 92019171 A 1 29 0.8334 G -chr1 92094461 92094462 A/G 2 11,11 0.8387,0.8452 G -chr1 92176304 92176305 A/T 2 11,12 0.8571,0.8825 A -chr1 92327876 92327877 A/T 2 17,21 0.8573,0.8449 A -chr1 92638778 92638779 G 1 10 0.8614 A -chr1 92736618 92736619 A/G 2 13,22 0.8496,0.8584 G -chr1 93146457 93146458 A/G 2 10,11 0.8576,0.8693 G -chr1 93537426 93537427 A 1 20 0.8305 G -chr1 93772970 93772971 C 1 9 0.8659 T -chr1 94244509 94244510 A 1 34 0.8917 G -chr1 95056634 95056635 A/T 2 14,9 0.8692,0.8540 A -chr1 95567853 95567854 A 1 27 0.8594 G -chr1 95745538 95745539 A/G 2 12,18 0.8339,0.8525 G -chr1 96168894 96168895 C/G 2 12,9 0.8600,0.8885 C -chr1 96796629 96796630 G/T 2 11,11 0.7776,0.7876 T -chr1 96817217 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0.8470 T -chr1 104945356 104945357 C/G 2 17,14 0.8257,0.8341 C -chr1 105161587 105161588 A/G 2 10,6 0.8231,0.8482 A -chr1 105297627 105297628 C/T 2 10,20 0.9008,0.8927 C -chr1 105326234 105326235 A 1 18 0.8313 G -chr1 105326248 105326249 G 1 11 0.8589 A -chr1 105661965 105661966 A/G 2 12,10 0.7819,0.7430 A -chr1 105759370 105759371 T 1 32 0.8712 C -chr1 105840667 105840668 C/G 2 19,14 0.8759,0.8684 C -chr1 106518709 106518710 A/G 2 19,12 0.8481,0.8208 A -chr1 106647217 106647218 A 1 36 0.8156 G -chr1 106818954 106818955 G 1 32 0.8705 C -chr1 107198202 107198203 T 1 30 0.8733 C -chr1 107206521 107206522 A/T 2 14,17 0.7824,0.7969 A -chr1 107482856 107482857 A/G 2 5,5 0.9175,0.9054 A -chr1 108086096 108086097 T 1 3 0.9153 C -chr1 108136472 108136473 G 1 32 0.8372 A -chr1 108516398 108516399 T 1 16 0.8247 G -chr1 108568921 108568922 A/G 2 19,6 0.8476,0.7586 A -chr1 109212670 109212671 A 1 8 0.8722 G -chr1 109718618 109718619 G/T 2 12,7 0.8453,0.8636 G -chr1 110016438 110016439 T 1 6 0.8657 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A -chr1 207183082 207183083 C/G 2 6,15 0.8519,0.8605 C -chr1 207539810 207539811 G 1 7 0.8791 A -chr1 207555357 207555358 T 1 8 0.8748 A -chr1 208026180 208026181 A/C 2 11,9 0.8127,0.7822 C -chr1 208190110 208190111 A/C 2 13,14 0.8358,0.8384 C -chr1 208562852 208562853 C 1 8 0.8844 T -chr1 208615658 208615659 G/T 2 3,5 0.8252,0.8497 T -chr1 208996827 208996828 C/T 2 6,11 0.8684,0.8583 T -chr1 209329544 209329545 A/G 2 7,3 0.8403,0.8390 A -chr1 209575390 209575391 G 1 24 0.8690 A -chr1 210579320 210579321 C/T 2 18,19 0.8552,0.8563 T -chr1 210798670 210798671 C/G 2 5,11 0.8343,0.8338 G -chr1 211476422 211476423 G 1 30 0.8526 C -chr1 211481940 211481941 A/G 2 6,3 0.6470,0.8036 A -chr1 211643016 211643017 C 1 24 0.8333 T -chr1 211914502 211914503 G 1 3 0.7604 A -chr1 212329293 212329294 T 1 3 0.8092 G -chr1 213597715 213597716 C/T 2 6,14 0.7945,0.8423 T -chr1 214045056 214045057 C/T 2 23,24 0.8777,0.8951 T -chr1 214068998 214068999 A/G 2 25,15 0.8485,0.8616 G -chr1 214103670 214103671 C/T 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230291995 A/T 2 3,4 0.8791,0.8600 T -chr1 230951171 230951172 A 1 32 0.8229 G -chr1 231053781 231053782 A/G 2 17,17 0.8623,0.8455 A -chr1 231103890 231103891 C/T 2 5,3 0.8889,0.7771 C -chr1 231154598 231154599 C/G 2 4,10 0.8617,0.8305 G -chr1 231636999 231637000 A/T 2 11,8 0.8378,0.8090 A -chr1 232080713 232080714 A/G 2 2,3 0.9202,0.8234 G -chr1 233412103 233412104 C/T 2 17,16 0.8650,0.8753 T -chr1 233951924 233951925 A/G 2 27,11 0.8057,0.8350 G -chr1 234291143 234291144 G/T 2 4,3 0.8473,0.8278 T -chr1 234348401 234348402 G 1 3 0.8864 A -chr1 234414262 234414263 A 1 6 0.8803 G -chr1 234797592 234797593 C/G 2 6,4 0.8934,0.9133 G -chr1 235077995 235077996 C/T 2 13,22 0.8707,0.8648 T -chr1 235105581 235105582 A/G 2 5,4 0.8579,0.8379 G -chr1 235263161 235263162 C/T 2 4,11 0.8418,0.8821 T -chr1 235532857 235532858 C 1 5 0.8874 T -chr1 235713077 235713078 C/T 2 12,8 0.8280,0.8221 C -chr1 235806793 235806794 A/G 2 16,11 0.8601,0.8949 A -chr1 235945293 235945294 C/T 2 16,15 0.8649,0.8682 T -chr1 236359345 236359346 G 1 3 0.8857 C -chr1 236697550 236697551 C/T 2 18,10 0.8298,0.8576 C -chr1 236795086 236795087 G 1 22 0.8452 A -chr1 236924145 236924146 A/C 2 9,14 0.8400,0.8507 C -chr1 237171418 237171419 A/G 2 11,5 0.8728,0.8370 A -chr1 237274018 237274019 C/T 2 21,20 0.8567,0.8457 C -chr1 237299348 237299349 C/T 2 16,17 0.8320,0.8497 T -chr1 237642241 237642242 C/G 2 16,10 0.8995,0.8829 C -chr1 237716911 237716912 A/G 2 11,17 0.8582,0.8566 A -chr1 237840899 237840900 A/G 2 8,5 0.8725,0.7936 A -chr1 237937873 237937874 C/T 2 13,5 0.8315,0.8745 C -chr1 238501614 238501615 C/G 2 15,8 0.8887,0.8268 C -chr1 238568913 238568914 A/G 2 10,11 0.8066,0.7737 A -chr1 238609915 238609916 A/G 2 9,12 0.8429,0.8730 A -chr1 239963180 239963181 G 1 23 0.8592 T -chr1 240177789 240177790 A/G 2 10,8 0.8891,0.8787 A -chr1 240181721 240181722 A/T 2 18,14 0.8630,0.8654 A -chr1 240641731 240641732 C 1 22 0.8261 T -chr1 240704716 240704717 A/G 2 26,15 0.8618,0.8797 A -chr1 241494577 241494578 A/G 2 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5431442 5431443 C/G 2 9,8 0.8222,0.8594 C -chr2 5495697 5495698 G 1 11 0.8673 C -chr2 5569322 5569323 A/G 2 9,9 0.8129,0.8307 G -chr2 5644933 5644934 T 1 43 0.8603 C -chr2 5652570 5652571 A/G 2 12,14 0.8323,0.8336 G -chr2 5849523 5849524 C/G 2 5,5 0.8411,0.8043 C -chr2 6043193 6043194 A 1 18 0.8760 G -chr2 6061369 6061370 G/T 2 16,12 0.8778,0.8678 T -chr2 6119476 6119477 G 1 21 0.8453 A -chr2 6126431 6126432 A/G 2 7,7 0.8294,0.8595 G -chr2 6152872 6152873 A/C 2 7,10 0.8917,0.9049 A -chr2 6241442 6241443 A/G 2 6,16 0.8581,0.8773 G -chr2 6329062 6329063 A/G 2 10,20 0.8713,0.8290 A -chr2 6340561 6340562 A/C 2 23,18 0.8662,0.8773 A -chr2 6639367 6639368 C/G 2 17,8 0.8312,0.8450 C -chr2 6646176 6646177 T 1 33 0.8480 C -chr2 6745043 6745044 C/T 2 11,16 0.8930,0.8880 T -chr2 7812916 7812917 C/T 2 12,12 0.8994,0.8533 C -chr2 7918751 7918752 A/G 2 8,3 0.8422,0.8894 A -chr2 7928406 7928407 A/G 2 13,8 0.8287,0.8062 A -chr2 8690489 8690490 C/T 2 10,9 0.8507,0.8444 C -chr2 8766167 8766168 C/T 2 5,7 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-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 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35899283 G 1 21 0.8731 T -chr2 35901325 35901326 A/T 2 7,7 0.8574,0.8522 T -chr2 36044285 36044286 C/T 2 17,12 0.8508,0.8655 C -chr2 36244685 36244686 A 1 36 0.8394 G -chr2 36468338 36468339 C/T 2 17,23 0.8574,0.8560 T -chr2 36471031 36471032 C/T 2 14,13 0.8662,0.8756 T -chr2 36494401 36494402 A/G 2 15,20 0.8430,0.8574 A -chr2 36511536 36511537 A 1 13 0.8915 G -chr2 36593909 36593910 A/T 2 3,4 0.9253,0.9202 T -chr2 36756287 36756288 C 1 22 0.8367 T -chr2 36886629 36886630 A/G 2 11,9 0.7783,0.7995 A -chr2 36946350 36946351 C/T 2 8,12 0.8675,0.8836 T -chr2 37031745 37031746 G 1 2 0.9482 A -chr2 37123298 37123299 G 1 3 0.8873 A -chr2 37440613 37440614 G 1 4 0.8654 C -chr2 37475113 37475114 C/G 2 4,8 0.8708,0.8717 C -chr2 37848875 37848876 C/G 2 15,14 0.8833,0.8930 C -chr2 38063479 38063480 G 1 9 0.8596 A -chr2 38371475 38371476 C/G 2 14,18 0.8482,0.8685 G -chr2 38375960 38375961 T 1 19 0.8371 C -chr2 39982697 39982698 G 1 11 0.8545 C -chr2 40209999 40210000 A/G 2 6,11 0.8434,0.8394 G -chr2 40257636 40257637 A 1 20 0.8681 T -chr2 40390261 40390262 A/G 2 25,14 0.8587,0.8616 G -chr2 40433419 40433420 G/T 2 17,19 0.8582,0.8618 T -chr2 40648155 40648156 A/T 2 14,20 0.8808,0.8689 T -chr2 41213459 41213460 A/C 2 9,16 0.8474,0.8460 A -chr2 41302220 41302221 A/T 2 13,13 0.8106,0.8109 T -chr2 41318244 41318245 G/T 2 9,10 0.8527,0.8722 G -chr2 41431084 41431085 C/T 2 22,10 0.8352,0.8304 T -chr2 41561331 41561332 C/T 2 15,10 0.8705,0.8573 T -chr2 41651449 41651450 G/T 2 10,7 0.8815,0.8401 T -chr2 41670349 41670350 A/C 2 15,13 0.8421,0.8731 A -chr2 41836312 41836313 C 1 31 0.8913 T -chr2 41870894 41870895 A/G 2 10,17 0.8469,0.8621 G -chr2 41871140 41871141 C/T 2 22,7 0.8939,0.8894 T -chr2 42253745 42253746 G/T 2 19,11 0.8599,0.8363 T -chr2 42571485 42571486 C/T 2 21,15 0.8820,0.8794 C -chr2 42751484 42751485 A 1 6 0.7769 G -chr2 43100437 43100438 C 1 5 0.8458 A -chr2 43102326 43102327 T 1 27 0.8234 C -chr2 43281210 43281211 A/G 2 18,21 0.8254,0.8269 G -chr2 43317252 43317253 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54060138 A/G 2 12,13 0.8953,0.8877 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 62023584 C 1 4 0.8330 G -chr2 62095993 62095994 G 1 13 0.8684 A -chr2 62152367 62152368 A/G 2 11,8 0.8627,0.8590 G -chr2 62342904 62342905 G/T 2 15,14 0.8610,0.8493 G -chr2 62535081 62535082 T 1 17 0.8231 G -chr2 62708402 62708403 C 1 12 0.8653 G -chr2 63502532 63502533 T 1 22 0.8790 A -chr2 63966633 63966634 A/G 2 17,22 0.8688,0.8922 A -chr2 63991958 63991959 T 1 34 0.8472 C -chr2 64256900 64256901 C/T 2 12,16 0.8295,0.8111 C -chr2 64559902 64559903 C/T 2 8,11 0.8130,0.8625 C -chr2 64733280 64733281 A 1 3 0.8400 T -chr2 64838891 64838892 G 1 16 0.8751 A -chr2 65164505 65164506 C/G 2 13,13 0.8823,0.8801 C -chr2 65209379 65209380 A/G 2 14,24 0.8638,0.8579 G -chr2 65640820 65640821 A/G 2 17,10 0.8518,0.8518 A -chr2 65654363 65654364 C/T 2 3,4 0.9017,0.8840 C -chr2 65806960 65806961 T 1 18 0.8154 C -chr2 65961564 65961565 G/T 2 7,7 0.8607,0.8990 G -chr2 66001264 66001265 C/G 2 13,6 0.8694,0.8799 C -chr2 66107663 66107664 C/T 2 16,14 0.8448,0.8557 C -chr2 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C 1 29 0.8384 T -chr2 71780214 71780215 C 1 3 0.8881 T -chr2 71872153 71872154 C 1 14 0.9126 T -chr2 72128778 72128779 C/T 2 14,12 0.8226,0.8432 T -chr2 73248749 73248750 C 1 4 0.8482 T -chr2 73249890 73249891 C/T 2 14,8 0.8496,0.8838 C -chr2 73701668 73701669 A/T 2 9,10 0.8618,0.8741 T -chr2 73936321 73936322 C/T 2 16,23 0.8390,0.8786 T -chr2 75039613 75039614 A 1 44 0.8398 C -chr2 75561788 75561789 C/T 2 14,17 0.8630,0.8751 C -chr2 76149762 76149763 C 1 20 0.8638 T -chr2 76227225 76227226 A/C 2 20,14 0.8595,0.8493 A -chr2 76453761 76453762 A/G 2 8,7 0.8161,0.8830 G -chr2 76495413 76495414 C 1 18 0.8523 A -chr2 76819975 76819976 A/G 2 4,3 0.8981,0.8943 G -chr2 76962949 76962950 C/T 2 6,13 0.9108,0.8704 T -chr2 77465283 77465284 A/G 2 3,9 0.8418,0.8365 G -chr2 78205266 78205267 C/G 2 12,20 0.8280,0.8586 G -chr2 78424568 78424569 T 1 30 0.8761 C -chr2 78534494 78534495 C/G 2 11,8 0.8683,0.8472 G -chr2 79226105 79226106 G/T 2 9,9 0.8992,0.9014 T -chr2 79759525 79759526 A/G 2 15,14 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-chr2 91633604 91633605 A/G 2 9,12 0.8427,0.8544 A -chr2 91703770 91703771 T 1 10 0.8694 A -chr2 92255470 92255471 A/G 2 5,5 0.8311,0.8065 A -chr2 92270000 92270001 A/C 2 12,33 0.8254,0.8159 C -chr2 92309832 92309833 A/G 2 46,39 0.8467,0.8469 A -chr2 92317637 92317638 C/G 2 18,24 0.8511,0.8565 C -chr2 95557772 95557773 G/T 2 12,41 0.8678,0.8549 T -chr2 96002694 96002695 G 1 24 0.8618 T -chr2 96037314 96037315 A/C 2 17,10 0.8879,0.8745 A -chr2 96521296 96521297 C 1 11 0.8407 T -chr2 97036195 97036196 G 1 30 0.8741 T -chr2 98317664 98317665 A/T 2 9,15 0.8558,0.8515 A -chr2 99102809 99102810 C/T 2 23,19 0.8600,0.8673 T -chr2 99449535 99449536 G 1 17 0.8763 A -chr2 99865350 99865351 C/T 2 6,6 0.8837,0.8345 T -chr2 100059125 100059126 A/G 2 17,18 0.9050,0.8696 G -chr2 100375324 100375325 G/T 2 22,25 0.8421,0.8477 T -chr2 100992223 100992224 A/G 2 17,12 0.8740,0.8786 G -chr2 101179797 101179798 C/G 2 7,8 0.8604,0.8674 C -chr2 101565150 101565151 G 1 31 0.8622 A -chr2 101652796 101652797 C 1 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106725928 T 1 26 0.8678 C -chr2 106872988 106872989 G 1 3 0.8438 A -chr2 106891236 106891237 C/G 2 11,14 0.8153,0.7996 G -chr2 107248223 107248224 G 1 6 0.8555 A -chr2 107540111 107540112 T 1 3 0.8678 G -chr2 107674320 107674321 C 1 5 0.7503 A -chr2 107883104 107883105 A 1 23 0.8436 G -chr2 107985237 107985238 C/T 2 6,5 0.8914,0.8901 T -chr2 108656279 108656280 A 1 15 0.8518 G -chr2 109457831 109457832 A/G 2 18,17 0.8798,0.8839 A -chr2 109497505 109497506 C/T 2 22,18 0.8200,0.8478 C -chr2 110004169 110004170 C 1 48 0.8462 T -chr2 110022218 110022219 A 1 17 0.8701 G -chr2 110028383 110028384 C 1 25 0.8334 G -chr2 110453976 110453977 A/G 2 7,12 0.8617,0.8349 A -chr2 111762159 111762160 T 1 29 0.8358 C -chr2 113076576 113076577 G 1 24 0.8674 A -chr2 113544825 113544826 A/G 2 9,10 0.8528,0.8501 G -chr2 113723913 113723914 T 1 13 0.8892 C -chr2 113744318 113744319 A/C 2 9,7 0.8821,0.8841 A -chr2 113798387 113798388 A 1 9 0.8726 G -chr2 114461691 114461692 C/T 2 6,3 0.8192,0.7602 T -chr2 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A/G 2 14,17 0.8750,0.8728 A -chr2 122047042 122047043 A/C 2 14,7 0.8756,0.8828 C -chr2 122536454 122536455 G 1 36 0.8550 A -chr2 122953458 122953459 A/T 2 13,5 0.7783,0.7993 A -chr2 123110168 123110169 C/T 2 15,12 0.8706,0.8962 C -chr2 123406903 123406904 C 1 21 0.8739 T -chr2 123564876 123564877 C/T 2 18,19 0.8261,0.7820 C -chr2 123874332 123874333 A/T 2 7,11 0.8475,0.8551 T -chr2 124092428 124092429 C/T 2 10,10 0.8572,0.8708 C -chr2 124413820 124413821 A/G 2 16,13 0.8704,0.8884 G -chr2 124800341 124800342 A/G 2 17,16 0.8483,0.8480 A -chr2 125021959 125021960 C/G 2 10,4 0.8821,0.9071 C -chr2 125112974 125112975 G 1 26 0.8617 A -chr2 125269890 125269891 G 1 19 0.8657 T -chr2 125410732 125410733 G/T 2 11,17 0.8284,0.8168 T -chr2 125470283 125470284 T 1 29 0.8602 C -chr2 125820393 125820394 G 1 22 0.8061 A -chr2 125915376 125915377 C 1 21 0.8597 T -chr2 126017806 126017807 C/T 2 3,3 0.8585,0.8707 C -chr2 126196708 126196709 G 1 12 0.8379 A -chr2 127462263 127462264 A/G 2 5,13 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140986295 C 1 18 0.8501 A -chr2 142219512 142219513 A 1 31 0.8191 G -chr2 143244376 143244377 C/G 2 7,14 0.8440,0.8075 G -chr2 143342732 143342733 A 1 23 0.8743 T -chr2 143988476 143988477 A 1 11 0.8436 G -chr2 144352436 144352437 A/C 2 4,8 0.8024,0.8489 A -chr2 144614826 144614827 A 1 35 0.8657 C -chr2 144665823 144665824 T 1 4 0.7615 G -chr2 144682963 144682964 C/T 2 23,10 0.8706,0.8596 C -chr2 145495249 145495250 A/G 2 28,13 0.8255,0.8547 A -chr2 145564922 145564923 A/G 2 9,5 0.8472,0.8234 A -chr2 146282217 146282218 A/T 2 19,12 0.8332,0.8448 A -chr2 146284171 146284172 A/T 2 8,8 0.8178,0.8491 T -chr2 150223214 150223215 G 1 23 0.8313 A -chr2 151073732 151073733 A/T 2 9,5 0.8612,0.8240 A -chr2 151870611 151870612 A 1 28 0.8717 G -chr2 151886687 151886688 A 1 15 0.8339 G -chr2 151904663 151904664 G 1 16 0.8893 A -chr2 152591188 152591189 A 1 21 0.8957 G -chr2 152836454 152836455 G 1 31 0.8582 A -chr2 152860648 152860649 C 1 4 0.8384 G -chr2 153234434 153234435 C/T 2 12,7 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C/T 2 12,11 0.8804,0.8932 C -chr2 170439090 170439091 C 1 33 0.8461 G -chr2 170837018 170837019 T 1 16 0.8875 A -chr2 171090317 171090318 G 1 25 0.8449 T -chr2 171167261 171167262 T 1 31 0.8762 A -chr2 171287813 171287814 A 1 21 0.8595 G -chr2 171429350 171429351 C/T 2 14,17 0.8626,0.8671 C -chr2 171725122 171725123 A/C 2 5,7 0.7945,0.8266 C -chr2 171907724 171907725 A/T 2 10,9 0.7375,0.8245 A -chr2 171988808 171988809 C/T 2 17,6 0.8498,0.8723 C -chr2 172832023 172832024 G/T 2 26,8 0.8962,0.8933 G -chr2 173317497 173317498 T 1 19 0.8678 G -chr2 173677056 173677057 A/G 2 13,22 0.8513,0.8595 G -chr2 173877349 173877350 A/G 2 15,16 0.8482,0.8356 G -chr2 174522940 174522941 T 1 30 0.8463 C -chr2 174652981 174652982 A/G 2 17,23 0.8545,0.8328 A -chr2 174844361 174844362 A 1 11 0.8638 G -chr2 175059682 175059683 C/T 2 13,5 0.8663,0.8515 C -chr2 175254026 175254027 C/T 2 3,6 0.8526,0.8814 T -chr2 175524346 175524347 C/G 2 21,22 0.8463,0.8580 G -chr2 175906889 175906890 C 1 5 0.8805 T -chr2 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A/C 2 16,21 0.8549,0.8918 C -chr2 222077465 222077466 G 1 26 0.8485 A -chr2 222943875 222943876 A/G 2 7,11 0.8280,0.8133 G -chr2 224172135 224172136 T 1 24 0.8623 C -chr2 224228653 224228654 C/T 2 14,9 0.8816,0.8801 T -chr2 224576598 224576599 A/G 2 14,13 0.8331,0.8441 G -chr2 224578061 224578062 A 1 2 0.9283 G -chr2 224609478 224609479 A/G 2 20,20 0.8356,0.8652 G -chr2 225764869 225764870 G 1 21 0.8698 A -chr2 226138793 226138794 A/G 2 9,9 0.8363,0.8672 G -chr2 226168965 226168966 C/T 2 14,12 0.8645,0.8463 C -chr2 226194352 226194353 C 1 29 0.8666 T -chr2 226750222 226750223 C/T 2 14,19 0.8595,0.8582 C -chr2 227326460 227326461 A/G 2 15,15 0.8696,0.8569 G -chr2 227451413 227451414 A/G 2 11,12 0.8897,0.8930 A -chr2 228053693 228053694 A/C 2 9,8 0.8307,0.9031 C -chr2 228412995 228412996 A/C 2 4,13 0.8436,0.8738 C -chr2 228569338 228569339 G 1 16 0.8654 C -chr2 229091494 229091495 A/T 2 11,12 0.8423,0.8376 A -chr2 229115092 229115093 C/T 2 7,10 0.8534,0.7687 T -chr2 229137678 229137679 C/T 2 16,5 0.8607,0.8915 C -chr2 229368811 229368812 C/G 2 8,12 0.8764,0.8618 C -chr2 229827678 229827679 C/G 2 12,12 0.8230,0.8538 G -chr2 229871995 229871996 C/T 2 12,14 0.8614,0.9014 T -chr2 229951736 229951737 A/G 2 12,15 0.8112,0.8438 A -chr2 230108324 230108325 A/T 2 6,4 0.8269,0.8507 T -chr2 231057231 231057232 A/G 2 6,7 0.8561,0.8403 G -chr2 231255308 231255309 T 1 3 0.8048 C -chr2 231440158 231440159 C 1 3 0.8857 T -chr2 231483476 231483477 A/G 2 9,4 0.8870,0.8327 A -chr2 233469465 233469466 C/T 2 4,8 0.8190,0.8718 C -chr2 233509850 233509851 C 1 23 0.8382 T -chr2 233654626 233654627 A/G 2 16,19 0.8774,0.8501 A -chr2 233957463 233957464 A/G 2 9,4 0.8847,0.8803 A -chr2 234758613 234758614 A/G 2 25,10 0.8630,0.8628 A -chr2 235039425 235039426 C 1 20 0.8737 T -chr2 235299766 235299767 C/T 2 14,18 0.8380,0.8359 C -chr2 235363266 235363267 C 1 25 0.8184 T -chr2 235426710 235426711 G 1 24 0.8735 A -chr2 236017838 236017839 C 1 30 0.8367 T -chr2 236906093 236906094 C/G 2 13,11 0.8126,0.8506 G -chr2 237001368 237001369 A/G 2 9,7 0.7809,0.7179 A -chr2 237231761 237231762 C 1 16 0.8513 G -chr2 237493593 237493594 A/G 2 19,11 0.8807,0.8977 A -chr2 237587954 237587955 A 1 30 0.8546 G -chr2 237761726 237761727 C/T 2 15,19 0.8455,0.8390 T -chr2 237794077 237794078 T 1 16 0.8209 C -chr2 237804208 237804209 G/T 2 9,9 0.7559,0.7945 T -chr2 237845915 237845916 C 1 18 0.8594 T -chr2 238189503 238189504 C 1 16 0.8731 T -chr2 238215382 238215383 G/T 2 4,9 0.8337,0.8438 T -chr2 238388372 238388373 C/T 2 14,6 0.7973,0.8047 C -chr2 238567766 238567767 T 1 11 0.8503 C -chr2 239636948 239636949 T 1 25 0.8565 G -chr2 240325621 240325622 A 1 14 0.8680 C -chr2 240340045 240340046 A 1 16 0.8701 G -chr2 240617791 240617792 A 1 6 0.8680 T -chr2 240673990 240673991 A/G 2 9,18 0.8915,0.8657 G -chr2 240776691 240776692 C/G 2 6,12 0.8626,0.8619 C -chr2 240871017 240871018 C/T 2 9,8 0.8265,0.8579 C -chr2 241089218 241089219 A/C 2 3,4 0.8734,0.8969 C -chr2 241140183 241140184 C/T 2 3,5 0.8246,0.8326 C -chr2 241314456 241314457 C/T 2 8,4 0.8642,0.8719 T -chr2 242323118 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 A/G 2 10,21 0.8643,0.8565 G -chr3 2979470 2979471 A/G 2 13,8 0.8698,0.8236 A -chr3 3147195 3147196 A/G 2 11,16 0.8251,0.8584 A -chr3 3204888 3204889 C 1 30 0.8639 T -chr3 3444680 3444681 G/T 2 8,7 0.8417,0.8969 T -chr3 3554054 3554055 A 1 15 0.8228 C -chr3 3557874 3557875 A/G 2 16,14 0.8782,0.8617 A -chr3 3878208 3878209 G/T 2 10,18 0.8604,0.8716 T -chr3 3963034 3963035 C/G 2 14,10 0.8455,0.8306 C -chr3 4196995 4196996 C/T 2 15,13 0.8366,0.8306 T -chr3 4339146 4339147 A 1 9 0.8491 G -chr3 4401637 4401638 C/T 2 10,4 0.7586,0.7557 T -chr3 4403356 4403357 C 1 16 0.7873 A -chr3 4426300 4426301 A/G 2 14,6 0.8164,0.8714 G -chr3 4696843 4696844 C 1 15 0.8888 T -chr3 4905104 4905105 A/G 2 5,4 0.8993,0.8872 A -chr3 4906185 4906186 C 1 31 0.8320 T -chr3 4907323 4907324 A/C 2 11,9 0.8825,0.8418 A -chr3 5173634 5173635 C/T 2 11,5 0.8635,0.8345 C -chr3 5468172 5468173 G 1 15 0.8775 C -chr3 5477374 5477375 C/T 2 7,3 0.8407,0.8877 T -chr3 5617877 5617878 A 1 23 0.8568 G -chr3 5977208 5977209 C/T 2 3,4 0.8542,0.9092 T -chr3 6534097 6534098 C/G 2 4,4 0.8301,0.8584 G -chr3 6659000 6659001 A/G 2 12,22 0.8758,0.8630 G -chr3 6764280 6764281 C 1 16 0.8638 T -chr3 6786561 6786562 G 1 22 0.8634 A -chr3 6788795 6788796 G 1 26 0.8363 A -chr3 7120414 7120415 A/G 2 7,11 0.8231,0.8696 G -chr3 7140145 7140146 T 1 20 0.8108 A -chr3 7255105 7255106 A/G 2 17,13 0.8372,0.8349 G -chr3 7354206 7354207 A/G 2 21,15 0.8560,0.8364 A -chr3 7378832 7378833 A 1 28 0.8326 G -chr3 7845138 7845139 C 1 29 0.8476 G -chr3 7876435 7876436 C/T 2 8,20 0.8598,0.8555 T -chr3 8185281 8185282 G 1 12 0.8326 T -chr3 8203313 8203314 A/G 2 14,10 0.8730,0.8436 G -chr3 8216238 8216239 A/G 2 4,5 0.9001,0.8885 G -chr3 8373145 8373146 A/G 2 7,10 0.8992,0.8373 A -chr3 8873281 8873282 C/T 2 10,20 0.8122,0.8155 T -chr3 9115804 9115805 T 1 22 0.8556 C -chr3 9402285 9402286 T 1 6 0.8786 G -chr3 9672077 9672078 G 1 26 0.8538 A -chr3 9795542 9795543 A/G 2 17,17 0.8474,0.8578 A -chr3 10108744 10108745 C/G 2 6,17 0.8585,0.8729 G -chr3 10243036 10243037 A/G 2 6,10 0.8430,0.8548 G -chr3 10250172 10250173 C/T 2 8,4 0.8466,0.8644 C -chr3 10696723 10696724 G/T 2 11,11 0.8413,0.8756 T -chr3 10757707 10757708 A/G 2 19,21 0.8756,0.8803 G -chr3 10771816 10771817 G/T 2 19,15 0.8395,0.8392 G -chr3 11164743 11164744 A 1 20 0.8484 G -chr3 11305371 11305372 A/G 2 6,4 0.8874,0.8598 A -chr3 11723959 11723960 G 1 10 0.8398 A -chr3 12408277 12408278 A/G 2 17,13 0.8374,0.8225 A -chr3 12825900 12825901 T 1 21 0.8525 C -chr3 12833078 12833079 C/G 2 22,18 0.8350,0.8084 C -chr3 13042981 13042982 A 1 32 0.8698 G -chr3 13052051 13052052 G 1 22 0.8840 A -chr3 13426609 13426610 C 1 17 0.8681 T -chr3 13625598 13625599 A/G 2 5,7 0.8319,0.7995 G -chr3 13693310 13693311 A/T 2 15,19 0.8938,0.8638 T -chr3 13779639 13779640 A/G 2 9,9 0.8865,0.8918 A -chr3 14318852 14318853 C/T 2 18,11 0.8644,0.8602 C -chr3 14484112 14484113 C/T 2 6,15 0.8323,0.8530 T -chr3 14505913 14505914 A 1 14 0.8635 C -chr3 14709231 14709232 C/T 2 10,9 0.8343,0.8347 C -chr3 14720134 14720135 C/T 2 20,19 0.8618,0.8805 T -chr3 14821040 14821041 C/T 2 10,7 0.8628,0.8347 C -chr3 15509326 15509327 C/G 2 8,11 0.8459,0.8599 C -chr3 15572071 15572072 C/T 2 8,15 0.8860,0.8814 T -chr3 15742821 15742822 C 1 8 0.7984 T -chr3 15928309 15928310 C 1 11 0.8483 G -chr3 16062814 16062815 G/T 2 10,16 0.8447,0.8467 G -chr3 16112492 16112493 A/G 2 15,19 0.8382,0.8194 G -chr3 16178870 16178871 T 1 14 0.8503 C -chr3 16366219 16366220 C 1 6 0.8714 T -chr3 16799932 16799933 A 1 20 0.8772 T -chr3 17137367 17137368 C/T 2 12,24 0.8677,0.8617 T -chr3 18425380 18425381 T 1 8 0.8688 C -chr3 19136802 19136803 G/T 2 21,19 0.8397,0.8302 G -chr3 19151226 19151227 C/G 2 4,7 0.8568,0.8758 G -chr3 19962997 19962998 T 1 28 0.8514 G -chr3 20607112 20607113 C/G 2 8,6 0.8754,0.8741 C -chr3 20648996 20648997 C/T 2 14,10 0.8268,0.8212 C -chr3 21072048 21072049 A/G 2 17,10 0.8515,0.8512 A -chr3 21235639 21235640 G 1 4 0.9064 T -chr3 21297909 21297910 T 1 5 0.8095 C -chr3 21357863 21357864 A/C 2 8,14 0.8299,0.8457 C -chr3 21974922 21974923 C/T 2 10,14 0.8590,0.8516 T -chr3 22022815 22022816 C/T 2 6,7 0.9019,0.8811 T -chr3 22042307 22042308 A/G 2 14,16 0.7800,0.7899 A -chr3 22049719 22049720 T 1 12 0.8678 C -chr3 22164859 22164860 T 1 12 0.8434 C -chr3 22164906 22164907 G 1 6 0.8042 A -chr3 22223597 22223598 C/T 2 21,17 0.8808,0.8595 C -chr3 22240683 22240684 A/T 2 24,8 0.8559,0.8706 A -chr3 22461099 22461100 C/T 2 18,8 0.8623,0.8527 C -chr3 22563443 22563444 T 1 32 0.8321 G -chr3 23129657 23129658 T 1 4 0.8685 G -chr3 23159552 23159553 A/T 2 15,13 0.8834,0.8685 A -chr3 23481112 23481113 A/G 2 15,15 0.8447,0.8695 G -chr3 24191198 24191199 A 1 4 0.8580 T -chr3 24364672 24364673 C/G 2 10,23 0.8360,0.8526 C -chr3 24723985 24723986 A/G 2 7,7 0.8431,0.8446 G -chr3 24973846 24973847 A/G 2 26,15 0.8618,0.8726 A -chr3 25461744 25461745 G 1 3 0.8731 A -chr3 25548204 25548205 G 1 19 0.8802 A -chr3 25785332 25785333 C/T 2 13,6 0.8629,0.8326 C -chr3 26241695 26241696 C/T 2 11,4 0.8669,0.8512 T -chr3 27050780 27050781 A/G 2 9,18 0.8364,0.8650 G -chr3 27079101 27079102 A 1 21 0.8463 C -chr3 27371842 27371843 C/T 2 15,18 0.8678,0.8727 T -chr3 27486374 27486375 C/G 2 5,8 0.8077,0.8487 G -chr3 27871375 27871376 C/T 2 10,4 0.8327,0.8208 C -chr3 28479716 28479717 C/T 2 5,10 0.8460,0.8813 T -chr3 29246180 29246181 A/C 2 12,6 0.8931,0.8708 A -chr3 30367146 30367147 A/G 2 14,7 0.8778,0.8853 A -chr3 30691472 30691473 A 1 17 0.8833 G -chr3 30923559 30923560 A/G 2 11,16 0.8906,0.8765 G -chr3 30949052 30949053 A/G 2 24,15 0.8729,0.8594 A -chr3 31299774 31299775 G 1 29 0.8232 T -chr3 31435576 31435577 A 1 34 0.8536 G -chr3 31783325 31783326 A/G 2 10,11 0.8099,0.8024 A -chr3 32033747 32033748 C/G 2 15,20 0.9040,0.9017 C -chr3 32234674 32234675 C 1 7 0.8057 T -chr3 32257820 32257821 A 1 19 0.8551 T -chr3 32445245 32445246 A/G 2 3,3 0.8767,0.8950 A -chr3 32900865 32900866 C/T 2 2,2 0.9275,0.8586 C -chr3 33078220 33078221 C 1 3 0.8197 G -chr3 33103427 33103428 C 1 22 0.8686 T -chr3 33242341 33242342 T 1 26 0.8675 C -chr3 33480586 33480587 A/C 2 7,13 0.8376,0.8512 A -chr3 33531799 33531800 A/G 2 8,4 0.8412,0.8344 A -chr3 33665651 33665652 C/T 2 10,14 0.8567,0.8606 T -chr3 33791753 33791754 C 1 6 0.8135 A -chr3 33796931 33796932 G/T 2 10,10 0.8481,0.8577 G -chr3 34054737 34054738 A/G 2 12,9 0.8551,0.8807 A -chr3 34209327 34209328 C/T 2 19,19 0.8374,0.7817 C -chr3 34238216 34238217 A/G 2 8,5 0.8299,0.8314 G -chr3 34367510 34367511 C/T 2 18,10 0.8675,0.8633 C -chr3 34720121 34720122 C 1 13 0.8936 T -chr3 34793711 34793712 A 1 19 0.8308 T -chr3 35229807 35229808 G 1 4 0.8712 A -chr3 35427134 35427135 C/T 2 13,17 0.8811,0.8677 T -chr3 35450285 35450286 A 1 12 0.7948 C -chr3 35460957 35460958 T 1 11 0.8742 C -chr3 35961895 35961896 C/T 2 12,12 0.8670,0.8599 T -chr3 36487695 36487696 T 1 27 0.8583 C -chr3 36687851 36687852 A/G 2 7,7 0.8165,0.8200 A -chr3 37199349 37199350 A/T 2 6,7 0.8951,0.8921 A -chr3 37507448 37507449 A/G 2 19,20 0.8664,0.8846 G -chr3 38406792 38406793 G 1 25 0.8695 T -chr3 38565937 38565938 A 1 4 0.7900 T -chr3 38804667 38804668 A/C 2 12,10 0.8487,0.7817 A -chr3 39011225 39011226 A/G 2 19,19 0.8746,0.8503 A -chr3 39054634 39054635 C/T 2 4,5 0.7974,0.9065 T -chr3 39331971 39331972 A/C 2 15,11 0.8381,0.8309 A -chr3 39578257 39578258 C 1 21 0.8444 T -chr3 39639753 39639754 C/T 2 29,31 0.8506,0.8672 T -chr3 39640994 39640995 C/T 2 17,14 0.8410,0.8592 C -chr3 39850445 39850446 G/T 2 16,9 0.8643,0.8393 G -chr3 40012717 40012718 C/T 2 14,17 0.8555,0.8480 C -chr3 40458040 40458041 C 1 24 0.8698 T -chr3 41010581 41010582 C/G 2 10,16 0.8727,0.8533 C -chr3 41583038 41583039 T 1 3 0.7862 G -chr3 41632668 41632669 C 1 38 0.8605 A -chr3 41636663 41636664 C/G 2 9,7 0.8693,0.8456 C -chr3 41794936 41794937 G/T 2 17,20 0.8523,0.8579 T -chr3 41859851 41859852 G/T 2 4,6 0.8840,0.8915 T -chr3 41946902 41946903 A/G 2 14,14 0.8826,0.8801 G -chr3 42203992 42203993 G 1 7 0.8771 A -chr3 42270680 42270681 T 1 11 0.8511 C -chr3 42374628 42374629 C/T 2 6,8 0.8660,0.8675 T -chr3 42409827 42409828 C/T 2 7,4 0.8317,0.8682 C -chr3 42503533 42503534 A/G 2 17,19 0.8686,0.8363 G -chr3 42784629 42784630 A/G 2 24,14 0.8509,0.8521 A -chr3 43140032 43140033 A/T 2 11,20 0.8564,0.8662 T -chr3 43256120 43256121 A/T 2 28,19 0.8752,0.9149 T -chr3 45124876 45124877 G/T 2 20,17 0.8805,0.8718 G -chr3 45202837 45202838 C 1 22 0.8669 T -chr3 45434708 45434709 C/T 2 16,11 0.8374,0.8497 C -chr3 45648152 45648153 C/T 2 19,13 0.8655,0.8802 C -chr3 45996760 45996761 A 1 31 0.8392 G -chr3 46589167 46589168 T 1 4 0.8838 A -chr3 46625654 46625655 C/T 2 7,9 0.8894,0.8462 C -chr3 46743933 46743934 G/T 2 3,6 0.8261,0.8434 G -chr3 46985862 46985863 G 1 13 0.8791 A -chr3 49936101 49936102 C/T 2 7,11 0.8812,0.8706 T -chr3 50352199 50352200 A/G 2 17,13 0.8465,0.8580 A -chr3 50837082 50837083 C 1 28 0.8501 A -chr3 50851987 50851988 A 1 17 0.8225 G -chr3 50900968 50900969 C 1 24 0.8554 C -chr3 50987193 50987194 A 1 25 0.8454 G -chr3 51006236 51006237 C 1 11 0.9004 T -chr3 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 57701937 C/T 2 10,3 0.8890,0.9208 C -chr3 57834310 57834311 C/T 2 6,3 0.8965,0.8655 C -chr3 57846576 57846577 A/C 2 5,9 0.8268,0.8325 C -chr3 59415537 59415538 C/T 2 3,4 0.8835,0.9050 T -chr3 59446925 59446926 C 1 2 0.8953 T -chr3 59576384 59576385 G 1 15 0.8759 A -chr3 59711016 59711017 C/T 2 16,18 0.8549,0.8571 C -chr3 59733522 59733523 A/G 2 13,5 0.8759,0.9030 G -chr3 59935242 59935243 A 1 24 0.8670 G -chr3 60190058 60190059 A 1 3 0.8704 G -chr3 60696312 60696313 G/T 2 10,4 0.8906,0.9056 T -chr3 61170596 61170597 C/T 2 18,12 0.8419,0.8354 C -chr3 61402546 61402547 A/G 2 7,12 0.8093,0.8672 G -chr3 61503137 61503138 C/G 2 6,11 0.8179,0.8734 G -chr3 61612839 61612840 C/T 2 13,12 0.8676,0.8470 C -chr3 61669671 61669672 A/G 2 11,21 0.8558,0.8555 G -chr3 62103206 62103207 C/T 2 5,7 0.7560,0.8673 T -chr3 62542636 62542637 C/T 2 7,19 0.8560,0.8422 C -chr3 62710807 62710808 C/G 2 18,12 0.8751,0.8712 C -chr3 63010708 63010709 C/T 2 7,11 0.8788,0.8823 C -chr3 63049584 63049585 A/G 2 15,9 0.8652,0.8692 A -chr3 63166595 63166596 G 1 34 0.7937 A -chr3 63376646 63376647 C 1 8 0.8426 A -chr3 63588758 63588759 G 1 17 0.8766 A -chr3 63617362 63617363 C 1 25 0.8485 T -chr3 64653895 64653896 A/T 2 8,22 0.8559,0.8602 T -chr3 64655814 64655815 A/T 2 24,11 0.8469,0.8609 A -chr3 64902863 64902864 A/T 2 10,14 0.8811,0.8716 A -chr3 65186244 65186245 G 1 19 0.8735 A -chr3 65802554 65802555 C/T 2 11,6 0.8778,0.8995 C -chr3 65886518 65886519 A/G 2 13,17 0.8170,0.8198 A -chr3 66057490 66057491 A/G 2 11,10 0.8810,0.8626 A -chr3 67305724 67305725 G 1 15 0.8558 T -chr3 67338407 67338408 C/T 2 11,13 0.8546,0.8271 C -chr3 67430279 67430280 A/C 2 18,18 0.8792,0.8782 C -chr3 67456178 67456179 C 1 16 0.8502 G -chr3 67519386 67519387 A 1 41 0.8677 G -chr3 68106466 68106467 A/G 2 22,19 0.8068,0.8243 G -chr3 68328673 68328674 C/T 2 16,25 0.8532,0.8611 T -chr3 68561318 68561319 A/G 2 5,8 0.8481,0.8715 A -chr3 68594318 68594319 A/G 2 4,6 0.8575,0.8526 G -chr3 68628730 68628731 A/G 2 18,11 0.8271,0.8525 G -chr3 69209055 69209056 C/T 2 4,6 0.8877,0.8473 C -chr3 69282460 69282461 C 1 17 0.8409 T -chr3 69440853 69440854 C/T 2 23,14 0.8626,0.8720 C -chr3 69686550 69686551 A/T 2 3,5 0.8799,0.8796 T -chr3 69728894 69728895 C 1 21 0.9032 A -chr3 70260205 70260206 C/T 2 13,10 0.8594,0.8516 T -chr3 71174438 71174439 A 1 29 0.8794 G -chr3 71744800 71744801 A 1 37 0.8731 G -chr3 72049287 72049288 G/T 2 4,4 0.8546,0.7967 T -chr3 72158909 72158910 G 1 26 0.8587 A -chr3 72199038 72199039 C 1 16 0.8925 A -chr3 72366388 72366389 C/T 2 10,7 0.8367,0.9121 C -chr3 72596704 72596705 A/G 2 13,16 0.8740,0.8573 G -chr3 73340113 73340114 A/G 2 8,10 0.8804,0.8834 G -chr3 73371681 73371682 A/T 2 11,11 0.8282,0.8190 A -chr3 73771359 73771360 T 1 20 0.8571 C -chr3 73779273 73779274 C/G 2 6,4 0.8793,0.8763 G -chr3 74589482 74589483 A/G 2 17,17 0.8511,0.8282 G -chr3 74621971 74621972 A/C 2 17,22 0.8758,0.8512 A -chr3 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0.8718 T -chr3 83759824 83759825 C 1 12 0.8688 G -chr3 83949184 83949185 C/T 2 15,14 0.8687,0.8747 C -chr3 84128384 84128385 A/C 2 3,5 0.7550,0.8664 C -chr3 84299714 84299715 A 1 13 0.8191 T -chr3 84339957 84339958 C/T 2 14,10 0.8663,0.8421 C -chr3 84720460 84720461 T 1 26 0.8656 G -chr3 84876249 84876250 C/T 2 15,11 0.8642,0.8552 C -chr3 84936395 84936396 C/T 2 9,6 0.8862,0.8727 C -chr3 85853952 85853953 A 1 3 0.8768 G -chr3 86106302 86106303 A/G 2 22,12 0.8762,0.8469 G -chr3 86209359 86209360 A/C 2 12,18 0.8841,0.8748 C -chr3 86278208 86278209 A/G 2 21,12 0.8237,0.8277 A -chr3 86286880 86286881 A/C 2 12,13 0.8754,0.8719 C -chr3 86794432 86794433 A/G 2 17,18 0.8608,0.8842 G -chr3 86935861 86935862 A/G 2 10,9 0.8648,0.8448 A -chr3 86952655 86952656 A/T 2 6,3 0.8983,0.7956 A -chr3 87015149 87015150 A/T 2 11,12 0.8532,0.8587 T -chr3 87194995 87194996 C 1 9 0.8897 T -chr3 88065830 88065831 C 1 13 0.9039 T -chr3 88492143 88492144 C/T 2 10,4 0.8565,0.8253 C -chr3 88747634 88747635 G 1 4 0.8805 A -chr3 88917128 88917129 A/T 2 14,20 0.7889,0.8460 T -chr3 89104979 89104980 A/G 2 9,11 0.8990,0.8893 A -chr3 89316026 89316027 C/T 2 18,18 0.8407,0.8602 C -chr3 89427194 89427195 A/G 2 6,3 0.9066,0.7876 A -chr3 89980402 89980403 G/T 2 5,6 0.8664,0.8732 G -chr3 90333848 90333849 G/T 2 3,4 0.9041,0.8452 T -chr3 90379808 90379809 A/C 2 5,4 0.8467,0.8707 A -chr3 90405601 90405602 A/G 2 6,6 0.8672,0.8861 G -chr3 94021191 94021192 T 1 8 0.8946 G -chr3 94038828 94038829 C/T 2 10,21 0.8875,0.8903 T -chr3 94106811 94106812 C/T 2 12,12 0.8470,0.8418 C -chr3 94422946 94422947 G 1 5 0.9074 A -chr3 94964527 94964528 A/G 2 18,9 0.8506,0.8863 A -chr3 95230267 95230268 C/G 2 14,7 0.8084,0.7979 C -chr3 95712518 95712519 T 1 4 0.8596 G -chr3 96275861 96275862 A/T 2 13,10 0.8993,0.8695 T -chr3 96484353 96484354 A/G 2 6,12 0.8410,0.8060 A -chr3 96549128 96549129 A/T 2 8,15 0.8666,0.8677 T -chr3 96900440 96900441 A/G 2 4,8 0.8420,0.9083 G -chr3 96936264 96936265 A/G 2 12,17 0.8577,0.8836 G -chr3 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111518038 C/T 2 6,3 0.8626,0.9004 T -chr3 111610854 111610855 A/G 2 13,12 0.8420,0.8472 A -chr3 111647455 111647456 A/G 2 16,17 0.8595,0.8721 A -chr3 111694437 111694438 C 1 9 0.8804 T -chr3 111875921 111875922 C 1 10 0.8038 T -chr3 111884172 111884173 C/G 2 4,7 0.9056,0.8664 C -chr3 111971879 111971880 A/T 2 16,17 0.8450,0.8981 T -chr3 112536239 112536240 A/T 2 12,14 0.8940,0.8726 T -chr3 112973063 112973064 G/T 2 16,9 0.8720,0.8627 T -chr3 113017486 113017487 G/T 2 5,8 0.9090,0.8943 G -chr3 113239021 113239022 A/G 2 6,4 0.8933,0.8849 A -chr3 115175457 115175458 G/T 2 14,9 0.8740,0.8665 G -chr3 115818342 115818343 A/G 2 20,15 0.8694,0.8616 A -chr3 115844505 115844506 T 1 25 0.8601 C -chr3 116028663 116028664 C/T 2 10,15 0.8661,0.8406 C -chr3 116114622 116114623 C/T 2 9,11 0.8732,0.8653 T -chr3 116289944 116289945 T 1 44 0.8356 C -chr3 116419418 116419419 G 1 24 0.8418 C -chr3 116867346 116867347 T 1 40 0.8778 C -chr3 117318038 117318039 A 1 35 0.8349 C -chr3 117495688 117495689 A/G 2 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2 3,7 0.8271,0.8790 C -chr3 125836156 125836157 C/G 2 4,5 0.8896,0.9162 C -chr3 126178389 126178390 A/C 2 11,7 0.8502,0.8827 A -chr3 126356546 126356547 C/T 2 9,6 0.8540,0.8688 C -chr3 127020360 127020361 G 1 19 0.8970 C -chr3 127748733 127748734 G/T 2 22,26 0.8788,0.8874 T -chr3 127913262 127913263 A/G 2 12,13 0.8624,0.8509 A -chr3 128129039 128129040 C/T 2 4,4 0.8389,0.8351 T -chr3 128159585 128159586 A/C 2 8,10 0.8641,0.8704 A -chr3 128704289 128704290 A/T 2 7,5 0.8460,0.8901 A -chr3 128887526 128887527 G 1 9 0.8940 A -chr3 129084989 129084990 A/G 2 10,11 0.8607,0.8505 G -chr3 129136059 129136060 A/C 2 5,4 0.8817,0.7976 C -chr3 129276112 129276113 C/G 2 6,8 0.8466,0.8759 C -chr3 129698702 129698703 C 1 25 0.8172 T -chr3 130133619 130133620 C/T 2 8,12 0.8375,0.8616 T -chr3 130135574 130135575 A/T 2 6,7 0.8531,0.8183 A -chr3 130304773 130304774 C/T 2 6,8 0.8546,0.8378 T -chr3 130511024 130511025 C 1 20 0.8958 T -chr3 131066312 131066313 A/C 2 11,15 0.8319,0.8761 C -chr3 131805810 131805811 C/T 2 12,9 0.8227,0.8438 C -chr3 131843596 131843597 C/G 2 30,17 0.8434,0.8338 C -chr3 132727356 132727357 A 1 12 0.8482 G -chr3 133375033 133375034 G 1 24 0.8709 A -chr3 133595332 133595333 C/T 2 8,7 0.8296,0.8382 T -chr3 134007732 134007733 T 1 10 0.8479 G -chr3 134054044 134054045 T 1 14 0.8819 A -chr3 134219018 134219019 C/T 2 7,7 0.8600,0.8564 C -chr3 134296512 134296513 C 1 3 0.8369 G -chr3 134530097 134530098 G 1 4 0.8131 T -chr3 134761039 134761040 C 1 17 0.8895 T -chr3 135110410 135110411 A/C 2 13,5 0.8558,0.8458 A -chr3 135363557 135363558 C/T 2 17,7 0.8518,0.8796 C -chr3 135771729 135771730 C 1 35 0.8286 T -chr3 136098558 136098559 A/C 2 3,4 0.8333,0.8577 C -chr3 136413838 136413839 T 1 31 0.8445 C -chr3 136455955 136455956 C/G 2 12,7 0.9005,0.8785 C -chr3 136498168 136498169 A/C 2 17,13 0.8878,0.8777 A -chr3 137395602 137395603 C/T 2 15,6 0.8700,0.8943 C -chr3 137795666 137795667 G/T 2 5,7 0.9082,0.9035 T -chr3 138402353 138402354 A/G 2 6,7 0.8959,0.6744 A -chr3 138872625 138872626 A/T 2 7,3 0.8595,0.8421 A -chr3 140892820 140892821 C 1 31 0.8849 T -chr3 140951391 140951392 T 1 4 0.8451 G -chr3 141359254 141359255 C 1 2 0.9450 T -chr3 142395071 142395072 A/G 2 16,10 0.8230,0.8823 A -chr3 142921927 142921928 G 1 20 0.8438 A -chr3 143360567 143360568 A/C 2 10,15 0.8421,0.8340 C -chr3 143587925 143587926 G 1 2 0.9188 A -chr3 143595445 143595446 G 1 24 0.8372 A -chr3 143601887 143601888 A/C 2 7,5 0.8259,0.8474 A -chr3 143605433 143605434 A/G 2 9,4 0.8822,0.8881 A -chr3 143658933 143658934 G 1 15 0.8591 C -chr3 144090889 144090890 A/T 2 7,6 0.8946,0.9251 A -chr3 144246106 144246107 A/C 2 17,17 0.7954,0.7681 A -chr3 144271653 144271654 C/T 2 14,9 0.8432,0.7523 C -chr3 144655655 144655656 C 1 27 0.8502 T -chr3 144681634 144681635 C 1 15 0.8898 T -chr3 144859261 144859262 A/T 2 11,4 0.8595,0.8450 A -chr3 145131672 145131673 A/G 2 4,9 0.8444,0.8201 G -chr3 145133375 145133376 A/G 2 3,5 0.8470,0.8943 G -chr3 145245466 145245467 C/T 2 13,10 0.8539,0.8606 C -chr3 145564367 145564368 C 1 18 0.8544 G -chr3 145758563 145758564 A/C 2 27,17 0.8228,0.8537 A -chr3 145775424 145775425 C 1 20 0.8638 T -chr3 145807639 145807640 A/G 2 11,17 0.8571,0.8635 G -chr3 146045525 146045526 C/T 2 12,5 0.8486,0.8367 C -chr3 146123635 146123636 C/T 2 6,6 0.9004,0.8638 C -chr3 146634034 146634035 T 1 16 0.8767 C -chr3 147331126 147331127 C/T 2 5,3 0.8574,0.7820 C -chr3 147334137 147334138 T 1 13 0.8801 G -chr3 147348030 147348031 C/T 2 12,6 0.8704,0.8724 T -chr3 147920677 147920678 C/G 2 7,13 0.8796,0.8699 G -chr3 148263686 148263687 C/T 2 9,6 0.8962,0.8722 C -chr3 148344396 148344397 A/G 2 9,12 0.8554,0.8760 G -chr3 148902354 148902355 A/G 2 9,18 0.8053,0.8355 G -chr3 149033528 149033529 G/T 2 5,6 0.8431,0.8511 T -chr3 149099644 149099645 C 1 22 0.8693 T -chr3 149787921 149787922 A/C 2 16,7 0.8666,0.8489 A -chr3 149789085 149789086 A/G 2 14,18 0.8479,0.8641 G -chr3 149849838 149849839 A/G 2 11,13 0.8137,0.8272 G -chr3 150013986 150013987 T 1 19 0.8532 C -chr3 150091656 150091657 A/G 2 5,18 0.8186,0.8348 G -chr3 150125238 150125239 C/G 2 10,5 0.8407,0.8599 G -chr3 150181917 150181918 C/T 2 12,6 0.8545,0.8214 C -chr3 150238548 150238549 C/T 2 5,15 0.8698,0.8868 T -chr3 150423630 150423631 C/T 2 11,12 0.8637,0.8376 C -chr3 150565052 150565053 G/T 2 9,5 0.8592,0.7952 G -chr3 150727495 150727496 C/T 2 23,20 0.8439,0.8477 T -chr3 150852991 150852992 C/T 2 11,6 0.8428,0.8800 C -chr3 151057174 151057175 A 1 8 0.8247 G -chr3 151238772 151238773 A/G 2 12,7 0.8878,0.8938 A -chr3 151759592 151759593 A/C 2 5,6 0.8524,0.8526 A -chr3 152054221 152054222 A/G 2 15,16 0.8468,0.8508 A -chr3 152213085 152213086 T 1 35 0.8502 C -chr3 153489810 153489811 A 1 5 0.8479 G -chr3 153733728 153733729 T 1 34 0.8479 C -chr3 153988465 153988466 C/T 2 6,4 0.8907,0.8659 T -chr3 154363227 154363228 C/T 2 13,15 0.8480,0.8485 T -chr3 154725997 154725998 G/T 2 4,3 0.8832,0.8791 T -chr3 155235298 155235299 C/T 2 11,20 0.8749,0.8951 T -chr3 155327875 155327876 T 1 16 0.8426 C -chr3 155338104 155338105 A 1 10 0.8167 G -chr3 155964465 155964466 A/G 2 10,6 0.8827,0.8410 A -chr3 156417088 156417089 G 1 14 0.8439 A -chr3 156672894 156672895 T 1 5 0.7972 A -chr3 157177117 157177118 A 1 29 0.8383 G -chr3 157494083 157494084 C 1 14 0.8220 T -chr3 157993936 157993937 A 1 8 0.8396 G -chr3 158018164 158018165 A 1 29 0.8395 G -chr3 158099781 158099782 C 1 9 0.8384 T -chr3 158299400 158299401 G 1 13 0.8795 C -chr3 158569224 158569225 A/G 2 29,14 0.8799,0.9029 A -chr3 159100164 159100165 C/T 2 4,2 0.9238,0.8952 C -chr3 159523087 159523088 T 1 30 0.8770 C -chr3 160034573 160034574 A/G 2 13,12 0.7917,0.8431 A -chr3 160165607 160165608 G/T 2 7,4 0.7957,0.8048 G -chr3 160340208 160340209 A/C 2 22,8 0.8095,0.8199 A -chr3 161914911 161914912 C/T 2 19,16 0.8703,0.8808 T -chr3 162142997 162142998 A 1 13 0.8514 G -chr3 162412771 162412772 C 1 16 0.8976 T -chr3 162426027 162426028 C 1 9 0.8443 T -chr3 162484911 162484912 C/G 2 15,10 0.8585,0.8490 C -chr3 162497012 162497013 C/T 2 15,9 0.8364,0.8319 T -chr3 162730802 162730803 A/G 2 4,3 0.8399,0.8161 A -chr3 163451235 163451236 A 1 10 0.8797 G -chr3 163700664 163700665 A/T 2 5,11 0.8892,0.8535 T -chr3 164127325 164127326 A/G 2 9,12 0.8498,0.8785 G -chr3 164164951 164164952 T 1 16 0.8669 C -chr3 165393628 165393629 A/T 2 10,22 0.8617,0.8549 T -chr3 165553586 165553587 G/T 2 7,8 0.8855,0.8926 G -chr3 165788381 165788382 C 1 20 0.8712 A -chr3 165842802 165842803 C/T 2 11,10 0.8809,0.8958 T -chr3 166179861 166179862 C/T 2 14,17 0.8486,0.8533 T -chr3 166441703 166441704 G 1 21 0.8698 C -chr3 166644880 166644881 C/T 2 16,16 0.8534,0.8505 C -chr3 167533457 167533458 A 1 5 0.9072 G -chr3 167668103 167668104 A 1 31 0.8451 G -chr3 167826653 167826654 A/G 2 12,8 0.8367,0.8891 G -chr3 168226051 168226052 T 1 4 0.8751 C -chr3 168610223 168610224 C/T 2 12,7 0.8802,0.8337 T -chr3 168852681 168852682 C/T 2 12,17 0.8711,0.8629 T -chr3 169239577 169239578 G 1 28 0.8448 A -chr3 170448936 170448937 C/T 2 17,18 0.8672,0.8477 C -chr3 170542839 170542840 G/T 2 3,5 0.7524,0.8619 T -chr3 170575551 170575552 C/T 2 14,15 0.8537,0.8276 C -chr3 170732299 170732300 A/G 2 15,11 0.8577,0.8776 G -chr3 170755991 170755992 A/G 2 18,15 0.8734,0.8851 A -chr3 170970129 170970130 G/T 2 6,5 0.8799,0.8700 T -chr3 171027046 171027047 A/G 2 11,7 0.8315,0.8253 G -chr3 171422524 171422525 A/G 2 12,15 0.8840,0.8963 A -chr3 171631325 171631326 C 1 3 0.8272 T -chr3 171961932 171961933 C/G 2 12,5 0.8599,0.8676 C -chr3 172529850 172529851 C 1 4 0.8986 T -chr3 173023607 173023608 A/G 2 7,5 0.8502,0.8176 A -chr3 173028174 173028175 A/C 2 5,12 0.8518,0.8712 A -chr3 173308201 173308202 C/T 2 8,8 0.8870,0.8736 C -chr3 173310567 173310568 C 1 32 0.8722 G -chr3 173362742 173362743 A/C 2 18,14 0.8295,0.8214 A -chr3 173638602 173638603 G 1 31 0.8554 T -chr3 173707576 173707577 A/T 2 16,12 0.8766,0.8644 T -chr3 173814237 173814238 A 1 10 0.8220 G -chr3 173874967 173874968 T 1 14 0.8608 G -chr3 174065179 174065180 A/G 2 17,13 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0.8482 G -chr3 179392153 179392154 A/G 2 15,17 0.8847,0.8733 G -chr3 179477954 179477955 G 1 4 0.9056 A -chr3 180103128 180103129 A/G 2 11,17 0.8367,0.8327 G -chr3 180352876 180352877 G/T 2 7,8 0.7822,0.8622 T -chr3 180726597 180726598 A 1 6 0.8747 G -chr3 181009687 181009688 A/G 2 14,16 0.8123,0.8231 G -chr3 181462477 181462478 C/T 2 10,13 0.8592,0.8845 C -chr3 182172158 182172159 G/T 2 13,13 0.8602,0.8639 G -chr3 182496387 182496388 A/G 2 3,6 0.8770,0.8828 G -chr3 183110862 183110863 G 1 17 0.8786 A -chr3 183274961 183274962 C/T 2 18,17 0.8303,0.8525 T -chr3 183461023 183461024 C/T 2 6,10 0.8897,0.8775 T -chr3 184126526 184126527 C/T 2 8,11 0.7898,0.8237 C -chr3 184442091 184442092 C/T 2 5,3 0.8641,0.8581 C -chr3 184549538 184549539 A/G 2 15,13 0.8511,0.8450 G -chr3 184783350 184783351 C/T 2 3,3 0.8870,0.8053 C -chr3 185035085 185035086 A/G 2 16,16 0.8468,0.8615 G -chr3 185132807 185132808 A/T 2 7,9 0.8614,0.8888 T -chr3 185253525 185253526 A 1 4 0.8863 G -chr3 185297831 185297832 T 1 3 0.8682 C -chr3 185606530 185606531 A/G 2 3,3 0.8471,0.8251 G -chr3 185705293 185705294 C 1 10 0.9016 A -chr3 186056896 186056897 C 1 27 0.8276 T -chr3 186208283 186208284 A/G 2 9,11 0.8470,0.8506 G -chr3 186377548 186377549 C 1 4 0.8858 T -chr3 186469660 186469661 A/G 2 13,12 0.8736,0.8752 G -chr3 186570439 186570440 A/G 2 17,20 0.8793,0.8640 G -chr3 186804056 186804057 A/G 2 4,3 0.8395,0.8482 G -chr3 187048819 187048820 A 1 31 0.8325 G -chr3 187219487 187219488 C/T 2 18,10 0.8883,0.8702 C -chr3 187503247 187503248 C/T 2 8,6 0.8626,0.8595 T -chr3 187695753 187695754 A/G 2 15,11 0.9095,0.8999 A -chr3 188204331 188204332 A/G 2 7,8 0.8803,0.9084 A -chr3 188212142 188212143 C/T 2 19,19 0.8491,0.8838 T -chr3 188372257 188372258 T 1 37 0.8808 C -chr3 189264322 189264323 A/T 2 7,5 0.8732,0.8778 A -chr3 189265528 189265529 A 1 14 0.8548 G -chr3 189845962 189845963 T 1 7 0.8074 C -chr3 189937948 189937949 A/G 2 8,11 0.8533,0.8594 G -chr3 190066111 190066112 A/G 2 16,16 0.8925,0.8692 A -chr3 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193557255 G 1 14 0.8129 A -chr3 193577306 193577307 C/T 2 13,13 0.8396,0.8632 T -chr3 194078986 194078987 T 1 27 0.8552 T -chr3 194538501 194538502 G 1 25 0.8443 A -chr3 194833310 194833311 C/T 2 7,9 0.8846,0.8769 C -chr3 195449688 195449689 A/G 2 7,4 0.8568,0.8138 A -chr3 195596635 195596636 T 1 4 0.8479 C -chr3 195884838 195884839 A/G 2 3,7 0.8598,0.8514 G -chr3 196182320 196182321 C 1 7 0.8712 T -chr3 196478212 196478213 A/G 2 4,9 0.8589,0.8650 G -chr3 197198848 197198849 A/C 2 20,15 0.8554,0.8444 C -chr3 197672761 197672762 C/T 2 11,11 0.8769,0.8611 T -chr4 415568 415569 G 1 3 0.8814 C -chr4 1046426 1046427 C/T 2 7,3 0.7907,0.8610 C -chr4 2195632 2195633 C/G 2 13,15 0.8578,0.8317 C -chr4 2793544 2793545 C 1 7 0.8762 G -chr4 3473638 3473639 C 1 7 0.8987 A -chr4 3622257 3622258 A/G 2 10,7 0.8712,0.8108 G -chr4 3710794 3710795 C/T 2 12,8 0.8194,0.7876 C -chr4 3731276 3731277 A/G 2 21,26 0.8782,0.8840 G -chr4 3829806 3829807 C 1 5 0.8689 T -chr4 4183869 4183870 A/C 2 6,3 0.8513,0.7424 A -chr4 4585243 4585244 A/G 2 9,4 0.8818,0.8507 A -chr4 4809042 4809043 T 1 19 0.8088 C -chr4 4880295 4880296 T 1 4 0.8832 G -chr4 4935308 4935309 G 1 42 0.8443 T -chr4 4951993 4951994 A/G 2 13,23 0.8546,0.8568 G -chr4 5163100 5163101 A/G 2 8,9 0.8614,0.8727 A -chr4 5283250 5283251 G 1 9 0.8952 A -chr4 5385750 5385751 G/T 2 13,11 0.8498,0.8513 G -chr4 5629203 5629204 A/G 2 15,5 0.8428,0.8372 A -chr4 5932063 5932064 A/T 2 11,13 0.8533,0.8545 T -chr4 6293801 6293802 C/T 2 4,7 0.8926,0.8770 T -chr4 6370720 6370721 C/T 2 6,13 0.8350,0.8365 T -chr4 6605003 6605004 C/T 2 10,3 0.8493,0.8416 C -chr4 6697765 6697766 G/T 2 18,17 0.8351,0.8249 T -chr4 6710738 6710739 T 1 15 0.8673 C -chr4 6737964 6737965 C 1 2 0.8641 T -chr4 6738957 6738958 C 1 10 0.8504 T -chr4 7256987 7256988 G 1 22 0.8309 A -chr4 7381430 7381431 A/G 2 5,12 0.8646,0.8511 G -chr4 7638945 7638946 G 1 17 0.8710 A -chr4 7829446 7829447 C/G 2 7,7 0.8264,0.7957 G -chr4 7889095 7889096 C/T 2 13,14 0.8387,0.8350 C -chr4 8040857 8040858 A/T 2 11,14 0.8601,0.8692 A -chr4 8318445 8318446 G 1 12 0.8869 A -chr4 8355801 8355802 C/T 2 19,8 0.8340,0.8406 C -chr4 8599042 8599043 C 1 24 0.8685 G -chr4 8692551 8692552 C/T 2 14,10 0.8510,0.8711 C -chr4 9706341 9706342 G 1 4 0.8426 T -chr4 9825813 9825814 C 1 8 0.8726 A -chr4 9941261 9941262 C/T 2 10,5 0.8541,0.8955 C -chr4 9994582 9994583 C/T 2 16,17 0.8627,0.8811 T -chr4 10193898 10193899 C/G 2 6,12 0.8801,0.8624 C -chr4 10205717 10205718 G 1 19 0.8789 A -chr4 10652412 10652413 C/T 2 4,6 0.8695,0.8601 C -chr4 10658921 10658922 A/C 2 12,22 0.8274,0.8559 C -chr4 10670045 10670046 A/G 2 15,6 0.8432,0.8613 G -chr4 11455517 11455518 C/T 2 27,15 0.8625,0.8537 C -chr4 11834959 11834960 G/T 2 16,13 0.8527,0.8405 G -chr4 12362388 12362389 A 1 38 0.8639 T -chr4 12586592 12586593 C/T 2 6,12 0.8698,0.8845 T -chr4 13229443 13229444 C/G 2 3,4 0.8896,0.8751 C -chr4 13292300 13292301 G 1 28 0.8659 A -chr4 13319487 13319488 C/T 2 7,9 0.8750,0.8898 C -chr4 13490657 13490658 A/G 2 17,8 0.8583,0.8410 A -chr4 13787260 13787261 T 1 32 0.8647 A -chr4 14157415 14157416 G/T 2 20,20 0.8196,0.8285 T -chr4 14318505 14318506 C/G 2 11,11 0.9091,0.9017 C -chr4 15725765 15725766 C/T 2 16,24 0.8923,0.8809 T -chr4 15816669 15816670 C 1 8 0.8382 T -chr4 16348945 16348946 C/T 2 9,13 0.8541,0.8197 T -chr4 16508710 16508711 T 1 3 0.9327 C -chr4 16601008 16601009 C 1 23 0.8739 T -chr4 16864700 16864701 G/T 2 8,7 0.8981,0.8852 G -chr4 17192625 17192626 G/T 2 15,8 0.8453,0.8438 G -chr4 17676436 17676437 C/G 2 12,22 0.8498,0.8484 C -chr4 17682833 17682834 C/T 2 5,9 0.8725,0.8666 T -chr4 18025483 18025484 A 1 23 0.8580 G -chr4 18084933 18084934 G/T 2 17,5 0.8512,0.8756 G -chr4 18147150 18147151 C 1 28 0.8574 T -chr4 18220072 18220073 C/T 2 15,14 0.8579,0.8460 C -chr4 18272772 18272773 T 1 7 0.8382 C -chr4 18530936 18530937 A/G 2 10,4 0.8662,0.8865 A -chr4 18667647 18667648 A/G 2 7,13 0.8384,0.8955 G -chr4 18803427 18803428 C 1 31 0.8736 A -chr4 18990113 18990114 C/T 2 17,12 0.8869,0.8660 T -chr4 19573155 19573156 C 1 27 0.8832 T -chr4 20157722 20157723 C/T 2 12,19 0.8086,0.8093 C -chr4 20629037 20629038 A/G 2 20,19 0.8502,0.8647 G -chr4 20693553 20693554 C 1 30 0.8434 T -chr4 20781305 20781306 C/T 2 10,17 0.8460,0.8452 T -chr4 20955282 20955283 T 1 16 0.8181 A -chr4 20992090 20992091 A/G 2 13,18 0.8478,0.8356 G -chr4 21216229 21216230 A/T 2 15,7 0.8099,0.8335 T -chr4 22122580 22122581 C 1 18 0.8326 T -chr4 22141981 22141982 C/T 2 17,16 0.8720,0.8420 T -chr4 22234591 22234592 A 1 20 0.8388 G -chr4 22371521 22371522 C 1 15 0.8703 T -chr4 22379216 22379217 G/T 2 4,3 0.9095,0.9443 G -chr4 22590175 22590176 A/G 2 6,4 0.8397,0.8596 G -chr4 23940851 23940852 A 1 14 0.8226 C -chr4 23967766 23967767 C 1 14 0.8566 T -chr4 24016472 24016473 T 1 11 0.8205 C -chr4 24079266 24079267 G/T 2 3,9 0.9110,0.8585 T -chr4 24214556 24214557 A/T 2 15,16 0.8802,0.8870 A -chr4 24230322 24230323 A 1 30 0.8625 C -chr4 24351176 24351177 A 1 2 0.8457 G -chr4 24883582 24883583 A 1 19 0.8342 G -chr4 25237390 25237391 A 1 17 0.8224 G -chr4 25320464 25320465 C/T 2 11,14 0.8419,0.8393 T -chr4 25825328 25825329 A/G 2 13,9 0.8418,0.8553 A -chr4 26052090 26052091 A/G 2 7,12 0.7814,0.8277 G -chr4 26232779 26232780 A/G 2 14,15 0.8694,0.8810 G -chr4 26510490 26510491 G 1 8 0.8858 C -chr4 26701975 26701976 A 1 37 0.8815 T -chr4 26806741 26806742 C 1 23 0.8654 T -chr4 27439768 27439769 C/G 2 27,25 0.8461,0.8703 G -chr4 27640443 27640444 G 1 3 0.8009 A -chr4 27843378 27843379 C/T 2 10,6 0.8988,0.8318 T -chr4 28110445 28110446 A/G 2 17,18 0.8325,0.8594 G -chr4 28232674 28232675 G 1 17 0.8648 A -chr4 29072406 29072407 C 1 14 0.8783 T -chr4 29123695 29123696 G 1 23 0.8784 A -chr4 29336229 29336230 A/C 2 13,9 0.8587,0.8903 A -chr4 29453672 29453673 A/G 2 21,11 0.8465,0.8505 A -chr4 29459791 29459792 A 1 3 0.9024 C -chr4 29614693 29614694 A 1 9 0.8421 G -chr4 29717108 29717109 C/T 2 11,8 0.8599,0.8824 C -chr4 29794232 29794233 C/T 2 13,17 0.7821,0.8063 T -chr4 29877238 29877239 A/G 2 3,5 0.8470,0.8643 A -chr4 30007360 30007361 C/T 2 6,11 0.9116,0.8798 T -chr4 30078834 30078835 C/T 2 22,9 0.8291,0.8429 C -chr4 30081946 30081947 A/G 2 9,11 0.8775,0.8626 G -chr4 30431091 30431092 C/T 2 10,6 0.8618,0.8571 T -chr4 30582181 30582182 A/G 2 3,4 0.8893,0.8531 A -chr4 30910107 30910108 C 1 17 0.8638 T -chr4 30925712 30925713 G 1 13 0.8557 T -chr4 30959459 30959460 C/T 2 10,13 0.8542,0.8542 C -chr4 31059378 31059379 A/G 2 18,15 0.8421,0.8594 A -chr4 31174877 31174878 A 1 6 0.8509 G -chr4 31321087 31321088 A 1 15 0.8494 C -chr4 31336411 31336412 G 1 24 0.7915 T -chr4 31426980 31426981 C/T 2 5,4 0.8267,0.8241 C -chr4 31984084 31984085 A/T 2 5,12 0.8752,0.8641 T -chr4 32190245 32190246 C 1 13 0.8749 T -chr4 32222281 32222282 C 1 31 0.8637 T -chr4 32233990 32233991 C/G 2 20,14 0.8468,0.8836 C -chr4 32391384 32391385 C/T 2 14,14 0.8438,0.8538 C -chr4 32446549 32446550 T 1 3 0.8542 C -chr4 32538499 32538500 C/T 2 17,13 0.8806,0.8613 C -chr4 33030780 33030781 A/G 2 14,13 0.8454,0.8732 G -chr4 33347432 33347433 G 1 5 0.8615 A -chr4 33360258 33360259 T 1 24 0.8480 C -chr4 33747043 33747044 A/C 2 5,7 0.9238,0.8671 A -chr4 33818941 33818942 C/T 2 11,17 0.8599,0.8355 T -chr4 33910281 33910282 A/C 2 4,8 0.8640,0.8268 C -chr4 34695682 34695683 C/T 2 17,7 0.8746,0.8396 C -chr4 34713272 34713273 A/C 2 10,11 0.8481,0.8655 C -chr4 35395742 35395743 A/G 2 12,5 0.8525,0.8728 G -chr4 35606307 35606308 A/G 2 3,8 0.7799,0.8468 G -chr4 35948082 35948083 T 1 3 0.8834 G -chr4 36116042 36116043 C/T 2 11,20 0.8442,0.8703 C -chr4 36802522 36802523 A/G 2 6,12 0.8634,0.8707 G -chr4 37046139 37046140 A/T 2 15,9 0.8553,0.8712 T -chr4 37342619 37342620 A/G 2 18,21 0.8470,0.8624 G -chr4 37362637 37362638 A/T 2 27,20 0.8603,0.8457 A -chr4 37762569 37762570 G/T 2 9,21 0.9082,0.8775 T -chr4 37787099 37787100 A/G 2 27,15 0.8774,0.8768 A -chr4 38038842 38038843 G 1 23 0.8005 C -chr4 38079713 38079714 A 1 9 0.8226 T -chr4 38626281 38626282 C 1 20 0.8676 T -chr4 38944590 38944591 G 1 11 0.8900 A -chr4 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C/T 2 8,5 0.8680,0.8683 C -chr4 44970265 44970266 C/T 2 20,16 0.8647,0.8539 T -chr4 44986056 44986057 C/T 2 12,14 0.8347,0.8550 T -chr4 45694769 45694770 A 1 14 0.9029 G -chr4 45834347 45834348 C/T 2 10,14 0.9095,0.9052 T -chr4 46007542 46007543 G/T 2 14,11 0.8565,0.8756 T -chr4 46045230 46045231 T 1 10 0.8251 G -chr4 46292598 46292599 T 1 17 0.8288 G -chr4 46718441 46718442 A/G 2 17,18 0.8707,0.8874 A -chr4 46851002 46851003 C/T 2 8,7 0.8807,0.8736 T -chr4 46885129 46885130 C 1 24 0.8766 G -chr4 46949661 46949662 A 1 37 0.8226 G -chr4 47067921 47067922 A/G 2 3,9 0.8923,0.8909 A -chr4 47190211 47190212 C/G 2 5,13 0.8104,0.8456 G -chr4 47256062 47256063 A 1 8 0.8907 G -chr4 47296510 47296511 C/T 2 5,4 0.8838,0.8568 C -chr4 47418220 47418221 G 1 32 0.8313 A -chr4 47446465 47446466 T 1 27 0.8657 C -chr4 47680412 47680413 A/G 2 5,9 0.7981,0.8253 G -chr4 47742767 47742768 G 1 17 0.8600 A -chr4 47886318 47886319 A/C 2 14,7 0.8831,0.8759 A -chr4 48273745 48273746 C 1 13 0.8539 A -chr4 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-chr4 119399110 119399111 C 1 4 0.8316 T -chr4 119737675 119737676 C 1 20 0.8664 T -chr4 119831056 119831057 A/G 2 6,17 0.8584,0.8599 G -chr4 119917478 119917479 A/G 2 12,18 0.8344,0.8488 A -chr4 120530501 120530502 A/G 2 17,17 0.8595,0.8616 A -chr4 121138148 121138149 A/G 2 11,15 0.8772,0.8485 G -chr4 121290613 121290614 C/T 2 13,17 0.8295,0.8376 T -chr4 121648477 121648478 A/G 2 8,3 0.8886,0.8125 A -chr4 122034920 122034921 C 1 11 0.8728 T -chr4 122344723 122344724 A/T 2 10,9 0.8497,0.8454 A -chr4 122391276 122391277 A/C 2 15,10 0.8453,0.8732 A -chr4 123515265 123515266 G/T 2 13,23 0.8684,0.8663 T -chr4 124763464 124763465 A/G 2 13,13 0.8547,0.8341 A -chr4 124933070 124933071 A 1 4 0.9172 G -chr4 125852097 125852098 A/G 2 17,10 0.8430,0.8327 A -chr4 126097734 126097735 C/T 2 9,8 0.8637,0.8065 T -chr4 126182809 126182810 C/T 2 25,10 0.8766,0.8713 C -chr4 126367985 126367986 T 1 4 0.8845 C -chr4 126391141 126391142 A/G 2 5,3 0.8893,0.9025 G -chr4 126423686 126423687 A/G 2 13,14 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-chr4 140526505 140526506 A/G 2 11,21 0.8915,0.8714 A -chr4 140548470 140548471 C 1 25 0.8624 G -chr4 140632482 140632483 C/T 2 4,3 0.8048,0.8025 C -chr4 140992196 140992197 C/T 2 4,5 0.8607,0.8336 C -chr4 141077001 141077002 G 1 17 0.8324 C -chr4 141506190 141506191 A/G 2 9,17 0.8736,0.8643 G -chr4 141800023 141800024 A/G 2 16,16 0.8645,0.8591 G -chr4 142257511 142257512 A/G 2 17,11 0.8548,0.8577 A -chr4 142539393 142539394 C 1 10 0.8476 A -chr4 142578161 142578162 A/G 2 10,10 0.8213,0.8311 A -chr4 143095287 143095288 A/C 2 8,7 0.7314,0.6391 A -chr4 143140405 143140406 G/T 2 21,14 0.8491,0.8229 T -chr4 143458742 143458743 A/G 2 8,4 0.7948,0.7164 A -chr4 143529012 143529013 G 1 24 0.8366 A -chr4 144012289 144012290 C/T 2 4,3 0.8225,0.8383 T -chr4 144710069 144710070 C 1 3 0.9114 G -chr4 144953371 144953372 C 1 3 0.9119 T -chr4 144966079 144966080 C/T 2 10,15 0.8150,0.8317 C -chr4 144978043 144978044 C/T 2 10,8 0.8341,0.8542 C -chr4 145009867 145009868 A 1 10 0.8524 G -chr4 145125391 145125392 G 1 30 0.8749 C -chr4 145174461 145174462 C 1 21 0.8551 G -chr4 145210058 145210059 T 1 41 0.8594 G -chr4 145511574 145511575 C 1 5 0.8125 T -chr4 145776775 145776776 T 1 7 0.8402 C -chr4 146388357 146388358 C/T 2 10,8 0.8705,0.8719 C -chr4 147268324 147268325 C 1 27 0.8590 T -chr4 147830498 147830499 C/T 2 25,17 0.8586,0.8715 C -chr4 149261650 149261651 A/G 2 15,17 0.8600,0.8462 A -chr4 149367122 149367123 C 1 9 0.8745 G -chr4 149391823 149391824 A/C 2 28,12 0.8790,0.8587 A -chr4 149417096 149417097 C/G 2 7,11 0.9064,0.8826 C -chr4 149570763 149570764 A/G 2 12,4 0.8074,0.8745 A -chr4 149903797 149903798 A 1 25 0.8804 G -chr4 150106121 150106122 A/G 2 14,7 0.8236,0.8157 G -chr4 150225784 150225785 G/T 2 6,5 0.8439,0.8687 T -chr4 150960084 150960085 C/T 2 7,19 0.8643,0.8781 T -chr4 151017089 151017090 G/T 2 22,7 0.8611,0.8586 G -chr4 151111249 151111250 G 1 11 0.8159 A -chr4 153088563 153088564 G/T 2 11,14 0.8428,0.8357 T -chr4 153590964 153590965 A 1 15 0.8939 G -chr4 153798941 153798942 A/G 2 5,3 0.8672,0.8517 A -chr4 153899180 153899181 C/T 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 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0.8953,0.8887 T -chr4 163758756 163758757 C/T 2 10,7 0.8753,0.8723 C -chr4 163825871 163825872 A/G 2 5,8 0.8905,0.8674 G -chr4 164536633 164536634 G 1 17 0.8748 A -chr4 164833011 164833012 C/T 2 10,15 0.8610,0.8712 T -chr4 165019029 165019030 C/T 2 10,8 0.9009,0.8867 C -chr4 165405165 165405166 A/G 2 17,20 0.8482,0.8562 G -chr4 165496865 165496866 C/T 2 9,14 0.8669,0.8576 T -chr4 165893485 165893486 T 1 28 0.8725 C -chr4 166337460 166337461 A/C 2 6,12 0.8376,0.7955 C -chr4 166504313 166504314 A/G 2 12,7 0.8807,0.9098 A -chr4 166567512 166567513 C/T 2 11,13 0.8142,0.8298 C -chr4 166592848 166592849 C/T 2 27,21 0.8354,0.8503 C -chr4 166649372 166649373 C/T 2 18,14 0.9065,0.8779 T -chr4 166793324 166793325 G/T 2 8,11 0.8259,0.8428 G -chr4 167161470 167161471 A/C 2 4,5 0.6663,0.8515 A -chr4 167390779 167390780 A/G 2 7,6 0.8941,0.8767 G -chr4 167571705 167571706 C 1 14 0.8505 T -chr4 167654119 167654120 T 1 15 0.8528 C -chr4 167661861 167661862 G 1 5 0.8719 A -chr4 167780914 167780915 C 1 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A -chr4 179446957 179446958 C/T 2 5,8 0.8468,0.8752 C -chr4 180003384 180003385 C/T 2 7,4 0.8558,0.7582 C -chr4 180099816 180099817 C 1 9 0.7652 A -chr4 180197506 180197507 C/T 2 15,13 0.8628,0.8572 C -chr4 180207898 180207899 C/G 2 7,5 0.8950,0.8458 C -chr4 180483793 180483794 C/T 2 10,18 0.8865,0.8535 T -chr4 181635425 181635426 A/G 2 12,7 0.8623,0.8486 G -chr4 181677514 181677515 G/T 2 18,12 0.8561,0.8623 G -chr4 181728669 181728670 C/T 2 9,17 0.8618,0.8424 T -chr4 181773694 181773695 G 1 15 0.8360 T -chr4 182010232 182010233 A 1 10 0.9094 G -chr4 182198560 182198561 G/T 2 8,15 0.8990,0.8485 G -chr4 182595647 182595648 G 1 7 0.8720 A -chr4 183349617 183349618 C 1 30 0.8599 T -chr4 183840666 183840667 C/T 2 11,10 0.8602,0.8637 C -chr4 184539986 184539987 C/T 2 10,13 0.8744,0.8763 C -chr4 184577347 184577348 A/G 2 17,12 0.8594,0.8638 G -chr4 184848690 184848691 C/T 2 6,3 0.8055,0.9124 T -chr4 184869465 184869466 C/T 2 7,10 0.8680,0.8602 C -chr4 185152833 185152834 C/T 2 6,14 0.8938,0.8922 T -chr4 185295724 185295725 A/G 2 6,7 0.8510,0.8971 G -chr4 185799820 185799821 C 1 3 0.8723 T -chr4 186036531 186036532 A/G 2 4,6 0.8536,0.8347 G -chr4 186501340 186501341 A 1 3 0.8728 T -chr4 186874161 186874162 C 1 22 0.8707 T -chr4 187042710 187042711 C/T 2 17,13 0.8236,0.8531 T -chr4 187721783 187721784 A/G 2 5,6 0.8210,0.8750 G -chr4 188191974 188191975 A 1 19 0.7509 T -chr4 188245373 188245374 C/T 2 9,6 0.8171,0.7736 T -chr4 188275669 188275670 A/G 2 19,18 0.8357,0.8459 G -chr4 188449086 188449087 T 1 5 0.8718 C -chr4 188482419 188482420 C/G 2 2,2 0.9478,0.9539 C -chr4 188732986 188732987 C/T 2 19,16 0.8559,0.8991 C -chr4 189238092 189238093 A/G 2 8,4 0.8540,0.8684 G -chr4 189496091 189496092 C/G 2 9,19 0.8694,0.8708 G -chr4 189651011 189651012 G 1 14 0.8630 A -chr4 189833278 189833279 A/G 2 18,16 0.8835,0.8680 A -chr4 190023777 190023778 T 1 10 0.8380 C -chr4 190032906 190032907 T 1 14 0.8361 C -chr4 190186671 190186672 A/G 2 6,12 0.8941,0.8636 A -chr4 190308182 190308183 A/G 2 3,4 0.8554,0.9005 A -chr4 190375157 190375158 A/G 2 10,10 0.8439,0.8479 G -chr4 190479011 190479012 A/G 2 58,24 0.8732,0.8875 A -chr4 190485467 190485468 A/C 2 14,14 0.8614,0.8775 C -chr4 190503737 190503738 C/T 2 7,3 0.8353,0.8366 C -chr4 190520423 190520424 A/G 2 29,38 0.8601,0.8588 G -chr4 190532686 190532687 C/T 2 14,11 0.8235,0.8314 C -chr4 190573499 190573500 A/T 2 10,10 0.8771,0.8733 A -chr4 190576416 190576417 C/T 2 17,24 0.8469,0.8301 C -chr4 190578133 190578134 C 1 24 0.7795 T -chr4 190589089 190589090 A/C 2 40,35 0.8463,0.8563 C -chr4 190645527 190645528 A/G 2 23,19 0.8465,0.8885 G -chr4 190648252 190648253 C/T 2 24,8 0.8835,0.9145 T -chr4 190673613 190673614 T 1 39 0.8641 C -chr4 190674529 190674530 C/T 2 16,21 0.8313,0.8457 T -chr4 190842899 190842900 A/C 2 34,10 0.8396,0.8646 A -chr4 190917661 190917662 A 1 13 0.8333 T -chr5 164709 164710 T 1 4 0.7607 A -chr5 517374 517375 C/T 2 14,5 0.8583,0.8698 C -chr5 788185 788186 A/T 2 5,5 0.8658,0.8520 A -chr5 788913 788914 T 1 16 0.8119 G -chr5 952242 952243 C/G 2 6,6 0.8494,0.8451 C -chr5 1075291 1075292 A/G 2 4,4 0.7630,0.7999 G -chr5 1120563 1120564 T 1 10 0.7684 C -chr5 1632069 1632070 A 1 3 0.8416 C -chr5 1976499 1976500 A/G 2 20,9 0.8645,0.8797 A -chr5 2147011 2147012 C/T 2 6,4 0.8651,0.8826 C -chr5 2740609 2740610 C/T 2 5,5 0.8770,0.8683 T -chr5 3162078 3162079 A 1 20 0.8633 G -chr5 3385735 3385736 A/G 2 11,6 0.8447,0.8203 G -chr5 3671849 3671850 G/T 2 17,18 0.8499,0.8412 G -chr5 4271116 4271117 A/G 2 18,19 0.8485,0.8402 A -chr5 4398976 4398977 G/T 2 10,20 0.8544,0.8067 T -chr5 4485754 4485755 C/T 2 15,9 0.8270,0.8363 C -chr5 4539817 4539818 A/G 2 14,18 0.8678,0.8681 A -chr5 5105552 5105553 C/T 2 9,17 0.8836,0.8841 C -chr5 5198321 5198322 C/G 2 12,14 0.8509,0.8491 G -chr5 5375675 5375676 G 1 14 0.8552 T -chr5 5418604 5418605 C/G 2 6,11 0.8664,0.8501 G -chr5 5534458 5534459 A/G 2 10,11 0.8362,0.8861 G -chr5 5627110 5627111 G 1 4 0.8849 A -chr5 6009955 6009956 A/G 2 10,8 0.8730,0.8716 A -chr5 6215462 6215463 C/T 2 12,19 0.8790,0.8843 C -chr5 6410109 6410110 A/C 2 10,15 0.8467,0.8582 C -chr5 6564234 6564235 A/G 2 15,13 0.8526,0.8310 A -chr5 6658002 6658003 C 1 27 0.8647 T -chr5 7247134 7247135 T 1 6 0.8787 C -chr5 7250292 7250293 A/T 2 15,12 0.8592,0.8580 T -chr5 7746159 7746160 A/G 2 4,4 0.8225,0.8312 G -chr5 7814869 7814870 C/T 2 3,7 0.7890,0.8348 T -chr5 7978190 7978191 A/G 2 18,13 0.8506,0.8666 G -chr5 8125495 8125496 G 1 15 0.8217 A -chr5 8233696 8233697 C 1 17 0.8466 G -chr5 8240091 8240092 G/T 2 14,5 0.8195,0.8078 G -chr5 8624662 8624663 C/T 2 10,24 0.8524,0.8495 T -chr5 9182097 9182098 C/T 2 13,15 0.8423,0.8085 T -chr5 9441719 9441720 G 1 29 0.8535 A -chr5 9601954 9601955 T 1 31 0.8539 C -chr5 9758915 9758916 T 1 29 0.8504 C -chr5 9915398 9915399 A/G 2 16,15 0.8387,0.8492 G -chr5 10580940 10580941 T 1 19 0.8466 C -chr5 10789569 10789570 C 1 37 0.8568 T -chr5 10860896 10860897 G/T 2 8,12 0.9006,0.9003 T -chr5 11123850 11123851 C/G 2 20,24 0.8285,0.8524 C -chr5 11125497 11125498 A/G 2 8,11 0.8682,0.8504 A -chr5 11291602 11291603 A/G 2 13,24 0.8164,0.8216 A -chr5 11556439 11556440 A/T 2 3,3 0.5454,0.6812 T -chr5 11911753 11911754 G/T 2 19,9 0.8696,0.8810 G -chr5 12502066 12502067 C/G 2 14,13 0.8617,0.8676 G -chr5 12727752 12727753 A 1 6 0.9091 G -chr5 12786539 12786540 A 1 28 0.8439 G -chr5 12797636 12797637 C 1 6 0.9092 A -chr5 13032838 13032839 A/G 2 4,7 0.9001,0.8601 A -chr5 13337586 13337587 T 1 4 0.7551 C -chr5 13496096 13496097 A 1 30 0.8491 G -chr5 13828391 13828392 C/T 2 15,18 0.8400,0.8676 T -chr5 13918290 13918291 C 1 34 0.8536 T -chr5 13932116 13932117 G 1 22 0.8466 A -chr5 14060164 14060165 C/T 2 11,11 0.8300,0.8165 T -chr5 15534172 15534173 A 1 21 0.8726 T -chr5 15695931 15695932 C/T 2 16,18 0.8503,0.8517 T -chr5 15738674 15738675 C/G 2 16,15 0.8624,0.8592 G -chr5 16070391 16070392 C/T 2 11,8 0.8781,0.8775 C -chr5 16136837 16136838 A/G 2 4,11 0.8448,0.8592 A -chr5 16301523 16301524 T 1 26 0.8381 G -chr5 16443444 16443445 C/T 2 8,11 0.8885,0.8679 C -chr5 16532972 16532973 A/C 2 13,19 0.8154,0.7879 A -chr5 16974867 16974868 T 1 5 0.8470 C -chr5 17040053 17040054 T 1 13 0.8393 C -chr5 17502643 17502644 A/G 2 20,34 0.8328,0.8749 G -chr5 17793459 17793460 G 1 24 0.8491 A -chr5 17978599 17978600 G 1 35 0.8565 T -chr5 18367711 18367712 A/G 2 7,4 0.9048,0.8786 A -chr5 19385093 19385094 A/G 2 13,15 0.8445,0.8500 G -chr5 19693342 19693343 A/G 2 16,13 0.8771,0.8807 G -chr5 19966296 19966297 A/G 2 14,18 0.8887,0.8281 A -chr5 20230890 20230891 A/C 2 3,7 0.8819,0.8843 A -chr5 20321184 20321185 C/T 2 14,16 0.8253,0.8362 C -chr5 20327384 20327385 C/T 2 26,16 0.8511,0.8917 C -chr5 20789541 20789542 C 1 4 0.7505 T -chr5 21440362 21440363 A 1 10 0.8740 G -chr5 21450653 21450654 T 1 3 0.8619 C -chr5 21542704 21542705 C/T 2 3,7 0.9227,0.8928 T -chr5 21543855 21543856 C/T 2 31,30 0.8580,0.8497 T -chr5 21548152 21548153 C/T 2 20,14 0.8572,0.8411 C -chr5 21552064 21552065 A/G 2 23,33 0.8717,0.8666 G -chr5 21560041 21560042 G/T 2 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26801678 26801679 G 1 25 0.8607 A -chr5 26900585 26900586 A 1 5 0.8349 T -chr5 27102207 27102208 G/T 2 4,4 0.7684,0.8197 T -chr5 27176619 27176620 C/T 2 12,20 0.8832,0.8879 T -chr5 28006649 28006650 C/T 2 13,18 0.8043,0.8222 T -chr5 28369591 28369592 A/G 2 8,14 0.7839,0.7796 G -chr5 28386891 28386892 A/G 2 13,12 0.8208,0.7901 G -chr5 29569247 29569248 A 1 27 0.8358 G -chr5 29609673 29609674 A/G 2 20,14 0.8341,0.8545 A -chr5 29881507 29881508 T 1 25 0.8700 C -chr5 30095707 30095708 C 1 10 0.8572 T -chr5 30108505 30108506 C/T 2 5,6 0.8529,0.9126 C -chr5 30423252 30423253 A 1 5 0.8977 G -chr5 30500156 30500157 C 1 12 0.8325 T -chr5 31074929 31074930 C/T 2 5,4 0.8659,0.8911 C -chr5 31175747 31175748 A 1 28 0.8277 G -chr5 31357366 31357367 T 1 7 0.8537 C -chr5 31485756 31485757 A/C 2 4,3 0.8314,0.8686 A -chr5 31632898 31632899 A/G 2 4,13 0.8465,0.8825 G -chr5 31652930 31652931 G 1 5 0.8045 A -chr5 32186075 32186076 C/T 2 14,8 0.8559,0.8483 C -chr5 32766416 32766417 C/T 2 15,14 0.8606,0.8858 T -chr5 32786705 32786706 C/G 2 25,19 0.8347,0.8263 C -chr5 33024226 33024227 A 1 11 0.8491 T -chr5 33165839 33165840 C/T 2 19,19 0.8681,0.8802 C -chr5 33355272 33355273 C 1 25 0.8673 T -chr5 33629795 33629796 C/T 2 13,12 0.8700,0.8448 C -chr5 33630838 33630839 A/G 2 8,7 0.8364,0.9031 A -chr5 33638713 33638714 C/T 2 9,10 0.8507,0.8746 C -chr5 33699373 33699374 C 1 24 0.8813 T -chr5 34238196 34238197 C/G 2 3,3 0.9118,0.8843 G -chr5 34262511 34262512 C 1 12 0.8619 G -chr5 34297800 34297801 G 1 5 0.8721 A -chr5 35369279 35369280 C 1 34 0.8767 A -chr5 35557743 35557744 C/G 2 17,17 0.8773,0.8574 C -chr5 35632842 35632843 C/T 2 9,7 0.8544,0.8084 T -chr5 35888202 35888203 A/G 2 8,5 0.8665,0.8539 G -chr5 36366113 36366114 T 1 36 0.8218 G -chr5 36471424 36471425 C/T 2 7,4 0.8289,0.8883 C -chr5 36713032 36713033 C/T 2 9,17 0.8637,0.8799 T -chr5 37493250 37493251 G 1 9 0.8285 A -chr5 38005970 38005971 T 1 3 0.9259 G -chr5 38036782 38036783 C/T 2 8,8 0.8624,0.8667 T -chr5 38060409 38060410 A/T 2 11,14 0.8420,0.8861 T -chr5 38180319 38180320 A/C 2 14,14 0.8624,0.8777 C -chr5 38226051 38226052 T 1 21 0.8461 C -chr5 38767811 38767812 G 1 40 0.8490 A -chr5 39084470 39084471 A/G 2 15,10 0.8948,0.8500 G -chr5 39676276 39676277 C 1 17 0.8801 T -chr5 39904401 39904402 A/G 2 16,21 0.8751,0.8680 G -chr5 39945884 39945885 C 1 19 0.8802 T -chr5 39946437 39946438 T 1 22 0.8046 C -chr5 40112580 40112581 C 1 20 0.8605 T -chr5 40173866 40173867 A 1 18 0.8708 G -chr5 41080760 41080761 A 1 14 0.8781 T -chr5 41578614 41578615 A/G 2 8,12 0.8697,0.8575 G -chr5 41654166 41654167 A/G 2 6,5 0.7318,0.7887 A -chr5 42129545 42129546 C/T 2 11,7 0.8610,0.8499 C -chr5 42162285 42162286 C/T 2 9,11 0.8795,0.8695 C -chr5 42184327 42184328 A/T 2 9,8 0.8651,0.8499 A -chr5 42988421 42988422 A/G 2 6,4 0.8333,0.8072 G -chr5 43362388 43362389 C/T 2 11,5 0.8427,0.8372 C -chr5 43370845 43370846 T 1 4 0.8387 C -chr5 43520023 43520024 A/G 2 4,8 0.8575,0.8238 G -chr5 43738687 43738688 G/T 2 17,16 0.8559,0.8320 T -chr5 43797465 43797466 C/T 2 3,6 0.9034,0.9043 T -chr5 44303759 44303760 C 1 7 0.8985 T -chr5 44693533 44693534 A/T 2 23,12 0.8735,0.8864 A -chr5 44766052 44766053 A/G 2 6,9 0.8415,0.8603 G -chr5 45157587 45157588 A/G 2 6,13 0.8712,0.8753 A -chr5 45504018 45504019 T 1 15 0.8751 C -chr5 45511609 45511610 C/G 2 16,18 0.8351,0.8187 C -chr5 45842162 45842163 T 1 11 0.8752 C -chr5 46078652 46078653 C/T 2 11,17 0.8781,0.8589 T -chr5 46145634 46145635 G 1 6 0.7565 A -chr5 46382713 46382714 A/C 2 11,23 0.8679,0.8523 A -chr5 46387284 46387285 C 1 16 0.8756 T -chr5 49514537 49514538 A/T 2 19,20 0.8938,0.8687 T -chr5 49514638 49514639 G 1 4 0.8456 A -chr5 49612753 49612754 A/T 2 15,15 0.8569,0.8746 A -chr5 49652066 49652067 C 1 26 0.8763 T -chr5 50480850 50480851 C/T 2 14,5 0.8522,0.8341 T -chr5 50781972 50781973 A/G 2 8,13 0.9003,0.8400 A -chr5 51155291 51155292 G 1 21 0.8293 A -chr5 51223214 51223215 A/G 2 8,20 0.8410,0.8275 G -chr5 51656464 51656465 A/G 2 16,23 0.8455,0.9000 G -chr5 51752284 51752285 T 1 15 0.8869 C -chr5 51783567 51783568 T 1 15 0.8101 G -chr5 52006123 52006124 C/G 2 15,10 0.8517,0.8096 C -chr5 52220742 52220743 C/T 2 6,14 0.8232,0.8372 T -chr5 52332434 52332435 A 1 25 0.8622 G -chr5 52934404 52934405 A/G 2 10,5 0.8926,0.8368 G -chr5 53381728 53381729 C/T 2 8,5 0.8716,0.8970 T -chr5 53430181 53430182 A 1 18 0.8366 C -chr5 53654384 53654385 G/T 2 14,17 0.8546,0.8464 G -chr5 53692884 53692885 G/T 2 13,16 0.8799,0.8667 G -chr5 53926317 53926318 C/T 2 13,24 0.8357,0.8627 T -chr5 54304793 54304794 A/G 2 7,4 0.8244,0.8531 G -chr5 54718389 54718390 C/T 2 18,21 0.8683,0.8501 T -chr5 54942394 54942395 A 1 22 0.8660 T -chr5 55983584 55983585 A 1 5 0.9115 C -chr5 57073043 57073044 A/G 2 11,13 0.8797,0.8632 A -chr5 57201665 57201666 C/T 2 7,2 0.9277,0.9449 C -chr5 57440255 57440256 C/T 2 6,6 0.8933,0.8904 C -chr5 57677111 57677112 A 1 26 0.8498 G -chr5 57948729 57948730 C 1 11 0.8234 T -chr5 58119345 58119346 G 1 3 0.8029 A -chr5 58810585 58810586 C/T 2 12,18 0.8694,0.8611 T -chr5 58927155 58927156 C/T 2 10,11 0.8739,0.8239 T -chr5 59629369 59629370 G/T 2 20,28 0.8789,0.8400 G -chr5 60237983 60237984 T 1 16 0.8770 C -chr5 60285618 60285619 C/T 2 6,4 0.8523,0.8376 C -chr5 60382972 60382973 A/G 2 8,10 0.8238,0.8481 G -chr5 60585888 60585889 C 1 17 0.8652 T -chr5 62539654 62539655 G 1 2 0.8856 A -chr5 62803311 62803312 G 1 6 0.8941 A -chr5 63524109 63524110 A/G 2 5,4 0.8675,0.9057 G -chr5 64197072 64197073 C 1 9 0.8439 A -chr5 64712515 64712516 A/G 2 3,3 0.8891,0.9301 G -chr5 65202946 65202947 A 1 13 0.8487 T -chr5 65828486 65828487 C 1 3 0.9024 A -chr5 66675527 66675528 A/G 2 13,10 0.8299,0.8445 A -chr5 66692400 66692401 T 1 25 0.8349 C -chr5 66949005 66949006 G 1 25 0.8051 A -chr5 66959256 66959257 G 1 7 0.8629 T -chr5 66992865 66992866 T 1 37 0.8577 C -chr5 66996303 66996304 G 1 29 0.8634 A -chr5 67287770 67287771 C 1 22 0.8693 G -chr5 67432790 67432791 C 1 26 0.8669 T -chr5 67529751 67529752 A 1 34 0.8713 G -chr5 68181338 68181339 C 1 16 0.8723 T -chr5 68295564 68295565 G 1 11 0.8366 T -chr5 70972437 70972438 G 1 9 0.8638 A -chr5 71097023 71097024 A/C 2 17,23 0.8152,0.8255 C -chr5 71525467 71525468 A/T 2 15,14 0.8409,0.8420 A -chr5 72044090 72044091 A/G 2 11,7 0.8712,0.8857 A -chr5 72071989 72071990 A/C 2 10,14 0.8442,0.8017 A -chr5 72206861 72206862 G 1 28 0.8607 T -chr5 72434268 72434269 C/G 2 16,10 0.8374,0.8438 C -chr5 72453957 72453958 T 1 20 0.8744 C -chr5 72488282 72488283 C 1 2 0.9501 T -chr5 72493265 72493266 G 1 29 0.8740 A -chr5 72707103 72707104 C/T 2 11,17 0.8837,0.8436 T -chr5 72766227 72766228 A 1 24 0.8370 G -chr5 73149866 73149867 A 1 23 0.8500 G -chr5 73386230 73386231 C/T 2 12,20 0.8312,0.8586 T -chr5 73693428 73693429 A/G 2 9,5 0.8840,0.9065 A -chr5 73710928 73710929 C 1 25 0.8497 G -chr5 73725737 73725738 C/T 2 17,10 0.8223,0.8184 T -chr5 73986825 73986826 C 1 35 0.8578 T -chr5 73992405 73992406 G 1 17 0.8747 T -chr5 74460044 74460045 G 1 22 0.8587 A -chr5 74502796 74502797 A 1 21 0.8719 G -chr5 74617238 74617239 A/G 2 14,21 0.8583,0.8514 G -chr5 75044076 75044077 C/G 2 14,15 0.8698,0.8760 C -chr5 75131412 75131413 A/G 2 7,6 0.8523,0.9112 A -chr5 75161290 75161291 A/G 2 17,14 0.9037,0.8834 A -chr5 75817815 75817816 A/G 2 15,9 0.8857,0.9078 A -chr5 76038054 76038055 A/C 2 11,13 0.8747,0.8994 C -chr5 76090950 76090951 A/G 2 11,12 0.8647,0.8880 G -chr5 76730566 76730567 C/T 2 11,26 0.8746,0.8867 T -chr5 76806357 76806358 C/G 2 15,18 0.8696,0.8614 G -chr5 77015982 77015983 C/T 2 24,25 0.8656,0.8643 T -chr5 77173521 77173522 A/G 2 14,18 0.8524,0.8567 G -chr5 77579204 77579205 T 1 25 0.8072 C -chr5 77788790 77788791 G 1 18 0.8776 A -chr5 77805424 77805425 A/T 2 10,10 0.8151,0.8021 A -chr5 77818841 77818842 A/G 2 7,10 0.8339,0.8590 G -chr5 78306691 78306692 C/G 2 3,6 0.8619,0.8462 G -chr5 79112166 79112167 A/G 2 11,13 0.8521,0.8557 A -chr5 79279954 79279955 C 1 3 0.7728 G -chr5 79455797 79455798 A/G 2 9,15 0.8697,0.8804 A -chr5 80008999 80009000 A/G 2 14,22 0.8980,0.8836 G -chr5 80111738 80111739 C 1 15 0.8640 T -chr5 80526621 80526622 A/G 2 11,13 0.8693,0.8852 A -chr5 80751554 80751555 A/G 2 3,10 0.8221,0.8384 A -chr5 80800748 80800749 A/T 2 10,19 0.8869,0.8831 A -chr5 81049186 81049187 C/T 2 5,5 0.8691,0.8659 T -chr5 81097613 81097614 A/G 2 4,5 0.8011,0.8048 G -chr5 81900906 81900907 A/G 2 20,16 0.8535,0.8460 A -chr5 81988067 81988068 C/T 2 13,17 0.8810,0.8944 T -chr5 82125242 82125243 A 1 26 0.8627 G -chr5 82958620 82958621 G 1 26 0.8125 A -chr5 83144570 83144571 A 1 35 0.8626 G -chr5 83360505 83360506 G 1 18 0.7721 A -chr5 84898772 84898773 G 1 4 0.8161 T -chr5 84943739 84943740 G 1 5 0.8772 A -chr5 85223830 85223831 A 1 23 0.8700 G -chr5 85398494 85398495 C 1 11 0.8706 T -chr5 85611399 85611400 G 1 16 0.8487 A -chr5 88398647 88398648 C 1 13 0.8874 A -chr5 88610498 88610499 A 1 23 0.8320 G -chr5 88845147 88845148 G 1 16 0.8272 A -chr5 90202962 90202963 C 1 13 0.8891 T -chr5 90505598 90505599 G 1 11 0.8777 A -chr5 90915267 90915268 A 1 24 0.8686 G -chr5 91495980 91495981 A 1 9 0.8958 C -chr5 91570561 91570562 C/G 2 4,4 0.7648,0.8735 G -chr5 91588031 91588032 T 1 9 0.8161 C -chr5 92344845 92344846 C 1 16 0.8600 T -chr5 93488607 93488608 A 1 6 0.8746 T -chr5 93664161 93664162 A/G 2 5,12 0.8460,0.7708 A -chr5 94030179 94030180 A/G 2 23,15 0.8702,0.8901 A -chr5 94665840 94665841 G 1 11 0.8757 T -chr5 94797363 94797364 A/G 2 18,23 0.8644,0.8567 G -chr5 95246127 95246128 A/G 2 3,5 0.8478,0.8469 G -chr5 95774816 95774817 A/G 2 11,4 0.8767,0.8827 G -chr5 95837671 95837672 A/C 2 5,6 0.8110,0.8340 C -chr5 95939748 95939749 A/G 2 8,11 0.8734,0.8369 G -chr5 96061698 96061699 C/T 2 5,10 0.8462,0.8627 C -chr5 96169938 96169939 C/T 2 13,4 0.8453,0.8537 C -chr5 96946899 96946900 T 1 18 0.8258 G -chr5 96978348 96978349 A 1 4 0.9408 G -chr5 97026465 97026466 C/T 2 17,9 0.8244,0.8509 T -chr5 97153608 97153609 A 1 27 0.8697 G -chr5 97911703 97911704 C/T 2 22,30 0.8582,0.8516 T -chr5 98190219 98190220 C 1 11 0.8635 T -chr5 99502938 99502939 T 1 28 0.8480 C -chr5 99580287 99580288 G/T 2 20,9 0.8345,0.8820 G -chr5 99590042 99590043 C/G 2 6,15 0.8940,0.8942 G -chr5 99596296 99596297 G 1 11 0.8250 T -chr5 99804492 99804493 C/T 2 11,14 0.8661,0.8592 T -chr5 99849873 99849874 T 1 4 0.7670 A -chr5 100466501 100466502 G 1 13 0.8808 A -chr5 100706405 100706406 C 1 14 0.8498 A -chr5 100951780 100951781 C 1 23 0.8570 T -chr5 100968066 100968067 C 1 14 0.8386 A -chr5 101640997 101640998 A/G 2 8,9 0.8579,0.8741 A -chr5 101838810 101838811 C/G 2 18,19 0.8679,0.8616 G -chr5 102632399 102632400 G/T 2 15,20 0.8917,0.8548 G -chr5 102834119 102834120 A 1 25 0.8567 T -chr5 102863526 102863527 G 1 14 0.8565 T -chr5 103287604 103287605 A/G 2 9,9 0.8520,0.8381 G -chr5 103443155 103443156 C 1 8 0.8633 T -chr5 103916348 103916349 C/T 2 14,15 0.8297,0.8302 T -chr5 103999961 103999962 C/T 2 19,18 0.8631,0.8605 C -chr5 104582044 104582045 A/T 2 15,15 0.8630,0.8758 T -chr5 104616018 104616019 A/G 2 13,7 0.8697,0.8830 A -chr5 104892944 104892945 C 1 22 0.8591 T 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0.8620 A -chr5 110973036 110973037 G 1 17 0.8441 C -chr5 111382387 111382388 A 1 21 0.8274 T -chr5 111509231 111509232 G 1 7 0.8687 A -chr5 111673686 111673687 G 1 18 0.8569 A -chr5 111725642 111725643 A/G 2 14,12 0.8614,0.8434 A -chr5 111874892 111874893 C/G 2 11,8 0.8335,0.8579 C -chr5 112229687 112229688 C/T 2 5,11 0.8730,0.8869 T -chr5 112329577 112329578 C 1 3 0.8881 A -chr5 112428762 112428763 C/T 2 16,26 0.8688,0.8661 T -chr5 112434465 112434466 A 1 38 0.8360 G -chr5 112812456 112812457 A/G 2 10,11 0.8395,0.8754 G -chr5 112829304 112829305 A/G 2 16,9 0.8618,0.8935 A -chr5 113961147 113961148 A/G 2 22,13 0.8454,0.8388 G -chr5 114171343 114171344 C/T 2 11,11 0.8174,0.8180 T -chr5 114346885 114346886 A/G 2 9,10 0.8557,0.8798 G -chr5 114624217 114624218 C 1 16 0.8771 T -chr5 114794246 114794247 G 1 39 0.8511 C -chr5 114813281 114813282 C 1 26 0.8905 T -chr5 114951079 114951080 G 1 9 0.8026 T -chr5 115574359 115574360 C/T 2 11,10 0.8663,0.8507 T -chr5 115677362 115677363 A/G 2 3,4 0.8627,0.7461 A -chr5 115952512 115952513 C/G 2 9,11 0.8545,0.8401 C -chr5 116617232 116617233 C 1 21 0.8859 T -chr5 116680619 116680620 A/C 2 16,15 0.8500,0.8468 A -chr5 116924168 116924169 C/T 2 11,7 0.8509,0.8532 C -chr5 117117129 117117130 A 1 15 0.8545 C -chr5 117131868 117131869 A/T 2 6,10 0.8500,0.8452 T -chr5 117209041 117209042 A/T 2 4,8 0.8851,0.8556 T -chr5 117443654 117443655 G 1 18 0.8968 A -chr5 117517709 117517710 G 1 7 0.8742 A -chr5 117833500 117833501 G/T 2 16,14 0.8670,0.8930 T -chr5 117979363 117979364 T 1 8 0.8422 A -chr5 118117002 118117003 A/G 2 20,18 0.8941,0.8821 A -chr5 118618287 118618288 A/C 2 4,7 0.8744,0.8704 C -chr5 118646392 118646393 A 1 4 0.8454 G -chr5 118664644 118664645 C/T 2 18,8 0.8300,0.8379 C -chr5 119097251 119097252 A/G 2 14,10 0.8878,0.8851 A -chr5 119205921 119205922 C/T 2 21,15 0.7903,0.8344 C -chr5 119211483 119211484 A 1 17 0.8104 G -chr5 119226698 119226699 C/G 2 7,3 0.9081,0.7617 C -chr5 119329149 119329150 A/T 2 4,7 0.8689,0.8600 T -chr5 119378917 119378918 T 1 5 0.8824 C -chr5 119404894 119404895 C/T 2 8,9 0.8543,0.8436 T -chr5 119450415 119450416 C/T 2 13,9 0.8625,0.8317 C -chr5 119450944 119450945 G 1 20 0.8797 A -chr5 119657615 119657616 C/G 2 10,13 0.8452,0.8519 G -chr5 119775269 119775270 C 1 25 0.8606 T -chr5 120479321 120479322 A/G 2 14,14 0.8882,0.8813 A -chr5 120560043 120560044 A/G 2 6,6 0.8786,0.8518 G -chr5 120585596 120585597 C/G 2 10,16 0.8801,0.8935 C -chr5 120796611 120796612 A 1 6 0.8649 G -chr5 121077156 121077157 C/T 2 3,4 0.7817,0.8797 T -chr5 121326121 121326122 A/C 2 19,10 0.8483,0.8647 C -chr5 121944482 121944483 A/C 2 5,4 0.8778,0.8711 A -chr5 122296699 122296700 C 1 10 0.8775 T -chr5 122446354 122446355 T 1 2 0.9366 C -chr5 123621601 123621602 C/G 2 14,11 0.8823,0.8793 C -chr5 123850955 123850956 A/C 2 30,14 0.8774,0.8613 C -chr5 123853590 123853591 T 1 12 0.7670 G -chr5 123997974 123997975 C/T 2 15,8 0.8654,0.8575 C -chr5 124559008 124559009 A/G 2 17,13 0.8959,0.8844 A -chr5 124579157 124579158 C/T 2 4,2 0.8523,0.9474 C -chr5 124639550 124639551 T 1 28 0.8391 G -chr5 124834211 124834212 C 1 4 0.8715 T -chr5 125051773 125051774 A 1 27 0.8585 G -chr5 126378194 126378195 A/C 2 12,16 0.8335,0.8342 C -chr5 126858443 126858444 A/G 2 4,3 0.8795,0.9071 G -chr5 127104163 127104164 A/G 2 14,8 0.8885,0.9167 A -chr5 127977033 127977034 T 1 16 0.8786 C -chr5 128525420 128525421 A/G 2 8,6 0.8116,0.8233 A -chr5 129360657 129360658 A 1 12 0.8552 G -chr5 130067490 130067491 G 1 34 0.8757 C -chr5 131304741 131304742 C/T 2 11,16 0.8794,0.8572 T -chr5 131357796 131357797 C/G 2 19,16 0.8749,0.9006 C -chr5 131481738 131481739 C/G 2 6,3 0.8704,0.7647 C -chr5 131515412 131515413 T 1 33 0.8686 C -chr5 131524687 131524688 A/G 2 17,21 0.8508,0.8397 G -chr5 131537623 131537624 A/G 2 8,12 0.8909,0.8459 G -chr5 132421989 132421990 A 1 22 0.8613 G -chr5 132664762 132664763 C 1 14 0.8721 T -chr5 132846172 132846173 C/T 2 14,16 0.8504,0.8563 C -chr5 133019914 133019915 G 1 6 0.8840 A -chr5 133156221 133156222 A/T 2 8,9 0.8469,0.8263 A -chr5 133184082 133184083 C/G 2 5,14 0.9116,0.8729 G -chr5 133258177 133258178 C 1 15 0.8488 A -chr5 133909956 133909957 T 1 14 0.8735 C -chr5 134113557 134113558 A 1 23 0.8605 G -chr5 134116554 134116555 C 1 3 0.8536 T -chr5 134461403 134461404 A/T 2 13,15 0.8581,0.8458 T -chr5 134692055 134692056 A/C 2 18,11 0.8483,0.8741 A -chr5 135041808 135041809 A 1 9 0.8527 G -chr5 135380058 135380059 A 1 14 0.8356 G -chr5 136636656 136636657 C 1 20 0.8723 G -chr5 136849572 136849573 A 1 25 0.8643 C -chr5 137402497 137402498 A 1 5 0.7827 T -chr5 137777609 137777610 T 1 4 0.8290 C -chr5 137945750 137945751 C/G 2 18,6 0.8722,0.8780 C -chr5 138886845 138886846 T 1 6 0.8261 C -chr5 139539089 139539090 C/T 2 22,15 0.8388,0.8231 C -chr5 139614262 139614263 A/G 2 13,14 0.8569,0.8449 G -chr5 139961782 139961783 A/T 2 11,8 0.8612,0.8488 A -chr5 140070028 140070029 C 1 4 0.8425 T -chr5 140685274 140685275 A/G 2 12,8 0.8614,0.8945 A -chr5 141248805 141248806 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0.8579,0.7831 C -chr5 146814431 146814432 A/G 2 8,13 0.8796,0.8635 G -chr5 147060558 147060559 C/T 2 18,27 0.8119,0.8119 T -chr5 147082563 147082564 C/T 2 12,16 0.8798,0.8653 T -chr5 147327045 147327046 A/G 2 11,13 0.8676,0.8677 G -chr5 147827666 147827667 A/G 2 19,7 0.8577,0.8673 A -chr5 148060816 148060817 C 1 22 0.8478 T -chr5 148197428 148197429 C 1 27 0.8511 A -chr5 148716421 148716422 A 1 34 0.8798 G -chr5 148753207 148753208 T 1 3 0.7547 C -chr5 148823172 148823173 A/T 2 3,5 0.8137,0.8375 T -chr5 149058361 149058362 A/G 2 11,9 0.8610,0.8800 G -chr5 149117003 149117004 C 1 21 0.8616 T -chr5 149149558 149149559 G 1 40 0.8834 A -chr5 149273553 149273554 A/G 2 12,11 0.8620,0.8547 A -chr5 149591705 149591706 G 1 33 0.8378 A -chr5 149704805 149704806 T 1 25 0.8465 C -chr5 149706271 149706272 G/T 2 8,5 0.9076,0.7994 G -chr5 149827493 149827494 T 1 12 0.8899 C -chr5 149891728 149891729 A/C 2 16,10 0.8415,0.8443 C -chr5 150375257 150375258 C 1 25 0.8689 T -chr5 150392652 150392653 G 1 17 0.8202 T -chr5 150623551 150623552 A/C 2 21,24 0.8633,0.8748 C -chr5 150661585 150661586 C 1 22 0.8980 T -chr5 151321016 151321017 A/G 2 17,13 0.8402,0.8183 G -chr5 151542533 151542534 C 1 19 0.8064 T -chr5 151836513 151836514 A/G 2 10,9 0.8386,0.8160 G -chr5 152759447 152759448 A/G 2 11,6 0.8750,0.9029 A -chr5 153010981 153010982 A/G 2 8,10 0.8718,0.8674 A -chr5 153413389 153413390 C/T 2 5,5 0.8633,0.8453 C -chr5 153577918 153577919 C 1 39 0.8678 T -chr5 153775492 153775493 C/T 2 6,8 0.8681,0.8629 C -chr5 153856593 153856594 A/G 2 5,12 0.8370,0.8697 G -chr5 153882514 153882515 G 1 12 0.8952 A -chr5 154531296 154531297 C/T 2 18,21 0.8803,0.8626 C -chr5 154762554 154762555 C/T 2 14,8 0.8732,0.8574 C -chr5 155050553 155050554 C 1 3 0.8928 T -chr5 155607463 155607464 A 1 4 0.8612 C -chr5 155804140 155804141 G 1 12 0.8992 A -chr5 155924869 155924870 C 1 28 0.8316 G -chr5 156002437 156002438 A 1 31 0.8523 G -chr5 156514815 156514816 A/G 2 7,3 0.8890,0.8786 A -chr5 156628286 156628287 C/T 2 8,19 0.8702,0.8754 T -chr5 156832250 156832251 A/G 2 9,4 0.8598,0.8574 A -chr5 157227468 157227469 C/T 2 17,10 0.8510,0.8389 C -chr5 157360164 157360165 A/C 2 9,16 0.8459,0.8478 A -chr5 157718285 157718286 A/G 2 7,22 0.8640,0.7796 A -chr5 157877476 157877477 C/T 2 18,24 0.8741,0.8791 T -chr5 158377709 158377710 T 1 31 0.8617 C -chr5 158432456 158432457 A/T 2 17,12 0.8310,0.8413 A -chr5 158531776 158531777 T 1 12 0.8679 C -chr5 158821492 158821493 A/C 2 15,7 0.8656,0.8341 A -chr5 159072450 159072451 C 1 27 0.8622 T -chr5 159327343 159327344 C/T 2 17,8 0.8448,0.8646 C -chr5 159579781 159579782 G 1 4 0.8207 A -chr5 159629047 159629048 G 1 4 0.8449 C -chr5 159823098 159823099 C/T 2 5,5 0.8817,0.9108 C -chr5 159854550 159854551 C/G 2 11,11 0.8760,0.8566 G -chr5 160791731 160791732 A 1 16 0.7789 T -chr5 161082776 161082777 C/T 2 16,5 0.8638,0.8325 T -chr5 161462720 161462721 C/T 2 7,4 0.9038,0.9130 C -chr5 162462911 162462912 A/G 2 7,5 0.8579,0.8679 A -chr5 162601148 162601149 A 1 21 0.8530 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167170710 A/G 2 9,7 0.8568,0.9047 A -chr5 167380982 167380983 A/T 2 10,6 0.8057,0.8200 A -chr5 167942597 167942598 A/G 2 11,27 0.8355,0.8496 G -chr5 168268663 168268664 A/G 2 18,15 0.8322,0.8544 G -chr5 168637289 168637290 C/T 2 3,9 0.8606,0.8351 T -chr5 168642438 168642439 A/G 2 14,12 0.8612,0.8355 A -chr5 170379854 170379855 G 1 25 0.8535 A -chr5 170935060 170935061 A/G 2 9,3 0.8565,0.8550 G -chr5 171084814 171084815 A/G 2 11,23 0.8477,0.8506 G -chr5 171288319 171288320 G 1 20 0.8157 C -chr5 171604337 171604338 A 1 20 0.8697 T -chr5 172646002 172646003 T 1 13 0.8850 C -chr5 172923031 172923032 G 1 3 0.8263 C -chr5 172978275 172978276 C 1 36 0.8627 T -chr5 173517622 173517623 A/G 2 8,11 0.8025,0.8067 G -chr5 173754761 173754762 C 1 11 0.8729 T -chr5 173855868 173855869 A/G 2 9,15 0.8370,0.8534 A -chr5 174059631 174059632 G/T 2 18,10 0.8532,0.8724 G -chr5 174143293 174143294 G/T 2 3,3 0.8957,0.8668 T -chr5 174180940 174180941 C/T 2 16,6 0.8835,0.8880 C -chr5 174659316 174659317 A 1 8 0.8580 G -chr5 175208534 175208535 A/T 2 10,12 0.8134,0.8011 T -chr5 175810713 175810714 A 1 3 0.8323 C -chr5 177493866 177493867 A/G 2 19,9 0.8584,0.8351 A -chr5 177562250 177562251 A 1 9 0.8766 G -chr5 177990885 177990886 C/T 2 19,8 0.8593,0.8365 C -chr5 178541940 178541941 A/G 2 17,23 0.8959,0.8810 A -chr5 178894465 178894466 A 1 23 0.8642 T -chr5 179311941 179311942 C/T 2 19,16 0.8929,0.8715 T -chr5 179522728 179522729 C/T 2 5,5 0.9107,0.8847 T -chr5 180194817 180194818 C 1 12 0.8384 T -chr5 180508875 180508876 A/G 2 17,11 0.8608,0.8674 A -chr5 180554657 180554658 G 1 11 0.8922 A -chr5 180628825 180628826 A/G 2 10,8 0.8643,0.8243 A -chr6 231637 231638 T 1 40 0.8467 G -chr6 240304 240305 A/G 2 6,5 0.8385,0.7591 G -chr6 240483 240484 A/G 2 9,7 0.8786,0.8660 A -chr6 445705 445706 A 1 8 0.9004 G -chr6 1059967 1059968 C/T 2 14,13 0.8549,0.8637 C -chr6 1766895 1766896 A 1 13 0.7657 G -chr6 2132291 2132292 C/T 2 17,15 0.8738,0.8667 C -chr6 2582912 2582913 T 1 22 0.8507 C -chr6 2937199 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C 1 14 0.8386 T -chr6 9344143 9344144 C/T 2 11,5 0.7998,0.7788 T -chr6 9646597 9646598 G/T 2 4,8 0.7325,0.8665 T -chr6 9819564 9819565 A/C 2 16,18 0.8914,0.8985 C -chr6 10153618 10153619 G/T 2 14,7 0.8496,0.8360 G -chr6 10527045 10527046 A/G 2 14,12 0.8570,0.8488 G -chr6 10810348 10810349 A 1 3 0.8166 G -chr6 11379145 11379146 C/T 2 20,12 0.8422,0.8224 T -chr6 11455417 11455418 C 1 2 0.9648 A -chr6 11497706 11497707 A/G 2 8,9 0.7957,0.7839 G -chr6 11896278 11896279 A 1 4 0.9112 G -chr6 11902749 11902750 G 1 24 0.8644 C -chr6 11945806 11945807 A 1 11 0.8829 G -chr6 12336122 12336123 A/T 2 9,13 0.8663,0.8514 T -chr6 12353791 12353792 T 1 26 0.8353 G -chr6 12432026 12432027 A/G 2 7,3 0.8616,0.7461 A -chr6 12653264 12653265 C/G 2 6,6 0.8951,0.8713 G -chr6 12823469 12823470 A/T 2 11,12 0.8735,0.8749 A -chr6 13006409 13006410 G 1 19 0.8765 C -chr6 13311651 13311652 G 1 20 0.8302 A -chr6 13420144 13420145 A 1 8 0.8641 G -chr6 13430465 13430466 T 1 2 0.9123 C -chr6 13763596 13763597 A/G 2 12,8 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31348252 C 1 11 0.8472 G -chr6 31543030 31543031 A/G 2 3,6 0.8797,0.8715 G -chr6 32187636 32187637 G/T 2 13,13 0.8708,0.8207 G -chr6 32341718 32341719 C/T 2 14,8 0.8696,0.8865 C -chr6 32355604 32355605 A/G 2 10,12 0.8252,0.8288 G -chr6 32453893 32453894 A/G 2 9,6 0.8218,0.8079 A -chr6 32487927 32487928 G/T 2 4,4 0.8182,0.7976 T -chr6 32520906 32520907 C 1 6 0.8688 T -chr6 32572081 32572082 T 1 3 0.8896 C -chr6 32590832 32590833 G 1 19 0.8468 A -chr6 32654201 32654202 C/T 2 6,8 0.8833,0.9109 T -chr6 32695432 32695433 C 1 10 0.8823 T -chr6 32778655 32778656 G 1 2 0.9455 A -chr6 32827592 32827593 C/T 2 4,5 0.8632,0.7774 C -chr6 32900759 32900760 A/T 2 11,13 0.9065,0.8961 T -chr6 32987119 32987120 G/T 2 21,27 0.8570,0.8699 T -chr6 33026552 33026553 A 1 18 0.8576 G -chr6 33032702 33032703 T 1 6 0.8369 C -chr6 33039979 33039980 G 1 24 0.7529 A -chr6 33074611 33074612 A 1 22 0.8660 C -chr6 33121677 33121678 C/T 2 14,19 0.8479,0.8335 C -chr6 33124963 33124964 A/G 2 15,14 0.8315,0.8731 G -chr6 33280628 33280629 G 1 20 0.8308 C -chr6 33452808 33452809 C/T 2 6,6 0.8702,0.8652 T -chr6 33579447 33579448 A 1 4 0.8855 T -chr6 33672602 33672603 C 1 7 0.8774 T -chr6 33813073 33813074 A/G 2 17,18 0.8618,0.8571 G -chr6 34025331 34025332 C/T 2 6,16 0.8886,0.8579 T -chr6 34323072 34323073 C/T 2 4,8 0.8067,0.8181 T -chr6 34572027 34572028 C 1 18 0.8911 A -chr6 35080915 35080916 T 1 2 0.9204 C -chr6 35407373 35407374 C/G 2 12,8 0.8594,0.8596 C -chr6 36621358 36621359 G/T 2 14,13 0.8253,0.8499 T -chr6 36732541 36732542 C/G 2 9,5 0.8448,0.8277 G -chr6 36815375 36815376 A/T 2 12,10 0.8582,0.8665 A -chr6 36897484 36897485 C/T 2 20,11 0.8866,0.8918 C -chr6 37021259 37021260 A 1 24 0.8455 T -chr6 37319582 37319583 A/G 2 12,10 0.8636,0.8746 G -chr6 37627809 37627810 C/T 2 4,5 0.8625,0.8425 C -chr6 37684077 37684078 C/T 2 14,5 0.8350,0.7979 C -chr6 37824130 37824131 A/G 2 5,13 0.8675,0.8389 G -chr6 38126762 38126763 G/T 2 7,5 0.8204,0.8393 G -chr6 38271198 38271199 G/T 2 10,8 0.8499,0.8365 G -chr6 38286537 38286538 C/G 2 4,6 0.8383,0.8710 C -chr6 38859073 38859074 A/T 2 21,16 0.8654,0.8580 T -chr6 38984373 38984374 A 1 25 0.8592 G -chr6 39232712 39232713 C/T 2 5,4 0.8286,0.8639 C -chr6 39264455 39264456 C/T 2 7,7 0.8241,0.8361 C -chr6 39593812 39593813 C 1 27 0.8519 G -chr6 39625610 39625611 T 1 21 0.8802 G -chr6 39744401 39744402 G/T 2 12,13 0.8409,0.8310 G -chr6 40085244 40085245 C/T 2 13,18 0.8126,0.8401 T -chr6 40255276 40255277 A/G 2 17,17 0.8200,0.8408 G -chr6 40853381 40853382 C/T 2 17,27 0.8507,0.8497 C -chr6 40919337 40919338 C/T 2 6,7 0.9165,0.8947 T -chr6 41489374 41489375 A/G 2 10,11 0.8345,0.8343 A -chr6 41783248 41783249 A/G 2 25,9 0.8819,0.8437 A -chr6 43261766 43261767 C 1 25 0.8640 G -chr6 43868985 43868986 G 1 26 0.8939 A -chr6 44468053 44468054 A/G 2 9,3 0.8245,0.8429 G -chr6 45671068 45671069 A 1 16 0.8736 C -chr6 45790055 45790056 T 1 23 0.8616 C -chr6 46130905 46130906 C/G 2 17,8 0.8824,0.9038 C -chr6 46134705 46134706 C/T 2 15,9 0.8356,0.8424 T -chr6 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-chr6 50946011 50946012 G 1 7 0.8522 A -chr6 51013675 51013676 A/T 2 5,7 0.8895,0.8701 A -chr6 51147199 51147200 A/G 2 18,17 0.8382,0.8542 G -chr6 51410775 51410776 G 1 6 0.8794 A -chr6 51591159 51591160 C/T 2 6,6 0.8170,0.8432 T -chr6 51648627 51648628 A/T 2 8,11 0.8537,0.8296 A -chr6 51966393 51966394 A/G 2 9,10 0.8667,0.8728 G -chr6 52393013 52393014 C/G 2 6,6 0.9065,0.8798 C -chr6 52860374 52860375 T 1 26 0.8753 C -chr6 53276000 53276001 G 1 41 0.8263 T -chr6 53348716 53348717 A/G 2 6,10 0.8036,0.7994 A -chr6 53795212 53795213 C/T 2 23,15 0.8613,0.8510 C -chr6 53997200 53997201 A/G 2 16,5 0.8521,0.8991 G -chr6 54048181 54048182 T 1 11 0.8608 C -chr6 54081196 54081197 G 1 28 0.8569 A -chr6 54163990 54163991 A/C 2 13,6 0.8768,0.8929 A -chr6 54504525 54504526 A/G 2 15,11 0.8692,0.8371 A -chr6 54552209 54552210 G 1 20 0.8870 A -chr6 54632535 54632536 G/T 2 5,6 0.7421,0.7739 T -chr6 54680756 54680757 T 1 5 0.8742 A -chr6 55073412 55073413 C/T 2 22,10 0.8349,0.8726 C -chr6 55185535 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64579532 64579533 A 1 21 0.8457 G -chr6 64679903 64679904 G 1 27 0.8641 C -chr6 64976763 64976764 A 1 32 0.8707 G -chr6 65176406 65176407 C 1 12 0.8432 G -chr6 65338598 65338599 C/T 2 9,6 0.8814,0.8488 C -chr6 65875243 65875244 A/T 2 8,5 0.8512,0.8336 T -chr6 66810803 66810804 A/C 2 5,10 0.8458,0.8350 C -chr6 66876020 66876021 G 1 14 0.8659 C -chr6 66927537 66927538 T 1 12 0.8082 A -chr6 67250007 67250008 A/G 2 13,9 0.8722,0.8271 A -chr6 67352211 67352212 C/T 2 11,20 0.8785,0.8737 C -chr6 67786258 67786259 C/T 2 12,7 0.8742,0.8470 C -chr6 67887155 67887156 A 1 8 0.8236 C -chr6 68037284 68037285 G 1 19 0.8440 A -chr6 68393626 68393627 A/T 2 4,3 0.8802,0.8693 T -chr6 68517692 68517693 A 1 20 0.8993 T -chr6 68539307 68539308 G/T 2 9,3 0.8807,0.8936 T -chr6 68598658 68598659 A 1 17 0.8779 G -chr6 68838782 68838783 A/C 2 12,22 0.8416,0.8465 C -chr6 69000282 69000283 A/G 2 12,13 0.8435,0.8548 A -chr6 69198836 69198837 C/T 2 16,11 0.8514,0.8140 T -chr6 69221232 69221233 G/T 2 8,6 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C -chr6 110368302 110368303 C 1 2 0.9159 T -chr6 110397284 110397285 C 1 23 0.8447 T -chr6 110655674 110655675 C/T 2 15,15 0.8679,0.8665 C -chr6 111378648 111378649 A 1 17 0.8431 C -chr6 111796192 111796193 T 1 4 0.8341 C -chr6 111812471 111812472 G/T 2 5,11 0.8262,0.8628 T -chr6 112250254 112250255 A/C 2 6,3 0.8638,0.8743 A -chr6 112266346 112266347 C 1 24 0.8573 T -chr6 112330809 112330810 G 1 13 0.8713 A -chr6 112448889 112448890 A/G 2 21,14 0.8482,0.8428 G -chr6 112466655 112466656 G 1 16 0.8347 A -chr6 112509716 112509717 T 1 28 0.8421 A -chr6 112527306 112527307 C/T 2 12,8 0.8609,0.8700 C -chr6 112612293 112612294 C/T 2 10,7 0.8384,0.8265 C -chr6 113637476 113637477 A 1 9 0.8649 G -chr6 113951216 113951217 T 1 14 0.8373 G -chr6 113974571 113974572 C 1 3 0.8870 T -chr6 113997164 113997165 C/T 2 15,18 0.8650,0.8728 T -chr6 114036279 114036280 C/T 2 10,11 0.8495,0.8607 T -chr6 114810789 114810790 C/T 2 13,10 0.8454,0.8345 C -chr6 115048196 115048197 A 1 37 0.8225 C -chr6 115120099 115120100 T 1 27 0.8458 C -chr6 115143772 115143773 T 1 8 0.8672 G -chr6 116478950 116478951 C/G 2 21,8 0.8596,0.8571 C -chr6 116546865 116546866 G/T 2 24,9 0.8644,0.8966 G -chr6 117358916 117358917 A/T 2 10,12 0.8244,0.8716 T -chr6 117493421 117493422 C/T 2 16,11 0.8108,0.8412 T -chr6 117854299 117854300 C 1 12 0.8511 T -chr6 117899670 117899671 A 1 13 0.8426 G -chr6 117919702 117919703 A 1 23 0.8517 G -chr6 117947066 117947067 A 1 10 0.8429 G -chr6 118103839 118103840 A/G 2 17,20 0.8551,0.8570 G -chr6 118643121 118643122 C 1 28 0.8705 T -chr6 118914256 118914257 T 1 13 0.8364 G -chr6 119101007 119101008 C/T 2 8,9 0.8563,0.8719 T -chr6 119512984 119512985 C/T 2 25,21 0.8518,0.8627 C -chr6 119528355 119528356 C/T 2 8,8 0.8785,0.8929 T -chr6 119745228 119745229 T 1 18 0.8176 A -chr6 119814526 119814527 A/G 2 8,4 0.8319,0.7994 A -chr6 120142180 120142181 C/T 2 15,9 0.8711,0.8602 C -chr6 120509775 120509776 A/G 2 6,11 0.8275,0.7911 A -chr6 120560221 120560222 T 1 14 0.8687 C -chr6 120630251 120630252 C/T 2 16,10 0.8673,0.8396 C -chr6 120892437 120892438 C/G 2 12,10 0.8449,0.8591 C -chr6 121441201 121441202 C 1 19 0.8349 T -chr6 121511606 121511607 A/T 2 21,8 0.8713,0.8988 A -chr6 121762087 121762088 G/T 2 5,5 0.8829,0.8467 G -chr6 122265119 122265120 A 1 31 0.8560 G -chr6 122585022 122585023 G 1 18 0.8661 A -chr6 122594826 122594827 C/T 2 9,4 0.8644,0.8518 C -chr6 123035437 123035438 A/G 2 7,10 0.8611,0.8114 G -chr6 123185618 123185619 C 1 17 0.8658 T -chr6 123277697 123277698 T 1 25 0.8450 C -chr6 123373944 123373945 A/G 2 13,8 0.8908,0.8919 A -chr6 123545880 123545881 C 1 21 0.8197 T -chr6 124065838 124065839 G 1 3 0.8651 A -chr6 125013302 125013303 A/G 2 13,20 0.8310,0.8551 A -chr6 125035784 125035785 C/T 2 18,8 0.8401,0.7804 C -chr6 125140346 125140347 G/T 2 3,3 0.7785,0.9004 T -chr6 125146970 125146971 C/T 2 10,13 0.8499,0.8692 C -chr6 125488218 125488219 A/C 2 3,7 0.8736,0.8739 A -chr6 125806062 125806063 T 1 21 0.8088 G -chr6 126051355 126051356 A/G 2 5,5 0.8698,0.8054 G -chr6 126317922 126317923 C/T 2 6,3 0.8813,0.7266 C -chr6 126498670 126498671 G 1 26 0.7501 A -chr6 126524798 126524799 C/T 2 16,11 0.8845,0.8800 C -chr6 127283783 127283784 A/G 2 11,13 0.8360,0.8657 G -chr6 127432656 127432657 A/G 2 18,14 0.8929,0.8790 A -chr6 127552224 127552225 A/T 2 6,7 0.8920,0.8091 T -chr6 127772126 127772127 T 1 13 0.8741 C -chr6 127817626 127817627 G/T 2 12,19 0.8838,0.8457 T -chr6 127982200 127982201 G 1 2 0.8712 A -chr6 127984420 127984421 A/G 2 4,12 0.8545,0.8693 G -chr6 128477979 128477980 A/G 2 6,3 0.8747,0.8050 A -chr6 129269141 129269142 A/G 2 9,5 0.8352,0.8787 A -chr6 129366900 129366901 C/G 2 7,17 0.8567,0.8502 G -chr6 129628812 129628813 G/T 2 3,5 0.5731,0.7511 T -chr6 131055585 131055586 A/G 2 6,17 0.9001,0.8928 G -chr6 131714636 131714637 T 1 24 0.8636 C -chr6 132005538 132005539 A 1 9 0.8432 G -chr6 132107542 132107543 A/G 2 17,11 0.8844,0.8922 G -chr6 133002442 133002443 A/C 2 11,14 0.8186,0.8155 A -chr6 133180113 133180114 C/G 2 8,14 0.8403,0.8573 C -chr6 134417321 134417322 A 1 8 0.8485 C -chr6 134464772 134464773 A 1 4 0.8730 G -chr6 134792983 134792984 C 1 23 0.8550 T -chr6 134848564 134848565 A/G 2 19,16 0.8554,0.8499 A -chr6 135260659 135260660 A/G 2 18,24 0.8517,0.8609 G -chr6 135668850 135668851 C/T 2 7,4 0.8513,0.8684 C -chr6 135685353 135685354 A 1 2 0.9197 G -chr6 135912209 135912210 A/G 2 12,12 0.8468,0.8377 A -chr6 135969673 135969674 A/G 2 7,7 0.8729,0.8186 G -chr6 136034388 136034389 C/G 2 28,19 0.8332,0.8200 G -chr6 136099417 136099418 G 1 9 0.7748 A -chr6 136134950 136134951 A 1 3 0.7698 T -chr6 136549093 136549094 G 1 21 0.8629 A -chr6 136860204 136860205 A/G 2 9,12 0.8198,0.8482 G -chr6 137025465 137025466 G 1 10 0.8583 C -chr6 137050116 137050117 A/G 2 3,5 0.8426,0.7986 G -chr6 137588942 137588943 C/T 2 12,11 0.8769,0.9154 C -chr6 137926894 137926895 C/T 2 17,13 0.8252,0.8436 C -chr6 138287456 138287457 A/G 2 13,9 0.8411,0.8112 G -chr6 138561259 138561260 A/C 2 5,6 0.8705,0.8651 A -chr6 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-chr6 154815664 154815665 A/G 2 12,19 0.8667,0.8694 A -chr6 154825271 154825272 A/T 2 15,7 0.9097,0.8780 A -chr6 154877790 154877791 G 1 8 0.8629 A -chr6 154936312 154936313 C/T 2 11,17 0.8901,0.8833 T -chr6 155251978 155251979 A/G 2 6,10 0.8171,0.8264 G -chr6 155552687 155552688 C/T 2 10,13 0.8778,0.8766 T -chr6 155822101 155822102 T 1 7 0.8914 A -chr6 156118549 156118550 T 1 24 0.8846 C -chr6 156141802 156141803 A/G 2 13,7 0.8483,0.8080 A -chr6 156237058 156237059 C 1 21 0.8487 T -chr6 156315443 156315444 C/T 2 11,10 0.8552,0.8546 C -chr6 156435988 156435989 A 1 25 0.8525 T -chr6 156617791 156617792 A/G 2 7,5 0.8749,0.8560 A -chr6 156641516 156641517 C 1 4 0.8742 T -chr6 157284312 157284313 C/T 2 24,17 0.8081,0.8419 C -chr6 157309959 157309960 C/T 2 17,15 0.8614,0.8773 T -chr6 157734458 157734459 A/G 2 9,5 0.8174,0.8215 G -chr6 157977527 157977528 C 1 22 0.8519 T -chr6 158019568 158019569 C 1 30 0.8725 T -chr6 158237369 158237370 A/G 2 19,15 0.8277,0.8438 G -chr6 158494260 158494261 G 1 9 0.8382 A -chr6 158515706 158515707 C/T 2 16,6 0.8873,0.8748 C -chr6 158586681 158586682 C 1 19 0.8443 T -chr6 158596200 158596201 C/T 2 11,10 0.8455,0.8095 T -chr6 158822743 158822744 A/G 2 11,18 0.8752,0.8605 A -chr6 159032669 159032670 A 1 19 0.8605 C -chr6 159414898 159414899 C/T 2 7,14 0.8961,0.8684 T -chr6 159563284 159563285 C/T 2 6,3 0.8797,0.8788 C -chr6 159605827 159605828 A/C 2 19,10 0.8548,0.8793 C -chr6 159610533 159610534 C/T 2 19,18 0.8108,0.8354 T -chr6 159713535 159713536 G 1 18 0.8577 C -chr6 159720955 159720956 A 1 3 0.8698 C -chr6 159772226 159772227 A/C 2 24,21 0.8657,0.8458 C -chr6 160296611 160296612 C/T 2 18,8 0.8222,0.8702 T -chr6 160353821 160353822 T 1 14 0.8473 C -chr6 160363576 160363577 A/G 2 19,10 0.8580,0.8709 A -chr6 160525186 160525187 A/G 2 10,19 0.8165,0.8612 G -chr6 160729346 160729347 T 1 7 0.8782 G -chr6 161133684 161133685 A/G 2 3,4 0.9038,0.8529 A -chr6 161213046 161213047 C/T 2 7,4 0.8231,0.8523 T -chr6 161266374 161266375 C/T 2 3,6 0.7771,0.9254 T -chr6 161305277 161305278 C/T 2 6,7 0.8460,0.8283 C -chr6 161321587 161321588 A/C 2 10,7 0.8944,0.9084 A -chr6 161341053 161341054 A/G 2 8,21 0.8537,0.8486 G -chr6 161998692 161998693 C/T 2 12,19 0.8474,0.8723 C -chr6 162305401 162305402 C/T 2 15,12 0.8726,0.8846 C -chr6 162510796 162510797 T 1 26 0.8428 C -chr6 162583638 162583639 A/C 2 7,14 0.8508,0.8291 C -chr6 162898885 162898886 A/C 2 23,19 0.8470,0.8758 C -chr6 162928415 162928416 C/T 2 13,13 0.8390,0.8527 T -chr6 162947410 162947411 T 1 7 0.9016 C -chr6 162962844 162962845 A/G 2 3,7 0.8710,0.8618 G -chr6 163151776 163151777 C 1 12 0.8362 T -chr6 163157131 163157132 C/T 2 3,9 0.8045,0.9016 T -chr6 163254936 163254937 C/T 2 3,7 0.8714,0.8566 C -chr6 163265399 163265400 A/C 2 7,3 0.8874,0.8254 A -chr6 163759776 163759777 G/T 2 17,23 0.8198,0.8438 G -chr6 163769151 163769152 A/G 2 12,13 0.8485,0.8675 G -chr6 163908941 163908942 A/G 2 7,7 0.9018,0.8923 A -chr6 163921921 163921922 A/G 2 13,9 0.8857,0.8800 A -chr6 164655659 164655660 A/G 2 14,19 0.8354,0.8693 G -chr6 164699403 164699404 T 1 21 0.8561 A -chr6 164828838 164828839 A/T 2 12,18 0.8895,0.8818 T -chr6 165504609 165504610 A/G 2 13,6 0.8584,0.8260 A -chr6 165522784 165522785 C 1 20 0.8459 A -chr6 166142455 166142456 T 1 7 0.8970 A -chr6 166165884 166165885 C/T 2 6,8 0.8885,0.8757 C -chr6 166284442 166284443 A/G 2 19,21 0.8429,0.8193 G -chr6 166534741 166534742 A/C 2 9,12 0.9043,0.8830 A -chr6 166545377 166545378 G 1 40 0.8512 A -chr6 166747795 166747796 C/T 2 7,9 0.8469,0.8453 C -chr6 166832735 166832736 C/G 2 10,5 0.8330,0.8235 C -chr6 167333895 167333896 C/T 2 9,5 0.8910,0.9102 C -chr6 167341773 167341774 A/G 2 23,15 0.8506,0.8468 G -chr6 167419670 167419671 C/T 2 16,15 0.8669,0.8801 T -chr6 167562968 167562969 C/T 2 15,17 0.8829,0.8578 T -chr6 167691797 167691798 A 1 32 0.8694 G -chr6 167719353 167719354 C/T 2 5,12 0.8466,0.8569 C -chr6 168095846 168095847 G 1 3 0.7830 A -chr6 168348154 168348155 A/G 2 6,3 0.8960,0.9020 A -chr6 168480543 168480544 T 1 3 0.8584 C -chr6 168648435 168648436 T 1 10 0.8693 C -chr6 168721220 168721221 A 1 20 0.8333 G -chr6 168782995 168782996 C/T 2 12,7 0.8342,0.8253 C -chr6 168939749 168939750 A/G 2 12,16 0.8615,0.8985 G -chr6 169355794 169355795 A/G 2 13,17 0.8542,0.8501 G -chr6 169784466 169784467 A 1 4 0.8780 G -chr6 170455574 170455575 A/G 2 8,8 0.8408,0.8242 G -chr6 170587305 170587306 C 1 15 0.8620 A -chr6 170595429 170595430 C 1 11 0.8779 G -chr6 170719668 170719669 C/T 2 10,18 0.8531,0.8850 T -chr6 170781530 170781531 G 1 23 0.8477 C -chr7 102450 102451 T 1 25 0.8620 G -chr7 124276 124277 G/T 2 13,5 0.8427,0.8955 G -chr7 652658 652659 C 1 18 0.8448 T -chr7 1842753 1842754 G 1 19 0.8880 A -chr7 2153540 2153541 A/G 2 12,6 0.9029,0.9168 G -chr7 2200972 2200973 T 1 6 0.8245 C -chr7 2261467 2261468 A/G 2 10,8 0.8406,0.8643 G -chr7 2705265 2705266 G 1 11 0.8893 A -chr7 3387047 3387048 G 1 33 0.8759 C -chr7 3544919 3544920 A 1 3 0.7593 C -chr7 3861547 3861548 C/G 2 7,10 0.8291,0.8337 C -chr7 3882331 3882332 A/C 2 8,9 0.8593,0.8460 C -chr7 4453381 4453382 A/G 2 14,5 0.8985,0.8857 A -chr7 4692260 4692261 G/T 2 10,9 0.8249,0.8342 T -chr7 4962687 4962688 A 1 33 0.8140 G -chr7 5148819 5148820 G 1 35 0.8852 A -chr7 5486081 5486082 G 1 15 0.8783 A -chr7 5538211 5538212 T 1 7 0.8148 G -chr7 5816851 5816852 C/G 2 13,10 0.8751,0.8428 C -chr7 5868462 5868463 C/T 2 4,4 0.8842,0.8587 C -chr7 6199634 6199635 A 1 14 0.8218 G -chr7 6394190 6394191 C 1 10 0.8506 T -chr7 6431295 6431296 A/G 2 10,8 0.8579,0.8410 A -chr7 7133154 7133155 T 1 12 0.8850 G -chr7 7170775 7170776 A/G 2 7,10 0.8604,0.8632 G -chr7 7902348 7902349 G 1 18 0.8796 C -chr7 8374930 8374931 G/T 2 12,10 0.8703,0.8637 T -chr7 8548620 8548621 A 1 11 0.8719 G -chr7 8706086 8706087 G 1 31 0.8564 A -chr7 9543074 9543075 A/G 2 5,12 0.8460,0.8561 G -chr7 9700424 9700425 C 1 39 0.8804 T -chr7 10099271 10099272 A/C 2 5,8 0.8762,0.8776 A -chr7 10574018 10574019 C 1 5 0.8738 T -chr7 10895413 10895414 C/T 2 4,3 0.8764,0.8383 C -chr7 10899369 10899370 A/G 2 12,16 0.8662,0.7996 A -chr7 11008220 11008221 G 1 25 0.8651 A -chr7 11371571 11371572 C/G 2 10,15 0.8871,0.8539 G -chr7 11460950 11460951 A/G 2 5,8 0.9256,0.9026 G -chr7 11473560 11473561 A/G 2 17,13 0.8488,0.8570 G -chr7 11551804 11551805 G 1 2 0.9563 A -chr7 11577647 11577648 C/G 2 17,13 0.8454,0.8584 C -chr7 11926515 11926516 A/T 2 11,9 0.8753,0.8861 T -chr7 11930908 11930909 T 1 11 0.8938 C -chr7 12133936 12133937 G/T 2 7,14 0.8400,0.8659 G -chr7 12220152 12220153 A/T 2 11,21 0.8545,0.8691 T -chr7 12263233 12263234 T 1 35 0.8231 C -chr7 12400709 12400710 A/C 2 10,9 0.8671,0.8432 C -chr7 12633910 12633911 C/G 2 8,10 0.8505,0.8322 G -chr7 12701459 12701460 A 1 4 0.8568 C -chr7 13049520 13049521 C/T 2 4,3 0.8313,0.8154 C -chr7 13054901 13054902 G/T 2 7,15 0.8292,0.8716 T -chr7 13434228 13434229 C/T 2 16,6 0.8901,0.8840 C -chr7 13757128 13757129 T 1 5 0.8103 A -chr7 14068173 14068174 A/C 2 8,10 0.8655,0.8646 C -chr7 14668099 14668100 A/G 2 17,9 0.8294,0.8273 A -chr7 14878544 14878545 T 1 3 0.9097 C -chr7 15223116 15223117 T 1 21 0.8410 C -chr7 15417629 15417630 C/T 2 12,18 0.7998,0.8048 T -chr7 15623080 15623081 C/G 2 9,12 0.8396,0.8398 C -chr7 15838346 15838347 C/T 2 3,6 0.9049,0.8872 T -chr7 15886269 15886270 C/T 2 4,4 0.8308,0.8097 C -chr7 15979021 15979022 A/G 2 9,9 0.8693,0.8806 A -chr7 16249812 16249813 C/T 2 5,8 0.8849,0.8771 T -chr7 16473830 16473831 A/C 2 10,14 0.8480,0.8568 C -chr7 16571972 16571973 A/G 2 9,5 0.8728,0.8323 A -chr7 16766930 16766931 C/T 2 11,10 0.8405,0.8794 C -chr7 17270821 17270822 C/T 2 18,17 0.8612,0.8705 C -chr7 17601249 17601250 G 1 12 0.8359 A -chr7 17764374 17764375 C 1 4 0.8229 A -chr7 17960826 17960827 A/T 2 10,21 0.8693,0.8579 T -chr7 18044209 18044210 C/G 2 10,11 0.8451,0.8833 G -chr7 19086657 19086658 C/G 2 3,5 0.9247,0.8357 G -chr7 19240383 19240384 T 1 11 0.8656 C -chr7 19381418 19381419 A/G 2 12,6 0.8657,0.8578 G -chr7 22078499 22078500 C/T 2 11,10 0.8560,0.8473 T -chr7 22295359 22295360 A/G 2 7,6 0.8965,0.8760 A -chr7 23145288 23145289 A/G 2 3,4 0.8723,0.8709 G -chr7 23223838 23223839 C/T 2 9,10 0.8870,0.8899 T -chr7 23357828 23357829 A/G 2 15,17 0.8353,0.8379 G -chr7 23392270 23392271 C 1 22 0.7918 T -chr7 24050042 24050043 A/C 2 16,21 0.8357,0.8325 C -chr7 24416304 24416305 A/G 2 28,13 0.8541,0.8472 G -chr7 24600382 24600383 C/T 2 11,12 0.8542,0.8393 C -chr7 25208327 25208328 G/T 2 6,5 0.8965,0.8462 G -chr7 26133434 26133435 C/T 2 7,9 0.8379,0.8386 C -chr7 26134758 26134759 A/C 2 16,18 0.8395,0.8523 A -chr7 26196818 26196819 A 1 16 0.8199 G -chr7 26541923 26541924 C 1 38 0.8363 T -chr7 26589888 26589889 A 1 10 0.8734 G -chr7 26645071 26645072 G/T 2 12,17 0.8496,0.8243 T -chr7 27358451 27358452 A/G 2 7,8 0.8678,0.8858 A -chr7 28110018 28110019 C/G 2 17,11 0.8906,0.8586 C -chr7 28310468 28310469 G 1 10 0.8619 A -chr7 28689586 28689587 G 1 24 0.8505 A -chr7 28775342 28775343 A 1 7 0.8483 T -chr7 29536291 29536292 A 1 10 0.7779 T -chr7 29567392 29567393 C 1 37 0.8683 G -chr7 29683761 29683762 G/T 2 4,14 0.8833,0.8371 T -chr7 30180408 30180409 G 1 28 0.8614 A -chr7 31334525 31334526 A/T 2 9,6 0.8145,0.8241 A -chr7 32098934 32098935 C/T 2 10,6 0.8217,0.8041 C -chr7 32280814 32280815 A/G 2 10,17 0.8651,0.8758 G -chr7 32364603 32364604 A/G 2 18,13 0.8795,0.8561 G -chr7 32604221 32604222 A/G 2 8,18 0.8473,0.8581 A -chr7 32894330 32894331 T 1 7 0.8280 G -chr7 33183158 33183159 C/T 2 6,5 0.8776,0.9015 C -chr7 33527553 33527554 A 1 19 0.8426 C -chr7 33848365 33848366 A/G 2 4,6 0.8879,0.8919 G -chr7 34926258 34926259 C/T 2 9,16 0.8860,0.8740 C -chr7 35042640 35042641 A/C 2 2,3 0.8051,0.8794 C -chr7 35322461 35322462 C 1 19 0.8492 T -chr7 35421612 35421613 G 1 5 0.7511 A -chr7 35467069 35467070 C/T 2 12,17 0.8591,0.8569 C -chr7 35595821 35595822 T 1 17 0.8408 C -chr7 35596240 35596241 A/G 2 9,12 0.8792,0.8636 G -chr7 36602295 36602296 C 1 27 0.8558 G -chr7 36696573 36696574 A/G 2 14,17 0.8743,0.8336 G -chr7 36706967 36706968 T 1 32 0.8611 C -chr7 36721031 36721032 T 1 16 0.8619 C -chr7 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 0.8440,0.8397 T -chr7 41691875 41691876 C 1 19 0.8693 A -chr7 41813930 41813931 G 1 15 0.8700 A -chr7 42724094 42724095 G 1 14 0.8629 A -chr7 42866524 42866525 C 1 22 0.8464 T -chr7 43075374 43075375 C 1 17 0.8462 T -chr7 44585051 44585052 C 1 5 0.9119 T -chr7 44890982 44890983 A/G 2 8,22 0.8998,0.8666 G -chr7 45932668 45932669 G 1 36 0.8649 A -chr7 46022166 46022167 A/G 2 4,5 0.8578,0.8431 A -chr7 46045428 46045429 C 1 4 0.8942 T -chr7 46113669 46113670 C/T 2 25,22 0.8508,0.8338 C -chr7 46210927 46210928 A/G 2 20,13 0.8746,0.8862 A -chr7 46344626 46344627 A/G 2 11,7 0.7717,0.7814 A -chr7 46612608 46612609 C/T 2 16,7 0.8333,0.8799 C -chr7 46736235 46736236 C/T 2 22,16 0.8675,0.8726 T -chr7 47189518 47189519 G 1 24 0.8545 C -chr7 47469691 47469692 A 1 12 0.8546 G -chr7 47678871 47678872 G/T 2 13,16 0.8143,0.7873 T -chr7 48281177 48281178 C/T 2 16,10 0.8405,0.8669 C -chr7 49160302 49160303 A 1 23 0.8569 G -chr7 49480762 49480763 C/T 2 20,22 0.8555,0.8609 T -chr7 49783327 49783328 C/T 2 12,11 0.8778,0.8478 C -chr7 50002727 50002728 A 1 3 0.8871 G -chr7 50566670 50566671 A/G 2 13,22 0.8804,0.8536 G -chr7 50841993 50841994 A/G 2 11,8 0.8710,0.8740 G -chr7 51018801 51018802 G/T 2 6,6 0.8704,0.8367 G -chr7 51123821 51123822 G 1 10 0.8712 C -chr7 51306417 51306418 G 1 5 0.9015 A -chr7 51413455 51413456 A 1 14 0.8730 G -chr7 51562141 51562142 A 1 28 0.8481 G -chr7 51929596 51929597 C 1 27 0.8269 T -chr7 52069540 52069541 C 1 36 0.8620 T -chr7 52076059 52076060 A/G 2 7,7 0.8312,0.8700 A -chr7 52164272 52164273 G/T 2 15,14 0.8350,0.8238 G -chr7 52223510 52223511 C 1 15 0.8928 T -chr7 52389629 52389630 G 1 21 0.8416 C -chr7 52450193 52450194 C/T 2 29,15 0.8379,0.8310 C -chr7 52468998 52468999 A 1 22 0.8587 G -chr7 52660131 52660132 C/G 2 15,4 0.8668,0.8791 G -chr7 52908649 52908650 C/T 2 5,4 0.8312,0.8508 T -chr7 52987533 52987534 A 1 15 0.8405 G -chr7 53103553 53103554 G 1 9 0.8163 C -chr7 53196399 53196400 C/T 2 3,3 0.8770,0.7603 C -chr7 53339220 53339221 C 1 17 0.8477 T -chr7 53455602 53455603 A 1 21 0.8721 G -chr7 53584606 53584607 C 1 3 0.8319 T -chr7 54140522 54140523 A/G 2 16,16 0.8180,0.8479 G -chr7 54318258 54318259 C/G 2 3,4 0.7930,0.8497 G -chr7 54448415 54448416 C/T 2 9,4 0.8542,0.8660 C -chr7 54736639 54736640 C/T 2 12,12 0.8994,0.9097 T -chr7 54759765 54759766 G 1 9 0.7701 A -chr7 54905349 54905350 C/T 2 10,7 0.8868,0.8725 T -chr7 55169784 55169785 C/G 2 15,20 0.8572,0.8560 G -chr7 55255527 55255528 G 1 6 0.8617 A -chr7 55306098 55306099 A/C 2 11,8 0.8253,0.8209 C -chr7 55400333 55400334 T 1 24 0.8310 C -chr7 55475079 55475080 T 1 23 0.8275 C -chr7 55554214 55554215 G 1 27 0.8462 C -chr7 55724988 55724989 A/G 2 12,13 0.8735,0.8551 G -chr7 57715746 57715747 C/T 2 13,19 0.8158,0.8367 T -chr7 57800874 57800875 A 1 3 0.9110 G -chr7 57805093 57805094 C/T 2 4,8 0.7433,0.8275 T -chr7 57866416 57866417 C/T 2 3,4 0.9135,0.9282 T -chr7 57990109 57990110 A/C 2 7,10 0.8290,0.8096 C -chr7 61055321 61055322 C/T 2 40,18 0.8470,0.8431 C -chr7 61756164 61756165 C 1 51 0.7853 A -chr7 61782821 61782822 C/G 2 10,24 0.8341,0.8493 G -chr7 61784272 61784273 A/G 2 60,18 0.8443,0.8244 A -chr7 61790300 61790301 G/T 2 17,18 0.7904,0.8078 T -chr7 61871639 61871640 A 1 11 0.8687 G -chr7 61878999 61879000 C/T 2 18,8 0.8674,0.7902 C -chr7 61971556 61971557 C/T 2 8,5 0.8757,0.8700 C -chr7 61977255 61977256 C/T 2 4,11 0.8733,0.8557 C -chr7 62052672 62052673 G/T 2 5,7 0.8537,0.8729 T -chr7 62177098 62177099 G 1 19 0.8694 A -chr7 62509875 62509876 A/G 2 24,12 0.8831,0.8908 A -chr7 63112586 63112587 C 1 11 0.8448 T -chr7 63566814 63566815 A/G 2 8,16 0.8494,0.8567 G -chr7 63815358 63815359 T 1 19 0.8048 C -chr7 64166824 64166825 A/G 2 10,12 0.8652,0.8586 G -chr7 64448290 64448291 T 1 22 0.8232 C -chr7 65266054 65266055 G/T 2 16,13 0.8654,0.8822 G -chr7 66827405 66827406 A/G 2 15,12 0.8328,0.8222 G -chr7 66898108 66898109 T 1 11 0.8629 G -chr7 67104712 67104713 C 1 5 0.8693 G -chr7 67218020 67218021 A/G 2 3,4 0.8158,0.8074 A -chr7 67356815 67356816 A/C 2 18,11 0.8809,0.8615 A -chr7 67512324 67512325 A 1 12 0.8907 T -chr7 67697143 67697144 A/G 2 12,10 0.8702,0.8656 A -chr7 68343236 68343237 C 1 7 0.8001 T -chr7 68505468 68505469 C/T 2 14,14 0.8894,0.9005 T -chr7 68751894 68751895 A 1 29 0.8451 C -chr7 69373186 69373187 A/G 2 5,8 0.8483,0.7967 G -chr7 69682575 69682576 A/G 2 17,12 0.8634,0.8509 A -chr7 69722058 69722059 C/T 2 14,16 0.8595,0.8651 C -chr7 69942583 69942584 A/G 2 18,22 0.8813,0.8574 G -chr7 69946083 69946084 A 1 26 0.8199 G -chr7 70434659 70434660 C 1 35 0.8572 A -chr7 70543456 70543457 G 1 23 0.8329 A -chr7 70761808 70761809 A/C 2 5,4 0.8345,0.8654 A -chr7 72224051 72224052 C/T 2 10,10 0.8261,0.8368 C -chr7 72988068 72988069 C/T 2 11,6 0.8457,0.8659 C -chr7 73136141 73136142 A/C 2 4,12 0.8136,0.8323 C -chr7 73751837 73751838 T 1 5 0.8020 G -chr7 75264343 75264344 G 1 22 0.8654 A -chr7 75426361 75426362 A/T 2 4,9 0.8449,0.8602 A -chr7 75775957 75775958 A/C 2 5,3 0.8809,0.7617 A -chr7 75986093 75986094 C/G 2 13,21 0.8105,0.8223 G -chr7 77113700 77113701 A 1 32 0.8665 T -chr7 77730140 77730141 A 1 18 0.8448 G -chr7 77960228 77960229 C/T 2 17,21 0.8587,0.8710 C -chr7 77980234 77980235 C/G 2 3,6 0.7597,0.7631 G -chr7 78028377 78028378 A/T 2 15,10 0.8070,0.8213 T -chr7 78249293 78249294 C 1 19 0.8617 T -chr7 78401199 78401200 T 1 24 0.8560 G -chr7 78801464 78801465 G/T 2 15,19 0.8186,0.8148 T -chr7 79350509 79350510 C 1 15 0.8823 G -chr7 79377163 79377164 T 1 3 0.8372 A -chr7 79466730 79466731 C/G 2 14,6 0.8581,0.8312 C -chr7 80102151 80102152 A/T 2 11,14 0.8516,0.8782 A -chr7 80238116 80238117 A/C 2 11,17 0.8449,0.8425 C -chr7 81099183 81099184 C/T 2 10,16 0.6587,0.7250 T -chr7 81117607 81117608 C/G 2 8,4 0.8234,0.7442 C -chr7 81567118 81567119 A/C 2 7,8 0.8574,0.8818 C -chr7 81616000 81616001 A/G 2 16,10 0.8348,0.8184 A -chr7 81725372 81725373 A/G 2 8,9 0.8383,0.8549 G -chr7 81877687 81877688 A/G 2 11,7 0.8728,0.9005 A -chr7 82515875 82515876 A/C 2 5,8 0.8707,0.9016 A -chr7 83248205 83248206 T 1 15 0.8218 C -chr7 83595304 83595305 A/G 2 8,3 0.8633,0.8226 G -chr7 83786843 83786844 C/G 2 8,9 0.8141,0.8516 G -chr7 83884704 83884705 C/T 2 16,7 0.8567,0.8890 C -chr7 84088719 84088720 C/G 2 13,11 0.8404,0.8590 G -chr7 84187075 84187076 C 1 11 0.7838 T -chr7 84326169 84326170 A/G 2 7,10 0.8197,0.8368 G -chr7 84437921 84437922 A/G 2 7,14 0.8780,0.8744 G -chr7 84460926 84460927 A/G 2 10,20 0.8324,0.8435 G -chr7 84542155 84542156 C/T 2 12,12 0.8278,0.8631 T -chr7 84872364 84872365 C/T 2 11,14 0.8499,0.8686 C -chr7 85025568 85025569 C/T 2 23,21 0.8149,0.8199 C -chr7 85111666 85111667 T 1 9 0.8908 G -chr7 85293810 85293811 C 1 16 0.8647 T -chr7 85301896 85301897 G 1 6 0.8601 A -chr7 85825962 85825963 C 1 2 0.9510 T -chr7 86066601 86066602 A/G 2 4,10 0.8178,0.8551 G -chr7 86351216 86351217 C/T 2 16,19 0.8574,0.8682 T -chr7 86985567 86985568 C 1 25 0.8765 T -chr7 87098103 87098104 G 1 4 0.8978 A -chr7 87204904 87204905 T 1 30 0.8856 C -chr7 87411529 87411530 C/T 2 10,12 0.8618,0.8728 C -chr7 88354800 88354801 A/G 2 15,13 0.8550,0.8549 G -chr7 88402484 88402485 G 1 35 0.8734 A -chr7 88469359 88469360 C/T 2 13,18 0.8559,0.8441 T -chr7 88554874 88554875 G 1 43 0.8622 A -chr7 88969882 88969883 A/G 2 13,19 0.8635,0.8468 A -chr7 89432924 89432925 C 1 25 0.8637 T -chr7 89435249 89435250 C/T 2 12,4 0.8667,0.8672 T -chr7 89734103 89734104 A/G 2 12,15 0.8884,0.8661 G -chr7 91116722 91116723 C/T 2 17,24 0.8399,0.8552 T -chr7 91768614 91768615 A 1 18 0.8134 G -chr7 91952587 91952588 A/G 2 4,8 0.8471,0.8645 A -chr7 92095825 92095826 A/G 2 16,28 0.8696,0.8333 A -chr7 92103734 92103735 G/T 2 5,4 0.8510,0.7904 G -chr7 92131028 92131029 A/G 2 13,9 0.8574,0.8638 A -chr7 92759461 92759462 A/G 2 19,15 0.8734,0.8795 A -chr7 93005067 93005068 A 1 22 0.8725 T -chr7 93034746 93034747 G/T 2 13,8 0.8702,0.9143 T -chr7 93230165 93230166 A/G 2 4,5 0.9068,0.8338 G -chr7 93230496 93230497 C 1 19 0.8244 T -chr7 93364652 93364653 C/T 2 10,11 0.8715,0.8896 T -chr7 93365707 93365708 A/G 2 10,5 0.8600,0.9030 A -chr7 93414679 93414680 T 1 37 0.8344 G -chr7 93618625 93618626 A 1 13 0.8499 G -chr7 93815903 93815904 C/T 2 11,9 0.8445,0.8658 T -chr7 94261017 94261018 A/G 2 15,7 0.8396,0.8216 G -chr7 95438636 95438637 G/T 2 22,9 0.8749,0.8630 G -chr7 95622762 95622763 A 1 42 0.8645 G -chr7 95677804 95677805 C/T 2 10,14 0.9135,0.8438 C -chr7 96370867 96370868 A/C 2 13,20 0.8557,0.8415 C -chr7 96929255 96929256 A/G 2 10,20 0.8891,0.8633 G -chr7 97490927 97490928 C 1 11 0.8543 T -chr7 97506375 97506376 T 1 3 0.9079 C -chr7 98005537 98005538 G 1 11 0.8593 A -chr7 98618052 98618053 C/T 2 15,17 0.8764,0.8782 C -chr7 98961737 98961738 C/T 2 9,5 0.8691,0.8494 C -chr7 99675658 99675659 G/T 2 9,8 0.8641,0.8805 T -chr7 100457355 100457356 A/G 2 13,10 0.8947,0.8973 A -chr7 100550888 100550889 A/G 2 5,3 0.8763,0.8760 G -chr7 100680369 100680370 T 1 3 0.8480 C -chr7 101005925 101005926 C 1 8 0.8766 G -chr7 101103000 101103001 C/G 2 12,6 0.8839,0.8867 C -chr7 101129729 101129730 C/T 2 5,3 0.8496,0.8571 C -chr7 101339318 101339319 C 1 3 0.8585 A -chr7 101549006 101549007 A 1 24 0.8697 G -chr7 101586337 101586338 A/C 2 10,14 0.7809,0.8151 C -chr7 101700891 101700892 A 1 4 0.8537 G -chr7 101870479 101870480 A/C 2 8,6 0.8217,0.8551 A -chr7 102905689 102905690 C/T 2 7,6 0.8693,0.8826 C -chr7 103094407 103094408 A/G 2 6,5 0.8352,0.8103 G -chr7 103362483 103362484 C 1 27 0.8286 T -chr7 103586189 103586190 T 1 22 0.8648 C -chr7 104014983 104014984 G 1 10 0.8662 A -chr7 104028508 104028509 A/G 2 11,15 0.8488,0.8715 G -chr7 104156889 104156890 G 1 6 0.7775 A -chr7 104417275 104417276 C 1 20 0.8789 T -chr7 104691540 104691541 C 1 5 0.8632 T -chr7 104951836 104951837 A 1 3 0.7882 G -chr7 105875655 105875656 C 1 18 0.8570 T -chr7 106018493 106018494 G 1 21 0.8440 A -chr7 106129203 106129204 A/T 2 3,11 0.9220,0.8894 T -chr7 106639517 106639518 T 1 16 0.8291 C -chr7 107245132 107245133 G 1 4 0.8233 T -chr7 107283108 107283109 A/T 2 16,22 0.8583,0.8630 T -chr7 108270117 108270118 C 1 19 0.8517 T -chr7 108587028 108587029 C/T 2 4,8 0.8576,0.8478 C -chr7 108748624 108748625 G 1 9 0.8275 T -chr7 108840649 108840650 A/G 2 18,12 0.8757,0.8650 A -chr7 108908817 108908818 A/T 2 11,22 0.8593,0.8494 T -chr7 109085009 109085010 G 1 13 0.8221 T -chr7 109237803 109237804 T 1 9 0.8628 C -chr7 109693781 109693782 C 1 3 0.8903 A -chr7 109930337 109930338 A/G 2 11,8 0.8144,0.8135 A -chr7 109939206 109939207 C/G 2 7,5 0.8586,0.8792 C -chr7 109939319 109939320 A/G 2 8,6 0.7981,0.8568 A -chr7 109978464 109978465 A 1 4 0.8404 C -chr7 110011496 110011497 C/T 2 3,9 0.7858,0.8658 T -chr7 110901585 110901586 C/T 2 9,10 0.8731,0.8470 T -chr7 111763090 111763091 C/T 2 14,16 0.8769,0.8814 C -chr7 111813120 111813121 A/C 2 19,9 0.8840,0.8790 A -chr7 112137675 112137676 C 1 21 0.8307 T -chr7 112766081 112766082 A/G 2 13,11 0.8753,0.8667 A -chr7 113291872 113291873 T 1 37 0.8325 A -chr7 113322648 113322649 C/T 2 13,6 0.8646,0.8914 C -chr7 114367236 114367237 C 1 26 0.8605 A -chr7 115296243 115296244 A/C 2 9,11 0.8569,0.8202 C -chr7 115529244 115529245 G 1 8 0.8720 A -chr7 115705391 115705392 T 1 37 0.8589 G -chr7 115796253 115796254 A/G 2 15,17 0.8677,0.8774 G -chr7 115814741 115814742 C/T 2 14,8 0.8637,0.8659 C -chr7 115821379 115821380 C/G 2 6,8 0.8752,0.8366 C -chr7 116095005 116095006 A/G 2 14,11 0.8317,0.8663 A -chr7 116180849 116180850 A/C 2 13,7 0.8537,0.8325 C -chr7 116193704 116193705 A 1 13 0.8282 C -chr7 116282320 116282321 C 1 26 0.7990 T -chr7 117918346 117918347 A 1 19 0.8729 G -chr7 118082757 118082758 A 1 12 0.8636 G -chr7 118700084 118700085 A/T 2 12,17 0.8687,0.8697 T -chr7 118847502 118847503 A/G 2 6,10 0.8460,0.8715 G -chr7 118922597 118922598 C/T 2 3,6 0.7685,0.7965 T -chr7 119235089 119235090 C/G 2 11,11 0.8730,0.8592 G -chr7 119299156 119299157 A/G 2 10,11 0.8810,0.8637 G -chr7 119588746 119588747 G/T 2 13,5 0.7751,0.8015 T -chr7 120908821 120908822 A/G 2 11,10 0.8363,0.8490 G -chr7 120994672 120994673 C/T 2 9,14 0.8561,0.8160 T -chr7 121172354 121172355 A/C 2 6,15 0.8458,0.8552 A -chr7 121434597 121434598 C/T 2 3,4 0.8985,0.8884 C -chr7 121927774 121927775 A/G 2 18,12 0.8423,0.8519 A -chr7 122616641 122616642 A/T 2 11,22 0.8568,0.8535 T -chr7 122981617 122981618 G/T 2 5,7 0.8409,0.8686 T -chr7 123977174 123977175 G/T 2 8,10 0.8168,0.8565 T -chr7 124118262 124118263 G 1 6 0.8217 C -chr7 124379765 124379766 A/G 2 10,16 0.8661,0.8477 A -chr7 124532715 124532716 C/T 2 14,10 0.8558,0.8357 C -chr7 124540534 124540535 C/T 2 13,13 0.8272,0.8639 T -chr7 124640879 124640880 A/G 2 7,12 0.8610,0.8444 G -chr7 124713157 124713158 A/C 2 14,16 0.8264,0.8440 A -chr7 125105193 125105194 C/T 2 10,4 0.8724,0.8836 T -chr7 125318825 125318826 A/G 2 13,11 0.7950,0.7988 A -chr7 125330237 125330238 A/G 2 3,3 0.8838,0.8829 G -chr7 125356576 125356577 C/G 2 10,6 0.8685,0.8812 C -chr7 125397572 125397573 C/T 2 14,19 0.8680,0.8605 T -chr7 125463608 125463609 T 1 31 0.8739 A -chr7 125508146 125508147 C 1 34 0.8679 T -chr7 125713309 125713310 T 1 10 0.8157 C -chr7 125769502 125769503 G 1 4 0.8440 A -chr7 125777230 125777231 G 1 19 0.8622 A -chr7 125891154 125891155 C/T 2 11,14 0.8651,0.8738 T -chr7 126333115 126333116 T 1 21 0.8186 A -chr7 126697744 126697745 C/T 2 19,6 0.8742,0.8862 T -chr7 126986134 126986135 G 1 14 0.8517 C -chr7 127249097 127249098 C/T 2 7,8 0.8807,0.8086 C -chr7 127505576 127505577 C/T 2 17,7 0.8618,0.8334 C -chr7 127877783 127877784 A/G 2 7,5 0.8854,0.8704 A -chr7 128339293 128339294 A/C 2 6,3 0.7781,0.8016 C -chr7 130133152 130133153 C/T 2 10,9 0.8350,0.8113 T -chr7 130336138 130336139 C/T 2 5,3 0.9022,0.7939 C -chr7 130451670 130451671 A 1 2 0.9154 G -chr7 130565361 130565362 C/T 2 5,10 0.8760,0.8705 T -chr7 130743942 130743943 G 1 13 0.8585 A -chr7 130767581 130767582 A/G 2 9,8 0.8495,0.8832 G -chr7 130937473 130937474 C 1 30 0.8658 T -chr7 131039633 131039634 T 1 6 0.8318 C -chr7 131703335 131703336 C 1 4 0.8647 T -chr7 132014657 132014658 C 1 17 0.8774 T -chr7 133147073 133147074 G/T 2 13,22 0.8838,0.8835 T -chr7 133293803 133293804 A/C 2 12,20 0.8576,0.8760 C -chr7 133372864 133372865 C 1 9 0.8327 T -chr7 133570724 133570725 A 1 39 0.8707 T -chr7 133743040 133743041 G/T 2 19,11 0.8714,0.8858 G -chr7 133828020 133828021 A/G 2 18,13 0.8327,0.8577 G -chr7 133840014 133840015 A/C 2 14,9 0.8097,0.8619 A -chr7 134010670 134010671 C/T 2 25,16 0.8817,0.8636 T -chr7 134038637 134038638 C/T 2 19,16 0.8297,0.8306 C -chr7 134290790 134290791 T 1 3 0.8861 C -chr7 134497704 134497705 C/G 2 18,19 0.8678,0.8591 C -chr7 134816340 134816341 G/T 2 7,9 0.8490,0.8091 T -chr7 134849279 134849280 A 1 29 0.8628 T -chr7 135280031 135280032 G/T 2 13,10 0.8815,0.8593 T -chr7 135619033 135619034 C/T 2 19,21 0.8712,0.8633 T -chr7 136292346 136292347 C/T 2 10,22 0.8815,0.8599 T -chr7 136417171 136417172 G 1 11 0.8732 T -chr7 136418348 136418349 A 1 13 0.8662 G -chr7 136819400 136819401 A/C 2 7,4 0.8894,0.7810 A -chr7 137084996 137084997 A 1 15 0.8698 G -chr7 137215836 137215837 A/T 2 11,24 0.8435,0.8556 A -chr7 137794781 137794782 A/G 2 7,3 0.8421,0.7683 A -chr7 137918783 137918784 C/T 2 11,14 0.8621,0.8563 T -chr7 138421075 138421076 A/G 2 8,11 0.8318,0.8226 A -chr7 138561259 138561260 G 1 6 0.8649 A -chr7 139994132 139994133 A/G 2 13,5 0.8649,0.8769 G -chr7 141831660 141831661 G 1 29 0.8639 A -chr7 142187130 142187131 A 1 13 0.8838 C -chr7 142129340 142129341 C/T 2 9,6 0.8943,0.8491 G -chr7 142429103 142429104 A/G 2 3,8 0.8395,0.8273 G -chr7 142817551 142817552 C/G 2 8,10 0.8263,0.8111 C -chr7 143727849 143727850 G 1 20 0.8764 A -chr7 143746577 143746578 C/T 2 11,18 0.8576,0.8177 C -chr7 144485000 144485001 G/T 2 3,4 0.8144,0.7741 T -chr7 145160356 145160357 A 1 12 0.8165 G -chr7 145348709 145348710 T 1 8 0.8158 A -chr7 145434236 145434237 C/T 2 23,19 0.8684,0.8776 C -chr7 145468562 145468563 A/G 2 16,8 0.7781,0.7533 A -chr7 145494665 145494666 A/G 2 13,9 0.8354,0.8241 A -chr7 145515918 145515919 A/G 2 3,2 0.9056,0.9278 A -chr7 145749942 145749943 C/T 2 13,16 0.8925,0.8852 C -chr7 146027701 146027702 A/G 2 12,8 0.8227,0.8323 A -chr7 146216087 146216088 C 1 30 0.8757 T -chr7 146223305 146223306 G 1 17 0.8555 A -chr7 146481857 146481858 A/G 2 4,6 0.8231,0.8417 G -chr7 146808976 146808977 G/T 2 8,17 0.8016,0.8310 T -chr7 147159214 147159215 G 1 22 0.8741 A -chr7 147185966 147185967 C/T 2 21,18 0.8494,0.8188 C -chr7 147193814 147193815 A 1 25 0.8466 T -chr7 147392445 147392446 T 1 18 0.8447 A -chr7 147581160 147581161 C/T 2 20,18 0.8541,0.8550 T -chr7 147919634 147919635 T 1 3 0.8573 G -chr7 148163660 148163661 C/G 2 15,13 0.8502,0.8204 C -chr7 148246163 148246164 G/T 2 14,17 0.8370,0.8587 T -chr7 148313458 148313459 C/T 2 8,13 0.8921,0.8970 T -chr7 148440741 148440742 C/T 2 3,4 0.8815,0.8683 T -chr7 149322875 149322876 C 1 15 0.9017 T -chr7 149700860 149700861 G/T 2 34,25 0.8906,0.8934 G -chr7 151558713 151558714 C/G 2 6,6 0.8632,0.8345 G -chr7 151747426 151747427 A 1 9 0.8430 T -chr7 152036803 152036804 C 1 10 0.8961 T -chr7 152099760 152099761 A/T 2 22,67 0.8813,0.8665 A -chr7 152210459 152210460 A/G 2 4,8 0.8720,0.8392 G -chr7 152261843 152261844 C/T 2 20,20 0.8605,0.8594 T -chr7 152263476 152263477 C 1 7 0.8831 T -chr7 152432948 152432949 A 1 26 0.8140 C -chr7 152712217 152712218 A/G 2 15,16 0.8795,0.8657 G -chr7 152822115 152822116 A 1 25 0.8911 T -chr7 153018681 153018682 T 1 35 0.8620 A -chr7 153103741 153103742 C/T 2 15,10 0.8451,0.8418 C -chr7 153158187 153158188 A 1 20 0.7535 T -chr7 153281660 153281661 C/T 2 10,7 0.8799,0.8524 C -chr7 153545473 153545474 A/C 2 15,8 0.8784,0.8860 C -chr7 153554572 153554573 C/G 2 15,15 0.8530,0.8644 G -chr7 153645098 153645099 G 1 24 0.8772 A -chr7 154004141 154004142 A/G 2 18,18 0.8064,0.8045 A -chr7 154018163 154018164 A/G 2 18,17 0.8650,0.8747 G -chr7 154085728 154085729 T 1 19 0.8951 C -chr7 154187692 154187693 A/T 2 16,12 0.8362,0.8150 A -chr7 154541090 154541091 G 1 6 0.8748 A -chr7 154625859 154625860 C/T 2 9,16 0.8137,0.8461 C -chr7 154685611 154685612 T 1 14 0.8502 G -chr7 154779240 154779241 G/T 2 19,16 0.8179,0.8393 T -chr7 154999107 154999108 A 1 10 0.8442 G -chr7 155149073 155149074 T 1 24 0.8368 C -chr7 155248528 155248529 C/T 2 7,8 0.8693,0.8316 C -chr7 155494555 155494556 A 1 3 0.9386 G -chr7 155634075 155634076 C/T 2 8,13 0.8569,0.8643 C -chr7 156041418 156041419 A/G 2 20,21 0.8745,0.8751 A -chr7 156242109 156242110 G 1 15 0.8532 T -chr7 156269197 156269198 C/T 2 9,11 0.8290,0.8538 C -chr7 156562303 156562304 C 1 24 0.8018 T -chr7 156658140 156658141 C/G 2 8,16 0.8732,0.8633 G -chr7 156761817 156761818 A/G 2 18,15 0.8435,0.8628 G -chr7 157087918 157087919 G/T 2 9,8 0.8459,0.8496 G -chr7 157185399 157185400 C/T 2 22,14 0.8577,0.8824 T -chr7 157211607 157211608 G 1 4 0.8391 T -chr7 157227609 157227610 A 1 18 0.8586 T -chr7 157231794 157231795 A 1 15 0.8570 G -chr7 157555772 157555773 C/T 2 6,11 0.8622,0.8619 T -chr7 157564377 157564378 C/T 2 11,15 0.8592,0.8356 T -chr7 157571460 157571461 A 1 4 0.8280 G -chr7 157607816 157607817 A/C 2 5,5 0.8489,0.8503 C -chr7 157682113 157682114 G/T 2 9,19 0.8769,0.8431 T -chr7 157750646 157750647 A/G 2 23,16 0.8698,0.8884 G -chr7 157762230 157762231 G/T 2 10,9 0.8858,0.8363 G -chr7 157819324 157819325 C/T 2 7,13 0.8603,0.8445 T -chr7 157925271 157925272 C 1 4 0.8556 G -chr7 158122286 158122287 G/T 2 15,7 0.8685,0.8678 G -chr7 158164825 158164826 A/T 2 3,3 0.8953,0.8449 T -chr7 158166514 158166515 C/T 2 5,6 0.8360,0.8386 C -chr7 158525060 158525061 A/G 2 10,19 0.8696,0.8651 G -chr7 158540037 158540038 A 1 3 0.8866 G -chr7 158672618 158672619 G 1 22 0.8657 A -chr7 158989832 158989833 G/T 2 3,5 0.9425,0.7716 G -chr7 159007172 159007173 T 1 18 0.8649 A -chr8 418862 418863 C 1 26 0.8522 T -chr8 462698 462699 C 1 11 0.8842 T -chr8 516631 516632 G/T 2 6,7 0.8647,0.8635 T -chr8 638420 638421 G 1 3 0.8915 C -chr8 673081 673082 A/G 2 8,5 0.8413,0.8340 A -chr8 693202 693203 A/C 2 8,9 0.8465,0.9158 C -chr8 1167031 1167032 A 1 14 0.8520 T -chr8 1174140 1174141 C/G 2 14,14 0.8573,0.8379 C -chr8 1611292 1611293 G/T 2 9,4 0.8256,0.7291 G -chr8 1654912 1654913 A/C 2 16,15 0.8190,0.8496 C -chr8 1805200 1805201 C/G 2 11,12 0.8461,0.8849 G -chr8 2309327 2309328 C/G 2 8,14 0.8669,0.8716 G -chr8 2385045 2385046 A/G 2 12,5 0.8866,0.8707 A -chr8 3082863 3082864 A/G 2 6,14 0.8249,0.8499 G -chr8 3122962 3122963 A/C 2 19,30 0.8679,0.8635 C -chr8 3209448 3209449 T 1 26 0.8590 C -chr8 3241664 3241665 G 1 28 0.8849 C -chr8 3250046 3250047 T 1 32 0.8282 A -chr8 3265844 3265845 C/T 2 10,13 0.8625,0.8721 C -chr8 3404626 3404627 C 1 14 0.8548 T -chr8 3530444 3530445 C/G 2 10,11 0.8595,0.8625 G -chr8 3615559 3615560 A/G 2 2,4 0.9244,0.9010 G -chr8 3632970 3632971 A/G 2 18,9 0.8549,0.8286 A -chr8 3667450 3667451 C/T 2 18,21 0.8588,0.8807 T -chr8 3703111 3703112 A/T 2 17,14 0.8782,0.8557 A -chr8 3871843 3871844 C/T 2 16,19 0.8886,0.8718 C -chr8 3899806 3899807 T 1 35 0.8633 A -chr8 3927294 3927295 C/T 2 24,15 0.8617,0.8515 C -chr8 3938448 3938449 A/T 2 7,21 0.8971,0.8838 T -chr8 3949075 3949076 C/G 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 4,8 0.9009,0.8916 G -chr8 9708556 9708557 C 1 22 0.8572 A -chr8 9825048 9825049 T 1 29 0.8256 A -chr8 10046954 10046955 A/G 2 4,9 0.8309,0.8239 G -chr8 10064218 10064219 G/T 2 13,6 0.8715,0.8267 G -chr8 10136251 10136252 A/C 2 16,16 0.8500,0.8533 C -chr8 10352229 10352230 C/T 2 10,12 0.9004,0.9061 T -chr8 10480376 10480377 C 1 8 0.8438 G -chr8 10579622 10579623 C/G 2 10,13 0.8038,0.8313 G -chr8 10670073 10670074 A/G 2 17,7 0.8730,0.8856 A -chr8 10817190 10817191 A/G 2 12,6 0.8625,0.8898 A -chr8 10981572 10981573 C/T 2 10,20 0.9026,0.8797 T -chr8 11023871 11023872 A/G 2 10,22 0.8871,0.8937 A -chr8 11083681 11083682 C/G 2 15,18 0.8461,0.8571 G -chr8 11410137 11410138 C/T 2 10,17 0.8529,0.8478 T -chr8 11530145 11530146 G/T 2 3,4 0.6843,0.8362 T -chr8 11704718 11704719 A 1 3 0.8889 C -chr8 11778910 11778911 A 1 34 0.8481 C -chr8 11806268 11806269 C/T 2 15,19 0.8385,0.8381 T -chr8 12438658 12438659 A/G 2 10,5 0.7433,0.7885 A -chr8 12524126 12524127 A/T 2 9,5 0.8643,0.9084 T -chr8 12524149 12524150 A/G 2 9,6 0.8226,0.8761 G -chr8 12697893 12697894 T 1 3 0.8557 C -chr8 13180655 13180656 C 1 33 0.8726 A -chr8 13365365 13365366 G 1 19 0.8451 T -chr8 13590854 13590855 A/G 2 15,17 0.8697,0.9072 A -chr8 13622192 13622193 T 1 13 0.8454 C -chr8 13652156 13652157 C/G 2 12,12 0.7993,0.8345 G -chr8 14081651 14081652 C 1 10 0.8535 A -chr8 14474164 14474165 C/G 2 6,8 0.8635,0.9050 G -chr8 14520814 14520815 A 1 19 0.8572 G -chr8 14521175 14521176 C/T 2 19,9 0.7955,0.8856 T -chr8 14690924 14690925 G 1 17 0.8552 C -chr8 14868161 14868162 A/G 2 6,5 0.8921,0.8885 G -chr8 14961879 14961880 C/T 2 18,10 0.8791,0.8899 C -chr8 15152459 15152460 A/C 2 20,7 0.8418,0.8626 A -chr8 15192055 15192056 A/G 2 16,16 0.8426,0.8697 A -chr8 15281378 15281379 A/G 2 14,16 0.8926,0.8945 A -chr8 15534187 15534188 A/G 2 17,10 0.8844,0.8778 A -chr8 15603891 15603892 A/C 2 11,8 0.8362,0.8091 A -chr8 15813285 15813286 G 1 15 0.8624 A -chr8 16350771 16350772 C/G 2 5,6 0.8637,0.8684 G -chr8 16500456 16500457 C/G 2 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21453781 21453782 A/G 2 12,10 0.8427,0.8336 G -chr8 21561237 21561238 A/G 2 15,5 0.8537,0.8172 G -chr8 21601272 21601273 A/G 2 5,6 0.8762,0.8574 G -chr8 21610236 21610237 C/T 2 17,20 0.8577,0.8579 C -chr8 21934710 21934711 A/G 2 5,6 0.8849,0.8430 G -chr8 22205600 22205601 A/G 2 10,11 0.8166,0.8296 G -chr8 22371857 22371858 A 1 9 0.8267 G -chr8 23183856 23183857 A/T 2 14,16 0.8859,0.8831 T -chr8 23289535 23289536 A/G 2 7,9 0.8687,0.8630 G -chr8 23368737 23368738 A/G 2 21,12 0.8673,0.8767 A -chr8 23399772 23399773 A/G 2 16,10 0.8584,0.8526 A -chr8 23496415 23496416 T 1 17 0.8193 A -chr8 23547760 23547761 T 1 14 0.8419 C -chr8 23786071 23786072 A/C 2 21,18 0.8541,0.8597 A -chr8 23898416 23898417 C/T 2 13,9 0.8693,0.8508 C -chr8 23968624 23968625 A/G 2 8,7 0.8318,0.8563 G -chr8 24363791 24363792 A/G 2 12,12 0.8633,0.8476 G -chr8 24400772 24400773 C 1 25 0.8706 T -chr8 24456188 24456189 A/G 2 8,6 0.8688,0.8431 A -chr8 24565581 24565582 G 1 3 0.8823 A -chr8 24571920 24571921 C/T 2 8,5 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 27757178 27757179 C/G 2 17,13 0.8346,0.8287 C -chr8 27775116 27775117 T 1 15 0.8550 C -chr8 27897451 27897452 T 1 18 0.7900 C -chr8 28005309 28005310 A 1 15 0.8328 T -chr8 29561882 29561883 A/G 2 19,13 0.8517,0.8864 A -chr8 29882117 29882118 T 1 3 0.8160 A -chr8 29890870 29890871 A/G 2 15,13 0.8440,0.8489 A -chr8 30116936 30116937 C 1 4 0.8532 T -chr8 30512479 30512480 A/G 2 9,11 0.8301,0.8752 G -chr8 30996415 30996416 G 1 26 0.8782 A -chr8 31743057 31743058 G 1 14 0.8171 T -chr8 31824085 31824086 A 1 21 0.8492 G -chr8 33147296 33147297 C 1 29 0.8677 T -chr8 33156537 33156538 C 1 28 0.8792 T -chr8 34256990 34256991 A/T 2 20,15 0.8032,0.7886 A -chr8 34694769 34694770 C 1 4 0.9286 G -chr8 34696392 34696393 G 1 8 0.8812 A -chr8 36059448 36059449 A/G 2 7,7 0.8393,0.8420 G -chr8 36067271 36067272 A/G 2 16,18 0.8406,0.8350 G -chr8 36226616 36226617 C/T 2 19,9 0.8600,0.8473 C -chr8 36660186 36660187 A/G 2 18,16 0.8566,0.8697 G -chr8 36775083 36775084 G/T 2 13,13 0.8158,0.8173 G -chr8 36865148 36865149 A/G 2 13,15 0.8551,0.8924 A -chr8 37012837 37012838 A 1 26 0.8684 G -chr8 37962657 37962658 A/G 2 7,7 0.8456,0.8822 G -chr8 38408988 38408989 C 1 12 0.8517 G -chr8 39001988 39001989 C/T 2 19,11 0.8591,0.8761 C -chr8 39134247 39134248 A/G 2 12,12 0.8402,0.8589 G -chr8 39281416 39281417 G 1 3 0.8119 A -chr8 39571608 39571609 T 1 4 0.8667 C -chr8 39604373 39604374 C/T 2 12,12 0.8309,0.8520 C -chr8 39831199 39831200 T 1 6 0.8350 G -chr8 40038609 40038610 T 1 22 0.8735 C -chr8 40298862 40298863 C/T 2 10,14 0.8591,0.8567 T -chr8 40454566 40454567 A/C 2 5,3 0.8709,0.8540 A -chr8 40656015 40656016 C/T 2 17,17 0.8658,0.8625 T -chr8 40698231 40698232 C 1 28 0.8642 T -chr8 40839323 40839324 C/T 2 14,17 0.8427,0.8541 C -chr8 41639753 41639754 C 1 37 0.8647 G -chr8 41879824 41879825 C 1 27 0.8493 T -chr8 42350770 42350771 C/T 2 15,14 0.8619,0.8488 C -chr8 42454605 42454606 C 1 4 0.7974 T -chr8 43252715 43252716 G 1 23 0.8518 A -chr8 43644013 43644014 C/T 2 8,10 0.8532,0.8338 T -chr8 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 C/T 2 7,9 0.8794,0.8529 T -chr8 51961774 51961775 T 1 5 0.8391 G -chr8 52293017 52293018 T 1 39 0.8401 C -chr8 52420872 52420873 C/T 2 8,26 0.8635,0.8511 T -chr8 52453159 52453160 A/C 2 5,5 0.8517,0.8495 A -chr8 52567936 52567937 A/G 2 18,19 0.8702,0.8869 G -chr8 52577140 52577141 C/T 2 23,12 0.8402,0.8798 C -chr8 52691045 52691046 A/T 2 14,15 0.8068,0.8267 T -chr8 52782552 52782553 C/G 2 21,8 0.8430,0.8670 C -chr8 53251133 53251134 C/T 2 4,3 0.8585,0.8313 C -chr8 53271256 53271257 C 1 30 0.8702 T -chr8 53838178 53838179 T 1 36 0.8584 C -chr8 54230858 54230859 C/T 2 5,8 0.8371,0.8164 C -chr8 54242318 54242319 T 1 24 0.8605 C -chr8 54371220 54371221 C 1 34 0.8724 T -chr8 54521656 54521657 C 1 22 0.8446 T -chr8 54589509 54589510 C 1 7 0.8576 G -chr8 54915256 54915257 A/T 2 22,15 0.8401,0.8436 T -chr8 55010806 55010807 A/C 2 11,11 0.8541,0.8686 A -chr8 55309190 55309191 C 1 28 0.8712 T -chr8 55440636 55440637 G 1 7 0.8601 A -chr8 55943662 55943663 A/G 2 8,4 0.8487,0.8462 A -chr8 56121808 56121809 G 1 12 0.8655 A -chr8 56313540 56313541 A/C 2 13,13 0.8699,0.8670 A -chr8 56504422 56504423 T 1 18 0.8519 C -chr8 56662574 56662575 G 1 22 0.8888 A -chr8 58317729 58317730 A/C 2 12,13 0.8495,0.8579 C -chr8 58511442 58511443 C/T 2 8,5 0.8557,0.8396 T -chr8 58600422 58600423 A/C 2 17,13 0.8233,0.8006 A -chr8 59096533 59096534 G/T 2 10,7 0.8628,0.8503 G -chr8 59689369 59689370 T 1 2 0.9255 C -chr8 59854931 59854932 T 1 23 0.8837 C -chr8 60369637 60369638 G 1 2 0.8959 A -chr8 60769821 60769822 C/T 2 3,5 0.8358,0.8325 T -chr8 61170321 61170322 T 1 21 0.8684 C -chr8 61281343 61281344 A/G 2 13,13 0.8728,0.8601 G -chr8 61375328 61375329 G 1 3 0.9169 C -chr8 62209205 62209206 A/C 2 11,13 0.8048,0.8259 C -chr8 63106535 63106536 G 1 24 0.8808 A -chr8 63130205 63130206 A/C 2 10,17 0.8927,0.8596 C -chr8 63447590 63447591 G/T 2 10,9 0.8757,0.8678 T -chr8 63599111 63599112 C/T 2 7,10 0.8502,0.8601 T -chr8 63806991 63806992 T 1 20 0.8477 G -chr8 64045648 64045649 C/T 2 8,8 0.8494,0.8468 T -chr8 65076011 65076012 G/T 2 9,6 0.8726,0.8460 G -chr8 65442307 65442308 G 1 37 0.8359 A -chr8 65635652 65635653 C/T 2 3,9 0.9090,0.8761 T -chr8 65777436 65777437 C 1 29 0.8886 T -chr8 66069059 66069060 T 1 32 0.8709 G -chr8 66919021 66919022 C 1 9 0.8444 A -chr8 67978551 67978552 A/G 2 15,14 0.8566,0.8580 G -chr8 68619554 68619555 C/T 2 13,18 0.8311,0.8376 T -chr8 68675999 68676000 T 1 4 0.7540 G -chr8 68937540 68937541 T 1 24 0.8669 C -chr8 69695823 69695824 A/G 2 5,7 0.8343,0.8363 A -chr8 70060112 70060113 C/T 2 10,18 0.8657,0.8676 T -chr8 70443700 70443701 C/G 2 19,14 0.8726,0.8775 C -chr8 70450070 70450071 G/T 2 8,11 0.8408,0.8435 T -chr8 70607810 70607811 C/T 2 4,7 0.8812,0.8538 C -chr8 70787713 70787714 A/G 2 13,19 0.8622,0.8853 G -chr8 70802907 70802908 A/T 2 8,4 0.8241,0.7907 A -chr8 70846205 70846206 T 1 5 0.8723 C -chr8 71751236 71751237 A/C 2 11,14 0.8395,0.8514 C -chr8 72258962 72258963 C/T 2 7,13 0.8560,0.8625 T -chr8 72394990 72394991 T 1 25 0.8747 C -chr8 73218718 73218719 C 1 17 0.8439 T -chr8 73316692 73316693 C/G 2 8,6 0.8624,0.8741 G -chr8 73469386 73469387 T 1 25 0.8592 A -chr8 73870745 73870746 C/T 2 13,10 0.8767,0.8849 T -chr8 74275971 74275972 G/T 2 7,3 0.9037,0.8786 G -chr8 74935698 74935699 T 1 25 0.8629 C -chr8 75498176 75498177 T 1 32 0.8746 C -chr8 75553384 75553385 G 1 13 0.8503 T -chr8 75752083 75752084 G 1 26 0.8488 A -chr8 75814454 75814455 A/G 2 11,8 0.8881,0.8641 G -chr8 76007022 76007023 C/G 2 12,24 0.8804,0.8450 G -chr8 76091950 76091951 A/G 2 5,5 0.8294,0.8204 G -chr8 76299137 76299138 A/G 2 12,22 0.8757,0.8661 G -chr8 76477121 76477122 C/T 2 4,12 0.8333,0.8406 T -chr8 76481754 76481755 C/T 2 4,3 0.8546,0.8641 C -chr8 76794334 76794335 C/G 2 10,15 0.8416,0.8688 G -chr8 77188528 77188529 C 1 15 0.8354 T -chr8 77575476 77575477 C/T 2 9,10 0.8429,0.8519 T -chr8 78533184 78533185 C/T 2 11,9 0.8183,0.7984 C -chr8 78654193 78654194 T 1 6 0.9070 G -chr8 78680348 78680349 C/T 2 17,13 0.8556,0.8408 T -chr8 79210801 79210802 C/T 2 4,10 0.8275,0.8529 T -chr8 79285507 79285508 C/T 2 14,14 0.8884,0.8708 T -chr8 79299918 79299919 C/T 2 7,6 0.9221,0.9092 C -chr8 79822965 79822966 A/C 2 12,11 0.8468,0.8171 C -chr8 80608843 80608844 C/G 2 10,12 0.8121,0.8084 C -chr8 80800817 80800818 G 1 21 0.7974 A -chr8 81081365 81081366 A 1 3 0.8674 G -chr8 81505232 81505233 C/T 2 3,4 0.9018,0.8770 T -chr8 81746759 81746760 G/T 2 4,14 0.7844,0.8611 T -chr8 81973287 81973288 C 1 30 0.8668 T -chr8 82793650 82793651 G/T 2 14,16 0.8474,0.8536 G -chr8 83265967 83265968 C/T 2 11,6 0.8790,0.8546 C -chr8 83431530 83431531 C/T 2 3,4 0.8457,0.8266 T -chr8 83631036 83631037 G 1 6 0.8526 A -chr8 83708677 83708678 G/T 2 4,6 0.8400,0.8919 G -chr8 83967104 83967105 C 1 3 0.8496 T -chr8 84268650 84268651 A/G 2 10,8 0.8244,0.8255 A -chr8 84834863 84834864 G 1 7 0.8762 A -chr8 85202565 85202566 A/C 2 3,4 0.9157,0.7343 A -chr8 86009323 86009324 G 1 18 0.8488 A -chr8 87059015 87059016 A/T 2 5,3 0.8696,0.8093 A -chr8 87061098 87061099 A/T 2 11,6 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111479150 A/G 2 4,7 0.8839,0.8427 A -chr8 112094550 112094551 A/G 2 21,20 0.8367,0.8513 G -chr8 112394632 112394633 C 1 19 0.8252 T -chr8 113161292 113161293 C/T 2 14,7 0.8691,0.8704 C -chr8 113436231 113436232 A/T 2 9,5 0.8714,0.8785 T -chr8 113591848 113591849 T 1 5 0.8603 C -chr8 114393053 114393054 A 1 21 0.8816 G -chr8 114471588 114471589 A/T 2 8,6 0.8547,0.8557 A -chr8 114485068 114485069 A/G 2 4,9 0.8518,0.9029 G -chr8 114507203 114507204 C/T 2 13,23 0.8735,0.8821 T -chr8 114698418 114698419 A/G 2 8,8 0.8446,0.8171 G -chr8 115208201 115208202 C 1 7 0.8838 T -chr8 115292495 115292496 A/G 2 6,8 0.8553,0.8643 G -chr8 115918164 115918165 T 1 19 0.8441 A -chr8 116292006 116292007 G 1 19 0.8391 A -chr8 116570629 116570630 A 1 6 0.8812 G -chr8 116610179 116610180 C 1 39 0.8785 T -chr8 118053488 118053489 G 1 32 0.8594 A -chr8 118076788 118076789 A/T 2 3,8 0.7587,0.8741 T -chr8 118530547 118530548 C 1 14 0.8262 A -chr8 118824337 118824338 C/T 2 6,11 0.8857,0.9139 T -chr8 118984428 118984429 C 1 18 0.8688 A -chr8 119779881 119779882 C/T 2 11,19 0.8605,0.8703 T -chr8 120032524 120032525 C 1 8 0.8779 T -chr8 120086851 120086852 G 1 21 0.8560 A -chr8 121015482 121015483 T 1 13 0.8221 C -chr8 121968245 121968246 G/T 2 19,18 0.8382,0.8614 G -chr8 122194666 122194667 G/T 2 6,5 0.8545,0.8551 G -chr8 122582008 122582009 C/G 2 12,23 0.8373,0.8491 G -chr8 122709202 122709203 C/G 2 11,4 0.8983,0.8970 C -chr8 122723890 122723891 T 1 21 0.7948 A -chr8 123429954 123429955 A/C 2 17,17 0.8835,0.8817 A -chr8 124712647 124712648 A 1 25 0.8466 G -chr8 124773832 124773833 C 1 12 0.8588 T -chr8 125107200 125107201 A 1 27 0.8352 G -chr8 125300066 125300067 G 1 3 0.7892 T -chr8 125668045 125668046 A/G 2 20,21 0.8796,0.8861 G -chr8 125735715 125735716 A/G 2 16,8 0.8191,0.8622 A -chr8 125770453 125770454 G/T 2 5,8 0.8393,0.8477 G -chr8 126071843 126071844 A/G 2 7,11 0.8722,0.8552 G -chr8 126482076 126482077 A/G 2 6,12 0.8672,0.8790 A -chr8 126850824 126850825 A/G 2 7,5 0.8079,0.8444 G -chr8 127527953 127527954 G/T 2 4,11 0.8674,0.8528 G -chr8 127678825 127678826 A 1 10 0.8781 T -chr8 127914937 127914938 T 1 27 0.8339 C -chr8 128179875 128179876 A/G 2 10,7 0.8618,0.8554 A -chr8 128625777 128625778 A/G 2 9,12 0.8620,0.8727 G -chr8 128916146 128916147 C/T 2 7,5 0.8450,0.8237 C -chr8 129186364 129186365 G 1 11 0.8463 T -chr8 129552343 129552344 T 1 38 0.8718 C -chr8 130036145 130036146 A/G 2 9,6 0.8809,0.8481 A -chr8 130248919 130248920 C/T 2 6,10 0.8927,0.8937 T -chr8 130421284 130421285 C 1 18 0.8659 T -chr8 130451821 130451822 C/T 2 18,13 0.8732,0.8593 T -chr8 130759235 130759236 C 1 4 0.8902 T -chr8 131476883 131476884 C/T 2 11,20 0.8745,0.8589 T -chr8 131704525 131704526 A/G 2 11,12 0.8552,0.8807 G -chr8 131806648 131806649 C/T 2 4,7 0.7633,0.7886 C -chr8 131936654 131936655 G 1 21 0.8269 C -chr8 132088886 132088887 C/T 2 8,8 0.8597,0.8603 C -chr8 132365071 132365072 A/G 2 22,13 0.8601,0.8404 A -chr8 132477624 132477625 G 1 3 0.8826 C -chr8 132555249 132555250 A/G 2 16,10 0.7971,0.8158 G -chr8 132555281 132555282 G 1 33 0.8727 A -chr8 132588565 132588566 G/T 2 6,6 0.8550,0.8783 T -chr8 132701886 132701887 C/T 2 8,9 0.8843,0.8685 T -chr8 132772995 132772996 C/T 2 21,18 0.8391,0.8488 T -chr8 132790701 132790702 A/G 2 4,8 0.8199,0.8794 G -chr8 132882454 132882455 C/T 2 13,10 0.8742,0.8784 C -chr8 132885411 132885412 A/C 2 6,16 0.8853,0.8722 C -chr8 132902202 132902203 C 1 23 0.8586 T -chr8 132914564 132914565 A/G 2 18,10 0.8440,0.8459 A -chr8 133061422 133061423 C/G 2 18,14 0.8741,0.8840 C -chr8 134094437 134094438 C 1 22 0.9036 T -chr8 134509521 134509522 C/G 2 14,6 0.8333,0.8676 G -chr8 134580160 134580161 C/T 2 3,9 0.9066,0.8711 T -chr8 134618690 134618691 C/G 2 21,10 0.8458,0.8327 C -chr8 134653061 134653062 A 1 26 0.8486 G -chr8 134713030 134713031 A 1 17 0.8159 C -chr8 135440304 135440305 C/T 2 19,13 0.8379,0.8720 C -chr8 135783911 135783912 A/G 2 4,2 0.8952,0.9529 A -chr8 136149711 136149712 G 1 41 0.8323 C -chr8 136174681 136174682 T 1 41 0.8537 C -chr8 136215436 136215437 C/T 2 15,15 0.8564,0.8591 T -chr8 136268594 136268595 C/T 2 10,9 0.8778,0.9187 C -chr8 136306823 136306824 C/T 2 17,10 0.8544,0.8826 C -chr8 136374028 136374029 C/T 2 23,17 0.8503,0.8773 C -chr8 136453730 136453731 T 1 15 0.8438 G -chr8 136774189 136774190 C/T 2 5,3 0.8281,0.8577 C -chr8 137221826 137221827 C/T 2 17,9 0.8264,0.8294 T -chr8 137777901 137777902 A/G 2 8,3 0.8713,0.8522 A -chr8 138411013 138411014 C/T 2 21,17 0.8532,0.8669 C -chr8 138617981 138617982 A/G 2 18,14 0.8732,0.8581 A -chr8 138905619 138905620 C/T 2 15,16 0.8678,0.8431 T -chr8 139111500 139111501 A/G 2 6,7 0.8862,0.9037 A -chr8 139383976 139383977 C 1 43 0.8863 T -chr8 139554368 139554369 A 1 4 0.9089 G -chr8 139560406 139560407 C/T 2 20,13 0.8519,0.8556 C -chr8 139614581 139614582 C/T 2 6,9 0.8651,0.8550 C -chr8 139633680 139633681 G 1 34 0.8313 A -chr8 139931563 139931564 T 1 24 0.8648 C -chr8 140594431 140594432 G 1 31 0.8303 T -chr8 140637123 140637124 G 1 17 0.8790 T -chr8 140892870 140892871 A/C 2 27,17 0.8658,0.8481 C -chr8 141104736 141104737 C 1 19 0.8711 T -chr8 141425878 141425879 C/G 2 8,4 0.8865,0.8682 G -chr8 141516769 141516770 G 1 3 0.8224 T -chr8 142087749 142087750 C/T 2 8,12 0.8863,0.8452 C -chr8 142322652 142322653 C/T 2 8,16 0.8626,0.8322 C -chr8 142446623 142446624 T 1 4 0.8480 C -chr8 142839616 142839617 T 1 15 0.8652 C -chr8 142885889 142885890 T 1 20 0.8108 C -chr8 143052788 143052789 A/C 2 4,3 0.8853,0.9002 A -chr8 143148810 143148811 C/G 2 15,18 0.8491,0.8588 C -chr8 143227545 143227546 T 1 11 0.8897 A -chr8 143235367 143235368 G 1 18 0.8573 A -chr8 143378350 143378351 A 1 5 0.8964 G -chr8 144052172 144052173 C/T 2 3,10 0.8695,0.8482 C -chr8 145168823 145168824 C/T 2 5,9 0.8309,0.8940 T -chr8 145801187 145801188 C 1 17 0.8738 T -chr8 145956259 145956260 C/T 2 10,12 0.8287,0.7830 C -chr8 146042173 146042174 G/T 2 17,11 0.8714,0.8415 T -chr9 349825 349826 A/G 2 9,14 0.8737,0.8682 A -chr9 556991 556992 C/T 2 13,15 0.8399,0.8206 T -chr9 1106543 1106544 G 1 17 0.8484 A -chr9 1252595 1252596 C 1 18 0.8453 T -chr9 1465540 1465541 A/G 2 18,15 0.8818,0.8648 A -chr9 1540280 1540281 A/G 2 12,16 0.8477,0.8653 G -chr9 2010014 2010015 A/G 2 6,3 0.8694,0.8662 A -chr9 2033894 2033895 A 1 3 0.8397 G -chr9 2190295 2190296 A/G 2 9,5 0.8716,0.8960 A -chr9 2249783 2249784 T 1 20 0.8462 G -chr9 2435074 2435075 A/G 2 5,4 0.8345,0.7811 A -chr9 2654616 2654617 T 1 22 0.7949 C -chr9 2717921 2717922 G 1 20 0.8625 C -chr9 2809547 2809548 C 1 14 0.8944 A -chr9 2976393 2976394 C/T 2 8,12 0.8826,0.8835 T -chr9 3433404 3433405 C/T 2 5,7 0.8924,0.8472 C -chr9 3634919 3634920 A/C 2 11,18 0.7937,0.8277 C -chr9 3701676 3701677 C/T 2 9,15 0.8200,0.8377 T -chr9 4276661 4276662 G 1 28 0.8510 A -chr9 4364437 4364438 A 1 10 0.8739 C -chr9 4385201 4385202 C/G 2 15,13 0.8654,0.8372 C -chr9 4654962 4654963 C/T 2 9,11 0.8976,0.8592 T -chr9 4929403 4929404 C/G 2 10,17 0.8777,0.8781 C -chr9 5106279 5106280 G 1 6 0.8558 A -chr9 5297251 5297252 C/T 2 7,3 0.8671,0.8523 C -chr9 6073842 6073843 G 1 15 0.8675 A -chr9 6808784 6808785 A/T 2 6,9 0.8708,0.8588 A -chr9 7001239 7001240 C 1 27 0.8549 T -chr9 7060291 7060292 A/G 2 10,21 0.8726,0.8682 G -chr9 7076585 7076586 A 1 21 0.8583 G -chr9 7597682 7597683 A/G 2 21,15 0.8621,0.8565 A -chr9 7755442 7755443 A/G 2 10,12 0.8568,0.8943 A -chr9 7769851 7769852 A/C 2 6,4 0.8435,0.8657 C -chr9 7932781 7932782 C/T 2 19,12 0.8823,0.8824 T -chr9 8097027 8097028 C/G 2 5,5 0.8915,0.8598 C -chr9 8125683 8125684 A/C 2 17,17 0.8513,0.8816 A -chr9 8240002 8240003 A/T 2 28,17 0.7409,0.7566 A -chr9 8242653 8242654 G 1 42 0.8587 A -chr9 8329243 8329244 C/G 2 5,5 0.8745,0.8793 C -chr9 8345151 8345152 C/T 2 11,5 0.8778,0.8961 T -chr9 8424509 8424510 A/G 2 7,11 0.8372,0.8377 G -chr9 8804902 8804903 C/T 2 9,14 0.8310,0.8857 T -chr9 8946101 8946102 A/C 2 12,12 0.7716,0.8499 C -chr9 9032692 9032693 A/G 2 9,20 0.8708,0.8428 G -chr9 9390793 9390794 C/G 2 8,8 0.8665,0.8711 G -chr9 9480742 9480743 G 1 5 0.8799 A -chr9 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85087095 A/G 2 11,8 0.8756,0.8880 A -chr9 85137663 85137664 C 1 20 0.8252 T -chr9 85907515 85907516 A/G 2 7,6 0.8787,0.8931 A -chr9 86066115 86066116 C/T 2 19,12 0.8549,0.8396 C -chr9 86578447 86578448 C/T 2 15,9 0.8731,0.8801 C -chr9 86762038 86762039 G 1 29 0.8740 C -chr9 87020834 87020835 A/G 2 20,11 0.8250,0.8167 A -chr9 87028997 87028998 A/C 2 7,3 0.8197,0.7892 A -chr9 87166648 87166649 A/T 2 4,7 0.7951,0.8272 T -chr9 87278761 87278762 C/T 2 14,12 0.8552,0.7983 C -chr9 87304264 87304265 A/T 2 19,11 0.8583,0.8204 A -chr9 87416506 87416507 A 1 26 0.8776 G -chr9 87610941 87610942 A 1 21 0.8728 G -chr9 88002515 88002516 C/T 2 8,15 0.8790,0.8651 C -chr9 88471695 88471696 A/G 2 6,14 0.9040,0.8694 G -chr9 89058252 89058253 C 1 31 0.8354 G -chr9 89429680 89429681 A/G 2 11,14 0.8813,0.8994 A -chr9 89521622 89521623 A/C 2 17,12 0.8564,0.7573 A -chr9 89710825 89710826 C/T 2 11,22 0.8907,0.8610 T -chr9 89795516 89795517 A/C 2 13,18 0.8587,0.8810 C -chr9 90142205 90142206 T 1 41 0.8385 G -chr9 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G/T 2 12,9 0.7905,0.8184 G -chr9 99527052 99527053 C/T 2 12,5 0.8613,0.8110 C -chr9 100020156 100020157 G 1 9 0.8443 A -chr9 100060955 100060956 T 1 19 0.8820 C -chr9 100071727 100071728 A 1 6 0.8032 G -chr9 100197780 100197781 A/G 2 4,5 0.8428,0.8858 G -chr9 100212402 100212403 G 1 33 0.8654 C -chr9 100359000 100359001 A/C 2 9,12 0.8473,0.8434 C -chr9 100650258 100650259 A/T 2 7,5 0.8792,0.8569 A -chr9 101003444 101003445 C/T 2 20,11 0.8734,0.8634 C -chr9 101015058 101015059 C/T 2 13,16 0.8817,0.8767 T -chr9 101116545 101116546 A/C 2 6,7 0.9092,0.8698 A -chr9 101281838 101281839 A/C 2 19,7 0.8216,0.7520 A -chr9 101300962 101300963 A/C 2 12,10 0.8363,0.8732 C -chr9 101336040 101336041 G 1 25 0.9013 T -chr9 101619190 101619191 C/T 2 10,8 0.8684,0.8549 C -chr9 103119633 103119634 A/G 2 11,11 0.8890,0.8340 G -chr9 103424822 103424823 A 1 15 0.8568 G -chr9 103510679 103510680 G/T 2 7,3 0.8983,0.8910 G -chr9 103595998 103595999 T 1 20 0.8589 A -chr9 103642401 103642402 G/T 2 12,12 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-chr9 110596571 110596572 A/G 2 17,8 0.8606,0.8075 A -chr9 110731200 110731201 A/G 2 9,18 0.8334,0.8221 G -chr9 110854525 110854526 A 1 20 0.8873 G -chr9 110863375 110863376 C/T 2 14,25 0.8810,0.8828 T -chr9 110927519 110927520 G 1 21 0.8791 A -chr9 110945171 110945172 A/G 2 12,5 0.8632,0.8742 G -chr9 111069810 111069811 G 1 6 0.8133 A -chr9 111312163 111312164 C/T 2 9,9 0.8193,0.8166 C -chr9 111330416 111330417 G 1 4 0.8201 A -chr9 111626089 111626090 A 1 27 0.8485 G -chr9 111628401 111628402 A/T 2 12,16 0.8858,0.8749 T -chr9 111664673 111664674 C/T 2 19,25 0.8314,0.8398 T -chr9 113468896 113468897 A/G 2 8,20 0.8879,0.8451 G -chr9 113508507 113508508 C 1 15 0.8334 G -chr9 113614696 113614697 T 1 15 0.8681 C -chr9 113651670 113651671 A/C 2 4,6 0.8008,0.8230 C -chr9 113751323 113751324 C/T 2 16,14 0.8351,0.8608 T -chr9 114485749 114485750 C 1 46 0.8532 A -chr9 114902931 114902932 C/T 2 6,18 0.8335,0.8912 T -chr9 115228693 115228694 G 1 4 0.8919 A -chr9 115320642 115320643 A 1 7 0.8895 G 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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 0.8598,0.8558 T -chr11 10769318 10769319 C 1 22 0.8418 G -chr11 11090026 11090027 A/T 2 19,7 0.8374,0.8571 A -chr11 11169114 11169115 A 1 10 0.8506 G -chr11 11337738 11337739 C/G 2 14,11 0.8296,0.8437 G -chr11 11366273 11366274 A/T 2 11,9 0.8758,0.8562 T -chr11 12032704 12032705 C/T 2 19,22 0.8487,0.8556 T -chr11 12296625 12296626 A/G 2 14,17 0.8699,0.8557 A -chr11 12663833 12663834 C/T 2 22,10 0.8376,0.7950 C -chr11 13075866 13075867 A/G 2 6,7 0.8107,0.8353 G -chr11 14461000 14461001 C/G 2 6,8 0.8638,0.8578 G -chr11 14889604 14889605 A/C 2 13,10 0.8952,0.8831 A -chr11 14928266 14928267 C 1 5 0.8724 G -chr11 14956052 14956053 C 1 16 0.8905 T -chr11 15239599 15239600 A/G 2 11,11 0.8626,0.8435 A -chr11 15311716 15311717 A/G 2 13,9 0.8460,0.8231 A -chr11 15319568 15319569 G 1 35 0.8796 A -chr11 16007046 16007047 T 1 30 0.8427 G -chr11 16250182 16250183 T 1 24 0.8677 C -chr11 16346502 16346503 A/G 2 12,11 0.8706,0.8390 G -chr11 16659347 16659348 A/G 2 20,21 0.8490,0.8664 G -chr11 16675739 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-chr11 21534442 21534443 T 1 29 0.7921 A -chr11 21765089 21765090 A/T 2 14,11 0.8150,0.8301 A -chr11 21963691 21963692 C/T 2 15,7 0.8433,0.8961 T -chr11 22344214 22344215 A/G 2 15,12 0.8568,0.8941 A -chr11 23308040 23308041 C/T 2 9,11 0.8841,0.9095 T -chr11 23328573 23328574 G 1 7 0.9053 A -chr11 23619390 23619391 G 1 16 0.8596 T -chr11 23629289 23629290 A/T 2 11,14 0.8685,0.8742 T -chr11 23679324 23679325 G/T 2 14,14 0.8218,0.8487 G -chr11 23693364 23693365 G 1 21 0.8784 A -chr11 23788812 23788813 A/G 2 7,5 0.8227,0.8307 A -chr11 23794796 23794797 A/G 2 6,16 0.7720,0.7765 A -chr11 23897933 23897934 A/C 2 18,16 0.7970,0.8302 C -chr11 23957175 23957176 A 1 5 0.8239 G -chr11 24158799 24158800 T 1 6 0.8930 G -chr11 24168664 24168665 G/T 2 15,14 0.8430,0.8550 T -chr11 24298272 24298273 C/T 2 6,10 0.8885,0.8437 T -chr11 24321787 24321788 C/T 2 9,12 0.8837,0.8603 T -chr11 24441978 24441979 A/G 2 8,11 0.8486,0.8648 G -chr11 24532929 24532930 A 1 3 0.8678 G -chr11 24612503 24612504 A 1 5 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0.8337,0.8427 T -chr11 29871195 29871196 T 1 19 0.8795 A -chr11 29895928 29895929 C 1 17 0.8723 T -chr11 29988051 29988052 A/G 2 14,12 0.8762,0.8643 G -chr11 30644090 30644091 A/T 2 5,18 0.8641,0.8590 T -chr11 30990099 30990100 T 1 9 0.8391 C -chr11 31416012 31416013 A/T 2 9,13 0.8640,0.8585 T -chr11 32449485 32449486 T 1 3 0.7690 C -chr11 32476526 32476527 A/G 2 7,4 0.8347,0.8053 A -chr11 32485630 32485631 A 1 28 0.8641 G -chr11 33026226 33026227 A/G 2 4,6 0.9093,0.9056 A -chr11 33236643 33236644 A/G 2 18,21 0.8368,0.8412 G -chr11 33545287 33545288 A/G 2 7,9 0.9095,0.8945 G -chr11 33657559 33657560 C/T 2 21,9 0.8605,0.8706 C -chr11 34570207 34570208 G/T 2 7,16 0.8428,0.8521 T -chr11 34686868 34686869 A/G 2 15,18 0.8512,0.8432 G -chr11 34693536 34693537 A/G 2 11,16 0.7937,0.7509 A -chr11 34714451 34714452 A/G 2 9,7 0.8865,0.8495 A -chr11 34763647 34763648 C 1 7 0.8658 G -chr11 34830708 34830709 G/T 2 24,11 0.8861,0.8966 G -chr11 34853136 34853137 A/G 2 14,17 0.8509,0.8308 G -chr11 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C/T 2 4,5 0.8540,0.8312 T -chr11 41705820 41705821 A/T 2 5,3 0.8829,0.8295 A -chr11 41758493 41758494 C/G 2 15,10 0.8677,0.8703 G -chr11 41770185 41770186 G/T 2 16,16 0.8623,0.8527 G -chr11 41833306 41833307 T 1 23 0.8691 A -chr11 42119746 42119747 C/T 2 7,12 0.7744,0.7329 T -chr11 42498740 42498741 C 1 15 0.8561 T -chr11 42631934 42631935 A 1 38 0.8459 T -chr11 42751301 42751302 A/G 2 12,9 0.8482,0.8433 A -chr11 43144543 43144544 A/G 2 28,13 0.8712,0.8804 A -chr11 43383716 43383717 T 1 2 0.9473 G -chr11 43644331 43644332 C 1 19 0.8699 T -chr11 43794378 43794379 G 1 16 0.8566 A -chr11 43993918 43993919 A/G 2 3,3 0.7398,0.8747 G -chr11 44522372 44522373 C 1 18 0.8867 T -chr11 44522417 44522418 G 1 26 0.8480 C -chr11 44622156 44622157 A/G 2 9,6 0.8123,0.8413 G -chr11 44695283 44695284 T 1 41 0.8625 A -chr11 45558166 45558167 C/G 2 20,14 0.8333,0.8284 C -chr11 45608057 45608058 A/G 2 15,11 0.8366,0.8475 G -chr11 47737804 47737805 C 1 10 0.8895 A -chr11 48349424 48349425 C/T 2 12,17 0.8514,0.8479 T -chr11 48359408 48359409 C/T 2 33,15 0.8575,0.8370 C -chr11 48705273 48705274 G 1 14 0.8479 A -chr11 48814660 48814661 A/C 2 14,5 0.8308,0.8549 A -chr11 48940812 48940813 C/T 2 6,20 0.7948,0.8081 T -chr11 48995845 48995846 C/T 2 12,6 0.7986,0.8030 T -chr11 49020127 49020128 T 1 9 0.8578 C -chr11 50288600 50288601 A/C 2 5,3 0.8628,0.7489 A -chr11 50514340 50514341 C/T 2 6,5 0.8840,0.8511 T -chr11 50637847 50637848 A/T 2 6,13 0.8550,0.8783 A -chr11 50691157 50691158 C/T 2 14,6 0.8410,0.8451 C -chr11 50751357 50751358 G 1 14 0.8560 T -chr11 50771753 50771754 A/G 2 14,14 0.8804,0.8628 A -chr11 51195553 51195554 A 1 7 0.8280 C -chr11 51233479 51233480 C/G 2 12,5 0.8538,0.7924 C -chr11 51283080 51283081 G 1 5 0.9086 C -chr11 51365710 51365711 C/T 2 4,10 0.7577,0.7592 T -chr11 51405299 51405300 C/T 2 3,11 0.8596,0.8578 T -chr11 51577268 51577269 C/T 2 13,5 0.8869,0.8992 C -chr11 54864906 54864907 G/T 2 6,6 0.7635,0.7795 T -chr11 54926665 54926666 C/G 2 19,6 0.8893,0.9157 C -chr11 54971789 54971790 A/T 2 4,6 0.8967,0.8083 A -chr11 55271406 55271407 A/G 2 8,12 0.8413,0.9083 A -chr11 55850530 55850531 C/T 2 22,13 0.8705,0.8465 C -chr11 55879425 55879426 A 1 33 0.8630 G -chr11 55942684 55942685 A/G 2 5,10 0.8577,0.8223 G -chr11 56491873 56491874 T 1 17 0.8243 A -chr11 56510242 56510243 G 1 14 0.8765 A -chr11 56630962 56630963 C 1 23 0.8727 T -chr11 56915991 56915992 A/G 2 6,4 0.8850,0.8800 A -chr11 57836284 57836285 A 1 16 0.8408 G -chr11 57945417 57945418 A 1 39 0.8694 T -chr11 58528159 58528160 G 1 9 0.8848 C -chr11 58583517 58583518 A 1 18 0.8832 G -chr11 58628863 58628864 C 1 24 0.8592 A -chr11 58804952 58804953 A/T 2 6,3 0.8370,0.7406 A -chr11 59132881 59132882 G 1 11 0.8871 A -chr11 59205056 59205057 G/T 2 4,6 0.7450,0.8607 T -chr11 59587219 59587220 C 1 20 0.8587 T -chr11 59749651 59749652 T 1 3 0.9265 C -chr11 60061197 60061198 G 1 23 0.8620 T -chr11 61415654 61415655 G 1 3 0.8953 C -chr11 61640197 61640198 A 1 20 0.8289 G -chr11 62001316 62001317 C 1 13 0.8400 A -chr11 62838781 62838782 C/T 2 4,4 0.8621,0.8530 T -chr11 62947891 62947892 C 1 34 0.8425 T -chr11 63261980 63261981 T 1 20 0.8719 C -chr11 63383852 63383853 A/G 2 12,22 0.8377,0.8458 G -chr11 63681072 63681073 C/G 2 4,6 0.8296,0.8422 G -chr11 63917328 63917329 C 1 16 0.8721 T -chr11 64305018 64305019 C/T 2 7,4 0.8583,0.8632 C -chr11 64402026 64402027 C 1 9 0.8481 T -chr11 64766722 64766723 C/T 2 11,10 0.8395,0.8345 C -chr11 64882788 64882789 T 1 26 0.8519 C -chr11 66141276 66141277 C/T 2 16,17 0.8649,0.8742 T -chr11 66521889 66521890 C/G 2 13,9 0.8649,0.8851 C -chr11 66889298 66889299 C 1 32 0.8316 T -chr11 67151519 67151520 A/C 2 4,4 0.9087,0.9032 A -chr11 67536794 67536795 A 1 19 0.8466 G -chr11 67579424 67579425 A 1 3 0.8315 G -chr11 67960825 67960826 T 1 3 0.8411 G -chr11 68254327 68254328 A 1 16 0.8347 C -chr11 68679862 68679863 A/G 2 3,4 0.8855,0.8430 G -chr11 68788389 68788390 C/T 2 3,6 0.9191,0.8556 C -chr11 68948042 68948043 C 1 16 0.8601 A -chr11 69032645 69032646 A/T 2 5,5 0.8428,0.9066 A -chr11 69255365 69255366 T 1 5 0.8047 C -chr11 69974620 69974621 A/G 2 7,9 0.8211,0.8015 G -chr11 70213048 70213049 C/T 2 21,11 0.8436,0.8254 C -chr11 70539416 70539417 C/T 2 18,13 0.8733,0.8511 C -chr11 70682519 70682520 C 1 15 0.8242 T -chr11 70759837 70759838 A/G 2 11,14 0.8516,0.8390 G -chr11 71257594 71257595 C/T 2 11,4 0.8720,0.8928 C -chr11 71373302 71373303 T 1 13 0.8592 G -chr11 71560579 71560580 G 1 26 0.8911 A -chr11 72557206 72557207 G 1 15 0.9038 A -chr11 72598703 72598704 A 1 22 0.8639 G -chr11 73005732 73005733 C/T 2 7,4 0.8549,0.8806 C -chr11 73074057 73074058 G 1 13 0.8672 A -chr11 73696609 73696610 A/T 2 15,7 0.8135,0.8345 A -chr11 74299817 74299818 T 1 17 0.8560 C -chr11 74667585 74667586 T 1 4 0.7930 C -chr11 74751267 74751268 A 1 3 0.8545 C -chr11 74991349 74991350 A/G 2 13,12 0.8460,0.8401 G -chr11 75258756 75258757 A/G 2 12,13 0.8707,0.8459 A -chr11 75968199 75968200 C 1 3 0.8208 T -chr11 76439067 76439068 A/G 2 25,20 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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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-chr11 119816114 119816115 C 1 9 0.8511 T -chr11 119948737 119948738 G 1 4 0.8317 T -chr11 121819614 121819615 A/G 2 11,14 0.8475,0.8612 G -chr11 122198077 122198078 T 1 49 0.8442 A -chr11 122240273 122240274 G 1 29 0.8274 T -chr11 122489472 122489473 T 1 22 0.8389 C -chr11 122838744 122838745 T 1 35 0.8386 G -chr11 122883744 122883745 C 1 20 0.8582 T -chr11 123009750 123009751 T 1 27 0.8722 G -chr11 123152706 123152707 T 1 32 0.8621 C -chr11 123342341 123342342 A 1 12 0.8633 G -chr11 123390446 123390447 A/C 2 10,5 0.9040,0.8715 A -chr11 123493572 123493573 A/T 2 7,10 0.8602,0.8853 A -chr11 123575347 123575348 A 1 13 0.8499 G -chr11 124178227 124178228 G 1 18 0.8343 C -chr11 124338221 124338222 T 1 12 0.8460 C -chr11 124973036 124973037 A 1 6 0.8563 G -chr11 125072723 125072724 C/T 2 8,18 0.8720,0.8684 T -chr11 125106047 125106048 C/G 2 4,8 0.8284,0.8379 C -chr11 125244726 125244727 C/T 2 8,14 0.8534,0.8557 T -chr11 125265141 125265142 A/G 2 13,13 0.8723,0.8632 A -chr11 125641603 125641604 A 1 37 0.8476 G -chr11 126419719 126419720 C/T 2 11,6 0.8672,0.8842 C -chr11 126696844 126696845 A 1 10 0.8925 G -chr11 126726212 126726213 T 1 29 0.8603 C -chr11 126832385 126832386 C 1 35 0.8380 T -chr11 127317893 127317894 G 1 28 0.8521 A -chr11 127703159 127703160 T 1 32 0.8816 C -chr11 127803598 127803599 A/G 2 16,11 0.8834,0.8885 G -chr11 127862842 127862843 C/T 2 14,7 0.8656,0.8911 C -chr11 127919287 127919288 A/G 2 15,14 0.8253,0.8439 A -chr11 129475701 129475702 C/T 2 12,11 0.8717,0.8649 T -chr11 129649412 129649413 C 1 19 0.8627 T -chr11 129791502 129791503 C/G 2 15,10 0.8379,0.8403 C -chr11 130280083 130280084 A/G 2 18,20 0.8615,0.8730 G -chr11 130428109 130428110 A/G 2 18,13 0.8456,0.8477 A -chr11 130765705 130765706 A/G 2 15,18 0.8791,0.8321 A -chr11 131095826 131095827 A/G 2 4,6 0.8320,0.8428 G -chr11 131097788 131097789 G/T 2 11,8 0.8375,0.8708 G -chr11 132177632 132177633 C 1 20 0.8498 A -chr11 132250950 132250951 C/G 2 8,14 0.8711,0.8742 G -chr11 132689991 132689992 A/G 2 9,7 0.8296,0.8091 A -chr11 133010989 133010990 A 1 14 0.8530 G -chr11 133221986 133221987 A/C 2 14,12 0.8589,0.8814 C -chr11 133380610 133380611 A/G 2 12,16 0.8737,0.8793 G -chr11 133605449 133605450 C/T 2 9,19 0.8666,0.8776 C -chr11 133956457 133956458 C/G 2 8,11 0.8587,0.8570 G -chr11 134296383 134296384 C/T 2 12,8 0.8424,0.8394 C -chr11 134299605 134299606 C 1 24 0.8779 T -chr11 134465219 134465220 C 1 25 0.8801 T -chr11 134598567 134598568 T 1 32 0.8831 C -chr11 134724362 134724363 G/T 2 18,23 0.8466,0.8460 G -chr11 134799739 134799740 A 1 6 0.8672 T -chr12 245334 245335 C 1 38 0.8264 T -chr12 332859 332860 C/T 2 13,12 0.8585,0.8536 T -chr12 564406 564407 A 1 14 0.8509 G -chr12 1350706 1350707 C/T 2 3,9 0.8936,0.8790 T -chr12 1419374 1419375 A/T 2 3,6 0.8159,0.8497 T -chr12 1610252 1610253 G 1 3 0.8814 A -chr12 1856981 1856982 C/T 2 8,11 0.8560,0.8362 T -chr12 1909978 1909979 A 1 6 0.8712 G -chr12 2252633 2252634 A/T 2 10,4 0.8871,0.8622 A -chr12 3008142 3008143 C 1 10 0.8734 T -chr12 3596992 3596993 C 1 19 0.8235 G -chr12 4080115 4080116 C 1 40 0.8266 G -chr12 4232478 4232479 A 1 31 0.8572 G -chr12 4275037 4275038 C/T 2 12,13 0.8436,0.8714 T -chr12 4313641 4313642 C/T 2 6,10 0.9011,0.9062 C -chr12 4535773 4535774 C/T 2 10,10 0.8650,0.8353 T -chr12 4651059 4651060 C/G 2 9,8 0.8662,0.8252 C -chr12 4816889 4816890 G 1 9 0.8084 A -chr12 4826012 4826013 C/T 2 16,13 0.7746,0.7685 T -chr12 5210721 5210722 C/T 2 12,10 0.8413,0.8549 C -chr12 5329934 5329935 C/G 2 10,8 0.8714,0.8750 C -chr12 5340703 5340704 A/G 2 12,16 0.8564,0.8334 G -chr12 5400668 5400669 C/T 2 9,4 0.8193,0.8738 C -chr12 5825678 5825679 C 1 25 0.8684 T -chr12 6354663 6354664 C/G 2 9,4 0.8939,0.8960 C -chr12 6439254 6439255 G 1 12 0.8566 A -chr12 6627355 6627356 A 1 14 0.8950 G -chr12 6894785 6894786 A/G 2 3,8 0.8943,0.8695 G -chr12 7009207 7009208 A/C 2 20,14 0.8658,0.8763 C -chr12 7375920 7375921 C/T 2 10,8 0.8659,0.8462 C -chr12 7758580 7758581 G 1 19 0.8314 A -chr12 8125671 8125672 C 1 3 0.8712 T -chr12 8131119 8131120 G 1 13 0.8282 C -chr12 8276431 8276432 T 1 26 0.8734 C -chr12 8412698 8412699 G 1 4 0.8160 A -chr12 8639298 8639299 C 1 18 0.9008 A -chr12 8651795 8651796 A/T 2 26,23 0.8603,0.8639 T -chr12 8695016 8695017 A/G 2 16,15 0.8574,0.8687 A -chr12 8717934 8717935 C/T 2 11,6 0.8581,0.8508 C -chr12 8903768 8903769 A/G 2 7,8 0.7924,0.8301 A -chr12 8957045 8957046 A/C 2 10,22 0.8520,0.8605 C -chr12 9015157 9015158 A 1 3 0.8299 T -chr12 9018484 9018485 G 1 21 0.8643 A -chr12 9391383 9391384 C/T 2 13,14 0.8123,0.8353 C -chr12 9815866 9815867 A/G 2 31,24 0.8685,0.8554 A -chr12 9847132 9847133 C/T 2 15,23 0.8883,0.8702 C -chr12 9948991 9948992 A/G 2 6,7 0.8816,0.8496 G -chr12 10340326 10340327 C/G 2 6,9 0.8634,0.8367 G -chr12 10775194 10775195 C 1 30 0.8646 T -chr12 11201486 11201487 C/T 2 16,13 0.8628,0.8617 T -chr12 11209058 11209059 G/T 2 24,8 0.8840,0.8795 G -chr12 11226749 11226750 A/G 2 9,16 0.8713,0.8666 G -chr12 11261334 11261335 G 1 11 0.8920 A -chr12 11348295 11348296 C/T 2 7,10 0.9007,0.8887 C -chr12 11526214 11526215 A 1 6 0.8312 G -chr12 11696968 11696969 A/G 2 12,16 0.8902,0.8556 G -chr12 11939880 11939881 G/T 2 12,10 0.8691,0.8618 T -chr12 12040944 12040945 A/G 2 8,13 0.8680,0.8913 G -chr12 12051984 12051985 G 1 14 0.8631 T -chr12 12457441 12457442 C/T 2 5,3 0.8387,0.8449 C -chr12 12990258 12990259 A/G 2 7,12 0.8825,0.8755 G -chr12 12990868 12990869 C/T 2 5,11 0.8924,0.8878 T -chr12 13450143 13450144 G 1 11 0.8713 A -chr12 13491562 13491563 C 1 24 0.8645 T -chr12 13537177 13537178 T 1 5 0.8524 C -chr12 13796505 13796506 A 1 15 0.8712 C -chr12 14226832 14226833 A/G 2 11,13 0.8273,0.8465 G -chr12 14353436 14353437 C/T 2 4,6 0.8675,0.8693 T -chr12 14383855 14383856 T 1 14 0.8419 C -chr12 14674591 14674592 C 1 24 0.8296 T -chr12 15135230 15135231 C/T 2 3,7 0.8404,0.8651 T -chr12 15605319 15605320 T 1 4 0.8574 C -chr12 15846343 15846344 A 1 24 0.8464 G -chr12 16141874 16141875 C 1 3 0.9191 T -chr12 16407135 16407136 A 1 9 0.8468 T -chr12 17531534 17531535 A/G 2 13,18 0.8930,0.8356 G -chr12 17639212 17639213 A/G 2 11,9 0.8603,0.8227 A -chr12 17693859 17693860 C/T 2 5,8 0.8787,0.8866 T -chr12 17882330 17882331 A/T 2 5,12 0.8478,0.8580 T -chr12 18119414 18119415 C/T 2 13,11 0.8750,0.8687 C -chr12 18148716 18148717 A/T 2 15,9 0.8565,0.8245 A -chr12 18661500 18661501 A/G 2 8,22 0.8278,0.8444 G -chr12 18972364 18972365 A/G 2 8,19 0.8217,0.8442 G -chr12 19416863 19416864 A/G 2 17,14 0.8712,0.8789 A -chr12 20176318 20176319 G 1 14 0.8584 T -chr12 20651374 20651375 A/G 2 14,18 0.8845,0.8757 A -chr12 21742305 21742306 C/T 2 3,8 0.8446,0.8811 T -chr12 22065462 22065463 G 1 20 0.8672 A -chr12 22284010 22284011 A/T 2 13,14 0.7849,0.8392 T -chr12 22613230 22613231 A/T 2 4,4 0.7899,0.7250 A -chr12 23249445 23249446 C/T 2 5,12 0.8168,0.8463 T -chr12 24150932 24150933 A/G 2 12,23 0.8583,0.8966 G -chr12 24382036 24382037 G 1 19 0.8614 A -chr12 24483751 24483752 C/T 2 17,20 0.8596,0.8506 T -chr12 24675221 24675222 A/C 2 9,6 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-chr12 31088071 31088072 C/T 2 8,3 0.8496,0.8587 C -chr12 31822255 31822256 G/T 2 16,21 0.9046,0.8688 G -chr12 32397514 32397515 A/G 2 8,9 0.8234,0.8381 A -chr12 32531211 32531212 T 1 44 0.8735 G -chr12 32704907 32704908 A 1 32 0.8674 G -chr12 32707910 32707911 A/G 2 21,12 0.8569,0.8372 A -chr12 32737477 32737478 A 1 14 0.8401 C -chr12 32928880 32928881 A 1 27 0.8297 G -chr12 33127922 33127923 C 1 10 0.8778 T -chr12 33867587 33867588 C 1 30 0.8610 T -chr12 34341578 34341579 C/T 2 17,8 0.8098,0.8571 C -chr12 34459853 34459854 A/C 2 4,9 0.8120,0.8387 C -chr12 34561952 34561953 C/G 2 14,16 0.8266,0.8636 G -chr12 34577308 34577309 A 1 13 0.8631 T -chr12 37902847 37902848 A/C 2 3,3 0.8502,0.7302 A -chr12 38242125 38242126 A/C 2 6,3 0.9169,0.8867 A -chr12 38256508 38256509 C/G 2 3,3 0.8514,0.8634 G -chr12 38482865 38482866 A 1 10 0.8936 G -chr12 38653604 38653605 G 1 25 0.8776 A -chr12 39053567 39053568 C/T 2 10,11 0.8779,0.8289 C -chr12 39126148 39126149 C/G 2 14,11 0.8737,0.8828 C -chr12 39854145 39854146 A/C 2 3,3 0.7988,0.9260 C -chr12 40088033 40088034 A 1 17 0.8577 G -chr12 40204252 40204253 A/C 2 6,8 0.8464,0.8881 A -chr12 40876380 40876381 A/G 2 11,19 0.8348,0.8458 G -chr12 41184818 41184819 A/T 2 7,8 0.8590,0.8494 T -chr12 41236641 41236642 C/T 2 9,13 0.8346,0.8665 T -chr12 41298199 41298200 C 1 5 0.8990 T -chr12 41506912 41506913 G 1 33 0.8204 T -chr12 42430098 42430099 A/G 2 10,9 0.8323,0.8730 G -chr12 42810648 42810649 T 1 19 0.8608 A -chr12 42829384 42829385 A/G 2 7,11 0.8569,0.8547 G -chr12 42883859 42883860 A/G 2 9,7 0.9167,0.8652 A -chr12 43003342 43003343 A/G 2 19,15 0.8707,0.8571 A -chr12 43072514 43072515 C/T 2 15,13 0.8309,0.8693 T -chr12 43200014 43200015 G/T 2 13,11 0.8373,0.8850 T -chr12 43502766 43502767 A/G 2 16,11 0.8655,0.8532 A -chr12 43586048 43586049 C 1 13 0.8873 T -chr12 43594561 43594562 G 1 10 0.8454 A -chr12 44528102 44528103 C 1 8 0.8822 G -chr12 44535161 44535162 T 1 3 0.9041 C -chr12 45344602 45344603 A/G 2 4,5 0.8842,0.9139 G -chr12 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73347545 73347546 T 1 26 0.8613 C -chr12 73363140 73363141 C/G 2 15,20 0.8344,0.8536 C -chr12 73400003 73400004 C/G 2 7,6 0.8732,0.8810 G -chr12 73552731 73552732 A/T 2 3,6 0.6266,0.7868 T -chr12 73728335 73728336 A/G 2 15,11 0.8462,0.8526 A -chr12 73741941 73741942 A/G 2 3,2 0.9035,0.9257 G -chr12 73763826 73763827 C 1 9 0.8808 T -chr12 73826116 73826117 C/T 2 4,2 0.8823,0.9354 C -chr12 74047417 74047418 A/G 2 12,19 0.8238,0.8567 G -chr12 74256408 74256409 C/G 2 5,8 0.8769,0.8840 G -chr12 74657156 74657157 G 1 42 0.8456 C -chr12 74914227 74914228 C 1 22 0.8628 T -chr12 74946319 74946320 T 1 6 0.8860 C -chr12 75162083 75162084 C/T 2 18,6 0.8551,0.8265 C -chr12 75908321 75908322 A/G 2 13,6 0.8393,0.7859 A -chr12 76394874 76394875 A/G 2 14,12 0.8571,0.8434 A -chr12 76695980 76695981 A/C 2 22,10 0.8520,0.8772 A -chr12 77034324 77034325 C/G 2 11,14 0.8570,0.8567 G -chr12 77058607 77058608 G 1 31 0.8794 T -chr12 77314053 77314054 G 1 30 0.8584 A -chr12 77863516 77863517 G/T 2 11,19 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-chr12 122386764 122386765 C 1 4 0.8622 G -chr12 122462355 122462356 C/T 2 6,7 0.9072,0.8399 T -chr12 123719584 123719585 C/G 2 15,34 0.8759,0.8656 G -chr12 123722567 123722568 A/G 2 7,9 0.8631,0.8426 G -chr12 123832713 123832714 G 1 4 0.8672 A -chr12 124475155 124475156 G 1 19 0.8468 A -chr12 124537933 124537934 G/T 2 5,8 0.8080,0.8254 T -chr12 124664677 124664678 C/G 2 3,7 0.8895,0.8301 G -chr12 124701893 124701894 A/G 2 23,13 0.8862,0.8574 A -chr12 124772624 124772625 A/G 2 21,18 0.8862,0.8459 G -chr12 124859243 124859244 G/T 2 7,5 0.8150,0.8295 G -chr12 126266103 126266104 C 1 9 0.8675 G -chr12 126292098 126292099 C/G 2 10,12 0.8234,0.8441 C -chr12 126367913 126367914 A/G 2 10,11 0.8352,0.8866 G -chr12 126498823 126498824 A 1 21 0.8062 T -chr12 126549247 126549248 C 1 22 0.8118 T -chr12 126562260 126562261 C 1 12 0.8585 G -chr12 126620341 126620342 C/T 2 14,7 0.7317,0.7744 T -chr12 126683396 126683397 G 1 16 0.8262 A -chr12 126941374 126941375 A/G 2 8,16 0.8432,0.9000 G -chr12 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-chr12 130709663 130709664 A/G 2 16,12 0.8565,0.8731 G -chr12 130791112 130791113 A/G 2 14,7 0.9057,0.8421 A -chr12 130929598 130929599 A/G 2 12,15 0.8774,0.8584 A -chr12 131226982 131226983 T 1 45 0.8694 G -chr12 131439238 131439239 C/T 2 10,23 0.8716,0.8708 T -chr12 131501014 131501015 C 1 7 0.8851 T -chr12 131544896 131544897 G 1 29 0.8533 C -chr12 131830859 131830860 C 1 3 0.8848 A -chr12 131878987 131878988 A 1 5 0.8729 G -chr12 131893612 131893613 G 1 7 0.8791 A -chr12 132101076 132101077 G 1 5 0.8223 C -chr12 132120246 132120247 A 1 27 0.8502 G -chr12 132436293 132436294 C/T 2 3,3 0.9092,0.9207 C -chr12 132677904 132677905 G 1 7 0.9052 C -chr12 133024763 133024764 T 1 4 0.8797 C -chr12 133343593 133343594 C/T 2 7,5 0.8790,0.8682 T -chr12 133435401 133435402 C/T 2 6,14 0.8264,0.8322 C -chr12 133550488 133550489 A/T 2 3,9 0.8749,0.8632 T -chr13 19051223 19051224 A 1 3 0.8612 G -chr13 19509430 19509431 C 1 35 0.8588 T -chr13 19638885 19638886 A/G 2 10,13 0.8558,0.8756 A -chr13 19649878 19649879 A/G 2 34,12 0.8357,0.8435 A -chr13 19970569 19970570 T 1 16 0.8720 C -chr13 20293166 20293167 A 1 6 0.8099 G -chr13 20871317 20871318 T 1 27 0.8230 C -chr13 20886866 20886867 T 1 15 0.8473 C -chr13 20919045 20919046 C/G 2 11,10 0.8626,0.8509 C -chr13 20920057 20920058 A/G 2 11,16 0.8844,0.8345 G -chr13 21050769 21050770 A/G 2 12,9 0.8647,0.8666 A -chr13 21209511 21209512 A/G 2 19,24 0.8604,0.8278 G -chr13 21677330 21677331 C/T 2 6,12 0.8948,0.8550 T -chr13 21933292 21933293 G/T 2 11,12 0.8589,0.8609 G -chr13 22028869 22028870 A/G 2 14,17 0.8396,0.8430 A -chr13 22356809 22356810 A/G 2 11,11 0.8309,0.8264 G -chr13 22504971 22504972 A 1 17 0.8692 G -chr13 22798236 22798237 T 1 30 0.8833 C -chr13 23184851 23184852 A/C 2 6,9 0.8801,0.7443 A -chr13 23308439 23308440 G 1 22 0.8627 A -chr13 23447346 23447347 C/G 2 14,11 0.8743,0.8818 G -chr13 23466941 23466942 A/C 2 10,10 0.8315,0.8317 A -chr13 23507534 23507535 C 1 10 0.8278 G -chr13 23708316 23708317 T 1 6 0.8848 C -chr13 24062509 24062510 A/G 2 11,13 0.8924,0.8450 A -chr13 24080178 24080179 A/G 2 13,17 0.8567,0.8796 G -chr13 24229013 24229014 A/G 2 18,19 0.9002,0.8901 G -chr13 24230632 24230633 A/G 2 10,15 0.8434,0.8658 A -chr13 24651058 24651059 A/G 2 22,10 0.8666,0.8438 A -chr13 24738745 24738746 T 1 14 0.8415 C -chr13 25598516 25598517 T 1 22 0.8748 G -chr13 25792172 25792173 A/G 2 12,10 0.8326,0.7400 A -chr13 26329138 26329139 C 1 21 0.8493 T -chr13 26517458 26517459 C/T 2 17,14 0.8699,0.8402 C -chr13 26585392 26585393 C 1 23 0.7949 T -chr13 26672399 26672400 C 1 10 0.8478 T -chr13 26885599 26885600 A/G 2 20,14 0.8811,0.8538 A -chr13 26921003 26921004 T 1 26 0.8616 C -chr13 27263749 27263750 C/G 2 16,10 0.8797,0.8775 G -chr13 27375791 27375792 C/T 2 6,9 0.8376,0.8715 T -chr13 27411120 27411121 C/T 2 20,20 0.8340,0.8446 C -chr13 27577082 27577083 A/G 2 14,9 0.8296,0.8743 A -chr13 28457502 28457503 C 1 18 0.8524 G -chr13 28814654 28814655 A/T 2 12,11 0.8624,0.8560 A -chr13 29227655 29227656 C/T 2 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1 15 0.8042 G -chr13 44203062 44203063 C 1 22 0.8583 A -chr13 44888741 44888742 C 1 12 0.9104 T -chr13 45247390 45247391 A 1 7 0.8587 G -chr13 45649628 45649629 T 1 6 0.8585 C -chr13 45694138 45694139 C 1 21 0.8550 T -chr13 45789136 45789137 C/T 2 16,18 0.8449,0.8561 T -chr13 45810299 45810300 A/T 2 21,21 0.8401,0.8619 T -chr13 46326573 46326574 A 1 34 0.8604 G -chr13 46378624 46378625 G/T 2 12,9 0.8558,0.8648 T -chr13 46514970 46514971 G/T 2 13,16 0.8677,0.8443 G -chr13 46624629 46624630 C/T 2 15,7 0.8552,0.8539 T -chr13 46695270 46695271 A/T 2 12,23 0.8651,0.8690 A -chr13 46831270 46831271 A/T 2 18,17 0.8580,0.8637 A -chr13 47501453 47501454 A/G 2 5,8 0.8906,0.7856 A -chr13 48320454 48320455 C/T 2 14,16 0.8475,0.8318 T -chr13 48600958 48600959 C/T 2 7,3 0.8434,0.8490 T -chr13 48997212 48997213 C/G 2 16,7 0.8584,0.8472 C -chr13 49323997 49323998 G 1 15 0.8077 C -chr13 50147399 50147400 A 1 6 0.8906 C -chr13 50295960 50295961 A/G 2 10,17 0.8714,0.8823 A -chr13 51140910 51140911 A/G 2 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A/G 2 7,5 0.8899,0.8722 G -chr14 21115091 21115092 A/C 2 6,3 0.8645,0.6656 A -chr14 21204212 21204213 A 1 31 0.8436 G -chr14 21205671 21205672 A/G 2 24,22 0.8486,0.8565 A -chr14 21230319 21230320 C/T 2 11,11 0.8657,0.8451 C -chr14 21300475 21300476 C/T 2 12,10 0.8373,0.8641 C -chr14 21710111 21710112 C/T 2 8,16 0.8570,0.8267 T -chr14 21803269 21803270 C/G 2 10,13 0.8635,0.8792 G -chr14 22201149 22201150 T 1 7 0.8442 C -chr14 22657455 22657456 G 1 11 0.8437 C -chr14 23080678 23080679 A/G 2 9,5 0.8529,0.8253 A -chr14 23264601 23264602 G 1 4 0.8330 T -chr14 23291195 23291196 A/G 2 9,14 0.8739,0.8790 G -chr14 23856895 23856896 G 1 11 0.8824 A -chr14 24304865 24304866 A/G 2 14,9 0.8735,0.8812 A -chr14 24759677 24759678 G/T 2 3,7 0.8226,0.8848 T -chr14 24963559 24963560 G 1 17 0.8895 A -chr14 25443215 25443216 C/T 2 19,10 0.8641,0.8332 C -chr14 25450992 25450993 C/T 2 7,8 0.8500,0.8620 C -chr14 25479244 25479245 C/G 2 16,16 0.8608,0.8667 G -chr14 25542666 25542667 T 1 14 0.8514 G -chr14 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A -chr14 31901353 31901354 A 1 10 0.8583 G -chr14 32364722 32364723 G/T 2 17,15 0.8564,0.8655 G -chr14 32398195 32398196 A 1 3 0.9385 G -chr14 32404726 32404727 G/T 2 22,13 0.8583,0.8613 T -chr14 33338303 33338304 C/T 2 15,10 0.8707,0.8907 C -chr14 33377671 33377672 A 1 33 0.8766 C -chr14 33433902 33433903 A/G 2 7,4 0.8739,0.8449 G -chr14 34005408 34005409 T 1 28 0.8778 A -chr14 34018187 34018188 A 1 22 0.8805 T -chr14 34025101 34025102 G 1 8 0.8556 C -chr14 34134351 34134352 A 1 6 0.8753 G -chr14 34178303 34178304 A/G 2 7,18 0.8347,0.8691 G -chr14 34225216 34225217 C/T 2 10,9 0.8542,0.8871 C -chr14 34501057 34501058 C 1 22 0.8472 A -chr14 34609548 34609549 G 1 11 0.8731 A -chr14 34761390 34761391 C/T 2 11,11 0.8547,0.8780 T -chr14 34764243 34764244 T 1 3 0.8996 C -chr14 35247640 35247641 A 1 19 0.8479 G -chr14 35961617 35961618 C/G 2 6,9 0.8214,0.8533 G -chr14 36637482 36637483 A/G 2 20,12 0.8475,0.8729 A -chr14 37144000 37144001 A 1 22 0.8756 G -chr14 37239187 37239188 A/G 2 18,17 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-chr16 75220262 75220263 T 1 7 0.8100 C -chr16 75222783 75222784 C/G 2 11,23 0.8669,0.8383 G -chr16 75364882 75364883 A/C 2 8,5 0.8397,0.8288 A -chr16 75960517 75960518 A/G 2 5,16 0.8460,0.8265 G -chr16 76160187 76160188 A/G 2 9,3 0.8514,0.8006 A -chr16 76750257 76750258 C/T 2 8,8 0.8623,0.8623 C -chr16 76763096 76763097 A/T 2 8,3 0.8618,0.7812 A -chr16 77074143 77074144 A 1 10 0.7560 G -chr16 77297566 77297567 T 1 4 0.8261 G -chr16 77618187 77618188 C/T 2 26,20 0.8715,0.8811 C -chr16 77762147 77762148 C/G 2 6,5 0.8533,0.8549 C -chr16 77964314 77964315 C/T 2 7,15 0.8990,0.8911 C -chr16 78009571 78009572 G 1 23 0.8757 A -chr16 78284955 78284956 C/G 2 12,17 0.8379,0.8327 G -chr16 78307175 78307176 G/T 2 11,10 0.8674,0.8544 G -chr16 78324602 78324603 C 1 29 0.8237 T -chr16 78422925 78422926 T 1 19 0.8542 C -chr16 78423609 78423610 A/T 2 6,12 0.8490,0.8016 A -chr16 78611270 78611271 A 1 18 0.8357 C -chr16 78684697 78684698 T 1 9 0.8631 G -chr16 78785103 78785104 A/G 2 7,15 0.8702,0.8897 G 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39279082 T 1 14 0.8394 C -chr17 40198660 40198661 C/T 2 3,6 0.8227,0.8209 C -chr17 40257162 40257163 C 1 13 0.8705 T -chr17 40346275 40346276 A 1 6 0.8866 G -chr17 40728228 40728229 T 1 31 0.8416 C -chr17 41247603 41247604 C 1 3 0.8306 A -chr17 41922613 41922614 C 1 3 0.7658 A -chr17 42283797 42283798 A/T 2 8,12 0.8385,0.8675 A -chr17 42607950 42607951 A/T 2 14,17 0.8612,0.8539 A -chr17 43028980 43028981 A/T 2 7,10 0.8821,0.8523 A -chr17 43092634 43092635 C/T 2 10,8 0.8798,0.8703 C -chr17 43444132 43444133 C/T 2 9,8 0.8661,0.8272 C -chr17 43483676 43483677 A/G 2 12,16 0.8789,0.8827 G -chr17 45061737 45061738 T 1 5 0.7855 C -chr17 45228468 45228469 A/G 2 11,11 0.8457,0.8577 G -chr17 45278789 45278790 A/G 2 7,13 0.8710,0.8718 G -chr17 47218958 47218959 A/G 2 13,12 0.8691,0.8458 G -chr17 48131631 48131632 C 1 9 0.7714 T -chr17 48158842 48158843 C/G 2 13,16 0.8737,0.8428 G -chr17 48262774 48262775 A/G 2 7,4 0.8574,0.8698 A -chr17 48462238 48462239 C/T 2 8,13 0.8738,0.8766 T -chr17 48784154 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0.8419,0.8297 A -chr17 77154455 77154456 C/T 2 12,10 0.8561,0.8202 T -chr17 77333548 77333549 G 1 12 0.8467 A -chr17 77368162 77368163 A/C 2 4,6 0.8887,0.8263 C -chr17 77451430 77451431 A/G 2 10,9 0.8576,0.8620 G -chr17 78543795 78543796 C/G 2 3,5 0.7937,0.8323 G -chr17 78634299 78634300 A/G 2 8,12 0.8420,0.8296 G -chr17 79018753 79018754 C 1 9 0.8882 T -chr17 79112450 79112451 A/C 2 5,6 0.8743,0.8686 A -chr17 79124791 79124792 A/G 2 16,17 0.8900,0.8893 A -chr17 79608652 79608653 A 1 3 0.8701 T -chr17 79921773 79921774 C 1 11 0.8905 T -chr17 80659947 80659948 A 1 31 0.9061 G -chr18 11196 11197 A/G 2 7,18 0.8044,0.8097 G -chr18 106477 106478 A/C 2 11,8 0.8360,0.8536 A -chr18 275817 275818 C/G 2 14,11 0.8683,0.8430 G -chr18 492998 492999 C 1 4 0.8491 T -chr18 780110 780111 C/T 2 3,7 0.8662,0.8628 T -chr18 783619 783620 C/T 2 3,4 0.7900,0.8691 T -chr18 1533792 1533793 A/G 2 3,7 0.7992,0.8109 G -chr18 1989938 1989939 C/G 2 20,12 0.8265,0.8462 G -chr18 2285182 2285183 C/G 2 4,3 0.8563,0.8364 C -chr18 2342674 2342675 A/G 2 8,13 0.8570,0.8462 A -chr18 2523296 2523297 A/G 2 15,9 0.8168,0.7638 A -chr18 2837074 2837075 C 1 10 0.8744 T -chr18 3356364 3356365 C/T 2 10,4 0.8496,0.8199 T -chr18 3575440 3575441 A/G 2 10,19 0.8649,0.8605 A -chr18 3605149 3605150 G 1 14 0.8601 T -chr18 3872604 3872605 A/C 2 6,9 0.8564,0.8543 C -chr18 4589879 4589880 A/T 2 6,7 0.8465,0.8352 T -chr18 4798532 4798533 A/G 2 18,19 0.8679,0.8670 G -chr18 5122274 5122275 C/T 2 4,4 0.7851,0.8690 T -chr18 5272515 5272516 T 1 11 0.8447 G -chr18 5704655 5704656 A/G 2 11,12 0.8212,0.8416 G -chr18 6039720 6039721 C 1 20 0.8437 G -chr18 6466680 6466681 A/G 2 7,11 0.8359,0.8852 G -chr18 6724372 6724373 A/G 2 19,12 0.7616,0.7073 A -chr18 7327175 7327176 C/T 2 7,4 0.8214,0.8759 C -chr18 7373155 7373156 C/T 2 14,11 0.8569,0.8616 C -chr18 7467503 7467504 G 1 21 0.8709 T -chr18 8396289 8396290 A 1 5 0.8988 G -chr18 8621429 8621430 A/G 2 11,17 0.8797,0.8922 G -chr18 9015853 9015854 A/G 2 6,14 0.8514,0.8432 G -chr18 9526183 9526184 C 1 27 0.8617 T -chr18 9662428 9662429 A 1 10 0.8391 C -chr18 9744352 9744353 G 1 32 0.8697 A -chr18 9776655 9776656 C/T 2 16,16 0.8513,0.8630 C -chr18 10005778 10005779 C/T 2 15,8 0.8818,0.8584 T -chr18 10150261 10150262 C 1 21 0.8667 G -chr18 10566344 10566345 C 1 5 0.8802 T -chr18 10957769 10957770 A/G 2 11,12 0.8611,0.8490 A -chr18 11419098 11419099 A 1 17 0.8301 T -chr18 11479098 11479099 A/C 2 9,6 0.8652,0.8501 C -chr18 11992264 11992265 T 1 32 0.8480 C -chr18 12100527 12100528 C 1 23 0.8316 T -chr18 12234749 12234750 A 1 3 0.7588 C -chr18 12315720 12315721 C 1 18 0.8409 T -chr18 13174620 13174621 A 1 21 0.8159 G -chr18 14695828 14695829 G/T 2 4,4 0.8764,0.8179 G -chr18 14730001 14730002 A 1 23 0.8645 C -chr18 15389946 15389947 A/G 2 17,16 0.8690,0.8157 A -chr18 18940963 18940964 C/T 2 15,9 0.8439,0.8777 C -chr18 19236531 19236532 C/T 2 15,9 0.8633,0.8684 T -chr18 19608874 19608875 G 1 2 0.9279 C -chr18 19624815 19624816 C 1 21 0.8597 T -chr18 19761935 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27980550 A/G 2 6,7 0.8628,0.8621 A -chr18 28302027 28302028 C/T 2 13,13 0.7467,0.7623 T -chr18 28330628 28330629 C/T 2 16,10 0.8562,0.8153 T -chr18 28484026 28484027 A/G 2 5,5 0.8014,0.8379 A -chr18 28687195 28687196 A/G 2 11,11 0.8669,0.8417 A -chr18 28883506 28883507 T 1 39 0.8607 C -chr18 29748462 29748463 C/T 2 25,11 0.8636,0.8463 C -chr18 30147774 30147775 C/T 2 4,6 0.9020,0.8091 C -chr18 30825002 30825003 C/T 2 8,9 0.8897,0.8688 T -chr18 30986543 30986544 C 1 5 0.8103 T -chr18 31288566 31288567 C 1 13 0.8722 T -chr18 32611260 32611261 A/C 2 6,5 0.8622,0.8697 A -chr18 33273256 33273257 A/G 2 16,22 0.8963,0.8649 A -chr18 33966972 33966973 A/G 2 4,8 0.9067,0.8921 G -chr18 34179367 34179368 A 1 33 0.8437 C -chr18 35281729 35281730 A/G 2 15,8 0.8235,0.8503 G -chr18 35699082 35699083 C/T 2 6,18 0.8340,0.8689 T -chr18 35843141 35843142 A/G 2 5,4 0.8669,0.8863 G -chr18 36358215 36358216 C/G 2 7,9 0.8845,0.8701 G -chr18 36482492 36482493 C/T 2 16,17 0.8350,0.8092 C -chr18 36943320 36943321 C/T 2 9,8 0.8494,0.8640 C -chr18 37470735 37470736 C/T 2 24,11 0.8079,0.8229 C -chr18 38021902 38021903 A 1 14 0.8546 C -chr18 38497880 38497881 C/T 2 12,15 0.8243,0.8741 T -chr18 38530159 38530160 G 1 18 0.8563 A -chr18 38773853 38773854 G 1 12 0.8978 A -chr18 38837876 38837877 A/G 2 11,18 0.9020,0.8922 A -chr18 39462201 39462202 C 1 17 0.8596 G -chr18 39697095 39697096 G 1 22 0.8692 A -chr18 39976666 39976667 C/T 2 14,19 0.8779,0.8643 C -chr18 40158357 40158358 A 1 14 0.8303 G -chr18 40642404 40642405 G 1 14 0.8487 A -chr18 40764952 40764953 A/T 2 15,5 0.8538,0.7300 A -chr18 41235377 41235378 A/G 2 6,8 0.8922,0.8559 G -chr18 41272975 41272976 A/T 2 6,4 0.8362,0.8450 A -chr18 41568673 41568674 G 1 5 0.8671 A -chr18 42597182 42597183 A 1 8 0.8675 C -chr18 42603732 42603733 C/T 2 7,19 0.8275,0.8502 C -chr18 43072986 43072987 T 1 25 0.8327 C -chr18 43854859 43854860 A/G 2 16,9 0.8624,0.8703 A -chr18 44680093 44680094 C/G 2 13,7 0.8813,0.8042 C -chr18 44864822 44864823 A/T 2 12,18 0.8391,0.8494 T -chr18 45016362 45016363 G 1 16 0.8663 C -chr18 45506269 45506270 C/G 2 9,10 0.8699,0.8772 G -chr18 45528065 45528066 A/G 2 22,18 0.8521,0.8256 A -chr18 45664614 45664615 C/T 2 9,13 0.8318,0.8141 C -chr18 45981768 45981769 C 1 26 0.8271 T -chr18 46047357 46047358 T 1 17 0.8553 C -chr18 46234913 46234914 T 1 15 0.8408 C -chr18 46423344 46423345 C/T 2 7,11 0.8081,0.8300 C -chr18 46459322 46459323 T 1 14 0.8020 C -chr18 46508977 46508978 C/G 2 27,13 0.8776,0.8861 C -chr18 47107151 47107152 C/G 2 11,8 0.8655,0.8548 C -chr18 47224379 47224380 A/G 2 9,13 0.8523,0.8560 G -chr18 47608961 47608962 C/T 2 14,12 0.8449,0.8367 C -chr18 47609439 47609440 T 1 20 0.8437 C -chr18 47673669 47673670 A/G 2 16,21 0.8597,0.8779 G -chr18 48057621 48057622 G 1 24 0.8680 C -chr18 48546439 48546440 G/T 2 14,10 0.8542,0.8092 G -chr18 48718008 48718009 A/G 2 16,6 0.8627,0.8464 G -chr18 48721643 48721644 A/T 2 14,14 0.8555,0.8601 A -chr18 48936581 48936582 C/T 2 23,21 0.8514,0.8786 T -chr18 49214066 49214067 A/T 2 9,9 0.8581,0.8670 A -chr18 49293768 49293769 G/T 2 4,7 0.8424,0.8741 G -chr18 49463587 49463588 G/T 2 15,13 0.8566,0.8569 T -chr18 50131268 50131269 G 1 27 0.8444 A -chr18 50185399 50185400 C/T 2 14,16 0.8549,0.8612 T -chr18 50262152 50262153 T 1 14 0.8650 C -chr18 50821989 50821990 A/G 2 12,12 0.8611,0.8257 A -chr18 50887982 50887983 C/G 2 10,15 0.8540,0.8433 G -chr18 50964896 50964897 A 1 14 0.8721 T -chr18 51701795 51701796 T 1 25 0.8376 C -chr18 52290904 52290905 A/T 2 13,6 0.8394,0.8436 T -chr18 52484550 52484551 G/T 2 18,12 0.8667,0.8621 G -chr18 52628517 52628518 C/T 2 9,26 0.8851,0.8753 T -chr18 52771333 52771334 A 1 3 0.8058 T -chr18 52807374 52807375 A 1 28 0.8586 G -chr18 53334001 53334002 A 1 11 0.8247 G -chr18 54554697 54554698 A/C 2 10,17 0.8626,0.8532 C -chr18 55645542 55645543 C/T 2 12,6 0.8473,0.8270 C -chr18 55674068 55674069 A/G 2 13,19 0.8463,0.8263 G -chr18 55843509 55843510 G 1 9 0.8861 C -chr18 57246292 57246293 T 1 26 0.8668 G -chr18 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0.8210,0.8499 C -chr18 61602025 61602026 C/T 2 15,13 0.8437,0.8716 C -chr18 61652333 61652334 A/G 2 6,3 0.8556,0.7859 A -chr18 61809949 61809950 C/T 2 17,16 0.8592,0.8606 C -chr18 61823494 61823495 A/G 2 13,16 0.8577,0.8341 A -chr18 61834261 61834262 A/G 2 6,11 0.8841,0.8436 G -chr18 61854654 61854655 C/T 2 23,15 0.8533,0.8752 C -chr18 62163861 62163862 A/T 2 5,3 0.8210,0.7008 A -chr18 62176865 62176866 A/G 2 6,6 0.8603,0.8205 A -chr18 62222697 62222698 C/T 2 11,8 0.8577,0.8706 T -chr18 62253956 62253957 A/G 2 7,6 0.8263,0.8695 G -chr18 62280474 62280475 C/T 2 13,9 0.8614,0.8657 T -chr18 62348542 62348543 A/G 2 8,13 0.8518,0.8479 G -chr18 63804889 63804890 C/T 2 15,9 0.8707,0.8704 T -chr18 63921635 63921636 T 1 21 0.8622 C -chr18 64160369 64160370 A/C 2 3,8 0.9030,0.8740 C -chr18 64436510 64436511 G/T 2 18,18 0.8502,0.8478 G -chr18 64503342 64503343 A/C 2 13,15 0.8557,0.8533 C -chr18 64996139 64996140 A 1 31 0.8470 G -chr18 65080690 65080691 A/G 2 9,10 0.8414,0.8636 G -chr18 65335511 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 -chr18 69325822 69325823 G 1 12 0.8820 T -chr18 69387389 69387390 A/G 2 3,3 0.8466,0.8312 A -chr18 69661375 69661376 A 1 28 0.8595 G -chr18 69775301 69775302 C/T 2 4,3 0.8048,0.7689 T -chr18 70202507 70202508 C 1 38 0.8737 A -chr18 70245925 70245926 C/T 2 14,9 0.8582,0.8535 C -chr18 70700023 70700024 A/T 2 10,13 0.8224,0.8735 T -chr18 70769393 70769394 A/T 2 13,18 0.7700,0.8131 T -chr18 70963709 70963710 C 1 14 0.9067 T -chr18 71038292 71038293 A/T 2 10,15 0.8253,0.8473 T -chr18 71577690 71577691 T 1 11 0.8639 C -chr18 71610971 71610972 C/T 2 8,15 0.8341,0.8233 T -chr18 71713778 71713779 T 1 25 0.8442 G -chr18 71943921 71943922 A 1 9 0.8627 T -chr18 72039092 72039093 A/C 2 8,15 0.8602,0.8272 C -chr18 72072015 72072016 A/G 2 14,14 0.8331,0.8553 G -chr18 72091934 72091935 C/T 2 14,25 0.8284,0.8595 C -chr18 72980164 72980165 A 1 15 0.8490 G -chr18 73286425 73286426 A/C 2 21,18 0.8611,0.8523 C -chr18 73482682 73482683 A 1 10 0.8869 G -chr18 73648336 73648337 G 1 24 0.8641 C -chr18 74020384 74020385 G/T 2 12,18 0.8088,0.7878 T -chr18 74397490 74397491 A/C 2 7,12 0.7908,0.8528 C -chr18 75145286 75145287 C/G 2 10,7 0.8561,0.7951 G -chr18 75166485 75166486 C 1 3 0.7803 A -chr18 75177867 75177868 C/T 2 13,16 0.8752,0.8787 T -chr18 75533611 75533612 C 1 6 0.8145 T -chr18 75876648 75876649 G/T 2 16,12 0.8493,0.8147 G -chr18 76777153 76777154 A 1 3 0.7873 G -chr18 76875830 76875831 G/T 2 3,4 0.9106,0.9334 T -chr18 76888927 76888928 C/T 2 17,21 0.8500,0.8528 T -chr18 76945114 76945115 C/T 2 12,14 0.8599,0.8571 C -chr18 77220878 77220879 C/T 2 3,6 0.8948,0.8542 C -chr18 77256423 77256424 A/G 2 3,4 0.8346,0.8104 G -chr18 77322625 77322626 A 1 4 0.7722 G -chr18 77855776 77855777 T 1 29 0.8446 C -chr19 526479 526480 A/T 2 13,4 0.7582,0.7513 T -chr19 839947 839948 C/G 2 4,6 0.8062,0.8343 G -chr19 1400797 1400798 G 1 6 0.8853 A -chr19 1530059 1530060 T 1 5 0.8209 C -chr19 1718580 1718581 T 1 7 0.8621 A -chr19 1959241 1959242 C 1 4 0.7825 G -chr19 2363318 2363319 C/T 2 5,5 0.8569,0.8849 C -chr19 2372237 2372238 A/G 2 15,17 0.8259,0.8532 G -chr19 2578666 2578667 C 1 9 0.8179 G -chr19 2843205 2843206 C/T 2 3,3 0.8091,0.8521 T -chr19 2872598 2872599 T 1 2 0.8715 C -chr19 3775117 3775118 T 1 8 0.8466 C -chr19 3829812 3829813 A 1 5 0.8713 G -chr19 5202900 5202901 G/T 2 19,10 0.8408,0.8078 G -chr19 5685316 5685317 A/G 2 6,5 0.7671,0.8136 G -chr19 5868011 5868012 A/C 2 3,7 0.7258,0.8214 C -chr19 6325106 6325107 A/T 2 12,19 0.8642,0.8446 T -chr19 6523816 6523817 G 1 18 0.8268 A -chr19 6604017 6604018 C 1 25 0.8490 G -chr19 6710447 6710448 A/G 2 4,4 0.7987,0.9100 G -chr19 7101529 7101530 C/T 2 5,10 0.8470,0.8639 T -chr19 7166387 7166388 A/G 2 10,13 0.8352,0.8456 G -chr19 7265081 7265082 A/G 2 11,9 0.8638,0.8754 A -chr19 7506754 7506755 G 1 6 0.8842 A -chr19 7612265 7612266 C/G 2 7,11 0.8715,0.8852 G -chr19 7756190 7756191 C/T 2 13,9 0.8387,0.8506 C -chr19 8316764 8316765 A/G 2 7,18 0.7705,0.8359 G -chr19 8526444 8526445 C/G 2 13,15 0.8756,0.8662 C -chr19 8536531 8536532 C 1 20 0.8564 G -chr19 8788176 8788177 G/T 2 6,10 0.8579,0.8818 T -chr19 9018440 9018441 C 1 6 0.8357 G -chr19 9258487 9258488 G 1 22 0.8782 A -chr19 10028296 10028297 C/G 2 17,15 0.8655,0.8602 C -chr19 10592143 10592144 C 1 4 0.8509 T -chr19 10866887 10866888 C 1 6 0.8428 T -chr19 11034975 11034976 C/T 2 4,9 0.8120,0.8093 T -chr19 11408904 11408905 G/T 2 5,8 0.8775,0.8825 T -chr19 11443424 11443425 A/G 2 14,10 0.8446,0.8433 G -chr19 11676831 11676832 C 1 4 0.7872 T -chr19 12235070 12235071 C 1 28 0.7944 T -chr19 12462121 12462122 C/T 2 11,15 0.8153,0.8320 T -chr19 12562318 12562319 A 1 6 0.8642 G -chr19 12615464 12615465 A 1 8 0.8375 G -chr19 12619992 12619993 C 1 12 0.8493 T -chr19 12857336 12857337 G/T 2 6,4 0.8250,0.7571 G -chr19 13423687 13423688 T 1 23 0.8610 A -chr19 13496043 13496044 T 1 3 0.7978 C -chr19 13942566 13942567 A/G 2 7,6 0.8497,0.8549 G -chr19 13950205 13950206 A/G 2 11,5 0.8457,0.8589 A -chr19 14356257 14356258 C 1 6 0.8395 T -chr19 14954599 14954600 C/T 2 9,14 0.8330,0.8829 T -chr19 15023654 15023655 A 1 23 0.8416 G -chr19 15086707 15086708 G 1 3 0.7925 A -chr19 15703758 15703759 G 1 6 0.8697 C -chr19 15749886 15749887 A 1 17 0.8642 G -chr19 15774240 15774241 G/T 2 13,23 0.8544,0.8728 T -chr19 15844822 15844823 A 1 30 0.8284 G -chr19 16031665 16031666 A/C 2 18,19 0.8649,0.8562 A -chr19 16089232 16089233 A/G 2 5,3 0.8844,0.8031 G -chr19 16122949 16122950 A/T 2 22,10 0.8712,0.8763 A -chr19 16201222 16201223 C 1 8 0.8705 T -chr19 16268855 16268856 C/T 2 7,17 0.8141,0.8446 T -chr19 16612085 16612086 C/T 2 22,13 0.8438,0.8244 C -chr19 16809322 16809323 G 1 10 0.8943 A -chr19 16897704 16897705 A 1 20 0.8665 G -chr19 17502994 17502995 C 1 29 0.8462 A -chr19 17801921 17801922 C/T 2 10,10 0.8771,0.8910 T -chr19 17935625 17935626 C 1 10 0.8613 T -chr19 17954945 17954946 T 1 14 0.8066 C -chr19 18164198 18164199 A/G 2 5,12 0.8304,0.8455 G -chr19 18241707 18241708 A 1 16 0.8384 G -chr19 18250625 18250626 G 1 9 0.8045 T -chr19 18750441 18750442 A/G 2 5,4 0.8171,0.8257 A -chr19 18949923 18949924 A/G 2 3,5 0.7909,0.8015 G -chr19 19396280 19396281 C 1 15 0.8781 T -chr19 19443465 19443466 C/T 2 9,12 0.8084,0.8070 C -chr19 20070855 20070856 G 1 11 0.8530 C -chr19 20111993 20111994 G 1 28 0.8416 A -chr19 20219018 20219019 C/G 2 4,3 0.8839,0.8939 C -chr19 20668040 20668041 C 1 10 0.8806 T -chr19 20732330 20732331 G/T 2 4,7 0.8006,0.8658 G -chr19 20800904 20800905 T 1 13 0.8032 C -chr19 20805751 20805752 T 1 17 0.8402 C -chr19 20957542 20957543 A/G 2 9,4 0.8739,0.8680 A -chr19 21028538 21028539 T 1 2 0.9271 A -chr19 21045564 21045565 C/T 2 4,6 0.9243,0.8810 T -chr19 21143869 21143870 A/G 2 17,5 0.8879,0.8766 A -chr19 21404614 21404615 G 1 32 0.8677 A -chr19 21621090 21621091 A/C 2 12,13 0.8430,0.8265 C -chr19 21809100 21809101 C/T 2 4,4 0.8952,0.8890 C -chr19 21817017 21817018 C 1 2 0.9075 T -chr19 22096518 22096519 C/T 2 4,5 0.8542,0.8784 T -chr19 22172197 22172198 A/T 2 8,5 0.8312,0.8390 A -chr19 22244771 22244772 C/T 2 15,12 0.8711,0.8864 C -chr19 22284339 22284340 A/G 2 6,4 0.8485,0.7515 A -chr19 23074746 23074747 C/G 2 4,11 0.7827,0.8362 G -chr19 23080244 23080245 C/T 2 2,3 0.9372,0.9040 C -chr19 23536721 23536722 A/C 2 6,5 0.8249,0.8691 C -chr19 23603912 23603913 G 1 13 0.8613 A -chr19 24113683 24113684 A 1 9 0.8239 G -chr19 24128130 24128131 G/T 2 4,4 0.8904,0.8589 T -chr19 24225010 24225011 C 1 3 0.9264 T -chr19 24337638 24337639 T 1 11 0.8599 C -chr19 24516389 24516390 C/G 2 13,17 0.8651,0.8455 G -chr19 24556145 24556146 A/C 2 38,24 0.8501,0.8342 A -chr19 27792549 27792550 A/T 2 5,4 0.7859,0.8469 A -chr19 27800041 27800042 C/T 2 33,10 0.8543,0.8799 T -chr19 27827941 27827942 C/G 2 3,5 0.8530,0.8454 G -chr19 27851488 27851489 A/G 2 12,5 0.8659,0.8623 A -chr19 28016159 28016160 A 1 28 0.8471 T -chr19 28154865 28154866 A/C 2 3,3 0.8649,0.8964 A -chr19 28176315 28176316 T 1 13 0.8020 A -chr19 28832268 28832269 T 1 7 0.8404 C -chr19 28897300 28897301 G 1 28 0.8342 A -chr19 29193395 29193396 G/T 2 12,6 0.8493,0.8815 T -chr19 29312511 29312512 C 1 29 0.8562 T -chr19 29408396 29408397 C 1 31 0.8441 T -chr19 29535629 29535630 C 1 35 0.8369 T -chr19 29621334 29621335 T 1 4 0.7750 C -chr19 30040418 30040419 G 1 3 0.8575 A -chr19 30102476 30102477 C/T 2 23,17 0.8229,0.8676 C -chr19 30236552 30236553 A/G 2 10,10 0.7698,0.7254 A -chr19 30917637 30917638 A/G 2 10,9 0.8668,0.8416 A -chr19 31074110 31074111 G/T 2 10,15 0.8202,0.8472 T -chr19 31150366 31150367 A/G 2 12,7 0.8517,0.8582 A -chr19 31296080 31296081 C 1 17 0.8517 A -chr19 31357439 31357440 C/T 2 14,7 0.8274,0.8053 T -chr19 31372950 31372951 G/T 2 9,16 0.8004,0.8612 T -chr19 32083695 32083696 C 1 8 0.8053 T -chr19 32129867 32129868 A 1 13 0.8740 T -chr19 32289823 32289824 A/G 2 6,11 0.8683,0.8340 G -chr19 32485233 32485234 A 1 19 0.8124 G -chr19 32492959 32492960 A/T 2 6,3 0.8178,0.7683 A -chr19 32800709 32800710 C/T 2 5,11 0.8072,0.8717 T -chr19 32881052 32881053 G 1 16 0.8559 A -chr19 33406090 33406091 A/G 2 3,4 0.8576,0.8882 G -chr19 33492038 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0.8390 C -chr20 53830318 53830319 T 1 13 0.8849 A -chr20 54138719 54138720 C 1 3 0.7700 T -chr20 54139208 54139209 G 1 31 0.8691 C -chr20 54160830 54160831 C/G 2 9,19 0.8721,0.8857 C -chr20 54218125 54218126 A/G 2 6,3 0.8552,0.8895 A -chr20 54235871 54235872 A/G 2 12,8 0.8728,0.8569 G -chr20 54324505 54324506 A/T 2 6,20 0.8520,0.8562 T -chr20 54368148 54368149 G/T 2 8,9 0.8831,0.8742 T -chr20 55100256 55100257 T 1 7 0.8079 C -chr20 55451719 55451720 A 1 25 0.8403 T -chr20 55706840 55706841 C/T 2 8,11 0.8431,0.8628 C -chr20 55738046 55738047 C/T 2 16,13 0.8501,0.8344 C -chr20 56049866 56049867 A/G 2 13,15 0.8746,0.8714 A -chr20 56116726 56116727 A/G 2 11,8 0.8934,0.7865 A -chr20 56121829 56121830 A/G 2 16,12 0.8950,0.8770 A -chr20 56213125 56213126 A/G 2 13,14 0.8699,0.8684 G -chr20 56446750 56446751 C 1 23 0.8584 G -chr20 56869419 56869420 A/T 2 3,3 0.7395,0.8309 T -chr20 57009429 57009430 A/G 2 14,17 0.8264,0.8679 G -chr20 57179288 57179289 C/G 2 14,8 0.8843,0.8652 C -chr20 58252898 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61912715 C/T 2 4,6 0.8745,0.8206 T -chr20 61996220 61996221 A/C 2 4,4 0.8385,0.8373 C -chr21 10716551 10716552 G 1 13 0.9032 A -chr21 10792114 10792115 G 1 61 0.8618 A -chr21 10812291 10812292 G 1 32 0.8866 A -chr21 10817653 10817654 G 1 37 0.8634 A -chr21 10827838 10827839 A/C 2 19,15 0.8381,0.8241 C -chr21 11084819 11084820 C/T 2 31,12 0.8552,0.8180 C -chr21 11091695 11091696 C/T 2 47,39 0.8536,0.8452 C -chr21 11104483 11104484 A/T 2 13,6 0.8590,0.8602 T -chr21 11134519 11134520 A/G 2 12,22 0.8684,0.8851 G -chr21 14349797 14349798 T 1 16 0.8682 G -chr21 14429630 14429631 G/T 2 15,8 0.8676,0.8413 G -chr21 15229510 15229511 A/G 2 4,11 0.8434,0.8528 A -chr21 15632186 15632187 G 1 31 0.8681 C -chr21 15648178 15648179 A/G 2 11,17 0.8602,0.8606 A -chr21 15884321 15884322 C/T 2 8,6 0.8600,0.8284 C -chr21 15953223 15953224 A/G 2 16,16 0.8673,0.8707 G -chr21 15958167 15958168 G/T 2 12,5 0.7415,0.8307 T -chr21 16085636 16085637 C/T 2 6,9 0.8406,0.8506 T -chr21 16562430 16562431 A/C 2 12,11 0.7839,0.8030 A -chr21 16605508 16605509 G 1 3 0.7853 A -chr21 16801276 16801277 G 1 22 0.8572 C -chr21 16992119 16992120 A/G 2 6,13 0.8599,0.8664 G -chr21 17475391 17475392 C/T 2 8,20 0.7972,0.8212 T -chr21 17555068 17555069 C 1 3 0.7859 T -chr21 17647109 17647110 T 1 21 0.8687 C -chr21 17692390 17692391 C/T 2 10,7 0.8623,0.8552 C -chr21 17744452 17744453 A/G 2 10,7 0.8294,0.7539 A -chr21 17806827 17806828 C 1 16 0.8356 G -chr21 17812533 17812534 G/T 2 12,8 0.8683,0.8567 G -chr21 17918465 17918466 C/G 2 6,6 0.8351,0.8701 C -chr21 18321523 18321524 C/T 2 14,7 0.8646,0.8680 T -chr21 18346268 18346269 A 1 4 0.8458 G -chr21 18381339 18381340 A/G 2 10,10 0.8805,0.8425 A -chr21 18801578 18801579 A/G 2 11,9 0.8804,0.8441 A -chr21 18922426 18922427 C/G 2 3,3 0.8312,0.8372 C -chr21 19666529 19666530 C/T 2 10,17 0.8490,0.8648 T -chr21 19693401 19693402 T 1 13 0.8292 C -chr21 19918068 19918069 A/G 2 19,16 0.8531,0.8413 A -chr21 20079417 20079418 C/T 2 5,5 0.8473,0.8550 T -chr21 20179786 20179787 C/T 2 17,16 0.8587,0.8715 C -chr21 20216016 20216017 A 1 4 0.8700 G -chr21 20220052 20220053 C 1 18 0.8398 T -chr21 20842716 20842717 G/T 2 5,5 0.8431,0.8543 G -chr21 20878562 20878563 C 1 22 0.8787 T -chr21 21046852 21046853 A/G 2 8,12 0.8738,0.8710 G -chr21 21210381 21210382 G/T 2 9,8 0.8280,0.8411 T -chr21 21350132 21350133 A/G 2 9,7 0.8570,0.8918 G -chr21 21738552 21738553 G/T 2 9,17 0.8542,0.8508 T -chr21 21775823 21775824 G 1 11 0.8883 A -chr21 21840087 21840088 G 1 6 0.7829 A -chr21 21948540 21948541 G/T 2 14,19 0.8535,0.8584 G -chr21 22076437 22076438 C/T 2 9,7 0.8930,0.8290 C -chr21 22130212 22130213 A 1 36 0.8023 G -chr21 22202494 22202495 A/G 2 5,6 0.8544,0.8480 G -chr21 22351931 22351932 A 1 10 0.8036 G -chr21 22817231 22817232 C/T 2 10,8 0.8387,0.8541 T -chr21 23633808 23633809 A 1 14 0.8601 T -chr21 24168237 24168238 G 1 10 0.8217 C -chr21 24493730 24493731 A/G 2 3,4 0.8196,0.8179 A -chr21 24669668 24669669 A 1 3 0.9083 G -chr21 24675359 24675360 C/G 2 15,5 0.8509,0.8586 C -chr21 25263672 25263673 C/T 2 5,3 0.8843,0.8590 C -chr21 25643123 25643124 A/G 2 6,9 0.8733,0.8819 A -chr21 25789614 25789615 A/C 2 8,14 0.8508,0.8437 C -chr21 26100881 26100882 A/G 2 6,6 0.8195,0.8752 G -chr21 26589493 26589494 C/T 2 13,12 0.8593,0.8833 T -chr21 26774083 26774084 A/G 2 11,10 0.8154,0.8616 G -chr21 27028774 27028775 C/T 2 11,12 0.8346,0.8002 T -chr21 27356668 27356669 C/G 2 10,19 0.9061,0.9001 C -chr21 28319793 28319794 C/T 2 6,7 0.8771,0.8433 C -chr21 28416537 28416538 A/G 2 5,16 0.8487,0.8491 A -chr21 28521498 28521499 T 1 25 0.8407 C -chr21 28668746 28668747 C/T 2 20,11 0.8536,0.8640 T -chr21 28827867 28827868 C/T 2 7,5 0.8468,0.8851 C -chr21 28852034 28852035 A/G 2 15,12 0.8346,0.8506 G -chr21 29182321 29182322 A/G 2 8,7 0.8824,0.8464 A -chr21 29184690 29184691 C 1 3 0.8780 T -chr21 29282404 29282405 G/T 2 3,6 0.7851,0.8764 T -chr21 29795338 29795339 G 1 18 0.7939 C -chr21 29858917 29858918 T 1 19 0.8532 C -chr21 29882462 29882463 C 1 27 0.8815 A -chr21 30040808 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-chr21 34210104 34210105 A/T 2 7,9 0.8110,0.8051 T -chr21 34620450 34620451 A 1 41 0.8518 G -chr21 34820028 34820029 A/G 2 4,6 0.8933,0.8782 A -chr21 35461408 35461409 G/T 2 12,14 0.8843,0.8585 T -chr21 35819013 35819014 A 1 31 0.8486 G -chr21 36152544 36152545 C 1 22 0.8821 T -chr21 37335469 37335470 C/G 2 10,34 0.8751,0.8598 G -chr21 37365697 37365698 C/T 2 10,6 0.8348,0.8583 C -chr21 37984872 37984873 C/T 2 14,6 0.8668,0.8779 C -chr21 39018313 39018314 G 1 38 0.7847 A -chr21 39054665 39054666 G 1 7 0.8792 A -chr21 39436579 39436580 A/G 2 8,9 0.8653,0.8571 G -chr21 39900140 39900141 C/T 2 17,8 0.8065,0.8292 C -chr21 40171452 40171453 G 1 31 0.8611 A -chr21 40294367 40294368 A/G 2 10,6 0.8906,0.8646 A -chr21 40336890 40336891 A/G 2 8,11 0.8666,0.8527 A -chr21 40556681 40556682 A/G 2 16,21 0.8542,0.8462 G -chr21 41296490 41296491 C/T 2 9,5 0.8887,0.8575 C -chr21 41324335 41324336 C/T 2 7,16 0.8698,0.8832 C -chr21 41344731 41344732 C 1 27 0.8931 T -chr21 41358285 41358286 A/G 2 15,13 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A/G 2 10,10 0.8453,0.8721 A -chr22 37257854 37257855 A 1 10 0.8764 G -chr22 37366617 37366618 C/T 2 7,7 0.8754,0.8720 T -chr22 37544601 37544602 A/G 2 9,11 0.8584,0.8423 G -chr22 37680511 37680512 A/G 2 12,14 0.8428,0.8699 G -chr22 37738603 37738604 G 1 8 0.8684 C -chr22 37778334 37778335 C/T 2 4,5 0.8970,0.8235 T -chr22 38015670 38015671 C 1 5 0.8390 T -chr22 38043088 38043089 C/G 2 3,3 0.7488,0.8705 G -chr22 38155496 38155497 A/G 2 16,15 0.8815,0.8822 A -chr22 38417509 38417510 C 1 13 0.8227 T -chr22 38556259 38556260 G/T 2 19,22 0.8609,0.8333 T -chr22 38727779 38727780 C/T 2 8,16 0.9215,0.8898 T -chr22 38929607 38929608 C/T 2 16,10 0.8614,0.8457 C -chr22 39408320 39408321 T 1 2 0.9577 C -chr22 39595017 39595018 T 1 14 0.8712 C -chr22 39751710 39751711 A/G 2 15,19 0.8193,0.8468 G -chr22 40023048 40023049 T 1 12 0.8728 C -chr22 40238023 40238024 A/T 2 2,5 0.8966,0.9188 T -chr22 40599630 40599631 A 1 16 0.8411 G -chr22 41782055 41782056 C/G 2 5,4 0.8985,0.9002 C -chr22 41921664 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-chrX 35315745 35315746 A/C 2 4,3 0.8662,0.7468 A -chrX 35789989 35789990 A 1 3 0.8123 T -chrX 35992937 35992938 C 1 13 0.8731 T -chrX 36490437 36490438 A 1 10 0.8662 G -chrX 37085000 37085001 T 1 18 0.8537 C -chrX 37178485 37178486 A 1 14 0.8579 C -chrX 38074515 38074516 G 1 17 0.8297 T -chrX 39372518 39372519 C 1 24 0.8724 T -chrX 39813881 39813882 T 1 10 0.8437 A -chrX 39976425 39976426 G 1 21 0.8500 T -chrX 40350324 40350325 A 1 10 0.7945 G -chrX 41181659 41181660 C 1 3 0.8726 G -chrX 41463524 41463525 C 1 5 0.8683 T -chrX 41719451 41719452 C 1 3 0.8333 T -chrX 41730780 41730781 A 1 6 0.8503 G -chrX 42616823 42616824 C 1 3 0.8150 T -chrX 43453010 43453011 G 1 9 0.8464 A -chrX 45111367 45111368 C 1 15 0.8658 T -chrX 49174103 49174104 G 1 7 0.8846 T -chrX 49532456 49532457 T 1 8 0.8469 C -chrX 50771936 50771937 T 1 9 0.8708 C -chrX 50805301 50805302 G 1 8 0.8916 A -chrX 50925405 50925406 A 1 4 0.8439 G -chrX 50999285 50999286 C 1 6 0.8161 A -chrX 52885495 52885496 A 1 4 0.9122 G -chrX 54213019 54213020 A 1 18 0.8800 C -chrX 56420604 56420605 T 1 8 0.8883 C -chrX 56871875 56871876 C 1 10 0.8580 T -chrX 56948872 56948873 C 1 4 0.8172 A -chrX 57902643 57902644 A 1 9 0.7836 G -chrX 58301124 58301125 A 1 7 0.8434 G -chrX 58484431 58484432 A/T 2 9,6 0.8647,0.8610 T -chrX 58503769 58503770 G 1 25 0.7959 A -chrX 61749872 61749873 C/T 2 10,4 0.8385,0.8592 C -chrX 61833825 61833826 A/G 2 14,6 0.8253,0.8235 A -chrX 61919201 61919202 A/G 2 10,5 0.8537,0.7923 A -chrX 63258429 63258430 G 1 8 0.8680 A -chrX 63343420 63343421 A 1 9 0.8538 T -chrX 64737712 64737713 G 1 5 0.8869 A -chrX 65406742 65406743 T 1 4 0.8768 G -chrX 65412147 65412148 A 1 10 0.8658 G -chrX 66537962 66537963 C 1 17 0.8608 T -chrX 67432611 67432612 C 1 8 0.7687 T -chrX 67529773 67529774 A 1 9 0.8667 C -chrX 67750977 67750978 G/T 2 2,3 0.9262,0.8234 G -chrX 68448738 68448739 A 1 8 0.8699 C -chrX 68886838 68886839 G 1 9 0.8311 A -chrX 69329487 69329488 A 1 9 0.8952 G -chrX 69658653 69658654 C 1 15 0.8881 T -chrX 69732648 69732649 T 1 12 0.8422 C -chrX 70206153 70206154 T 1 5 0.8651 G -chrX 73441601 73441602 C 1 5 0.8836 T -chrX 73543878 73543879 C 1 4 0.8016 T -chrX 73937967 73937968 G 1 9 0.8925 T -chrX 75517734 75517735 C 1 4 0.8876 T -chrX 78589855 78589856 T 1 8 0.8474 C -chrX 79113846 79113847 A 1 20 0.8606 G -chrX 79119636 79119637 C 1 4 0.8348 T -chrX 79342693 79342694 A 1 17 0.8573 C -chrX 79511579 79511580 T 1 21 0.8551 C -chrX 81316714 81316715 C 1 12 0.8420 T -chrX 81708030 81708031 A 1 7 0.8155 G -chrX 82274661 82274662 A 1 14 0.8341 G -chrX 82824528 82824529 G 1 9 0.8385 A -chrX 83045786 83045787 C 1 8 0.9032 T -chrX 83780514 83780515 G 1 16 0.8759 A -chrX 83794996 83794997 T 1 3 0.8294 C -chrX 84409582 84409583 C 1 15 0.8399 T -chrX 84756646 84756647 A 1 13 0.8264 G -chrX 84962767 84962768 G 1 11 0.8589 T -chrX 85614077 85614078 G 1 10 0.8623 A -chrX 85982600 85982601 A 1 15 0.8453 G -chrX 87002508 87002509 A 1 3 0.8329 G -chrX 87148584 87148585 C 1 19 0.8965 T -chrX 87513187 87513188 T 1 8 0.8567 A -chrX 87929206 87929207 A 1 9 0.8775 G -chrX 89844598 89844599 A 1 6 0.8466 C -chrX 90353477 90353478 C 1 3 0.8541 A -chrX 93805734 93805735 C 1 13 0.8085 A -chrX 94568447 94568448 A 1 4 0.8169 T -chrX 94797072 94797073 C 1 9 0.8648 T -chrX 94827116 94827117 T 1 5 0.8475 C -chrX 95231813 95231814 G 1 8 0.8454 A -chrX 95416914 95416915 C 1 11 0.8852 T -chrX 96109235 96109236 A 1 3 0.8593 C -chrX 96508436 96508437 A 1 5 0.8617 T -chrX 96870738 96870739 C 1 19 0.8686 T -chrX 97423060 97423061 A 1 16 0.8309 G -chrX 98934383 98934384 T 1 9 0.8394 C -chrX 100541635 100541636 A/T 2 6,3 0.8734,0.7937 A -chrX 100557633 100557634 C 1 10 0.8602 T -chrX 100963372 100963373 C 1 10 0.8248 T -chrX 103117581 103117582 T 1 13 0.8609 C -chrX 103862864 103862865 C 1 13 0.8374 T -chrX 106721925 106721926 G 1 13 0.8762 C -chrX 109408982 109408983 C 1 10 0.8833 T -chrX 109754636 109754637 C 1 17 0.8492 T -chrX 109761593 109761594 T 1 11 0.8431 A -chrX 109907481 109907482 T 1 9 0.8497 C -chrX 110015919 110015920 T 1 15 0.8467 C -chrX 110264993 110264994 T 1 16 0.8362 A -chrX 111281679 111281680 A 1 13 0.8744 G -chrX 111364460 111364461 G 1 10 0.8721 A -chrX 111368560 111368561 A 1 16 0.8444 G -chrX 111531573 111531574 T 1 10 0.8944 C -chrX 111720465 111720466 A 1 14 0.8430 G -chrX 112170053 112170054 G 1 3 0.9248 A -chrX 112459169 112459170 A 1 19 0.8654 G -chrX 113279524 113279525 T 1 20 0.8246 A -chrX 113324217 113324218 C 1 9 0.8407 A -chrX 114056797 114056798 C 1 11 0.8067 T -chrX 115018183 115018184 G 1 13 0.8356 A -chrX 115733503 115733504 T 1 7 0.8198 G -chrX 116139363 116139364 G 1 7 0.9105 A -chrX 116488679 116488680 G 1 14 0.8564 A -chrX 117358634 117358635 A 1 8 0.8613 G -chrX 118498954 118498955 C 1 4 0.7954 T -chrX 118648794 118648795 T 1 14 0.8734 G -chrX 118693641 118693642 T 1 6 0.8303 C -chrX 118869589 118869590 G 1 8 0.9096 A -chrX 120306948 120306949 G 1 12 0.8546 A -chrX 120448877 120448878 A 1 25 0.8910 C -chrX 120872985 120872986 T 1 8 0.8337 C -chrX 121680281 121680282 C 1 12 0.8836 T -chrX 122435686 122435687 T 1 12 0.7835 C -chrX 123397991 123397992 A 1 4 0.8356 G -chrX 123907161 123907162 C 1 7 0.8753 T -chrX 124719518 124719519 C 1 14 0.8631 T -chrX 124768222 124768223 T 1 5 0.8839 C -chrX 125632363 125632364 C 1 10 0.8800 T -chrX 126053340 126053341 A 1 10 0.8392 C -chrX 126195634 126195635 A 1 7 0.8718 G -chrX 126716246 126716247 C 1 6 0.8763 T -chrX 127367145 127367146 A 1 17 0.8456 G -chrX 127457582 127457583 G 1 8 0.8587 C -chrX 128605962 128605963 T 1 20 0.8591 C -chrX 129569189 129569190 C 1 17 0.8282 G -chrX 129811001 129811002 G 1 20 0.8687 C -chrX 130409883 130409884 T 1 17 0.8126 A -chrX 132344700 132344701 C 1 3 0.8623 T -chrX 132915772 132915773 A 1 15 0.8894 C -chrX 133907790 133907791 A 1 12 0.8533 C -chrX 134518384 134518385 C 1 9 0.8196 A -chrX 134766489 134766490 A/G 2 15,9 0.8509,0.8127 A -chrX 134985459 134985460 G 1 3 0.8540 A -chrX 135190793 135190794 G 1 17 0.8961 A -chrX 136655716 136655717 G 1 6 0.8716 T -chrX 136733809 136733810 C 1 15 0.8669 T -chrX 137469231 137469232 C 1 18 0.8722 T -chrX 137852981 137852982 T 1 11 0.8276 G -chrX 139003000 139003001 A 1 13 0.8526 G -chrX 139110302 139110303 A 1 9 0.8564 G -chrX 139529487 139529488 C 1 18 0.8521 T -chrX 139531472 139531473 T 1 11 0.8682 C -chrX 139615864 139615865 G 1 9 0.8202 A -chrX 139702889 139702890 C 1 3 0.8590 T -chrX 140485622 140485623 G 1 3 0.8489 C -chrX 140511684 140511685 G 1 13 0.8238 A -chrX 140743414 140743415 C 1 4 0.8914 T -chrX 141082368 141082369 C 1 12 0.8648 T -chrX 141153066 141153067 G 1 7 0.8369 C -chrX 141213396 141213397 A 1 4 0.8604 C -chrX 142194135 142194136 A 1 10 0.8411 G -chrX 142652846 142652847 T 1 19 0.8740 C -chrX 142688444 142688445 A 1 6 0.8866 C -chrX 142756403 142756404 C 1 18 0.8646 T -chrX 144873543 144873544 C 1 12 0.8420 T -chrX 145351956 145351957 T 1 5 0.8467 C -chrX 145881542 145881543 G 1 3 0.8178 T -chrX 145924332 145924333 G 1 9 0.8605 A -chrX 145935548 145935549 C 1 14 0.7743 A -chrX 146079383 146079384 C 1 3 0.8542 A -chrX 146425710 146425711 G 1 9 0.8032 A -chrX 146613499 146613500 C 1 11 0.8771 A -chrX 147002991 147002992 G 1 4 0.8704 T -chrX 149466820 149466821 T 1 15 0.8550 C -chrX 149603761 149603762 A 1 3 0.8279 C -chrX 150053854 150053855 C 1 11 0.8358 A -chrX 150408360 150408361 T 1 11 0.8165 C -chrX 150451895 150451896 A 1 23 0.8775 G -chrX 150777182 150777183 T 1 16 0.8623 C -chrX 150808405 150808406 T 1 15 0.8428 G -chrX 150923430 150923431 G/T 2 3,3 0.8295,0.8593 T -chrX 150989778 150989779 C 1 8 0.8441 G -chrX 152584270 152584271 G 1 7 0.8157 A -chrX 152845290 152845291 T 1 12 0.8522 C -chrX 153055432 153055433 A 1 17 0.8461 G -chrX 153090059 153090060 G 1 3 0.8010 A -chrY 4223441 4223442 G 1 8 0.7722 A -chrY 9939199 9939200 C/T 2 20,13 0.8045,0.8191 C -chrY 9962146 9962147 G/T 2 3,5 0.8341,0.8751 T -chrY 9991556 9991557 G/T 2 31,22 0.8248,0.8247 T -chrY 10050627 10050628 C/T 2 4,5 0.8047,0.8279 T -chrY 10068141 10068142 A/T 2 15,20 0.7954,0.8232 A -chrY 13195465 13195466 G/T 2 8,8 0.8124,0.8215 G -chrY 13295972 13295973 C/T 2 16,10 0.8060,0.8173 C -chrY 13567253 13567254 A/C 2 5,6 0.8285,0.8351 A -chrY 18619115 18619116 C 1 4 0.8518 A -chrY 59026174 59026175 A/G 2 5,13 0.8138,0.8404 A
--- a/snp_analysis_conversion/test-data/sample.gd_snp Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,402 +0,0 @@ -#{"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 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0 2 54 Y 54 0.178 1 -Contig177_chr2_79559305_79560033 168 C T 5.67 chr2 79559476 A 2 0 2 33 3 0 2 36 1 0 2 30 2 0 2 33 0 0 -1 0 1 0 2 30 N 56 0.257 0 -Contig8_chr2_82945728_82945839 61 T C 223.0 chr2 -1 N 2 0 2 33 4 0 2 39 9 0 2 54 3 0 2 36 5 0 2 42 0 0 -1 0 N -1 +99. 1 -Contig59_chr2_85243022_85243758 506 G A 96.3 chr2 85243509 T 9 0 2 54 11 0 2 60 12 0 2 63 14 0 2 69 10 0 2 57 7 0 2 48 Y 6 0.459 0 -Contig56_chr3_17326225_17327548 387 G C 91.2 chr3 17326591 G 14 0 2 69 13 0 2 66 15 0 2 72 15 0 2 72 13 0 2 66 12 0 2 63 Y 20 0.225 3 -Contig108_chr3_46210055_46210874 367 A G 21.0 chr3 46210423 A 19 0 2 84 10 0 2 57 16 0 2 75 14 0 2 69 20 0 2 87 11 0 2 60 N 236 0.028 1 -Contig16_chr3_47113407_47114449 322 G A 105.0 chr3 47113713 G 13 0 2 66 17 0 2 78 15 0 2 72 6 0 2 45 11 0 2 60 11 0 2 60 Y 114 0.132 5 -Contig3_chr3_47564810_47565251 262 T G 112.0 chr3 47565104 T 14 0 2 69 16 0 2 75 20 0 2 87 10 0 2 57 9 0 2 54 8 0 2 51 Y 24 0.073 1 -Contig35_chr3_49662401_49662929 270 A T 96.1 chr3 49662652 A 14 0 2 69 11 0 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 -Contig53_chr3_86407941_86409349 1406 G A 86.9 chr3 86409317 A 5 0 2 42 5 0 2 42 4 0 2 39 10 0 2 57 8 0 2 51 12 0 2 63 N 14 3.285 1 -Contig13_chr3_92409738_92412300 718 A G 23.3 chr3 92410450 A 12 0 2 63 16 0 2 75 18 0 2 81 13 0 2 66 22 0 2 93 7 0 2 48 Y 23 0.224 2 -Contig134_chr4_12145648_12148225 1326 C T 164.0 chr4 12146961 C 9 0 2 54 8 0 2 51 7 0 2 48 3 0 2 36 5 0 2 42 5 0 2 42 Y 4 0.080 1 -Contig88_chr4_15557471_15557833 268 A G 145.0 chr4 15557737 A 6 0 2 45 6 0 2 45 11 0 2 60 9 0 2 54 5 0 2 42 6 0 2 45 Y 46 4.138 0 -Contig53_chr4_18823968_18824478 149 A G 91.3 chr4 18824115 A 18 0 2 81 15 0 2 72 21 0 2 90 13 0 2 66 9 0 2 54 12 0 2 63 N 51 0.251 0 -Contig86_chr4_24953866_24956222 1985 C T 76.4 chr4 24955841 T 8 0 2 51 1 0 2 30 3 0 2 36 7 0 2 48 2 0 2 33 6 0 2 45 Y 12 0.357 0 -Contig19_chr4_26233601_26233991 146 G C 51.6 chr4 26233744 G 10 0 2 57 8 0 2 51 9 0 2 54 5 0 2 42 9 0 2 54 4 0 2 39 N 41 0.163 3 -Contig78_chr4_28579975_28580134 30 T G 19.6 chr4 28579994 - 4 0 2 39 3 0 2 36 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 -Contig30_chr4_70978564_70979580 596 A G 164.0 chr4 70979151 A 15 0 2 72 12 0 2 63 20 0 2 87 14 0 2 69 15 0 2 72 15 0 2 72 Y 111 2.458 2 -Contig72_chr4_74225793_74226492 674 A G 110.0 chr4 74226472 A 5 0 2 42 3 0 2 36 2 0 2 33 3 0 2 36 7 0 2 48 4 0 2 39 Y 115 +99. 1 -Contig32_chr4_75618955_75620254 301 T C 333.0 chr4 75619257 C 10 0 2 57 8 0 2 51 12 0 2 63 20 0 2 87 12 0 2 63 14 0 2 69 Y 34 0.163 2 -Contig31_chr5_4734956_4736547 1166 C T 133.0 chr5 4736132 C 14 0 2 69 8 0 2 51 17 0 2 78 4 0 2 39 9 0 2 54 12 0 2 63 Y 1 0.021 0 -Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0 -Contig30_chr5_15698241_15699076 396 G T 76.6 chr5 15698633 T 8 0 2 51 9 0 2 54 10 0 2 57 7 0 2 48 11 0 2 60 8 0 2 54 Y 65 0.009 0 -Contig36_chr5_17709244_17710004 373 T C 281.0 chr5 17709624 T 6 0 2 45 9 0 2 54 7 0 2 48 4 0 2 39 10 0 2 57 4 0 2 39 Y 16 0.131 0 -Contig13_chr5_21881138_21881562 227 A G 251.0 chr5 21881356 A 11 0 2 60 20 0 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 -Contig380_chr6_18173971_18174169 180 C T 4.87 chr6 18174144 T 0 0 -1 0 4 0 2 39 7 0 2 48 2 0 2 33 2 0 2 33 1 0 2 30 N 56 2.589 0 -Contig51_chr6_20231207_20231785 161 A G 70.5 chr6 20231375 G 13 0 2 66 5 0 2 42 8 0 2 51 2 0 2 36 5 0 2 42 5 0 2 42 Y 153 1.754 0 -Contig102_chr6_30271329_30271577 39 T G 139.0 chr6 30271371 G 3 0 2 36 4 0 2 39 6 0 2 45 1 0 2 30 4 0 2 39 4 0 2 39 N 15 1.159 0 -Contig217_chr6_31393824_31394218 97 G A 115.0 chr6 31393921 G 9 0 2 54 19 0 2 84 15 0 2 72 12 0 2 63 7 0 2 48 10 0 2 57 N 45 0.477 0 -Contig186_chr6_31928098_31928245 73 G A 117.0 chr6 -1 N 5 0 2 42 8 0 2 51 2 0 2 33 4 0 2 39 1 0 2 30 5 0 2 42 N -1 0.276 1 -Contig52_chr6_33188498_33188724 123 G A 59.0 chr6 -1 N 5 0 2 42 13 0 2 66 8 0 2 51 4 0 2 39 9 0 2 54 9 0 2 54 N -1 0.880 1 -Contig102_chr6_38743009_38743435 290 A G 178.0 chr6 38743311 A 11 0 2 60 13 0 2 66 9 0 2 54 11 0 2 60 12 0 2 63 13 0 2 66 Y 34 0.148 4 -Contig81_chr6_49018353_49019532 179 C A 72.5 chr6 49018530 A 15 0 2 72 13 0 2 66 19 0 2 72 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 -Contig42_chr13_47730018_47730856 254 A G 75.1 chr13 47730294 A 13 0 2 66 6 0 2 45 12 0 2 63 9 0 2 54 16 0 2 75 11 0 2 63 Y 630 0.049 1 -Contig55_chr13_53467708_53468101 221 T G 132.0 chr13 53467925 T 25 0 2 102 12 0 2 63 26 0 2 105 7 0 2 48 16 0 2 75 16 0 2 75 N 20 5.717 1 -Contig49_chr13_55103679_55105532 503 G A 76.0 chr13 55104178 G 21 0 2 90 19 0 2 84 18 0 2 81 20 0 2 87 8 9 1 89 17 0 2 78 Y 20 0.259 1 -Contig42_chr13_64785759_64786045 14 C G 22.8 chr13 64785772 C 2 0 2 33 2 0 2 33 4 0 2 39 7 0 2 48 8 0 2 51 2 0 2 33 N 527 +99. 1 -Contig66_chr13_66021813_66022244 319 C T 125.0 chr13 66022136 C 11 0 2 60 16 0 2 75 15 0 2 75 12 0 2 63 17 0 2 78 8 0 2 51 N 14 0.055 3 -Contig48_chr14_11839435_11843272 3014 A G 163.0 chr14 11842446 A 10 0 2 57 8 0 2 51 13 0 2 66 10 0 2 57 5 0 2 42 10 0 2 57 Y 31 0.908 0 -Contig9_chr14_23353717_23354432 80 G A 61.3 chr14 23353797 G 3 0 2 36 6 0 2 45 11 0 2 60 8 0 2 51 4 0 2 39 2 4 1 35 Y 11 0.444 0 -Contig14_chr14_24131180_24133488 1633 G A 131.0 chr14 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 -Contig103_chr21_10177255_10177765 121 G A 125.0 chr21 10177367 G 12 0 2 63 10 0 2 57 10 0 2 57 17 0 2 78 14 0 2 69 7 0 2 51 Y 37 0.213 3 -Contig1_chr21_10805534_10806399 766 A G 146.0 chr21 10806301 G 10 0 2 57 6 0 2 45 9 0 2 54 6 0 2 45 7 0 2 48 5 0 2 42 Y 20 0.319 0 -Contig46_chr21_21029492_21030645 443 C T 5.37 chr21 21029910 C 15 0 2 72 11 0 2 60 16 0 2 75 15 0 2 72 13 0 2 66 6 0 2 45 Y 96 3.737 0 -Contig129_chr21_31045749_31046924 381 A G 129.0 chr21 31046141 A 19 0 2 84 8 0 2 51 23 0 2 96 12 0 2 63 15 0 2 72 18 0 2 81 Y 69 0.028 2 -Contig23_chr21_31651123_31651986 840 C T 71.3 chr21 31651957 T 6 0 2 45 9 0 2 54 8 0 2 51 10 0 2 57 4 0 2 39 7 0 2 48 Y 105 2.977 3 -Contig64_chr21_43341847_43342031 84 T C 114.0 chr21 43341926 T 11 0 2 60 9 0 2 54 10 0 2 57 6 0 2 45 6 0 2 45 7 0 2 48 N 10 3.954 2 -Contig60_chr21_43475347_43475824 175 C T 8.05 chr21 43475551 T 6 0 2 45 7 0 2 48 13 0 2 66 6 0 2 45 14 0 2 69 14 0 2 69 N 45 0.058 0 -Contig64_chr21_45377513_45377872 19 C T 60.7 chr21 -1 N 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 -Contig164_chr24_46598127_46599206 84 C T 105.0 chr24 46598214 C 13 0 2 66 12 0 2 63 15 0 2 72 15 0 2 72 11 0 2 60 8 0 2 51 Y 22 1.262 1 -Contig144_chr25_4011170_4013134 541 A G 160.0 chr25 4011690 A 12 0 2 63 17 0 2 78 13 0 2 66 13 0 2 66 13 0 2 66 13 0 2 66 Y 5 0.087 0 -Contig81_chr25_6103472_6104760 699 G A 378.0 chr25 6104190 A 14 0 2 69 16 0 2 75 13 0 2 66 11 0 2 60 11 0 2 60 12 0 2 63 Y 33 0.789 2 -Contig152_chr25_7486442_7487609 75 A G 11.6 chr25 7486515 A 17 0 2 78 13 0 2 66 8 0 2 51 16 0 2 75 8 0 2 51 6 0 2 45 N 2 0.158 0 -Contig24_chr25_7695778_7698612 2714 C T 130.0 chr25 7698446 C 16 0 2 75 13 0 2 66 22 0 2 93 17 0 2 78 10 0 2 57 17 0 2 78 Y 27 0.346 0 -Contig89_chr25_8635170_8636009 586 G C 209.0 chr25 8635744 G 13 0 2 66 13 0 2 66 21 0 2 93 14 0 2 69 15 0 2 72 15 0 2 72 Y 14 0.067 0 -Contig77_chr25_10796299_10796481 2 T C 17.3 chr25 -1 N 1 0 2 30 0 0 -1 0 1 0 2 30 0 0 -1 0 0 0 -1 0 0 0 -1 0 N -1 +99. 0 -Contig73_chr25_14177327_14177474 125 A C 6.85 chr25 14177464 A 0 0 -1 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 -Contig11_chr26_11062142_11062902 707 C A 108.0 chr26 11062836 T 7 0 2 48 8 0 2 51 16 0 2 75 10 0 2 57 6 0 2 45 14 0 2 69 Y -1 4.709 0 -Contig133_chr26_17695661_17696368 39 T G 98.7 chr26 17695700 T 10 0 2 57 3 0 2 36 11 0 2 60 9 0 2 54 2 0 2 33 1 0 2 30 N 85 3.402 0 -Contig157_chr26_23894107_23895229 25 C T 50.2 chr26 23894140 C 0 0 -1 0 4 0 2 39 2 0 2 33 4 0 2 39 3 0 2 36 3 0 2 36 Y 51 +99. 0 -Contig146_chr26_26622638_26623906 574 G A 186.0 chr26 26623219 A 11 0 2 60 12 0 2 63 9 0 2 54 11 0 2 60 9 0 2 54 12 0 2 63 Y 1 0.318 0 -Contig8_chr26_27834126_27834326 140 G A 41.7 chr26 27834268 G 13 0 2 66 7 0 2 48 13 0 2 66 11 0 2 60 12 0 2 63 6 0 2 45 N 29 0.142 1 -Contig78_chr26_31128839_31129005 123 T C 145.0 chr26 -1 N 11 0 2 60 3 0 2 36 7 0 2 48 8 0 2 51 10 0 2 46 7 0 2 48 N -1 1.230 1 -Contig28_chr26_32935355_32935833 289 T C 77.9 chr26 32935638 T 15 0 2 72 22 0 2 93 15 0 2 72 9 0 2 54 15 0 2 72 17 0 2 78 Y 10 2.258 1 -Contig36_chr26_36606876_36607240 115 A T 139.0 chr26 36606979 A 1 0 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 -Contig35_chr27_40596169_40596445 20 G C 133.0 chr27 40596189 G 8 0 2 51 3 0 2 36 4 0 2 39 2 0 2 33 4 0 2 39 4 0 2 39 Y 4 +99. 1 -Contig85_chr27_45471750_45472022 211 G A 53.1 chr27 45471964 G 18 0 2 81 10 0 2 57 15 0 2 72 0 13 0 36 16 0 2 75 14 0 2 69 N 75 2.502 1 -Contig131_chr28_6481806_6483783 138 C T 36.2 chr28 6481953 C 12 0 2 63 12 0 2 63 20 0 2 87 11 0 2 60 10 0 2 57 12 0 2 63 Y 10 0.387 0 -Contig141_chr28_10027332_10028242 780 T G 74.8 chr28 10028095 T 10 0 2 57 11 0 2 60 14 0 2 69 10 0 2 57 7 0 2 48 9 0 2 54 Y 19 3.348 0 -Contig144_chr28_15468203_15470548 743 G A 20.0 chr28 15468942 G 13 0 2 66 12 0 2 63 10 0 2 57 11 0 2 60 16 0 2 75 7 0 2 48 N 14 0.053 0 -Contig47_chr28_21311718_21312366 541 G A 116.0 chr28 21312258 G 9 0 2 54 6 0 2 45 12 0 2 63 6 0 2 45 5 0 2 45 12 0 2 63 N 9 0.240 0 -Contig60_chr28_30197166_30197364 92 T C 164.0 chr28 30197258 T 10 0 2 57 13 0 2 66 15 0 2 72 16 0 2 75 12 0 2 63 11 0 2 60 N 369 1.139 0 -Contig201_chr28_36339953_36341322 260 C T 6.36 chr28 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 -Contig113_chr34_13341080_13341643 236 C T 90.7 chr34 13341316 C 4 0 2 39 2 0 2 33 8 0 2 51 4 0 2 39 8 0 2 51 3 0 2 36 Y 47 0.412 3 -Contig405_chr34_14415672_14415979 59 A G 36.2 chr34 14415731 G 8 0 2 51 2 0 2 33 8 0 2 51 6 0 2 48 3 0 2 36 7 0 2 48 Y 45 0.405 1 -Contig21_chr34_16422980_16425681 2009 G A 19.4 chr34 16424960 G 0 0 -1 0 0 0 -1 0 0 0 -1 0 5 0 2 42 0 0 -1 0 0 0 -1 0 Y 28 0.196 0 -Contig41_chr34_16544482_16545449 46 T C 102.0 chr34 16544523 T 5 0 2 42 11 0 2 60 6 0 2 45 0 2 0 3 7 0 2 48 8 0 2 51 Y 215 1.156 0 -Contig8_chr34_18474513_18475673 1122 C A 129.0 chr34 18475628 A 8 0 2 51 15 0 2 72 13 0 2 66 17 0 2 78 13 0 2 66 6 0 2 45 Y 61 0.123 2 -Contig152_chr34_31794848_31795540 242 G A 93.2 chr34 31795093 G 11 0 2 60 24 0 2 99 17 0 2 78 15 0 2 72 18 0 2 81 17 0 2 78 Y 123 2.780 0 -Contig28_chr34_41708848_41712034 1381 A G 78.2 chr34 41710232 A 11 0 2 60 17 0 2 78 15 0 2 72 16 0 2 75 15 0 2 72 14 0 2 69 Y 236 0.234 0 -Contig85_chr34_42798284_42800584 1845 C T 171.0 chr34 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
--- a/snp_analysis_conversion/test-data/snpsForSubmission.text Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ -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: -||
--- a/snp_analysis_conversion/test-data/snpsForSubmission.vcf Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,407 +0,0 @@ -##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
--- a/snp_analysis_conversion/test-data/vcf2pgSnp_input.vcf Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -##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
--- a/snp_analysis_conversion/test-data/vcf2pgSnp_output.pgSnp Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -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
--- a/snp_analysis_conversion/vcf2pgSnp.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ -#!/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;
--- a/snp_analysis_conversion/vcf2pgSnp.xml Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -<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>
--- a/snp_analysis_conversion/vcf2pgSnpMult.pl Tue May 28 17:01:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -#!/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;